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wentorai/research-plugins

350+ academic research skills, MCP configs, and plugins for Research-Claw and AI agents

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Review weekly changes to SKILL.md before updating. Dates mark the weeks in which we observed each version; checks apply to the recorded commits.

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skills/analysis/dataviz/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/dataviz/algorithm-visualizer-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/dataviz/chart-image-generator/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/dataviz/color-accessibility-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/dataviz/d3-visualization-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/dataviz/echarts-visualization-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/dataviz/geospatial-viz-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/dataviz/interactive-viz-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/dataviz/metabase-analytics-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/dataviz/network-visualization-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/dataviz/plotly-interactive-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/dataviz/publication-figures-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/dataviz/python-dataviz-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/dataviz/redash-analytics-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/econometrics/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/econometrics/causal-inference-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/econometrics/econml-causal-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/econometrics/iv-regression-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/econometrics/mostly-harmless-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/econometrics/panel-data-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/econometrics/python-causality-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/econometrics/robustness-checks/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/econometrics/stata-analyst-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/econometrics/stata-reference-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/econometrics/time-series-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/statistics/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/statistics/bayesian-statistics-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/statistics/data-anomaly-detection/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/statistics/hypothesis-testing-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/statistics/meta-analysis-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/statistics/ml-experiment-tracker/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/statistics/modeling-strategy-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/statistics/nonparametric-tests-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/statistics/power-analysis-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/statistics/sem-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/statistics/survival-analysis-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/wrangling/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/wrangling/csv-data-analyzer/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/wrangling/data-cleaning-pipeline/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/wrangling/data-cog-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/wrangling/missing-data-handling/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/wrangling/pandas-data-wrangling/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/wrangling/questionnaire-design-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/analysis/wrangling/stata-data-cleaning/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/wrangling/streamline-analyst-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/wrangling/survey-data-processing/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/analysis/wrangling/text-mining-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/domains/ai-ml/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/domains/ai-ml/ai-agent-papers-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/domains/ai-ml/ai-model-benchmarking/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/domains/ai-ml/anomaly-detection-papers-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/autonomous-agents-papers-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/computer-vision-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/deep-learning-papers-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/dl-transformer-finetune/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/domains/ai-ml/domain-adaptation-papers-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/generative-ai-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/graph-learning-papers-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/domains/ai-ml/huggingface-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/huggingface-inference-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/keras-deep-learning/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/kolmogorov-arnold-networks-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/llm-evaluation-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/llm-from-scratch-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/ml-pipeline-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/nlp-toolkit-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/npcpy-research-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/prompt-engineering-research/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/pytorch-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/pytorch-lightning-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/reinforcement-learning-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/responsible-ai-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/tensorflow-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/transformer-architecture-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ai-ml/vmas-simulator-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/alphafold-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/bioagents-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/biothings-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/clawbio-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/clinical-dialogue-agents-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/clinical-research-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/clinicaltrials-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/clinicaltrials-api-v2/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/ena-sequence-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/enrichr-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/ensembl-rest-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/epidemiology-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/genomas-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/genomics-analysis-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/genotex-benchmark-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/med-researcher-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/med-researcher-r1-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/medgeclaw-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/medical-data-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/medical-imaging-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/ncbi-blast-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/ncbi-datasets-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/pdb-structure-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/biomedical/quickgo-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/business/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/business/architecture-design-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/business/innovation-management-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/business/market-analysis-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/business/operations-research-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/business/strategic-management-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/chemistry/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/chemistry/cactus-cheminformatics-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/chemistry/catalysis-hub-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/chemistry/chemeagle-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/chemistry/chemgraph-agent-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/chemistry/computational-chemistry-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/chemistry/molecular-dynamics-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/chemistry/pubchem-api-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/chemistry/retrosynthesis-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/chemistry/spectroscopy-analysis-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/cs/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/cs/ai-security-papers-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/cs/algorithms-complexity-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/cs/code-llm-papers-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/cs/dblp-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/cs/distributed-systems-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/cs/formal-verification-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Local scripts

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/cs/gaussian-splatting-papers-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/cs/llm-aiops-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/cs/software-engineering-research/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/cs/software-heritage-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ecology/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ecology/biodiversity-data-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ecology/conservation-biology-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ecology/gbif-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ecology/inaturalist-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/ecology/species-distribution-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/economics/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/economics/behavioral-economics-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/economics/development-economics-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/economics/fred-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/economics/imf-data-api-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/economics/nber-working-papers-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/economics/post-labor-economics/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/economics/pricing-psychology-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/economics/repec-economics-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/economics/world-bank-data-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/education/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/education/academic-study-methods/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/education/assessment-design-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/education/curriculum-design-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/education/educational-research-methods/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/education/learning-science-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/education/mooc-analytics-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/education/open-syllabus-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/finance/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/finance/akshare-finance-data/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/finance/financial-data-analysis/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/finance/finsight-research-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/finance/options-analytics-agent-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/finance/portfolio-optimization-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/finance/quantitative-finance-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/finance/risk-modeling-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/finance/stata-accounting-research/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/geoscience/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/geoscience/climate-modeling-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/geoscience/climate-science-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/geoscience/gis-remote-sensing-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/geoscience/pangaea-data-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/geoscience/satellite-remote-sensing/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/geoscience/seismology-data-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/humanities/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/humanities/digital-humanities-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/humanities/ethical-philosophy-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/humanities/history-research-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/humanities/philosophy-research-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/humanities/political-history-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/law/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/law/caselaw-access-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/law/courtlistener-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/law/legal-agent-skills-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/law/legal-nlp-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/law/legal-research-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/law/opencontracts-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/law/patent-analysis-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/law/regulatory-compliance-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/law/uk-legislation-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/math/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/math/lean-theorem-proving-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/math/linear-algebra-applications/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/math/numerical-methods-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/math/oeis-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/math/symbolic-computation-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/math/topology-data-analysis/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/pharma/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/pharma/clinical-pharmacology-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/pharma/clinical-trial-design-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/pharma/drug-development-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/pharma/drug-target-interaction/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/pharma/madd-drug-discovery-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/pharma/pharmacovigilance-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/physics/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/physics/astrophysics-data-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/physics/computational-physics-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/physics/nasa-ads-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/physics/particle-physics-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/physics/quantum-computing-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/social-science/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/social-science/ipums-microdata-api/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/social-science/network-analysis-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/social-science/psychology-research-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

Compare on GitHub

skills/domains/social-science/social-research-methods/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/social-science/sociology-research-methods/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/domains/social-science/survey-research-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/literature/discovery/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/literature/discovery/citation-alert-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/literature/discovery/conference-proceedings-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/literature/discovery/literature-mapping-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/literature/discovery/paper-recommendation-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/literature/discovery/papers-we-love-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/literature/discovery/rss-paper-feeds/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/literature/discovery/semantic-paper-radar/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/literature/discovery/semantic-scholar-recs-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/literature/discovery/zotero-arxiv-daily-guide/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/literature/fulltext/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → bf44b3cd617f

No earlier version was observed for comparison.

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skills/literature/fulltext/arxiv-latex-source/SKILL.md

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View on GitHubAdd to my skills

Verified commit bf44b3cd617fa94c8a1b254c5d1987142ca3d631

310GitHub stars
3stars in 7 days
473skills in this repository
0commits in 30 days

Heat

2.8
  • Star growth, last 7 daysNot available
  • Star growth, last 24 hoursNot available
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Heat never changes the order by stars, and sponsorship never touches it. How heat works

Stars over time

Oct 25, 2026Nov 5, 2026310

30-day change not yet available: not enough history.

Individual skills in this repository

How it works

dataviz-skills

When your agent uses it

14 data visualization skills. Trigger: charts, plots, figures, publication-quality graphics. Design: one skill per tool with code templates and academic formatting conventions.

What it loads into context

Frontmatter

42 tokens

Always available to the agent

SKILL.md

527 tokens

When the skill is activated

Reference documents

0 tokens

Loaded on request

Token counts are estimates. Scripts run separately; they are not counted as reference context.

The playbook

    Files

    • SKILL.mdcore2,299 bytes
    • SKILL.mdcore2,299 bytes
    Read SKILL.md
    
# Data Visualization — 14 Skills

Select the skill matching the user's need, then `read` its SKILL.md.

| Skill | Description |
|-------|-------------|
| [algorithm-visualizer-guide](./algorithm-visualizer-guide/SKILL.md) | Guide to Algorithm Visualizer for interactive algorithm exploration |
| [bokeh-visualization-guide](./bokeh-visualization-guide/SKILL.md) | Guide to Bokeh for interactive browser-based research visualizations |
| [chart-image-generator](./chart-image-generator/SKILL.md) | Generate publication-quality chart images from research data |
| [color-accessibility-guide](./color-accessibility-guide/SKILL.md) | Colorblind-friendly palettes and accessible visualization design |
| [d3-visualization-guide](./d3-visualization-guide/SKILL.md) | Guide to D3.js for building custom interactive data visualizations |
| [echarts-visualization-guide](./echarts-visualization-guide/SKILL.md) | Guide to Apache ECharts for interactive research data dashboards |
| [geospatial-viz-guide](./geospatial-viz-guide/SKILL.md) | Create maps, choropleths, and spatial data visualizations for research |
| [interactive-viz-guide](./interactive-viz-guide/SKILL.md) | Interactive data visualization with Plotly, ECharts, and D3 |
    View the complete source on GitHub

    Skills included

    • dataviz-skills
    • algorithm-visualizer-guide
    • bokeh-visualization-guide
    • chart-image-generator
    • color-accessibility-guide
    • d3-visualization-guide
    • echarts-visualization-guide
    • geospatial-viz-guide
    • interactive-viz-guide
    • metabase-analytics-guide
    • network-visualization-guide
    • plotly-interactive-guide
    • publication-figures-guide
    • python-dataviz-guide
    • redash-analytics-guide
    • econometrics-skills
    • causal-inference-guide
    • econml-causal-guide
    • iv-regression-guide
    • mostly-harmless-guide
    • panel-data-guide
    • python-causality-guide
    • robustness-checks
    • stata-analyst-guide
    • stata-reference-guide
    • time-series-guide
    • statistics-skills
    • bayesian-statistics-guide
    • data-anomaly-detection
    • hypothesis-testing-guide
    • meta-analysis-guide
    • ml-experiment-tracker
    • modeling-strategy-guide
    • nonparametric-tests-guide
    • power-analysis-guide
    • sem-guide
    • survival-analysis-guide
    • wrangling-skills
    • csv-data-analyzer
    • data-cleaning-pipeline
    • data-cog-guide
    • missing-data-handling
    • pandas-data-wrangling
    • questionnaire-design-guide
    • stata-data-cleaning
    • streamline-analyst-guide
    • survey-data-processing
    • text-mining-guide
    • ai-ml-skills
    • ai-agent-papers-guide
    • ai-model-benchmarking
    • anomaly-detection-papers-guide
    • autonomous-agents-papers-guide
    • computer-vision-guide
    • deep-learning-papers-guide
    • dl-transformer-finetune
    • domain-adaptation-papers-guide
    • generative-ai-guide
    • graph-learning-papers-guide
    • huggingface-api
    • huggingface-inference-guide
    • keras-deep-learning
    • kolmogorov-arnold-networks-guide
    • llm-evaluation-guide
    • llm-from-scratch-guide
    • ml-pipeline-guide
    • nlp-toolkit-guide
    • npcpy-research-guide
    • prompt-engineering-research
    • pytorch-guide
    • pytorch-lightning-guide
    • reinforcement-learning-guide
    • responsible-ai-guide
    • tensorflow-guide
    • transformer-architecture-guide
    • vmas-simulator-guide
    • biomedical-skills
    • alphafold-api
    • bioagents-guide
    • biothings-api
    • clawbio-guide
    • clinical-dialogue-agents-guide
    • clinical-research-guide
    • clinicaltrials-api
    • clinicaltrials-api-v2
    • ena-sequence-api
    • enrichr-api
    • ensembl-rest-api
    • epidemiology-guide
    • genomas-guide
    • genomics-analysis-guide
    • genotex-benchmark-guide
    • med-researcher-guide
    • med-researcher-r1-guide
    • medgeclaw-guide
    • medical-data-api
    • medical-imaging-guide
    • ncbi-blast-api
    • ncbi-datasets-api
    • pdb-structure-api
    • quickgo-api
    • business-skills
    • architecture-design-guide
    • innovation-management-guide
    • market-analysis-guide
    • operations-research-guide
    • strategic-management-guide
    • chemistry-skills
    • cactus-cheminformatics-guide
    • catalysis-hub-api
    • chemeagle-guide
    • chemgraph-agent-guide
    • computational-chemistry-guide
    • molecular-dynamics-guide
    • pubchem-api-guide
    • retrosynthesis-guide
    • spectroscopy-analysis-guide
    • cs-skills
    • ai-security-papers-guide
    • algorithms-complexity-guide
    • code-llm-papers-guide
    • dblp-api
    • distributed-systems-guide
    • formal-verification-guide
    • gaussian-splatting-papers-guide
    • llm-aiops-guide
    • software-engineering-research
    • software-heritage-api
    • ecology-skills
    • biodiversity-data-guide
    • conservation-biology-guide
    • gbif-api
    • inaturalist-api
    • species-distribution-guide
    • economics-skills
    • behavioral-economics-guide
    • development-economics-guide
    • fred-api
    • imf-data-api-guide
    • nber-working-papers-api
    • post-labor-economics
    • pricing-psychology-guide
    • repec-economics-api
    • world-bank-data-guide
    • education-skills
    • academic-study-methods
    • assessment-design-guide
    • curriculum-design-guide
    • educational-research-methods
    • learning-science-guide
    • mooc-analytics-guide
    • open-syllabus-api
    • finance-skills
    • akshare-finance-data
    • financial-data-analysis
    • finsight-research-guide
    • options-analytics-agent-guide
    • portfolio-optimization-guide
    • quantitative-finance-guide
    • risk-modeling-guide
    • stata-accounting-research
    • geoscience-skills
    • climate-modeling-guide
    • climate-science-guide
    • gis-remote-sensing-guide
    • pangaea-data-api
    • satellite-remote-sensing
    • seismology-data-guide
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    Showing 300 of 473 skills. See GitHub for the complete repository.

    Repository facts

    License
    MIT
    Created
    Mar 9, 2026
    Last pushed
    Jun 19, 2026
    Forks
    42
    Open issues
    0
    Project activity
    Slowing

    Before you install

    Network or broad shell

    Automated signals, not a guarantee

    Checked Nov 5, 2026

    Not fully analyzed: some files were too long, unreadable or missing. This never lowers the level.

    Show 1,825 notes
    • skills/analysis/dataviz/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
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    • skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    • skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    • skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    • skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    • skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    • skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    • skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    • skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    • skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    • skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    • skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    • skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    • skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    • skills/analysis/dataviz/chart-image-generator/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    • skills/analysis/dataviz/chart-image-generator/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    • skills/analysis/dataviz/chart-image-generator/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    • skills/analysis/dataviz/chart-image-generator/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
    Show all 4,217 signals by file

    .gitignore

    • Executable scriptline 1
      Executable file
    • Access to secretsline 28
      [Credential-related source omitted]

    skills/analysis/dataviz/algorithm-visualizer-guide/SKILL.md

    • Network accessline 8
      subcategory: "dataviz"     keywords: ["algorithm visualization", "interactive learning", "code animation", "computational methods", "data structures", "teaching tools"]     source: "https://github.com/algorithm-visualizer/algorithm-visualiz
    • Network accessline 9
      keywords: ["algorithm visualization", "interactive learning", "code animation", "computational methods", "data structures", "teaching tools"]     source: "https://github.com/algorithm-visualizer/algorithm-visualizer" ---
    • Network accessline 10
      source: "https://github.com/algorithm-visualizer/algorithm-visualizer"
    • Network accessline 36
      # Clone the repository git clone https://github.com/algorithm-visualizer/algorithm-visualizer.git
    • Network accessline 37
      git clone https://github.com/algorithm-visualizer/algorithm-visualizer.git
    • Network accessline 46
      # Access at http://localhost:3000
    • Network accessline 52
      # Clone all required components git clone https://github.com/algorithm-visualizer/algorithm-visualizer.git
    • Network accessline 53
      git clone https://github.com/algorithm-visualizer/algorithm-visualizer.git
    • Network accessline 54
      git clone https://github.com/algorithm-visualizer/server.git
    • Network accessline 61
      cd ../algorithm-visualizer # Set the server URL in environment configuration echo "REACT_APP_API_URL=http://localhost:8080" > .env.local
    • Network accessline 62
      # Set the server URL in environment configuration echo "REACT_APP_API_URL=http://localhost:8080" > .env.local npm install && npm run build
    • Network accessline 63
      echo "REACT_APP_API_URL=http://localhost:8080" > .env.local
    • Network accessline 256
      - Algorithm Visualizer website: https://algorithm-visualizer.org
    • Network accessline 257
      - Algorithm Visualizer GitHub: https://github.com/algorithm-visualizer/algorithm-visualizer
    • Network accessline 258
      - Algorithms repository: https://github.com/algorithm-visualizer/algorithms
    • Network accessline 259
      - Visualization API documentation: https://github.com/algorithm-visualizer/algorithm-visualizer/wiki

    skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md

    • Network accessline 8
      subcategory: "dataviz"     keywords: ["Bokeh", "interactive plots", "Python visualization", "web dashboards", "scientific charts", "data exploration"]     source: "https://github.com/bokeh/bokeh"
    • Network accessline 9
      keywords: ["Bokeh", "interactive plots", "Python visualization", "web dashboards", "scientific charts", "data exploration"]     source: "https://github.com/bokeh/bokeh" ---
    • Network accessline 10
      source: "https://github.com/bokeh/bokeh"
    • Network accessline 267
      - Bokeh documentation: https://docs.bokeh.org
    • Network accessline 268
      - Bokeh GitHub repository: https://github.com/bokeh/bokeh
    • Network accessline 269
      - Bokeh gallery: https://docs.bokeh.org/en/latest/docs/gallery.html
    • Network accessline 270
      - HoloViews (high-level Bokeh wrapper): https://holoviews.org

    skills/analysis/dataviz/d3-visualization-guide/SKILL.md

    • Network accessline 8
      subcategory: "dataviz"     keywords: ["data visualization", "D3.js", "interactive charts", "SVG", "web visualization", "scientific plots"]     source: "https://github.com/d3/d3"
    • Network accessline 9
      keywords: ["data visualization", "D3.js", "interactive charts", "SVG", "web visualization", "scientific plots"]     source: "https://github.com/d3/d3" ---
    • Network accessline 10
      source: "https://github.com/d3/d3"
    • Network accessline 278
      - D3.js official documentation: https://d3js.org
    • Network accessline 279
      - D3 GitHub repository: https://github.com/d3/d3
    • Network accessline 280
      - Observable D3 tutorials: https://observablehq.com/@d3
    • Network accessline 281
      - D3 Graph Gallery (examples): https://d3-graph-gallery.com

    skills/analysis/dataviz/echarts-visualization-guide/SKILL.md

    • Network accessline 8
      subcategory: "dataviz"     keywords: ["ECharts", "interactive charts", "data dashboard", "Apache ECharts", "scientific charts", "research visualization"]     source: "https://github.com/apache/echarts"
    • Network accessline 9
      keywords: ["ECharts", "interactive charts", "data dashboard", "Apache ECharts", "scientific charts", "research visualization"]     source: "https://github.com/apache/echarts" ---
    • Network accessline 10
      source: "https://github.com/apache/echarts"
    • Network accessline 30
      <div id="chart" style="width: 800px; height: 500px;"></div> <script src="https://cdn.jsdelivr.net/npm/echarts@5/dist/echarts.min.js"></script>
    • Network accessline 31
      <script src="https://cdn.jsdelivr.net/npm/echarts@5/dist/echarts.min.js"></script>
    • Network accessline 217
      // Load CSV data and convert to ECharts format async function loadExperimentData(csvUrl) {   const response = await fetch(csvUrl);
    • Network accessline 218
      async function loadExperimentData(csvUrl) {   const response = await fetch(csvUrl);   const text = await response.text();
    • Network accessline 219
      const response = await fetch(csvUrl);
    • Network accessline 247
      - Apache ECharts official site: https://echarts.apache.org
    • Network accessline 248
      - ECharts GitHub repository: https://github.com/apache/echarts
    • Network accessline 249
      - ECharts examples gallery: https://echarts.apache.org/examples
    • Network accessline 250
      - ECharts configuration handbook: https://echarts.apache.org/en/option.html

    skills/analysis/dataviz/interactive-viz-guide/SKILL.md

    • Network accessline 152
      <html> <head>   <script src="https://cdn.jsdelivr.net/npm/echarts@5/dist/echarts.min.js"></script>
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      <head>   <script src="https://cdn.jsdelivr.net/npm/echarts@5/dist/echarts.min.js"></script> </head>
    • Network accessline 154
      <script src="https://cdn.jsdelivr.net/npm/echarts@5/dist/echarts.min.js"></script>

    skills/analysis/dataviz/metabase-analytics-guide/SKILL.md

    • Network accessline 8
      subcategory: "dataviz"     keywords: ["Metabase", "business intelligence", "SQL analytics", "data dashboard", "research analytics", "self-hosted BI"]     source: "https://github.com/metabase/metabase"
    • Network accessline 9
      keywords: ["Metabase", "business intelligence", "SQL analytics", "data dashboard", "research analytics", "self-hosted BI"]     source: "https://github.com/metabase/metabase" ---
    • Network accessline 10
      source: "https://github.com/metabase/metabase"
    • Network accessline 40
      # Access at http://localhost:3000
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      <!-- Embed a dashboard in a lab portal --> <iframe   src="http://metabase.lab.internal/public/dashboard/abc123-def456"
    • Network accessline 201
      <iframe   src="http://metabase.lab.internal/public/dashboard/abc123-def456"   frameborder="0"
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      src="http://metabase.lab.internal/public/dashboard/abc123-def456"
    • Access to secretsline 216
      [Credential-related source omitted]
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      signed = jwt.encode(payload, embedding_secret, algorithm="HS256") embed_url = f"http://metabase.lab.internal/embed/dashboard/{signed}"
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      embed_url = f"http://metabase.lab.internal/embed/dashboard/{signed}"
    • Network accessline 239
      - Metabase official documentation: https://www.metabase.com/docs
    • Network accessline 240
      - Metabase GitHub repository: https://github.com/metabase/metabase
    • Network accessline 241
      - Metabase embedding documentation: https://www.metabase.com/docs/latest/embedding
    • Network accessline 242
      - Metabase API reference: https://www.metabase.com/docs/latest/api

    skills/analysis/dataviz/plotly-interactive-guide/SKILL.md

    • Network accessline 8
      subcategory: "dataviz"     keywords: ["Plotly", "interactive visualization", "Dash", "Python charts", "scientific plots", "research figures"]     source: "https://github.com/plotly/plotly.py"
    • Network accessline 9
      keywords: ["Plotly", "interactive visualization", "Dash", "Python charts", "scientific plots", "research figures"]     source: "https://github.com/plotly/plotly.py" ---
    • Network accessline 10
      source: "https://github.com/plotly/plotly.py"
    • Network accessline 263
      - Plotly Python documentation: https://plotly.com/python/
    • Network accessline 264
      - Plotly.py GitHub repository: https://github.com/plotly/plotly.py
    • Network accessline 265
      - Dash documentation: https://dash.plotly.com
    • Network accessline 266
      - Plotly Express reference: https://plotly.com/python/plotly-express/

    skills/analysis/dataviz/python-dataviz-guide/SKILL.md

    • Network accessline 191
      - [matplotlib Documentation](https://matplotlib.org/stable/) -- Official reference
    • Network accessline 192
      - [seaborn Documentation](https://seaborn.pydata.org/) -- Statistical visualization
    • Network accessline 193
      - [plotly Documentation](https://plotly.com/python/) -- Interactive charts
    • Network accessline 194
      - [Scientific Visualization: Python + Matplotlib](https://github.com/rougier/scientific-visualization-book) -- Nicolas Rougier
    • Network accessline 195
      - [Ten Simple Rules for Better Figures](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003833) -- Rougier et al.

    skills/analysis/dataviz/redash-analytics-guide/SKILL.md

    • Network accessline 8
      subcategory: "dataviz"     keywords: ["Redash", "SQL dashboards", "data visualization", "query tool", "research analytics", "collaborative BI"]     source: "https://github.com/getredash/redash"
    • Network accessline 9
      keywords: ["Redash", "SQL dashboards", "data visualization", "query tool", "research analytics", "collaborative BI"]     source: "https://github.com/getredash/redash" ---
    • Network accessline 10
      source: "https://github.com/getredash/redash"
    • Network accessline 28
      # Clone the Redash setup repository git clone https://github.com/getredash/setup.git redash-setup
    • Network accessline 29
      git clone https://github.com/getredash/setup.git redash-setup
    • Access to secretsline 51
      [Credential-related source omitted]
    • Network accessline 248
      REDASH_URL = "http://redash.lab.internal"
    • Access to secretsline 249
      [Credential-related source omitted]
    • Network accessline 257
      response = requests.post(url, json=payload, headers=headers)
    • Network accessline 260
      # Poll for results     while job.get("status") not in (3, 4):         result = requests.get(
    • Network accessline 261
      while job.get("status") not in (3, 4):         result = requests.get(             f"{REDASH_URL}/api/jobs/{job['id']}",
    • Network accessline 262
      result = requests.get(
    • Network accessline 268
      # Fetch final results     result = requests.get(
    • Network accessline 269
      result = requests.get(
    • Network accessline 281
      - Redash official documentation: https://redash.io/help
    • Network accessline 282
      - Redash GitHub repository: https://github.com/getredash/redash
    • Network accessline 283
      - Redash setup guide: https://redash.io/help/open-source/setup
    • Network accessline 284
      - Redash API reference: https://redash.io/help/user-guide/integrations-and-api/api

    skills/analysis/econometrics/econml-causal-guide/SKILL.md

    • Network accessline 8
      subcategory: "econometrics"     keywords: ["causal-inference", "machine-learning", "treatment-effects", "econometrics", "microsoft", "double-ml"]     source: "https://github.com/py-why/EconML"
    • Network accessline 9
      keywords: ["causal-inference", "machine-learning", "treatment-effects", "econometrics", "microsoft", "double-ml"]     source: "https://github.com/py-why/EconML" ---
    • Network accessline 10
      source: "https://github.com/py-why/EconML"
    • Network accessline 160
      - EconML repository: https://github.com/py-why/EconML
    • Network accessline 161
      - EconML documentation: https://econml.azurewebsites.net/

    skills/analysis/econometrics/mostly-harmless-guide/SKILL.md

    • Network accessline 8
      subcategory: "econometrics"     keywords: ["econometrics", "causal-inference", "replication", "regression", "instrumental-variables", "difference-in-differences"]     source: "https://github.com/vikjam/mostly-harmless-replication"
    • Network accessline 9
      keywords: ["econometrics", "causal-inference", "replication", "regression", "instrumental-variables", "difference-in-differences"]     source: "https://github.com/vikjam/mostly-harmless-replication" ---
    • Network accessline 10
      source: "https://github.com/vikjam/mostly-harmless-replication"

    skills/analysis/econometrics/python-causality-guide/SKILL.md

    • Network accessline 8
      subcategory: "econometrics"     keywords: ["causal-inference", "python", "econometrics", "statistics", "treatment-effects", "observational-studies"]     source: "https://github.com/matheusfacure/python-causality-handbook"
    • Network accessline 9
      keywords: ["causal-inference", "python", "econometrics", "statistics", "treatment-effects", "observational-studies"]     source: "https://github.com/matheusfacure/python-causality-handbook" ---
    • Network accessline 10
      source: "https://github.com/matheusfacure/python-causality-handbook"
    • Network accessline 28
      git clone https://github.com/matheusfacure/python-causality-handbook.git
    • Network accessline 131
      - Python Causality Handbook: https://github.com/matheusfacure/python-causality-handbook
    • Network accessline 132
      - Online version: https://matheusfacure.github.io/python-causality-handbook/

    skills/analysis/econometrics/stata-analyst-guide/SKILL.md

    • Network accessline 8
      subcategory: "econometrics"     keywords: ["Stata", "sociology", "social science", "survey data", "regression", "publication tables"]     source: "https://www.stata.com"
    • Network accessline 9
      keywords: ["Stata", "sociology", "social science", "survey data", "regression", "publication tables"]     source: "https://www.stata.com" ---
    • Network accessline 10
      source: "https://www.stata.com"
    • Network accessline 241
      - Stata Survey Data Reference Manual: https://www.stata.com/manuals/svy.pdf
    • Network accessline 242
      - Mitchell, M. (2021), A Visual Guide to Stata Graphics, 4th ed., Stata Press - Long & Freese (2014), Regression Models for Categorical Dependent Variables Using Stata, 3rd ed. - esttab/estout documentation: http://repec.sowi.unibe.ch/stata
    • Network accessline 243
      - Long & Freese (2014), Regression Models for Categorical Dependent Variables Using Stata, 3rd ed. - esttab/estout documentation: http://repec.sowi.unibe.ch/stata/estout/ - ASA Style Guide: https://www.asanet.org/publications/style-guide/
    • Network accessline 244
      - esttab/estout documentation: http://repec.sowi.unibe.ch/stata/estout/
    • Network accessline 245
      - ASA Style Guide: https://www.asanet.org/publications/style-guide/

    skills/analysis/econometrics/stata-reference-guide/SKILL.md

    • Network accessline 8
      subcategory: "econometrics"     keywords: ["stata", "econometrics", "panel data", "causal inference", "community packages", "data management", "regression"]     source: "https://github.com/dylantmoore/stata-skill"
    • Network accessline 9
      keywords: ["stata", "econometrics", "panel data", "causal inference", "community packages", "data management", "regression"]     source: "https://github.com/dylantmoore/stata-skill" ---
    • Network accessline 10
      source: "https://github.com/dylantmoore/stata-skill"
    • Network accessline 201
      * Install from GitHub net install did_multiplegt, from("https://raw.githubusercontent.com/chaisemartinDehejia/did_multiplegt/main")
    • Network accessline 202
      net install did_multiplegt, from("https://raw.githubusercontent.com/chaisemartinDehejia/did_multiplegt/main")
    • Network accessline 289
      - [Stata Official Documentation](https://www.stata.com/manuals/)
    • Network accessline 290
      - [UCLA Stata FAQ](https://stats.oarc.ucla.edu/stata/faq/)
    • Network accessline 291
      - [Stata Journal](https://www.stata-journal.com/)
    • Network accessline 292
      - [SSC Archive](https://ideas.repec.org/s/boc/bocode.html)
    • Network accessline 293
      - [dylantmoore/stata-skill](https://github.com/dylantmoore/stata-skill) — Source for this reference

    skills/analysis/statistics/hypothesis-testing-guide/SKILL.md

    • Network accessline 206
      - [scipy.stats Documentation](https://docs.scipy.org/doc/scipy/reference/stats.html)
    • Network accessline 207
      - [pingouin Documentation](https://pingouin-stats.org/) -- Friendly statistics in Python
    • Network accessline 208
      - [statsmodels Documentation](https://www.statsmodels.org/)
    • Network accessline 209
      - [APA 7th Edition Statistics Reporting Guide](https://apastyle.apa.org/instructional-aids/numbers-statistics-guide.pdf)
    • Network accessline 210
      - [Statistical Tests Cheat Sheet](https://machinelearningmastery.com/statistical-hypothesis-tests-in-python-cheat-sheet/)

    skills/analysis/wrangling/data-cog-guide/SKILL.md

    • Network accessline 176
      - Breck, E., et al. (2019). Data Validation for Machine Learning. *MLSys 2019*. - Hynes, N., et al. (2017). The Data Linter: Lightweight, Automated Sanity Checking for ML Data Sets. *NIPS MLSys Workshop*. - Pandas Development Team (2024). *
    • Network accessline 178
      - Pandas Development Team (2024). *pandas: Powerful Python Data Analysis Toolkit*. https://pandas.pydata.org/

    skills/analysis/wrangling/pandas-data-wrangling/SKILL.md

    • Network accessline 239
      - [pandas Documentation](https://pandas.pydata.org/docs/) -- Official reference
    • Network accessline 240
      - [Python for Data Analysis, 3rd Edition](https://wesmckinney.com/book/) -- Wes McKinney
    • Network accessline 241
      - [Effective Pandas](https://store.metasnake.com/effective-pandas-book) -- Matt Harrison
    • Network accessline 242
      - [pandas Cookbook](https://github.com/jvns/pandas-cookbook) -- Julia Evans

    skills/analysis/wrangling/stata-data-cleaning/SKILL.md

    • Network accessline 8
      subcategory: "wrangling"     keywords: ["Stata", "data cleaning", "data wrangling", "missing values", "recoding", "validation"]     source: "https://www.stata.com/manuals/d.pdf"
    • Network accessline 9
      keywords: ["Stata", "data cleaning", "data wrangling", "missing values", "recoding", "validation"]     source: "https://www.stata.com/manuals/d.pdf" ---
    • Network accessline 10
      source: "https://www.stata.com/manuals/d.pdf"
    • Network accessline 273
      - Stata Data Management Reference Manual: https://www.stata.com/manuals/d.pdf
    • Network accessline 274
      - DIME Analytics Data Management Wiki: https://dimewiki.worldbank.org/Data_Management
    • Network accessline 275
      - J-PAL Research Resources: https://www.povertyactionlab.org/resource/data-cleaning

    skills/analysis/wrangling/streamline-analyst-guide/SKILL.md

    • Network accessline 8
      subcategory: "wrangling"     keywords: ["data analysis", "Streamlit", "automated EDA", "machine learning", "data science", "AI analyst"]     source: "https://github.com/Wilson-ZheLin/Streamline-Analyst"
    • Network accessline 9
      keywords: ["data analysis", "Streamlit", "automated EDA", "machine learning", "data science", "AI analyst"]     source: "https://github.com/Wilson-ZheLin/Streamline-Analyst" ---
    • Network accessline 10
      source: "https://github.com/Wilson-ZheLin/Streamline-Analyst"
    • Network accessline 22
      git clone https://github.com/Wilson-ZheLin/Streamline-Analyst.git
    • Network accessline 118
      - [Streamline-Analyst GitHub](https://github.com/Wilson-ZheLin/Streamline-Analyst)
    • Network accessline 119
      - [Streamlit](https://streamlit.io/)

    skills/domains/ai-ml/ai-agent-papers-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["AI agents", "agent papers", "2024 research", "LLM agents", "agent frameworks", "survey"]     source: "https://github.com/VoltAgent/awesome-ai-agent-papers"
    • Network accessline 9
      keywords: ["AI agents", "agent papers", "2024 research", "LLM agents", "agent frameworks", "survey"]     source: "https://github.com/VoltAgent/awesome-ai-agent-papers" ---
    • Network accessline 10
      source: "https://github.com/VoltAgent/awesome-ai-agent-papers"
    • Network accessline 145
      - [awesome-ai-agent-papers](https://github.com/VoltAgent/awesome-ai-agent-papers)
    • Network accessline 146
      - [VoltAgent Framework](https://github.com/VoltAgent/voltagent)

    skills/domains/ai-ml/ai-model-benchmarking/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["benchmarking", "evaluation", "LLM", "MMLU", "leaderboard", "metrics", "lm-eval"]     source: "https://github.com/EleutherAI/lm-evaluation-harness"
    • Network accessline 9
      keywords: ["benchmarking", "evaluation", "LLM", "MMLU", "leaderboard", "metrics", "lm-eval"]     source: "https://github.com/EleutherAI/lm-evaluation-harness" ---
    • Network accessline 10
      source: "https://github.com/EleutherAI/lm-evaluation-harness"
    • Network accessline 205
      - [lm-evaluation-harness](https://github.com/EleutherAI/lm-evaluation-harness) -- EleutherAI's evaluation framework (12,000+ stars)
    • Network accessline 206
      - [Open LLM Leaderboard](https://huggingface.co/spaces/HuggingFaceH4/open_llm_leaderboard) -- Hugging Face community leaderboard
    • Network accessline 207
      - [MMLU paper](https://arxiv.org/abs/2009.03300) -- Hendrycks et al., 2021
    • Network accessline 208
      - [Holistic Evaluation of Language Models (HELM)](https://crfm.stanford.edu/helm/) -- Stanford CRFM
    • Network accessline 209
      - [Chatbot Arena](https://chat.lmsys.org/) -- Human preference-based evaluation (LMSYS)

    skills/domains/ai-ml/anomaly-detection-papers-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["anomaly detection", "industrial inspection", "defect detection", "MVTec", "unsupervised AD", "visual inspection"]     source: "https://github.com/M-3LAB/awesome-industrial-anomaly-detection"
    • Network accessline 9
      keywords: ["anomaly detection", "industrial inspection", "defect detection", "MVTec", "unsupervised AD", "visual inspection"]     source: "https://github.com/M-3LAB/awesome-industrial-anomaly-detection" ---
    • Network accessline 10
      source: "https://github.com/M-3LAB/awesome-industrial-anomaly-detection"
    • Network accessline 165
      - [awesome-industrial-anomaly-detection](https://github.com/M-3LAB/awesome-industrial-anomaly-detection)
    • Network accessline 166
      - [Anomalib Library](https://github.com/openvinotoolkit/anomalib)
    • Network accessline 167
      - [MVTec AD Dataset](https://www.mvtec.com/company/research/datasets/mvtec-ad)

    skills/domains/ai-ml/autonomous-agents-papers-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["autonomous agents", "AI agents", "LLM agents", "agent papers", "planning", "tool use"]     source: "https://github.com/tmgthb/Autonomous-Agents"
    • Network accessline 9
      keywords: ["autonomous agents", "AI agents", "LLM agents", "agent papers", "planning", "tool use"]     source: "https://github.com/tmgthb/Autonomous-Agents" ---
    • Network accessline 10
      source: "https://github.com/tmgthb/Autonomous-Agents"
    • Network accessline 176
      - [Autonomous-Agents GitHub](https://github.com/tmgthb/Autonomous-Agents)
    • Network accessline 177
      - [LLM-Agent-Paper-List](https://github.com/WooooDyy/LLM-Agent-Paper-List)
    • Network accessline 178
      - [Agent Survey](https://arxiv.org/abs/2308.11432)

    skills/domains/ai-ml/deep-learning-papers-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["deep learning", "neural network", "Transformer", "CNN", "NLP", "computer vision"]     source: "https://github.com/labmlai/annotated_deep_learning_paper_implementations"
    • Network accessline 9
      keywords: ["deep learning", "neural network", "Transformer", "CNN", "NLP", "computer vision"]     source: "https://github.com/labmlai/annotated_deep_learning_paper_implementations" ---
    • Network accessline 10
      source: "https://github.com/labmlai/annotated_deep_learning_paper_implementations"
    • Network accessline 196
      - [annotated_deep_learning_paper_implementations](https://github.com/labmlai/annotated_deep_learning_paper_implementations) -- Line-by-line annotated implementations (65,800+ stars)
    • Network accessline 197
      - [Attention Is All You Need](https://arxiv.org/abs/1706.03762) -- Original Transformer paper
    • Network accessline 198
      - [Deep Residual Learning](https://arxiv.org/abs/1512.03385) -- ResNet paper
    • Network accessline 199
      - [The Illustrated Transformer](https://jalammar.github.io/illustrated-transformer/) -- Jay Alammar's visual guide
    • Network accessline 200
      - [Papers With Code](https://paperswithcode.com/) -- Paper-implementation pairs with benchmarks

    skills/domains/ai-ml/dl-transformer-finetune/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["transformer", "fine-tuning", "BERT", "LoRA", "PEFT", "transfer learning", "NLP"]     source: "https://github.com/huggingface/peft"
    • Network accessline 9
      keywords: ["transformer", "fine-tuning", "BERT", "LoRA", "PEFT", "transfer learning", "NLP"]     source: "https://github.com/huggingface/peft" ---
    • Network accessline 10
      source: "https://github.com/huggingface/peft"
    • Network accessline 235
      - [LoRA paper](https://arxiv.org/abs/2106.09685) -- Hu et al., 2021
    • Network accessline 236
      - [QLoRA paper](https://arxiv.org/abs/2305.14314) -- Dettmers et al., 2023
    • Network accessline 237
      - [PEFT library](https://github.com/huggingface/peft) -- Hugging Face parameter-efficient fine-tuning
    • Network accessline 238
      - [ULMFiT](https://arxiv.org/abs/1801.06146) -- Howard & Ruder, 2018 (gradual unfreezing, discriminative LR)
    • Network accessline 239
      - [Hugging Face Transformers Trainer](https://huggingface.co/docs/transformers/main_classes/trainer) -- Training API documentation

    skills/domains/ai-ml/domain-adaptation-papers-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["domain adaptation", "transfer learning", "distribution shift", "domain gap", "UDA", "domain generalization"]     source: "https://github.com/zhaoxin94/awesome-domain-adaptation"
    • Network accessline 9
      keywords: ["domain adaptation", "transfer learning", "distribution shift", "domain gap", "UDA", "domain generalization"]     source: "https://github.com/zhaoxin94/awesome-domain-adaptation" ---
    • Network accessline 10
      source: "https://github.com/zhaoxin94/awesome-domain-adaptation"
    • Network accessline 171
      - [awesome-domain-adaptation](https://github.com/zhaoxin94/awesome-domain-adaptation)
    • Network accessline 172
      - [Transfer Learning Library](https://github.com/thuml/Transfer-Learning-Library)
    • Network accessline 173
      - [DomainBed](https://github.com/facebookresearch/DomainBed)

    skills/domains/ai-ml/generative-ai-guide/SKILL.md

    • Network accessline 2
      name: generative-ai-guide description: "Curated guide to generative AI covering LLMs and diffusion models" source: https://github.com/aishwaryanr/awesome-generative-ai-guide
    • Network accessline 3
      description: "Curated guide to generative AI covering LLMs and diffusion models" source: https://github.com/aishwaryanr/awesome-generative-ai-guide metadata:
    • Network accessline 4
      source: https://github.com/aishwaryanr/awesome-generative-ai-guide

    skills/domains/ai-ml/graph-learning-papers-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["graph neural network", "GNN", "graph learning", "graph transformer", "message passing", "node classification"]     source: "https://github.com/doujiang-zheng/Awesome-Graph-Learning-Papers-List"
    • Network accessline 9
      keywords: ["graph neural network", "GNN", "graph learning", "graph transformer", "message passing", "node classification"]     source: "https://github.com/doujiang-zheng/Awesome-Graph-Learning-Papers-List" ---
    • Network accessline 10
      source: "https://github.com/doujiang-zheng/Awesome-Graph-Learning-Papers-List"
    • Network accessline 122
      - [Awesome-Graph-Learning-Papers-List](https://github.com/doujiang-zheng/Awesome-Graph-Learning-Papers-List)
    • Network accessline 123
      - [Open Graph Benchmark](https://ogb.stanford.edu/)
    • Network accessline 124
      - [PyG (PyTorch Geometric)](https://pyg.org/)
    • Network accessline 125
      - [DGL (Deep Graph Library)](https://www.dgl.ai/)

    skills/domains/ai-ml/huggingface-api/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["Hugging Face", "ML models", "datasets", "model hub", "transformers", "NLP", "computer vision"]     source: "https://huggingface.co/docs/hub/api"
    • Network accessline 9
      keywords: ["Hugging Face", "ML models", "datasets", "model hub", "transformers", "NLP", "computer vision"]     source: "https://huggingface.co/docs/hub/api" ---
    • Network accessline 10
      source: "https://huggingface.co/docs/hub/api"
    • Network accessline 17
      The Hugging Face Hub is the largest open-source ML ecosystem, hosting over 1 million models, 200,000+ datasets, and 400,000+ Spaces (demo apps). The Hub API at `https://huggingface.co/api` provides programmatic access to search, discover, a
    • Network accessline 28
      [Credential-related source omitted]
    • Access to secretsline 28
      [Credential-related source omitted]
    • Network accessline 30
      [Credential-related source omitted]
    • Access to secretsline 30
      [Credential-related source omitted]
    • Network accessline 33
      Generate tokens at: https://huggingface.co/settings/tokens
    • Network accessline 40
      GET https://huggingface.co/api/models?search={query}&limit={n}&sort={field}&direction={-1|1}
    • Network accessline 48
      curl -s "https://huggingface.co/api/models?search=bert&limit=2&sort=downloads&direction=-1"
    • Network accessline 76
      GET https://huggingface.co/api/models/{owner}/{model_name}
    • Network accessline 82
      curl -s "https://huggingface.co/api/models/google-bert/bert-base-uncased"
    • Network accessline 102
      GET https://huggingface.co/api/datasets?search={query}&limit={n}
    • Network accessline 108
      curl -s "https://huggingface.co/api/datasets?search=squad&limit=2"
    • Network accessline 128
      GET https://huggingface.co/api/datasets/{owner}/{dataset_name}
    • Network accessline 132
      curl -s "https://huggingface.co/api/datasets/rajpurkar/squad_v2"
    • Network accessline 140
      GET https://huggingface.co/api/spaces?search={query}&limit={n}
    • Network accessline 144
      curl -s "https://huggingface.co/api/spaces?search=chatbot&limit=2"
    • Network accessline 168
      # PyTorch text-generation models with 1000+ likes curl -s "https://huggingface.co/api/models?filter=text-generation&library=pytorch&sort=likes&direction=-1&limit=5"
    • Network accessline 169
      curl -s "https://huggingface.co/api/models?filter=text-generation&library=pytorch&sort=likes&direction=-1&limit=5"
    • Network accessline 171
      # Datasets for NER tasks in Chinese curl -s "https://huggingface.co/api/datasets?filter=token-classification&language=zh&limit=10"
    • Network accessline 172
      curl -s "https://huggingface.co/api/datasets?filter=token-classification&language=zh&limit=10"
    • Network accessline 174
      # Gradio Spaces sorted by trending curl -s "https://huggingface.co/api/spaces?filter=gradio&sort=trending&direction=-1&limit=5"
    • Network accessline 175
      curl -s "https://huggingface.co/api/spaces?filter=gradio&sort=trending&direction=-1&limit=5"
    • Network accessline 200
      # Search for top text-classification models resp = requests.get("https://huggingface.co/api/models", params={
    • Network accessline 201
      resp = requests.get("https://huggingface.co/api/models", params={
    • Network accessline 211
      # Get specific model metadata detail = requests.get("https://huggingface.co/api/models/google-bert/bert-base-uncased").json()
    • Network accessline 212
      detail = requests.get("https://huggingface.co/api/models/google-bert/bert-base-uncased").json()
    • Network accessline 246
      - Hub API documentation: https://huggingface.co/docs/hub/api
    • Network accessline 247
      - huggingface_hub Python library: https://huggingface.co/docs/huggingface_hub/
    • Network accessline 248
      - Model Hub: https://huggingface.co/models
    • Network accessline 249
      - Dataset Hub: https://huggingface.co/datasets
    • Network accessline 250
      - Spaces: https://huggingface.co/spaces
    • Network accessline 251
      - OpenAPI spec: https://huggingface.co/docs/hub/api#openapi

    skills/domains/ai-ml/huggingface-inference-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["huggingface", "inference", "nlp", "machine-learning", "transformers", "models"]     source: "https://huggingface.co/docs/api-inference/index"
    • Network accessline 9
      keywords: ["huggingface", "inference", "nlp", "machine-learning", "transformers", "models"]     source: "https://huggingface.co/docs/api-inference/index" ---
    • Network accessline 10
      source: "https://huggingface.co/docs/api-inference/index"
    • Network accessline 25
      A free Hugging Face API token is required. Create an account and generate a token at https://huggingface.co/settings/tokens.
    • Access to secretsline 30
      [Credential-related source omitted]
    • Network accessline 34
      [Credential-related source omitted]
    • Access to secretsline 34
      [Credential-related source omitted]
    • Access to secretsline 35
      [Credential-related source omitted]
    • Network accessline 45
      POST https://api-inference.huggingface.co/models/{model_id}
    • Dangerous shell operationline 49
      [Credential-related source omitted]
    • Network accessline 49
      [Credential-related source omitted]
    • Access to secretsline 49
      [Credential-related source omitted]
    • Network accessline 50
      "https://api-inference.huggingface.co/models/distilbert-base-uncased-finetuned-sst-2-english" \
    • Access to secretsline 51
      [Credential-related source omitted]
    • Dangerous shell operationline 60
      [Credential-related source omitted]
    • Network accessline 60
      [Credential-related source omitted]
    • Access to secretsline 60
      [Credential-related source omitted]
    • Network accessline 61
      "https://api-inference.huggingface.co/models/dslim/bert-base-NER" \
    • Access to secretsline 62
      [Credential-related source omitted]
    • Network accessline 71
      [Credential-related source omitted]
    • Access to secretsline 71
      [Credential-related source omitted]
    • Network accessline 72
      "https://api-inference.huggingface.co/models/facebook/bart-large-cnn" \
    • Access to secretsline 73
      [Credential-related source omitted]
    • Network accessline 86
      [Credential-related source omitted]
    • Access to secretsline 86
      [Credential-related source omitted]
    • Network accessline 87
      "https://api-inference.huggingface.co/models/facebook/bart-large-mnli" \
    • Access to secretsline 88
      [Credential-related source omitted]
    • Network accessline 103
      API_URL = "https://api-inference.huggingface.co/models/distilbert-base-uncased-finetuned-sst-2-english"
    • Access to secretsline 104
      [Credential-related source omitted]
    • Network accessline 106
      def classify_sentiment(texts):     """Classify sentiment for a batch of texts."""     response = requests.post(API_URL, headers=HEADERS, json={"inputs": texts})
    • Network accessline 107
      """Classify sentiment for a batch of texts."""     response = requests.post(API_URL, headers=HEADERS, json={"inputs": texts})     if response.status_code == 503:
    • Network accessline 108
      response = requests.post(API_URL, headers=HEADERS, json={"inputs": texts})
    • Network accessline 112
      print(f"Model loading, waiting {wait_time:.0f}s...")         time.sleep(wait_time)         response = requests.post(API_URL, headers=HEADERS, json={"inputs": texts})
    • Network accessline 113
      time.sleep(wait_time)         response = requests.post(API_URL, headers=HEADERS, json={"inputs": texts})     response.raise_for_status()
    • Network accessline 114
      response = requests.post(API_URL, headers=HEADERS, json={"inputs": texts})
    • Network accessline 138
      ZSC_URL = "https://api-inference.huggingface.co/models/facebook/bart-large-mnli"
    • Access to secretsline 139
      [Credential-related source omitted]
    • Network accessline 145
      "parameters": {"candidate_labels": categories}     }     resp = requests.post(ZSC_URL, headers=HEADERS, json=payload)
    • Network accessline 146
      }     resp = requests.post(ZSC_URL, headers=HEADERS, json=payload)     resp.raise_for_status()
    • Network accessline 147
      resp = requests.post(ZSC_URL, headers=HEADERS, json=payload)
    • Network accessline 193
      - Hugging Face Inference API Documentation: https://huggingface.co/docs/api-inference/index
    • Network accessline 194
      - Hugging Face Model Hub: https://huggingface.co/models
    • Network accessline 195
      - Hugging Face API Token Settings: https://huggingface.co/settings/tokens
    • Network accessline 196
      - Hugging Face Tasks Overview: https://huggingface.co/tasks

    skills/domains/ai-ml/keras-deep-learning/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["Keras", "deep learning", "neural network", "model training", "TensorFlow", "classification"]     source: "https://github.com/fchollet/deep-learning-with-python-notebooks"
    • Network accessline 9
      keywords: ["Keras", "deep learning", "neural network", "model training", "TensorFlow", "classification"]     source: "https://github.com/fchollet/deep-learning-with-python-notebooks" ---
    • Network accessline 10
      source: "https://github.com/fchollet/deep-learning-with-python-notebooks"
    • Access to secretsline 123
      [Credential-related source omitted]
    • Network accessline 206
      - [Deep Learning with Python, 2nd Edition](https://www.manning.com/books/deep-learning-with-python-second-edition) -- Francois Chollet (Keras creator)
    • Network accessline 207
      - [Keras documentation](https://keras.io/) -- Official API reference and guides
    • Network accessline 208
      - [TensorFlow tutorials](https://www.tensorflow.org/tutorials) -- End-to-end examples
    • Network accessline 209
      - [fchollet/deep-learning-with-python-notebooks](https://github.com/fchollet/deep-learning-with-python-notebooks) -- Code companion to the book
    • Network accessline 210
      - [Keras examples gallery](https://keras.io/examples/) -- 100+ community-contributed examples

    skills/domains/ai-ml/kolmogorov-arnold-networks-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["KAN", "Kolmogorov-Arnold", "learnable activations", "spline networks", "neural architecture", "interpretability"]     source: "https://github.com/mintisan/awesome-kan"
    • Network accessline 9
      keywords: ["KAN", "Kolmogorov-Arnold", "learnable activations", "spline networks", "neural architecture", "interpretability"]     source: "https://github.com/mintisan/awesome-kan" ---
    • Network accessline 10
      source: "https://github.com/mintisan/awesome-kan"
    • Network accessline 182
      - [awesome-kan](https://github.com/mintisan/awesome-kan)
    • Network accessline 183
      - [KAN Paper](https://arxiv.org/abs/2404.19756)
    • Network accessline 184
      - [pykan Implementation](https://github.com/KindXiaoming/pykan)
    • Network accessline 185
      - [KAN 2.0 Paper](https://arxiv.org/abs/2408.10205)

    skills/domains/ai-ml/llm-from-scratch-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["llm", "pytorch", "transformer", "gpt", "pretraining", "finetuning"]     source: "https://github.com/rasbt/LLMs-from-scratch"
    • Network accessline 9
      keywords: ["llm", "pytorch", "transformer", "gpt", "pretraining", "finetuning"]     source: "https://github.com/rasbt/LLMs-from-scratch" ---
    • Network accessline 10
      source: "https://github.com/rasbt/LLMs-from-scratch"
    • Network accessline 28
      git clone https://github.com/rasbt/LLMs-from-scratch.git
    • Network accessline 121
      - Repository: https://github.com/rasbt/LLMs-from-scratch
    • Network accessline 122
      - Book: "Build a Large Language Model (From Scratch)" by Sebastian Raschka (Manning, 2024) - Author's blog: https://sebastianraschka.com/blog/ - PyTorch documentation: https://pytorch.org/docs/stable/
    • Network accessline 123
      - Author's blog: https://sebastianraschka.com/blog/
    • Network accessline 124
      - PyTorch documentation: https://pytorch.org/docs/stable/

    skills/domains/ai-ml/ml-pipeline-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["MLOps", "pipeline", "deployment", "reproducibility", "feature engineering", "CI/CD"]     source: "https://github.com/mlflow/mlflow"
    • Network accessline 9
      keywords: ["MLOps", "pipeline", "deployment", "reproducibility", "feature engineering", "CI/CD"]     source: "https://github.com/mlflow/mlflow" ---
    • Network accessline 10
      source: "https://github.com/mlflow/mlflow"
    • Dangerous shell operationline 276
      rm -rf outputs/ multirun/ __pycache__/
    • Network accessline 291
      - [MLflow documentation](https://mlflow.org/docs/latest/) -- Experiment tracking and model registry
    • Network accessline 292
      - [DVC documentation](https://dvc.org/doc) -- Data version control for ML
    • Network accessline 293
      - [Hydra documentation](https://hydra.cc/) -- Configuration management framework
    • Network accessline 294
      - [Cookiecutter Data Science](https://drivendata.github.io/cookiecutter-data-science/) -- Project structure template
    • Network accessline 295
      - [Made With ML](https://madewithml.com/) -- MLOps best practices for researchers

    skills/domains/ai-ml/nlp-toolkit-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["NLP", "perplexity", "burstiness", "entropy", "tokenization", "text analysis"]     source: "https://github.com/huggingface/transformers"
    • Network accessline 9
      keywords: ["NLP", "perplexity", "burstiness", "entropy", "tokenization", "text analysis"]     source: "https://github.com/huggingface/transformers" ---
    • Network accessline 10
      source: "https://github.com/huggingface/transformers"
    • Network accessline 243
      - [Hugging Face Transformers](https://huggingface.co/docs/transformers/) -- Model hub and tokenizer library
    • Network accessline 244
      - [DetectGPT](https://arxiv.org/abs/2301.11305) -- Perplexity-based AI text detection (Mitchell et al., 2023)
    • Network accessline 245
      - [Burstiness and Memory in Text](https://doi.org/10.1103/PhysRevLett.114.078101) -- Altmann et al., 2015
    • Network accessline 246
      - [NLTK documentation](https://www.nltk.org/) -- Classic NLP toolkit for feature engineering
    • Network accessline 247
      - [spaCy documentation](https://spacy.io/) -- Industrial-strength NLP for production pipelines

    skills/domains/ai-ml/npcpy-research-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["npcpy", "NLP", "agents", "knowledge graph", "all-in-one", "Python library"]     source: "https://github.com/NPC-Worldwide/npcpy"
    • Network accessline 9
      keywords: ["npcpy", "NLP", "agents", "knowledge graph", "all-in-one", "Python library"]     source: "https://github.com/NPC-Worldwide/npcpy" ---
    • Network accessline 10
      source: "https://github.com/NPC-Worldwide/npcpy"
    • Network accessline 137
      - [npcpy GitHub](https://github.com/NPC-Worldwide/npcpy)

    skills/domains/ai-ml/pytorch-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["PyTorch", "deep learning", "training loop", "GPU", "debugging", "autograd"]     source: "https://github.com/pytorch/pytorch"
    • Network accessline 9
      keywords: ["PyTorch", "deep learning", "training loop", "GPU", "debugging", "autograd"]     source: "https://github.com/pytorch/pytorch" ---
    • Network accessline 10
      source: "https://github.com/pytorch/pytorch"
    • Network accessline 277
      - [PyTorch documentation](https://pytorch.org/docs/stable/) -- Official API reference
    • Network accessline 278
      - [PyTorch tutorials](https://pytorch.org/tutorials/) -- End-to-end examples from the PyTorch team
    • Network accessline 279
      - [PyTorch best practices](https://pytorch.org/docs/stable/notes/cuda.html) -- CUDA semantics and best practices
    • Network accessline 280
      - [Effective PyTorch](https://github.com/vahidk/EffectivePyTorch) -- Community best practices guide
    • Network accessline 281
      - [PyTorch Lightning](https://lightning.ai/) -- High-level training framework built on PyTorch

    skills/domains/ai-ml/pytorch-lightning-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["pytorch-lightning", "training", "distributed", "finetuning", "scalability", "research"]     source: "https://github.com/Lightning-AI/pytorch-lightning"
    • Network accessline 9
      keywords: ["pytorch-lightning", "training", "distributed", "finetuning", "scalability", "research"]     source: "https://github.com/Lightning-AI/pytorch-lightning" ---
    • Network accessline 10
      source: "https://github.com/Lightning-AI/pytorch-lightning"
    • Network accessline 241
      - Repository: https://github.com/Lightning-AI/pytorch-lightning
    • Network accessline 242
      - Documentation: https://lightning.ai/docs/pytorch/stable/
    • Network accessline 243
      - Lightning AI platform: https://lightning.ai/
    • Network accessline 244
      - Migration guide from vanilla PyTorch: https://lightning.ai/docs/pytorch/stable/starter/converting.html

    skills/domains/ai-ml/responsible-ai-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["responsible AI", "AI ethics", "fairness", "trustworthy AI", "AI safety", "bias"]     source: "https://github.com/AthenaCore/AwesomeResponsibleAI"
    • Network accessline 9
      keywords: ["responsible AI", "AI ethics", "fairness", "trustworthy AI", "AI safety", "bias"]     source: "https://github.com/AthenaCore/AwesomeResponsibleAI" ---
    • Network accessline 10
      source: "https://github.com/AthenaCore/AwesomeResponsibleAI"
    • Network accessline 124
      - [AwesomeResponsibleAI](https://github.com/AthenaCore/AwesomeResponsibleAI)
    • Network accessline 125
      - [Fairlearn](https://fairlearn.org/)
    • Network accessline 126
      - [EU AI Act](https://artificialintelligenceact.eu/)

    skills/domains/ai-ml/tensorflow-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["TensorFlow", "tf.function", "GPU", "SavedModel", "distributed training", "XLA"]     source: "https://github.com/tensorflow/tensorflow"
    • Network accessline 9
      keywords: ["TensorFlow", "tf.function", "GPU", "SavedModel", "distributed training", "XLA"]     source: "https://github.com/tensorflow/tensorflow" ---
    • Network accessline 10
      source: "https://github.com/tensorflow/tensorflow"
    • Network accessline 237
      - [TensorFlow documentation](https://www.tensorflow.org/guide) -- Official guides and API reference
    • Network accessline 238
      - [Better performance with tf.function](https://www.tensorflow.org/guide/function) -- Tracing semantics deep dive
    • Network accessline 239
      - [Distributed training guide](https://www.tensorflow.org/guide/distributed_training) -- Multi-GPU and multi-node patterns
    • Network accessline 240
      - [TensorFlow Model Garden](https://github.com/tensorflow/models) -- Reference implementations of SOTA models
    • Network accessline 241
      - [XLA documentation](https://www.tensorflow.org/xla) -- Hardware-accelerated compilation

    skills/domains/ai-ml/vmas-simulator-guide/SKILL.md

    • Network accessline 8
      subcategory: "ai-ml"     keywords: ["multi-agent RL", "VMAS", "simulator", "reinforcement learning", "vectorized", "cooperative"]     source: "https://github.com/proroklab/VectorizedMultiAgentSimulator"
    • Network accessline 9
      keywords: ["multi-agent RL", "VMAS", "simulator", "reinforcement learning", "vectorized", "cooperative"]     source: "https://github.com/proroklab/VectorizedMultiAgentSimulator" ---
    • Network accessline 10
      source: "https://github.com/proroklab/VectorizedMultiAgentSimulator"
    • Network accessline 127
      - [VMAS GitHub](https://github.com/proroklab/VectorizedMultiAgentSimulator)
    • Network accessline 128
      - [VMAS Paper](https://arxiv.org/abs/2207.03530)
    • Network accessline 129
      - [BenchMARL](https://github.com/facebookresearch/BenchMARL)

    skills/domains/biomedical/alphafold-api/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["protein structure", "AlphaFold", "structure prediction", "UniProt", "pLDDT", "bioinformatics"]     source: "https://alphafold.ebi.ac.uk"
    • Network accessline 9
      keywords: ["protein structure", "AlphaFold", "structure prediction", "UniProt", "pLDDT", "bioinformatics"]     source: "https://alphafold.ebi.ac.uk" ---
    • Network accessline 10
      source: "https://alphafold.ebi.ac.uk"
    • Network accessline 25
      Base URL: `https://alphafold.ebi.ac.uk/api`
    • Network accessline 32
      curl "https://alphafold.ebi.ac.uk/api/prediction/P04637"
    • Network accessline 54
      "sequenceStart": 1,     "sequenceEnd": 393,     "pdbUrl": "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v6.pdb",
    • Network accessline 55
      "sequenceEnd": 393,     "pdbUrl": "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v6.pdb",     "cifUrl": "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v6.cif",
    • Network accessline 56
      "pdbUrl": "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v6.pdb",
    • Network accessline 57
      "cifUrl": "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v6.cif",
    • Network accessline 58
      "bcifUrl": "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v6.bcif",
    • Network accessline 59
      "paeImageUrl": "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-predicted_aligned_error_v6.png",
    • Network accessline 60
      "paeDocUrl": "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-predicted_aligned_error_v6.json",
    • Network accessline 61
      "plddtDocUrl": "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-confidence_v6.json",
    • Network accessline 62
      "amAnnotationsUrl": "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-aa-substitutions.csv"
    • Network accessline 72
      curl "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-confidence_v6.json"
    • Network accessline 92
      curl "https://alphafold.ebi.ac.uk/api/uniprot/summary/P04637.json"
    • Network accessline 106
      "summary": {         "model_identifier": "AF-P04637-F1",         "model_url": "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v6.cif",
    • Network accessline 107
      "model_identifier": "AF-P04637-F1",         "model_url": "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v6.cif",         "provider": "AlphaFold DB",
    • Network accessline 108
      "model_url": "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v6.cif",
    • Network accessline 124
      # PDB format curl -O "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v6.pdb"
    • Network accessline 125
      curl -O "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v6.pdb"
    • Network accessline 127
      # mmCIF format curl -O "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v6.cif"
    • Network accessline 128
      curl -O "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v6.cif"
    • Network accessline 130
      # Predicted Aligned Error (PAE) matrix curl -O "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-predicted_aligned_error_v6.json"
    • Network accessline 131
      curl -O "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-predicted_aligned_error_v6.json"
    • Network accessline 154
      The AlphaFold DB API has no published per-request rate limits. EMBL-EBI's general fair use policy applies: usage that degrades service for others may result in blocking. For bulk downloads (entire proteomes), use the FTP archive at `https:/
    • Network accessline 162
      def get_alphafold_prediction(uniprot_id: str) -> dict:     """Fetch AlphaFold structure prediction for a UniProt accession."""     url = f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}"
    • Network accessline 163
      """Fetch AlphaFold structure prediction for a UniProt accession."""     url = f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}"     resp = requests.get(url)
    • Network accessline 164
      url = f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}"     resp = requests.get(url)     resp.raise_for_status()
    • Network accessline 165
      resp = requests.get(url)
    • Network accessline 172
      def get_confidence_scores(prediction: dict) -> dict:     """Download per-residue pLDDT confidence scores."""     resp = requests.get(prediction["plddtDocUrl"])
    • Network accessline 173
      """Download per-residue pLDDT confidence scores."""     resp = requests.get(prediction["plddtDocUrl"])     resp.raise_for_status()
    • Network accessline 174
      resp = requests.get(prediction["plddtDocUrl"])
    • Network accessline 187
      resp = requests.get(url)
    • Network accessline 223
      - [AlphaFold Protein Structure Database](https://alphafold.ebi.ac.uk/)
    • Network accessline 224
      - [AlphaFold DB API Documentation](https://alphafold.ebi.ac.uk/api/openapi.json)
    • Network accessline 225
      - [AlphaFold DB FTP (Bulk Downloads)](https://ftp.ebi.ac.uk/pub/databases/alphafold/)

    skills/domains/biomedical/bioagents-guide/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["AI scientist", "biological research", "autonomous lab", "drug discovery", "protein design", "bioinformatics"]     source: "https://github.com/SakanaAI/AI-Scientist"
    • Network accessline 9
      keywords: ["AI scientist", "biological research", "autonomous lab", "drug discovery", "protein design", "bioinformatics"]     source: "https://github.com/SakanaAI/AI-Scientist" ---
    • Network accessline 10
      source: "https://github.com/SakanaAI/AI-Scientist"
    • Network accessline 304
      - [AI Scientist](https://github.com/SakanaAI/AI-Scientist) -- Sakana AI's autonomous research framework
    • Network accessline 305
      - [ESM-2](https://github.com/facebookresearch/esm) -- Meta's protein language model
    • Network accessline 306
      - [ChemCrow](https://arxiv.org/abs/2304.05376) -- LLM agent for chemistry research
    • Network accessline 307
      - [BioGPT](https://github.com/microsoft/BioGPT) -- Microsoft's biomedical text generation model
    • Network accessline 308
      - [OpenTargets](https://www.opentargets.org/) -- Target identification platform

    skills/domains/biomedical/biothings-api/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["gene annotation", "variant annotation", "drug data", "BioThings", "mygene", "myvariant", "bioinformatics"]     source: "https://biothings.io"
    • Network accessline 9
      keywords: ["gene annotation", "variant annotation", "drug data", "BioThings", "mygene", "myvariant", "bioinformatics"]     source: "https://biothings.io" ---
    • Network accessline 10
      source: "https://biothings.io"
    • Network accessline 30
      # No API key needed — just query directly curl "https://mygene.info/v3/query?q=BRCA1&size=1"
    • Network accessline 31
      curl "https://mygene.info/v3/query?q=BRCA1&size=1"
    • Network accessline 39
      GET https://mygene.info/v3/query?q={query}&size={n}
    • Network accessline 45
      curl -s "https://mygene.info/v3/query?q=BRCA1&size=1"
    • Network accessline 70
      GET https://mygene.info/v3/gene/{entrez_id}
    • Network accessline 76
      # Full annotation (large response) curl -s "https://mygene.info/v3/gene/1017"
    • Network accessline 77
      curl -s "https://mygene.info/v3/gene/1017"
    • Network accessline 79
      # Selective fields curl -s "https://mygene.info/v3/gene/1017?fields=symbol,name,summary,genomic_pos,go"
    • Network accessline 80
      curl -s "https://mygene.info/v3/gene/1017?fields=symbol,name,summary,genomic_pos,go"
    • Network accessline 105
      GET https://myvariant.info/v1/query?q={query}&size={n}
    • Network accessline 111
      curl -s "https://myvariant.info/v1/query?q=rs58991260&size=1"
    • Network accessline 150
      GET https://myvariant.info/v1/variant/{hgvs_id}
    • Network accessline 154
      curl -s "https://myvariant.info/v1/variant/chr1:g.218631822G>A?fields=dbsnp,cadd,clinvar"
    • Network accessline 162
      GET https://mychem.info/v1/query?q={query}&size={n}
    • Network accessline 168
      curl -s "https://mychem.info/v1/query?q=aspirin&size=1"
    • Network accessline 206
      GET https://mychem.info/v1/chem/{id}
    • Network accessline 210
      curl -s "https://mychem.info/v1/chem/CHEMBL25?fields=drugbank,chembl,pubchem"
    • Network accessline 241
      MYGENE = "https://mygene.info/v3"
    • Network accessline 242
      MYVARIANT = "https://myvariant.info/v1"
    • Network accessline 243
      MYCHEM = "https://mychem.info/v1"
    • Network accessline 245
      def search_gene(symbol):     resp = requests.get(f"{MYGENE}/query",
    • Network accessline 246
      resp = requests.get(f"{MYGENE}/query",
    • Network accessline 252
      def search_variants(gene_symbol, size=5):     resp = requests.get(f"{MYVARIANT}/query",
    • Network accessline 253
      resp = requests.get(f"{MYVARIANT}/query",
    • Network accessline 260
      def search_drug(name):     resp = requests.get(f"{MYCHEM}/query",
    • Network accessline 261
      resp = requests.get(f"{MYCHEM}/query",
    • Network accessline 292
      - BioThings API Hub: https://biothings.io
    • Network accessline 293
      - MyGene.info Documentation: https://docs.mygene.info
    • Network accessline 294
      - MyVariant.info Documentation: https://docs.myvariant.info
    • Network accessline 295
      - MyChem.info Documentation: https://docs.mychem.info
    • Network accessline 296
      - Publication: Xin J et al. *Genome Biology* 17:91 (2016). https://doi.org/10.1186/s13059-016-0953-9

    skills/domains/biomedical/clawbio-guide/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["ClawBio", "bioinformatics", "OpenClaw", "genomics", "pipeline", "biological analysis"]     source: "https://github.com/ClawBio/ClawBio"
    • Network accessline 9
      keywords: ["ClawBio", "bioinformatics", "OpenClaw", "genomics", "pipeline", "biological analysis"]     source: "https://github.com/ClawBio/ClawBio" ---
    • Network accessline 10
      source: "https://github.com/ClawBio/ClawBio"
    • Network accessline 165
      - [ClawBio GitHub](https://github.com/ClawBio/ClawBio)
    • Network accessline 166
      - [Bioconductor](https://www.bioconductor.org/)
    • Network accessline 167
      - [nf-core Pipelines](https://nf-co.re/)

    skills/domains/biomedical/clinical-dialogue-agents-guide/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["clinical dialogue", "medical QA", "patient interaction", "clinical agents", "healthcare AI", "diagnosis"]     source: "https://github.com/xqz614/Awesome-Agentic-Clinical-Dialogue"
    • Network accessline 9
      keywords: ["clinical dialogue", "medical QA", "patient interaction", "clinical agents", "healthcare AI", "diagnosis"]     source: "https://github.com/xqz614/Awesome-Agentic-Clinical-Dialogue" ---
    • Network accessline 10
      source: "https://github.com/xqz614/Awesome-Agentic-Clinical-Dialogue"
    • Network accessline 143
      - [Awesome-Agentic-Clinical-Dialogue](https://github.com/xqz614/Awesome-Agentic-Clinical-Dialogue)
    • Network accessline 144
      - [AMIE Paper](https://arxiv.org/abs/2401.05654)
    • Network accessline 145
      - [AgentClinic](https://arxiv.org/abs/2405.07960)

    skills/domains/biomedical/clinicaltrials-api-v2/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["clinical trials", "ClinicalTrials.gov", "medical research", "study design", "FDA", "drug trials"]     source: "https://clinicaltrials.gov/data-api/about-api"
    • Network accessline 9
      keywords: ["clinical trials", "ClinicalTrials.gov", "medical research", "study design", "FDA", "drug trials"]     source: "https://clinicaltrials.gov/data-api/about-api" ---
    • Network accessline 10
      source: "https://clinicaltrials.gov/data-api/about-api"
    • Network accessline 29
      - **URL**: `GET https://clinicaltrials.gov/api/v2/studies`
    • Network accessline 50
      curl "https://clinicaltrials.gov/api/v2/studies?query.cond=diabetes&query.intr=metformin&pageSize=1&fields=NCTId,BriefTitle,OverallStatus"
    • Network accessline 74
      - **URL**: `GET https://clinicaltrials.gov/api/v2/studies/{nctId}`
    • Network accessline 77
      curl "https://clinicaltrials.gov/api/v2/studies/NCT04280705?fields=NCTId,BriefTitle,OverallStatus,Phase,LeadSponsorName,EnrollmentCount,Condition,InterventionName"
    • Network accessline 106
      - **URL**: `GET https://clinicaltrials.gov/api/v2/stats/size`
    • Network accessline 109
      curl "https://clinicaltrials.gov/api/v2/stats/size"
    • Network accessline 125
      - **URL**: `GET https://clinicaltrials.gov/api/v2/stats/fieldValues/{fieldName}`
    • Network accessline 128
      curl "https://clinicaltrials.gov/api/v2/stats/fieldValues/Phase"
    • Network accessline 150
      No formal rate limits are published for the v2 API. Follow NCBI usage guidelines: stay under 3 requests/second without an API key, up to 10/second with one. For bulk data access, use the AACT relational database (https://aact.ctti-clinicalt
    • Network accessline 165
      def collect_trials(condition, intervention, status="COMPLETED"):     base = "https://clinicaltrials.gov/api/v2/studies"
    • Network accessline 166
      base = "https://clinicaltrials.gov/api/v2/studies"
    • Network accessline 174
      [Credential-related source omitted]
    • Network accessline 175
      params["pageToken"] = token         data = requests.get(base, params=params).json()         studies.extend(data.get("studies", []))
    • Network accessline 176
      data = requests.get(base, params=params).json()
    • Network accessline 194
      params = {"query.cond": "Alzheimer's Disease", "pageSize": 100,           "fields": "NCTId,Phase,LeadSponsorName"} data = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params).json()
    • Network accessline 196
      data = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params).json()
    • Network accessline 212
      - v2 API reference: https://clinicaltrials.gov/data-api/api
    • Network accessline 213
      - About the API: https://clinicaltrials.gov/data-api/about-api
    • Network accessline 214
      - AACT database (bulk access): https://aact.ctti-clinicaltrials.org/
    • Network accessline 215
      - WHO ICTRP: https://trialsearch.who.int/
    • Network accessline 216
      - NCBI usage policies: https://www.ncbi.nlm.nih.gov/home/about/policies/

    skills/domains/biomedical/clinicaltrials-api/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["clinical medicine", "epidemiology", "public health", "evidence-based medicine"]     source: "https://clinicaltrials.gov/api/"
    • Network accessline 9
      keywords: ["clinical medicine", "epidemiology", "public health", "evidence-based medicine"]     source: "https://clinicaltrials.gov/api/" ---
    • Network accessline 10
      source: "https://clinicaltrials.gov/api/"
    • Network accessline 33
      - **URL**: `GET https://clinicaltrials.gov/api/v2/studies`
    • Network accessline 53
      # Search for recruiting cancer immunotherapy trials curl "https://clinicaltrials.gov/api/v2/studies?query.cond=cancer&query.intr=immunotherapy&filter.overallStatus=RECRUITING&pageSize=5"
    • Network accessline 54
      curl "https://clinicaltrials.gov/api/v2/studies?query.cond=cancer&query.intr=immunotherapy&filter.overallStatus=RECRUITING&pageSize=5"
    • Network accessline 56
      # Search by sponsor curl "https://clinicaltrials.gov/api/v2/studies?query.spons=NIH&filter.phase=PHASE3&pageSize=10"
    • Network accessline 57
      curl "https://clinicaltrials.gov/api/v2/studies?query.spons=NIH&filter.phase=PHASE3&pageSize=10"
    • Network accessline 66
      - **URL**: `GET https://clinicaltrials.gov/api/v2/studies/{nctId}`
    • Network accessline 76
      curl "https://clinicaltrials.gov/api/v2/studies/NCT04280705"
    • Network accessline 83
      No formal rate limits are documented for the ClinicalTrials.gov API. However, the service follows NCBI usage guidelines which recommend no more than 3 requests per second without an API key, and up to 10 requests per second with an NCBI API
    • Network accessline 98
      "pageSize": 20 } resp = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params)
    • Network accessline 99
      } resp = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params) data = resp.json()
    • Network accessline 100
      resp = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params)
    • Network accessline 134
      resp = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params)
    • Network accessline 156
      "pageSize": 100 } resp = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params)
    • Network accessline 157
      } resp = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params) data = resp.json()
    • Network accessline 158
      resp = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params)
    • Network accessline 173
      - Official API documentation: https://clinicaltrials.gov/data-api/api
    • Network accessline 174
      - ClinicalTrials.gov homepage: https://clinicaltrials.gov/
    • Network accessline 175
      - AACT database for bulk analysis: https://aact.ctti-clinicaltrials.org/
    • Network accessline 176
      - WHO ICTRP (international registry portal): https://trialsearch.who.int/
    • Network accessline 177
      - NCBI usage policies: https://www.ncbi.nlm.nih.gov/home/about/policies/

    skills/domains/biomedical/ena-sequence-api/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["ENA", "nucleotide sequences", "genomics", "EMBL-EBI", "sequencing data", "NGS"]     source: "https://www.ebi.ac.uk/ena/"
    • Network accessline 9
      keywords: ["ENA", "nucleotide sequences", "genomics", "EMBL-EBI", "sequencing data", "NGS"]     source: "https://www.ebi.ac.uk/ena/" ---
    • Network accessline 10
      source: "https://www.ebi.ac.uk/ena/"
    • Network accessline 24
      # Search for studies curl "https://www.ebi.ac.uk/ena/portal/api/search?query=CRISPR+cas9&result=study&limit=20&format=json"
    • Network accessline 25
      curl "https://www.ebi.ac.uk/ena/portal/api/search?query=CRISPR+cas9&result=study&limit=20&format=json"
    • Network accessline 27
      # Search for samples curl "https://www.ebi.ac.uk/ena/portal/api/search?query=human+gut+microbiome&result=sample&limit=20&format=json"
    • Network accessline 28
      curl "https://www.ebi.ac.uk/ena/portal/api/search?query=human+gut+microbiome&result=sample&limit=20&format=json"
    • Network accessline 30
      # Search for runs (sequencing data) curl "https://www.ebi.ac.uk/ena/portal/api/search?query=RNA-seq+cancer&result=read_run&limit=20&format=json"
    • Network accessline 31
      curl "https://www.ebi.ac.uk/ena/portal/api/search?query=RNA-seq+cancer&result=read_run&limit=20&format=json"
    • Network accessline 37
      # Get record by accession curl "https://www.ebi.ac.uk/ena/browser/api/xml/PRJEB12345"
    • Network accessline 38
      curl "https://www.ebi.ac.uk/ena/browser/api/xml/PRJEB12345"
    • Network accessline 40
      # Get in JSON format curl "https://www.ebi.ac.uk/ena/browser/api/summary/PRJEB12345"
    • Network accessline 41
      curl "https://www.ebi.ac.uk/ena/browser/api/summary/PRJEB12345"
    • Network accessline 43
      # Get sequence in FASTA curl "https://www.ebi.ac.uk/ena/browser/api/fasta/AF123456"
    • Network accessline 44
      curl "https://www.ebi.ac.uk/ena/browser/api/fasta/AF123456"
    • Network accessline 46
      # Get in EMBL flat file format curl "https://www.ebi.ac.uk/ena/browser/api/embl/AF123456"
    • Network accessline 47
      curl "https://www.ebi.ac.uk/ena/browser/api/embl/AF123456"
    • Network accessline 53
      # Search by organism curl "https://www.ebi.ac.uk/ena/portal/api/search?query=tax_tree(9606)&result=study&limit=20&format=json"
    • Network accessline 54
      curl "https://www.ebi.ac.uk/ena/portal/api/search?query=tax_tree(9606)&result=study&limit=20&format=json"
    • Network accessline 56
      # Get taxonomy details curl "https://www.ebi.ac.uk/ena/taxonomy/rest/tax-id/9606"
    • Network accessline 57
      curl "https://www.ebi.ac.uk/ena/taxonomy/rest/tax-id/9606"
    • Network accessline 88
      PORTAL_URL = "https://www.ebi.ac.uk/ena/portal/api"
    • Network accessline 89
      BROWSER_URL = "https://www.ebi.ac.uk/ena/browser/api"
    • Network accessline 100
      "tax_id,scientific_name,center_name",     }     resp = requests.get(f"{PORTAL_URL}/search", params=params)
    • Network accessline 101
      }     resp = requests.get(f"{PORTAL_URL}/search", params=params)     resp.raise_for_status()
    • Network accessline 102
      resp = requests.get(f"{PORTAL_URL}/search", params=params)
    • Network accessline 115
      "library_strategy,read_count,base_count",     }     resp = requests.get(f"{PORTAL_URL}/search", params=params)
    • Network accessline 116
      }     resp = requests.get(f"{PORTAL_URL}/search", params=params)     resp.raise_for_status()
    • Network accessline 117
      resp = requests.get(f"{PORTAL_URL}/search", params=params)
    • Network accessline 122
      def get_fasta(accession: str) -> str:     """Retrieve sequence in FASTA format."""     resp = requests.get(f"{BROWSER_URL}/fasta/{accession}")
    • Network accessline 123
      """Retrieve sequence in FASTA format."""     resp = requests.get(f"{BROWSER_URL}/fasta/{accession}")     resp.raise_for_status()
    • Network accessline 124
      resp = requests.get(f"{BROWSER_URL}/fasta/{accession}")
    • Network accessline 136
      "limit": 1000,     }     resp = requests.get(f"{PORTAL_URL}/search", params=params)
    • Network accessline 137
      }     resp = requests.get(f"{PORTAL_URL}/search", params=params)     resp.raise_for_status()
    • Network accessline 138
      resp = requests.get(f"{PORTAL_URL}/search", params=params)
    • Network accessline 161
      # Download FASTQ files (from run metadata) # The fastq_ftp field provides FTP paths: wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR123/ERR123456/ERR123456_1.fastq.gz
    • Network accessline 163
      wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR123/ERR123456/ERR123456_1.fastq.gz
    • Network accessline 172
      - [ENA](https://www.ebi.ac.uk/ena/)
    • Network accessline 173
      - [ENA Portal API](https://www.ebi.ac.uk/ena/portal/api/)
    • Network accessline 174
      - [ENA Browser API](https://www.ebi.ac.uk/ena/browser/api/)

    skills/domains/biomedical/enrichr-api/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["gene set enrichment", "pathway analysis", "GO terms", "KEGG", "Enrichr", "functional analysis"]     source: "https://maayanlab.cloud/Enrichr"
    • Network accessline 9
      keywords: ["gene set enrichment", "pathway analysis", "GO terms", "KEGG", "Enrichr", "functional analysis"]     source: "https://maayanlab.cloud/Enrichr" ---
    • Network accessline 10
      source: "https://maayanlab.cloud/Enrichr"
    • Network accessline 33
      https://maayanlab.cloud/Enrichr
    • Network accessline 39
      curl -X POST "https://maayanlab.cloud/Enrichr/addList" \
    • Network accessline 67
      curl "https://maayanlab.cloud/Enrichr/enrich?userListId=124544426&backgroundType=KEGG_2021_Human"
    • Network accessline 93
      curl "https://maayanlab.cloud/Enrichr/view?userListId=124544426"
    • Network accessline 106
      curl "https://maayanlab.cloud/Enrichr/export?userListId=124544426&backgroundType=KEGG_2021_Human&filename=results" \
    • Network accessline 113
      curl "https://maayanlab.cloud/Enrichr/datasetStatistics"
    • Network accessline 191
      ENRICHR_URL = "https://maayanlab.cloud/Enrichr"
    • Network accessline 198
      "description": (None, description),     }     resp = requests.post(f"{ENRICHR_URL}/addList", files=payload)
    • Network accessline 199
      }     resp = requests.post(f"{ENRICHR_URL}/addList", files=payload)     resp.raise_for_status()
    • Network accessline 200
      resp = requests.post(f"{ENRICHR_URL}/addList", files=payload)
    • Network accessline 205
      def get_enrichment(user_list_id: int, library: str) -> list[dict]:     """Retrieve enrichment results for a given library."""     resp = requests.get(
    • Network accessline 206
      """Retrieve enrichment results for a given library."""     resp = requests.get(         f"{ENRICHR_URL}/enrich",
    • Network accessline 207
      resp = requests.get(
    • Network accessline 228
      def get_libraries() -> list[dict]:     """List all available Enrichr libraries."""     resp = requests.get(f"{ENRICHR_URL}/datasetStatistics")
    • Network accessline 229
      """List all available Enrichr libraries."""     resp = requests.get(f"{ENRICHR_URL}/datasetStatistics")     resp.raise_for_status()
    • Network accessline 230
      resp = requests.get(f"{ENRICHR_URL}/datasetStatistics")
    • Network accessline 260
      - [Enrichr Web App](https://maayanlab.cloud/Enrichr)
    • Network accessline 261
      - [Enrichr API Docs](https://maayanlab.cloud/Enrichr/help#api)

    skills/domains/biomedical/ensembl-rest-api/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["Ensembl", "gene lookup", "sequence retrieval", "genomics", "variant data", "bioinformatics"]     source: "https://rest.ensembl.org"
    • Network accessline 9
      keywords: ["Ensembl", "gene lookup", "sequence retrieval", "genomics", "variant data", "bioinformatics"]     source: "https://rest.ensembl.org" ---
    • Network accessline 10
      source: "https://rest.ensembl.org"
    • Network accessline 31
      - **URL**: `GET https://rest.ensembl.org/lookup/symbol/{species}/{symbol}`
    • Network accessline 44
      curl "https://rest.ensembl.org/lookup/symbol/homo_sapiens/BRCA1?content-type=application/json"
    • Network accessline 64
      - **URL**: `GET https://rest.ensembl.org/sequence/id/{id}`
    • Network accessline 78
      curl "https://rest.ensembl.org/sequence/id/ENSG00000012048?content-type=application/json&type=genomic"
    • Network accessline 96
      - **URL**: `GET https://rest.ensembl.org/xrefs/symbol/{species}/{symbol}`
    • Network accessline 101
      curl "https://rest.ensembl.org/xrefs/symbol/homo_sapiens/TP53?content-type=application/json"
    • Network accessline 112
      - **URL**: `GET https://rest.ensembl.org/variation/{species}/{id}`
    • Network accessline 117
      curl "https://rest.ensembl.org/variation/homo_sapiens/rs699?content-type=application/json"
    • Network accessline 134
      - **URL**: `GET https://rest.ensembl.org/info/assembly/{species}`
    • Network accessline 141
      - **Response headers**: `X-RateLimit-Limit`, `X-RateLimit-Remaining`, `X-RateLimit-Reset` on every response. - **Batch POST endpoints** (`/lookup/id`, `/sequence/id`): accept up to 1000 IDs per request. - **GRCh37 mirror**: `https://grch37.
    • Network accessline 143
      - **GRCh37 mirror**: `https://grch37.rest.ensembl.org`
    • Network accessline 160
      BASE = "https://rest.ensembl.org"
    • Network accessline 163
      gene = requests.get(f"{BASE}/lookup/symbol/homo_sapiens/BRCA1", headers=HEADERS).json()
    • Network accessline 166
      seq = requests.get(f"{BASE}/sequence/id/{gene['id']}?type=cds", headers=HEADERS).json()
    • Network accessline 175
      ids = ["ENSG00000012048", "ENSG00000141510", "ENSG00000157764"]  # BRCA1, TP53, BRAF resp = requests.post(
    • Network accessline 176
      resp = requests.post(
    • Network accessline 177
      "https://rest.ensembl.org/lookup/id",
    • Network accessline 190
      for rsid in ["rs699", "rs1042522", "rs334"]:     v = requests.get(
    • Network accessline 191
      v = requests.get(
    • Network accessline 192
      f"https://rest.ensembl.org/variation/homo_sapiens/{rsid}",
    • Network accessline 201
      - REST API docs: https://rest.ensembl.org/documentation
    • Network accessline 202
      - Ensembl browser: https://www.ensembl.org
    • Network accessline 203
      - gget toolkit (built on Ensembl REST): https://pachterlab.github.io/gget/
    • Network accessline 204
      - GRCh37 archive API: https://grch37.rest.ensembl.org

    skills/domains/biomedical/genomas-guide/SKILL.md

    • Network accessline 22
      pip install genomas # Or from source git clone https://github.com/futianfan/GenoMAS.git
    • Network accessline 23
      # Or from source git clone https://github.com/futianfan/GenoMAS.git cd GenoMAS && pip install -e .
    • Network accessline 24
      git clone https://github.com/futianfan/GenoMAS.git
    • Network accessline 68
      # Step 1: Retrieve data data_agent = DataAgent() dataset = data_agent.fetch("GSE12345", platform="RNA-seq")
    • Network accessline 70
      dataset = data_agent.fetch("GSE12345", platform="RNA-seq")
    • Network accessline 125
      - [GenoMAS GitHub](https://github.com/futianfan/GenoMAS)

    skills/domains/biomedical/genomics-analysis-guide/SKILL.md

    • Network accessline 266
      - [DESeq2 Vignette](https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html) -- Differential expression analysis
    • Network accessline 267
      - [GATK Best Practices](https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows) -- Variant calling
    • Network accessline 268
      - [PLINK2 Documentation](https://www.cog-genomics.org/plink/2.0/) -- Genetic association analysis
    • Network accessline 269
      - [nf-core Pipelines](https://nf-co.re/) -- Community Nextflow workflows
    • Network accessline 270
      - [RNA-seq Analysis Tutorial](https://rnabio.org/) -- Griffith Lab comprehensive tutorial

    skills/domains/biomedical/genotex-benchmark-guide/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["GenoTEX", "gene expression", "benchmark", "LLM agent", "bioinformatics", "GEO"]     source: "https://github.com/Liu-Hy/GenoTEX"
    • Network accessline 9
      keywords: ["GenoTEX", "gene expression", "benchmark", "LLM agent", "bioinformatics", "GEO"]     source: "https://github.com/Liu-Hy/GenoTEX" ---
    • Network accessline 10
      source: "https://github.com/Liu-Hy/GenoTEX"
    • Network accessline 123
      - [GenoTEX GitHub](https://github.com/Liu-Hy/GenoTEX)
    • Network accessline 124
      - [GEO Database](https://www.ncbi.nlm.nih.gov/geo/)
    • Network accessline 125
      - [MLCB 2025](https://mlcb.github.io/)

    skills/domains/biomedical/med-researcher-guide/SKILL.md

    • Network accessline 159
      - [Med-Researcher GitHub](https://github.com/mao1207/Med-Researcher)
    • Network accessline 160
      - [GRADE Handbook](https://gdt.gradepro.org/app/handbook/handbook.html)
    • Network accessline 161
      - [PubMed API (E-utilities)](https://www.ncbi.nlm.nih.gov/books/NBK25501/)

    skills/domains/biomedical/med-researcher-r1-guide/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["medical research", "deep research", "clinical reasoning", "PubMed", "medical agent", "evidence-based"]     source: "https://github.com/AQ-MedAI/MedResearcher-R1"
    • Network accessline 9
      keywords: ["medical research", "deep research", "clinical reasoning", "PubMed", "medical agent", "evidence-based"]     source: "https://github.com/AQ-MedAI/MedResearcher-R1" ---
    • Network accessline 10
      source: "https://github.com/AQ-MedAI/MedResearcher-R1"
    • Network accessline 144
      - [MedResearcher-R1 GitHub](https://github.com/AQ-MedAI/MedResearcher-R1)
    • Network accessline 145
      - [PubMed E-utilities](https://www.ncbi.nlm.nih.gov/books/NBK25501/)
    • Network accessline 146
      - [GRADE Handbook](https://gdt.gradepro.org/app/handbook/handbook.html)

    skills/domains/biomedical/medgeclaw-guide/SKILL.md

    • Network accessline 294
      response = requests.post(
    • Network accessline 295
      "https://api.platform.opentargets.org/api/v4/graphql",
    • Network accessline 341
      - [DESeq2](https://bioconductor.org/packages/DESeq2/) -- Standard RNA-seq differential expression tool
    • Network accessline 342
      - [scispaCy](https://allenai.github.io/scispacy/) -- Biomedical NLP models for spaCy
    • Network accessline 343
      - [Open Targets Platform](https://platform.opentargets.org/) -- Target-disease association evidence
    • Network accessline 344
      - [RDKit](https://www.rdkit.org/) -- Cheminformatics toolkit

    skills/domains/biomedical/medical-data-api/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["FDA", "drug safety", "WHO", "global health", "adverse events", "medical data", "pharmacovigilance"]     source: "https://open.fda.gov"
    • Network accessline 9
      keywords: ["FDA", "drug safety", "WHO", "global health", "adverse events", "medical data", "pharmacovigilance"]     source: "https://open.fda.gov" ---
    • Network accessline 10
      source: "https://open.fda.gov"
    • Network accessline 27
      [Credential-related source omitted]
    • Access to secretsline 27
      [Credential-related source omitted]
    • Network accessline 37
      - **URL**: `GET https://api.fda.gov/drug/label.json`
    • Network accessline 50
      curl "https://api.fda.gov/drug/label.json?search=aspirin&limit=1"
    • Network accessline 59
      - **URL**: `GET https://api.fda.gov/drug/event.json`
    • Network accessline 72
      curl 'https://api.fda.gov/drug/event.json?search=patient.drug.openfda.brand_name:"aspirin"&limit=1'
    • Network accessline 81
      - **URL**: `GET https://ghoapi.azureedge.net/api/{IndicatorCode}`
    • Network accessline 95
      # Life expectancy at birth (WHOSIS_000001) curl "https://ghoapi.azureedge.net/api/WHOSIS_000001?\$top=2"
    • Network accessline 96
      curl "https://ghoapi.azureedge.net/api/WHOSIS_000001?\$top=2"
    • Network accessline 105
      - **URL**: `GET https://ghoapi.azureedge.net/api/Indicator`
    • Network accessline 109
      curl "https://ghoapi.azureedge.net/api/Indicator?\$top=5"
    • Network accessline 122
      - No documented rate limits; the service runs on Azure CDN (azureedge.net) - Recommended: keep requests under 10/second for courtesy - For bulk downloads, use the GHO data portal CSV exports at https://www.who.int/data/gho
    • Network accessline 124
      - For bulk downloads, use the GHO data portal CSV exports at https://www.who.int/data/gho
    • Network accessline 135
      resp = requests.get("https://api.fda.gov/drug/event.json", params={
    • Network accessline 151
      resp = requests.get("https://ghoapi.azureedge.net/api/WHOSIS_000001", params={
    • Network accessline 167
      for drug in ["ibuprofen", "naproxen", "celecoxib"]:     resp = requests.get("https://api.fda.gov/drug/label.json",
    • Network accessline 168
      resp = requests.get("https://api.fda.gov/drug/label.json",
    • Network accessline 190
      - openFDA documentation: https://open.fda.gov/apis/
    • Network accessline 191
      - openFDA API key registration: https://open.fda.gov/apis/authentication/
    • Network accessline 192
      - openFDA query syntax: https://open.fda.gov/apis/query-syntax/
    • Network accessline 193
      - openFDA GitHub: https://github.com/FDA/openfda
    • Network accessline 194
      - WHO GHO API documentation: https://www.who.int/data/gho/info/gho-odata-api
    • Network accessline 195
      - WHO GHO OData endpoint: https://ghoapi.azureedge.net/api/
    • Network accessline 196
      - WHO GHO indicator list: https://ghoapi.azureedge.net/api/Indicator
    • Network accessline 197
      - WHO Global Health Observatory portal: https://www.who.int/data/gho

    skills/domains/biomedical/ncbi-blast-api/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["BLAST", "sequence alignment", "NCBI", "homology search", "protein similarity", "nucleotide search"]     source: "https://blast.ncbi.nlm.nih.gov/"
    • Network accessline 9
      keywords: ["BLAST", "sequence alignment", "NCBI", "homology search", "protein similarity", "nucleotide search"]     source: "https://blast.ncbi.nlm.nih.gov/" ---
    • Network accessline 10
      source: "https://blast.ncbi.nlm.nih.gov/"
    • Network accessline 26
      # Nucleotide BLAST (blastn) curl -X POST "https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi" \
    • Network accessline 27
      curl -X POST "https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi" \
    • Network accessline 30
      # Protein BLAST (blastp) curl -X POST "https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi" \
    • Network accessline 31
      curl -X POST "https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi" \
    • Network accessline 34
      # BLAST with specific parameters curl -X POST "https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi" \
    • Network accessline 35
      curl -X POST "https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi" \
    • Network accessline 43
      # Poll for completion (returns XML with Status field) curl "https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=YOUR_RID"
    • Network accessline 44
      curl "https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=YOUR_RID"
    • Network accessline 50
      # Get results in XML curl "https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&FORMAT_TYPE=XML&RID=YOUR_RID"
    • Network accessline 51
      curl "https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&FORMAT_TYPE=XML&RID=YOUR_RID"
    • Network accessline 53
      # Get results in JSON curl "https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&FORMAT_TYPE=JSON2_S&RID=YOUR_RID"
    • Network accessline 54
      curl "https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&FORMAT_TYPE=JSON2_S&RID=YOUR_RID"
    • Network accessline 56
      # Get results in tabular format curl "https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&FORMAT_TYPE=Tabular&RID=YOUR_RID"
    • Network accessline 57
      curl "https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&FORMAT_TYPE=Tabular&RID=YOUR_RID"
    • Network accessline 102
      BLAST_URL = "https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi"
    • Network accessline 107
      evalue: float = 0.001) -> str:     """Submit a BLAST search, return Request ID."""     resp = requests.post(BLAST_URL, data={
    • Network accessline 108
      """Submit a BLAST search, return Request ID."""     resp = requests.post(BLAST_URL, data={         "CMD": "Put",
    • Network accessline 109
      resp = requests.post(BLAST_URL, data={
    • Network accessline 128
      elapsed = 0     while elapsed < max_wait:         resp = requests.get(BLAST_URL, params={
    • Network accessline 129
      while elapsed < max_wait:         resp = requests.get(BLAST_URL, params={             "CMD": "Get",
    • Network accessline 130
      resp = requests.get(BLAST_URL, params={
    • Network accessline 144
      def get_results(rid: str) -> list:     """Retrieve BLAST results as parsed hits."""     resp = requests.get(BLAST_URL, params={
    • Network accessline 145
      """Retrieve BLAST results as parsed hits."""     resp = requests.get(BLAST_URL, params={         "CMD": "Get",
    • Network accessline 146
      resp = requests.get(BLAST_URL, params={
    • Network accessline 192
      - [NCBI BLAST](https://blast.ncbi.nlm.nih.gov/)
    • Network accessline 193
      - [BLAST URL API Guide](https://blast.ncbi.nlm.nih.gov/doc/blast-help/developerinfo.html)
    • Network accessline 194
      - [BLAST Command Line](https://www.ncbi.nlm.nih.gov/books/NBK279690/)

    skills/domains/biomedical/ncbi-datasets-api/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["NCBI", "genome data", "gene data", "taxonomy", "RefSeq", "GenBank"]     source: "https://www.ncbi.nlm.nih.gov/datasets/"
    • Network accessline 9
      keywords: ["NCBI", "genome data", "gene data", "taxonomy", "RefSeq", "GenBank"]     source: "https://www.ncbi.nlm.nih.gov/datasets/" ---
    • Network accessline 10
      source: "https://www.ncbi.nlm.nih.gov/datasets/"
    • Network accessline 24
      https://api.ncbi.nlm.nih.gov/datasets/v2
    • Network accessline 30
      # Search genome assemblies by organism curl "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/9606?page_size=5"
    • Network accessline 31
      curl "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/9606?page_size=5"
    • Network accessline 33
      # Get assembly by accession curl "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000001405.40"
    • Network accessline 34
      curl "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000001405.40"
    • Network accessline 36
      # Download genome package curl -o genome.zip \
    • Network accessline 37
      curl -o genome.zip \
    • Network accessline 38
      "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000001405.40/download?\
    • Network accessline 45
      # Search genes by symbol curl "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/symbol/TP53/taxon/human"
    • Network accessline 46
      curl "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/symbol/TP53/taxon/human"
    • Network accessline 48
      # Get gene by NCBI Gene ID curl "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/id/7157"
    • Network accessline 49
      curl "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/id/7157"
    • Network accessline 51
      # Search genes by keyword curl "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/search?query=BRCA&taxon=9606&page_size=20"
    • Network accessline 52
      curl "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/search?query=BRCA&taxon=9606&page_size=20"
    • Network accessline 54
      # Download gene data package curl -o gene.zip \
    • Network accessline 55
      curl -o gene.zip \
    • Network accessline 56
      "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/id/7157/download?include_annotation_type=FASTA_GENE"
    • Network accessline 62
      # Get taxonomy info curl "https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/taxon/9606"
    • Network accessline 63
      curl "https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/taxon/9606"
    • Network accessline 65
      # Search taxonomy by name curl "https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/name_report?taxon_query=Homo+sapiens"
    • Network accessline 66
      curl "https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/name_report?taxon_query=Homo+sapiens"
    • Network accessline 68
      # Get taxonomy tree (subtree) curl "https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/taxon/9443/subtree"
    • Network accessline 69
      curl "https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/taxon/9443/subtree"
    • Network accessline 122
      BASE_URL = "https://api.ncbi.nlm.nih.gov/datasets/v2"
    • Network accessline 126
      page_size: int = 20) -> list:     """Search NCBI genes by keyword."""     resp = requests.get(
    • Network accessline 127
      """Search NCBI genes by keyword."""     resp = requests.get(         f"{BASE_URL}/gene/search",
    • Network accessline 128
      resp = requests.get(
    • Network accessline 150
      def get_gene(gene_id: int) -> dict:     """Get detailed gene information."""     resp = requests.get(f"{BASE_URL}/gene/id/{gene_id}")
    • Network accessline 151
      """Get detailed gene information."""     resp = requests.get(f"{BASE_URL}/gene/id/{gene_id}")     resp.raise_for_status()
    • Network accessline 152
      resp = requests.get(f"{BASE_URL}/gene/id/{gene_id}")
    • Network accessline 165
      resp = requests.get(
    • Network accessline 205
      # Install curl -o datasets "https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets"
    • Network accessline 206
      curl -o datasets "https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets"
    • Network accessline 218
      - [NCBI Datasets](https://www.ncbi.nlm.nih.gov/datasets/) - [Datasets API Reference](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/rest-api/) - [Datasets CLI](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install
    • Network accessline 219
      - [Datasets API Reference](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/rest-api/)
    • Network accessline 220
      - [Datasets CLI](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/)

    skills/domains/biomedical/pdb-structure-api/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["protein structure", "PDB", "crystallography", "structural biology", "RCSB", "molecular structure"]     source: "https://data.rcsb.org"
    • Network accessline 9
      keywords: ["protein structure", "PDB", "crystallography", "structural biology", "RCSB", "molecular structure"]     source: "https://data.rcsb.org" ---
    • Network accessline 10
      source: "https://data.rcsb.org"
    • Network accessline 31
      - **URL**: `GET https://data.rcsb.org/rest/v1/core/entry/{pdb_id}`
    • Network accessline 34
      curl "https://data.rcsb.org/rest/v1/core/entry/4HHB"
    • Network accessline 61
      - **URL**: `GET https://data.rcsb.org/rest/v1/core/polymer_entity/{pdb_id}/{entity_id}`
    • Network accessline 64
      curl "https://data.rcsb.org/rest/v1/core/polymer_entity/4HHB/1"
    • Network accessline 89
      - **URL**: `GET https://data.rcsb.org/rest/v1/core/chemcomp/{comp_id}`
    • Network accessline 92
      curl "https://data.rcsb.org/rest/v1/core/chemcomp/HEM"
    • Network accessline 113
      - **URL**: `POST https://search.rcsb.org/rcsbsearch/v2/query`
    • Network accessline 118
      curl -X POST "https://search.rcsb.org/rcsbsearch/v2/query" \
    • Network accessline 153
      No formal rate limits or rate-limit headers are published. RCSB recommends reasonable request rates. For bulk data, use FTP downloads at `https://files.rcsb.org/pub/pdb/` or `ftp://ftp.wwpdb.org/pub/pdb/` instead of iterative API calls.
    • Network accessline 174
      "paginate": {"start": 0, "rows": 5}} } results = requests.post("https://search.rcsb.org/rcsbsearch/v2/query",
    • Network accessline 175
      } results = requests.post("https://search.rcsb.org/rcsbsearch/v2/query",                         json=search_body).json()
    • Network accessline 176
      results = requests.post("https://search.rcsb.org/rcsbsearch/v2/query",
    • Network accessline 181
      for hit in results["result_set"]:     pdb_id = hit["identifier"]     entry = requests.get(
    • Network accessline 182
      pdb_id = hit["identifier"]     entry = requests.get(         f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}").json()
    • Network accessline 183
      entry = requests.get(
    • Network accessline 184
      f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}").json()
    • Network accessline 196
      pdb_id = "4HHB" entry = requests.get(
    • Network accessline 197
      entry = requests.get(
    • Network accessline 198
      f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}").json()
    • Network accessline 200
      for eid in range(1, entry["rcsb_entry_info"]["polymer_entity_count"] + 1):     entity = requests.get(
    • Network accessline 201
      entity = requests.get(
    • Network accessline 202
      f"https://data.rcsb.org/rest/v1/core/polymer_entity/{pdb_id}/{eid}"
    • Network accessline 214
      - Data API docs: https://data.rcsb.org/redoc/index.html
    • Network accessline 215
      - Search API docs: https://search.rcsb.org/index.html
    • Network accessline 216
      - RCSB PDB homepage: https://www.rcsb.org/
    • Network accessline 217
      - Programmatic access guide: https://www.rcsb.org/docs/programmatic-access
    • Network accessline 218
      - PDB file format: https://www.wwpdb.org/documentation/file-format
    • Network accessline 219
      - Worldwide PDB: https://www.wwpdb.org/

    skills/domains/biomedical/quickgo-api/SKILL.md

    • Network accessline 8
      subcategory: "biomedical"     keywords: ["Gene Ontology", "GO annotations", "protein function", "QuickGO", "EBI", "functional genomics"]     source: "https://www.ebi.ac.uk/QuickGO/"
    • Network accessline 9
      keywords: ["Gene Ontology", "GO annotations", "protein function", "QuickGO", "EBI", "functional genomics"]     source: "https://www.ebi.ac.uk/QuickGO/" ---
    • Network accessline 10
      source: "https://www.ebi.ac.uk/QuickGO/"
    • Network accessline 24
      https://www.ebi.ac.uk/QuickGO/services
    • Network accessline 30
      # Search terms by keyword curl "https://www.ebi.ac.uk/QuickGO/services/ontology/go/search?query=apoptosis&limit=20"
    • Network accessline 31
      curl "https://www.ebi.ac.uk/QuickGO/services/ontology/go/search?query=apoptosis&limit=20"
    • Network accessline 33
      # Get term details curl "https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0006915"
    • Network accessline 34
      curl "https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0006915"
    • Network accessline 36
      # Get term ancestors/descendants curl "https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0006915/ancestors"
    • Network accessline 37
      curl "https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0006915/ancestors"
    • Network accessline 38
      curl "https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0006915/descendants"
    • Network accessline 44
      # Get annotations for a protein (UniProt ID) curl "https://www.ebi.ac.uk/QuickGO/services/annotation/search?geneProductId=P04637&limit=50"
    • Network accessline 45
      curl "https://www.ebi.ac.uk/QuickGO/services/annotation/search?geneProductId=P04637&limit=50"
    • Network accessline 47
      # Annotations for a GO term curl "https://www.ebi.ac.uk/QuickGO/services/annotation/search?goId=GO:0006915&taxonId=9606&limit=50"
    • Network accessline 48
      curl "https://www.ebi.ac.uk/QuickGO/services/annotation/search?goId=GO:0006915&taxonId=9606&limit=50"
    • Network accessline 50
      # Filter by evidence code curl "https://www.ebi.ac.uk/QuickGO/services/annotation/search?\
    • Network accessline 51
      curl "https://www.ebi.ac.uk/QuickGO/services/annotation/search?\
    • Network accessline 54
      # Filter by aspect (ontology branch) curl "https://www.ebi.ac.uk/QuickGO/services/annotation/search?\
    • Network accessline 55
      curl "https://www.ebi.ac.uk/QuickGO/services/annotation/search?\
    • Network accessline 62
      # Download as TSV curl "https://www.ebi.ac.uk/QuickGO/services/annotation/downloadSearch?\
    • Network accessline 63
      curl "https://www.ebi.ac.uk/QuickGO/services/annotation/downloadSearch?\
    • Network accessline 91
      BASE_URL = "https://www.ebi.ac.uk/QuickGO/services"
    • Network accessline 94
      def search_go_terms(query: str, limit: int = 20) -> list:     """Search Gene Ontology terms."""     resp = requests.get(
    • Network accessline 95
      """Search Gene Ontology terms."""     resp = requests.get(         f"{BASE_URL}/ontology/go/search",
    • Network accessline 96
      resp = requests.get(
    • Network accessline 124
      resp = requests.get(
    • Network accessline 149
      "limit": limit,     }     resp = requests.get(
    • Network accessline 150
      }     resp = requests.get(         f"{BASE_URL}/annotation/search",
    • Network accessline 151
      resp = requests.get(
    • Network accessline 178
      - [QuickGO](https://www.ebi.ac.uk/QuickGO/)
    • Network accessline 179
      - [QuickGO API Docs](https://www.ebi.ac.uk/QuickGO/api)
    • Network accessline 180
      - [Gene Ontology](http://geneontology.org/)

    skills/domains/business/architecture-design-guide/SKILL.md

    • Network accessline 275
      - Ching, F. D. K. (2014). Architecture: Form, Space, and Order, 4th ed. Wiley. - [ArchDaily](https://www.archdaily.com/) -- Architectural project database and analysis
    • Network accessline 276
      - [ArchDaily](https://www.archdaily.com/) -- Architectural project database and analysis
    • Network accessline 277
      - [Ladybug Tools](https://www.ladybug.tools/) -- Environmental analysis for Grasshopper
    • Network accessline 279
      - [RIBA 2030 Climate Challenge](https://www.architecture.com/about/policy/climate-action/2030-climate-challenge) -- Carbon benchmarks

    skills/domains/chemistry/cactus-cheminformatics-guide/SKILL.md

    • Network accessline 8
      subcategory: "chemistry"     keywords: ["CACTUS", "cheminformatics", "PNNL", "molecular analysis", "LLM chemistry", "chemical agent"]     source: "https://github.com/pnnl/cactus"
    • Network accessline 9
      keywords: ["CACTUS", "cheminformatics", "PNNL", "molecular analysis", "LLM chemistry", "chemical agent"]     source: "https://github.com/pnnl/cactus" ---
    • Network accessline 10
      source: "https://github.com/pnnl/cactus"
    • Network accessline 87
      - [CACTUS GitHub](https://github.com/pnnl/cactus)
    • Network accessline 88
      - [RDKit](https://www.rdkit.org/)
    • Network accessline 89
      - [PNNL](https://www.pnnl.gov/)

    skills/domains/chemistry/catalysis-hub-api/SKILL.md

    • Network accessline 8
      subcategory: "chemistry"     keywords: ["catalysis", "DFT", "reaction energy", "surface chemistry", "computational chemistry", "GraphQL"]     source: "https://www.catalysis-hub.org"
    • Network accessline 9
      keywords: ["catalysis", "DFT", "reaction energy", "surface chemistry", "computational chemistry", "GraphQL"]     source: "https://www.catalysis-hub.org" ---
    • Network accessline 10
      source: "https://www.catalysis-hub.org"
    • Network accessline 27
      **Endpoint:** `https://api.catalysis-hub.org/graphql`
    • Network accessline 53
      curl -s -X POST "https://api.catalysis-hub.org/graphql" \
    • Network accessline 70
      curl -s -X POST "https://api.catalysis-hub.org/graphql" \
    • Network accessline 86
      curl -s -X POST "https://api.catalysis-hub.org/graphql" \
    • Network accessline 103
      curl -s -X POST "https://api.catalysis-hub.org/graphql" \
    • Network accessline 133
      ENDPOINT = "https://api.catalysis-hub.org/graphql"
    • Network accessline 135
      def query_catalysis_hub(query):     """Execute a GraphQL query against Catalysis Hub."""     resp = requests.post(ENDPOINT, json={"query": query})
    • Network accessline 136
      """Execute a GraphQL query against Catalysis Hub."""     resp = requests.post(ENDPOINT, json={"query": query})     resp.raise_for_status()
    • Network accessline 137
      resp = requests.post(ENDPOINT, json={"query": query})
    • Network accessline 168
      - Catalysis Hub: https://www.catalysis-hub.org
    • Network accessline 169
      - GraphQL Endpoint: https://api.catalysis-hub.org/graphql
    • Network accessline 171
      - SUNCAT Center: https://suncat.stanford.edu

    skills/domains/chemistry/chemeagle-guide/SKILL.md

    • Network accessline 8
      subcategory: "chemistry"     keywords: ["ChemEagle", "chemical extraction", "literature mining", "reaction extraction", "chemistry NLP", "multi-agent"]     source: "https://github.com/CYF2000127/ChemEagle"
    • Network accessline 9
      keywords: ["ChemEagle", "chemical extraction", "literature mining", "reaction extraction", "chemistry NLP", "multi-agent"]     source: "https://github.com/CYF2000127/ChemEagle" ---
    • Network accessline 10
      source: "https://github.com/CYF2000127/ChemEagle"
    • Network accessline 145
      - [ChemEagle GitHub](https://github.com/CYF2000127/ChemEagle)
    • Network accessline 146
      - [RDKit](https://www.rdkit.org/) — Chemistry toolkit
    • Network accessline 147
      - [PubChem](https://pubchem.ncbi.nlm.nih.gov/) — Chemical database

    skills/domains/chemistry/chemgraph-agent-guide/SKILL.md

    • Network accessline 8
      subcategory: "chemistry"     keywords: ["ChemGraph", "molecular simulation", "computational chemistry", "DFT", "LangGraph", "ASE"]     source: "https://github.com/argonne-lcf/ChemGraph"
    • Network accessline 9
      keywords: ["ChemGraph", "molecular simulation", "computational chemistry", "DFT", "LangGraph", "ASE"]     source: "https://github.com/argonne-lcf/ChemGraph" ---
    • Network accessline 10
      source: "https://github.com/argonne-lcf/ChemGraph"
    • Network accessline 118
      - [ChemGraph GitHub](https://github.com/argonne-lcf/ChemGraph)
    • Network accessline 119
      - [ASE Documentation](https://wiki.fysik.dtu.dk/ase/)
    • Network accessline 120
      - [LangGraph](https://github.com/langchain-ai/langgraph)

    skills/domains/chemistry/computational-chemistry-guide/SKILL.md

    • Network accessline 262
      - [ORCA Documentation](https://www.faccts.de/docs/orca/6.0/manual/) -- Free quantum chemistry software
    • Network accessline 263
      - [OpenMM Documentation](http://docs.openmm.org/) -- GPU-accelerated molecular dynamics
    • Network accessline 264
      - [RDKit Documentation](https://www.rdkit.org/docs/) -- Cheminformatics toolkit
    • Network accessline 265
      - [Psi4 Documentation](https://psicode.org/) -- Open-source quantum chemistry
    • Network accessline 266
      - [A Hitchhiker's Guide to DFT](https://onlinelibrary.wiley.com/doi/book/10.1002/3527600043) -- Koch and Holthausen

    skills/domains/chemistry/pubchem-api-guide/SKILL.md

    • Network accessline 8
      subcategory: "chemistry"     keywords: ["pubchem", "chemistry", "compounds", "structures", "bioassay", "pharmacology"]     source: "https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest"
    • Network accessline 9
      keywords: ["pubchem", "chemistry", "compounds", "structures", "bioassay", "pharmacology"]     source: "https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest" ---
    • Network accessline 10
      source: "https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest"
    • Network accessline 28
      # No API key needed curl "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/JSON"
    • Network accessline 29
      curl "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/JSON"
    • Network accessline 37
      GET https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{name}/JSON
    • Dangerous shell operationline 41
      curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/caffeine/JSON"    | python3 -m json.tool
    • Network accessline 41
      curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/caffeine/JSON" \
    • Network accessline 50
      GET https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cid}/property/{properties}/JSON
    • Dangerous shell operationline 56
      curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/ibuprofen/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IUPACName,XLogP/JSON"    | python3 -m json.tool
    • Network accessline 56
      curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/ibuprofen/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IUPACName,XLogP/JSON" \
    • Dangerous shell operationline 63
      curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastformula/C8H10N4O2/property/IUPACName,MolecularWeight,CanonicalSMILES/JSON"    | python3 -m json.tool
    • Network accessline 63
      curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastformula/C8H10N4O2/property/IUPACName,MolecularWeight,CanonicalSMILES/JSON" \
    • Dangerous shell operationline 72
      curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/cid/2244/property/IUPACName,MolecularWeight,CanonicalSMILES/JSON?Threshold=90"    | python3 -m json.tool
    • Network accessline 72
      curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/cid/2244/property/IUPACName,MolecularWeight,CanonicalSMILES/JSON?Threshold=90" \
    • Dangerous shell operationline 81
      curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/assaysummary/JSON"    | python3 -m json.tool
    • Network accessline 81
      curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/assaysummary/JSON" \
    • Network accessline 91
      PUG_REST = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"
    • Network accessline 95
      props = "MolecularWeight,XLogP,HBondDonorCount,HBondAcceptorCount,TPSA,RotatableBondCount,IUPACName"     url = f"{PUG_REST}/compound/name/{name}/property/{props}/JSON"     resp = requests.get(url)
    • Network accessline 96
      url = f"{PUG_REST}/compound/name/{name}/property/{props}/JSON"     resp = requests.get(url)     resp.raise_for_status()
    • Network accessline 97
      resp = requests.get(url)
    • Network accessline 139
      props = "IUPACName,MolecularFormula,MolecularWeight,CanonicalSMILES,XLogP"     url = f"{PUG_REST}/compound/cid/{cids}/property/{props}/JSON"     resp = requests.get(url)
    • Network accessline 140
      url = f"{PUG_REST}/compound/cid/{cids}/property/{props}/JSON"     resp = requests.get(url)     resp.raise_for_status()
    • Network accessline 141
      resp = requests.get(url)
    • Network accessline 177
      - PubChem PUG REST Documentation: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest
    • Network accessline 178
      - PubChem PUG REST Tutorial: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest-tutorial
    • Network accessline 179
      - PubChem Compound Database: https://pubchem.ncbi.nlm.nih.gov/
    • Network accessline 180
      - PubChem Power User Gateway: https://pubchem.ncbi.nlm.nih.gov/docs/power-user-gateway

    skills/domains/chemistry/retrosynthesis-guide/SKILL.md

    • Network accessline 106
      # One-step retrosynthesis response = requests.post(
    • Network accessline 107
      response = requests.post(
    • Network accessline 108
      "https://askcos.mit.edu/api/retro/",
    • Access to secretsline 130
      [Credential-related source omitted]
    • Access to secretsline 131
      [Credential-related source omitted]

    skills/domains/cs/ai-security-papers-guide/SKILL.md

    • Network accessline 8
      subcategory: "cs"     keywords: ["AI security", "adversarial ML", "model attacks", "S&P", "CCS", "USENIX", "NDSS"]     source: "https://github.com/Zhou-Zi7/Awesome-AI-Security-BIG4"
    • Network accessline 9
      keywords: ["AI security", "adversarial ML", "model attacks", "S&P", "CCS", "USENIX", "NDSS"]     source: "https://github.com/Zhou-Zi7/Awesome-AI-Security-BIG4" ---
    • Network accessline 10
      source: "https://github.com/Zhou-Zi7/Awesome-AI-Security-BIG4"
    • Network accessline 101
      - [Awesome-AI-Security-BIG4](https://github.com/Zhou-Zi7/Awesome-AI-Security-BIG4)
    • Network accessline 102
      - [IEEE S&P](https://www.ieee-security.org/TC/SP-Index.html)
    • Network accessline 103
      - [ACM CCS](https://www.sigsac.org/ccs/)

    skills/domains/cs/code-llm-papers-guide/SKILL.md

    • Network accessline 8
      subcategory: "cs"     keywords: ["Code LLM", "code generation", "program synthesis", "Codex", "code intelligence", "software engineering"]     source: "https://github.com/codefuse-ai/Awesome-Code-LLM"
    • Network accessline 9
      keywords: ["Code LLM", "code generation", "program synthesis", "Codex", "code intelligence", "software engineering"]     source: "https://github.com/codefuse-ai/Awesome-Code-LLM" ---
    • Network accessline 10
      source: "https://github.com/codefuse-ai/Awesome-Code-LLM"
    • Network accessline 128
      - [Awesome-Code-LLM](https://github.com/codefuse-ai/Awesome-Code-LLM)
    • Network accessline 129
      - [TMLR Survey Paper](https://arxiv.org/abs/2311.07989)
    • Network accessline 130
      - [HumanEval](https://github.com/openai/human-eval)
    • Network accessline 131
      - [SWE-bench](https://www.swebench.com/)

    skills/domains/cs/dblp-api/SKILL.md

    • Network accessline 8
      subcategory: "cs"     keywords: ["algorithms", "data structures", "software engineering", "database", "academic database search"]     source: "https://dblp.org/faq/1474707.html"
    • Network accessline 9
      keywords: ["algorithms", "data structures", "software engineering", "database", "academic database search"]     source: "https://dblp.org/faq/1474707.html" ---
    • Network accessline 10
      source: "https://dblp.org/faq/1474707.html"
    • Network accessline 31
      - **URL**: `GET https://dblp.org/search/publ/api`
    • Network accessline 42
      curl "https://dblp.org/search/publ/api?q=graph+neural+networks&format=json&h=10&f=0"
    • Network accessline 48
      - **URL**: `GET https://dblp.org/search/author/api`
    • Network accessline 58
      curl "https://dblp.org/search/author/api?q=Yann+LeCun&format=json&h=5"
    • Network accessline 64
      - **URL**: `GET https://dblp.org/search/venue/api`
    • Network accessline 74
      curl "https://dblp.org/search/venue/api?q=NeurIPS&format=json&h=5"
    • Network accessline 80
      - **URL**: `GET https://dblp.org/pid/{pid}.json`
    • Network accessline 87
      curl "https://dblp.org/pid/h/GeoffreyEHinton.json"
    • Network accessline 102
      # Step 1: Find the author's DBLP PID curl "https://dblp.org/search/author/api?q=Jure+Leskovec&format=json&h=1"
    • Network accessline 103
      curl "https://dblp.org/search/author/api?q=Jure+Leskovec&format=json&h=1"
    • Network accessline 105
      # Step 2: Fetch their full profile curl "https://dblp.org/pid/l/JureLeskovec.json"
    • Network accessline 106
      curl "https://dblp.org/pid/l/JureLeskovec.json"
    • Network accessline 114
      curl "https://dblp.org/search/publ/api?q=venue:ICML+year:2024&format=json&h=50"
    • Network accessline 122
      curl "https://dblp.org/search/publ/api?q=attention+is+all+you+need&format=json&h=1" | jq '.result.hits.hit[0].info.doi'
    • Network accessline 127
      - Official documentation: https://dblp.org/faq/1474707.html
    • Network accessline 128
      - DBLP XML dump: https://dblp.org/xml/
    • Network accessline 129
      - DBLP statistics: https://dblp.org/statistics/

    skills/domains/cs/formal-verification-guide/SKILL.md

    • Dangerous shell operationline 39
      CONSTANTS RM  \* Set of resource managers
    • Dangerous shell operationline 55
      \* RM r prepares to commit
    • Dangerous shell operationline 62
      \* TM receives a Prepared message from RM r
    • Dangerous shell operationline 77
      \* Safety property: No RM commits unless TM has committed
    • Dangerous shell operationline 79
      \A r \in RM : rmState[r] = "committed" => tmState = "committed"
    • Dangerous shell operationline 88
      # RM = {"rm1", "rm2", "rm3"}

    skills/domains/cs/gaussian-splatting-papers-guide/SKILL.md

    • Network accessline 8
      subcategory: "cs"     keywords: ["3D Gaussian Splatting", "3DGS", "neural rendering", "NeRF", "novel view synthesis", "point cloud"]     source: "https://github.com/MrNeRF/awesome-3D-gaussian-splatting"
    • Network accessline 9
      keywords: ["3D Gaussian Splatting", "3DGS", "neural rendering", "NeRF", "novel view synthesis", "point cloud"]     source: "https://github.com/MrNeRF/awesome-3D-gaussian-splatting" ---
    • Network accessline 10
      source: "https://github.com/MrNeRF/awesome-3D-gaussian-splatting"
    • Network accessline 127
      # Original implementation git clone https://github.com/graphdeco-inria/gaussian-splatting
    • Network accessline 128
      git clone https://github.com/graphdeco-inria/gaussian-splatting
    • Network accessline 156
      - [awesome-3D-gaussian-splatting](https://github.com/MrNeRF/awesome-3D-gaussian-splatting)
    • Network accessline 157
      - [Original 3DGS](https://repo-sam.inria.fr/fungraph/3d-gaussian-splatting/)
    • Network accessline 158
      - [3DGS Papers Collection](https://3dgaussians.github.io/)

    skills/domains/cs/llm-aiops-guide/SKILL.md

    • Network accessline 8
      subcategory: "cs"     keywords: ["AIOps", "LLM operations", "IT automation", "log analysis", "incident management", "DevOps AI"]     source: "https://github.com/Jun-jie-Huang/awesome-LLM-AIOps"
    • Network accessline 9
      keywords: ["AIOps", "LLM operations", "IT automation", "log analysis", "incident management", "DevOps AI"]     source: "https://github.com/Jun-jie-Huang/awesome-LLM-AIOps" ---
    • Network accessline 10
      source: "https://github.com/Jun-jie-Huang/awesome-LLM-AIOps"
    • Network accessline 295
      - [awesome-LLM-AIOps](https://github.com/Jun-jie-Huang/awesome-LLM-AIOps)
    • Network accessline 296
      - [OpsEval Benchmark](https://arxiv.org/abs/2310.07637)
    • Network accessline 297
      - [vLLM: Easy, Fast, and Cheap LLM Serving](https://arxiv.org/abs/2309.06180)
    • Network accessline 298
      - [LangSmith Documentation](https://docs.smith.langchain.com/)
    • Network accessline 299
      - [MLflow LLM Evaluation](https://mlflow.org/docs/latest/llms/llm-evaluate/index.html)
    • Network accessline 300
      - [FrugalGPT: How to Use LLMs While Reducing Cost](https://arxiv.org/abs/2305.05176)
    • Network accessline 301
      - [RouteLLM: Learning to Route LLMs](https://arxiv.org/abs/2406.18665)

    skills/domains/cs/software-engineering-research/SKILL.md

    • Network accessline 62
      repo_url = "https://github.com/apache/kafka"

    skills/domains/cs/software-heritage-api/SKILL.md

    • Network accessline 8
      subcategory: "cs"     keywords: ["Software Heritage", "code archive", "source code preservation", "SWHID", "code provenance", "open source"]     source: "https://www.softwareheritage.org/"
    • Network accessline 9
      keywords: ["Software Heritage", "code archive", "source code preservation", "SWHID", "code provenance", "open source"]     source: "https://www.softwareheritage.org/" ---
    • Network accessline 10
      source: "https://www.softwareheritage.org/"
    • Network accessline 24
      https://archive.softwareheritage.org/api/1
    • Network accessline 30
      # Search for repositories curl "https://archive.softwareheritage.org/api/1/origin/search/scikit-learn/?limit=10"
    • Network accessline 31
      curl "https://archive.softwareheritage.org/api/1/origin/search/scikit-learn/?limit=10"
    • Network accessline 33
      # Get origin metadata curl "https://archive.softwareheritage.org/api/1/origin/https://github.com/scikit-learn/scikit-learn/get/"
    • Network accessline 34
      curl "https://archive.softwareheritage.org/api/1/origin/https://github.com/scikit-learn/scikit-learn/get/"
    • Network accessline 36
      # List visits (snapshots) of an origin curl "https://archive.softwareheritage.org/api/1/origin/https://github.com/scikit-learn/scikit-learn/visits/"
    • Network accessline 37
      curl "https://archive.softwareheritage.org/api/1/origin/https://github.com/scikit-learn/scikit-learn/visits/"
    • Network accessline 43
      # Get a specific file by its SHA1 hash curl "https://archive.softwareheritage.org/api/1/content/sha1:adc83b19e793491b1c6ea0fd8b46cd9f32e592fc/"
    • Network accessline 44
      curl "https://archive.softwareheritage.org/api/1/content/sha1:adc83b19e793491b1c6ea0fd8b46cd9f32e592fc/"
    • Network accessline 46
      # Get raw file content curl "https://archive.softwareheritage.org/api/1/content/sha1:adc83b19e793491b1c6ea0fd8b46cd9f32e592fc/raw/"
    • Network accessline 47
      curl "https://archive.softwareheritage.org/api/1/content/sha1:adc83b19e793491b1c6ea0fd8b46cd9f32e592fc/raw/"
    • Network accessline 49
      # Get directory listing curl "https://archive.softwareheritage.org/api/1/directory/{sha1_git}/"
    • Network accessline 50
      curl "https://archive.softwareheritage.org/api/1/directory/{sha1_git}/"
    • Network accessline 56
      # Resolve a SWHID to its object curl "https://archive.softwareheritage.org/api/1/resolve/swh:1:cnt:adc83b19e793491b1c6ea0fd8b46cd9f32e592fc/"
    • Network accessline 57
      curl "https://archive.softwareheritage.org/api/1/resolve/swh:1:cnt:adc83b19e793491b1c6ea0fd8b46cd9f32e592fc/"
    • Network accessline 59
      # Get snapshot curl "https://archive.softwareheritage.org/api/1/snapshot/{sha1_git}/"
    • Network accessline 60
      curl "https://archive.softwareheritage.org/api/1/snapshot/{sha1_git}/"
    • Network accessline 62
      # Get revision (commit) curl "https://archive.softwareheritage.org/api/1/revision/{sha1_git}/"
    • Network accessline 63
      curl "https://archive.softwareheritage.org/api/1/revision/{sha1_git}/"
    • Network accessline 69
      # Request archival of a repository curl -X POST "https://archive.softwareheritage.org/api/1/origin/save/git/url/https://github.com/user/repo/"
    • Network accessline 70
      curl -X POST "https://archive.softwareheritage.org/api/1/origin/save/git/url/https://github.com/user/repo/"
    • Network accessline 92
      With qualifiers:   swh:1:cnt:{hash};origin=https://github.com/user/repo;visit=swh:1:snp:{hash};path=/src/main.py
    • Network accessline 93
      swh:1:cnt:{hash};origin=https://github.com/user/repo;visit=swh:1:snp:{hash};path=/src/main.py
    • Network accessline 102
      BASE_URL = "https://archive.softwareheritage.org/api/1"
    • Network accessline 105
      def search_origins(query: str, limit: int = 10) -> list:     """Search Software Heritage for archived repositories."""     resp = requests.get(
    • Network accessline 106
      """Search Software Heritage for archived repositories."""     resp = requests.get(         f"{BASE_URL}/origin/search/{query}/",
    • Network accessline 107
      resp = requests.get(
    • Network accessline 122
      def get_origin_visits(origin_url: str) -> list:     """Get archival snapshots for a repository."""     resp = requests.get(
    • Network accessline 123
      """Get archival snapshots for a repository."""     resp = requests.get(         f"{BASE_URL}/origin/{origin_url}/visits/",
    • Network accessline 124
      resp = requests.get(
    • Network accessline 140
      def get_directory(sha1_git: str) -> list:     """List files in an archived directory."""     resp = requests.get(
    • Network accessline 141
      """List files in an archived directory."""     resp = requests.get(         f"{BASE_URL}/directory/{sha1_git}/",
    • Network accessline 142
      resp = requests.get(
    • Network accessline 157
      def save_code_now(repo_url: str) -> dict:     """Request Software Heritage to archive a repository."""     resp = requests.post(
    • Network accessline 158
      """Request Software Heritage to archive a repository."""     resp = requests.post(         f"{BASE_URL}/origin/save/git/url/{repo_url}/",
    • Network accessline 159
      resp = requests.post(
    • Network accessline 172
      # Example: get snapshot history visits = get_origin_visits("https://github.com/pytorch/pytorch")
    • Network accessline 173
      visits = get_origin_visits("https://github.com/pytorch/pytorch")
    • Network accessline 177
      # Example: request archival # result = save_code_now("https://github.com/my-org/my-research-code")
    • Network accessline 178
      # result = save_code_now("https://github.com/my-org/my-research-code")
    • Network accessline 197
      - [Software Heritage](https://www.softwareheritage.org/)
    • Network accessline 198
      - [API Documentation](https://archive.softwareheritage.org/api/)
    • Network accessline 199
      - [SWHID Specification](https://docs.softwareheritage.org/devel/swh-model/persistent-identifiers.html)

    skills/domains/ecology/conservation-biology-guide/SKILL.md

    • Network accessline 57
      [Credential-related source omitted]
    • Access to secretsline 57
      [Credential-related source omitted]
    • Network accessline 59
      [Credential-related source omitted]
    • Network accessline 61
      req = urllib.request.Request(url)
    • Network accessline 62
      response = urllib.request.urlopen(req)

    skills/domains/ecology/gbif-api/SKILL.md

    • Network accessline 8
      subcategory: "ecology"     keywords: ["ecology", "biodiversity", "taxonomy", "environmental science"]     source: "https://www.gbif.org/developer/summary"
    • Network accessline 9
      keywords: ["ecology", "biodiversity", "taxonomy", "environmental science"]     source: "https://www.gbif.org/developer/summary" ---
    • Network accessline 10
      source: "https://www.gbif.org/developer/summary"
    • Network accessline 33
      - **URL**: `GET https://api.gbif.org/v1/occurrence/search`
    • Network accessline 50
      curl "https://api.gbif.org/v1/occurrence/search?scientificName=Panthera+tigris&hasCoordinate=true&limit=10"
    • Network accessline 59
      - **URL**: `GET https://api.gbif.org/v1/species/match`
    • Network accessline 71
      curl "https://api.gbif.org/v1/species/match?name=Homo+sapiens"
    • Network accessline 80
      - **URL**: `GET https://api.gbif.org/v1/dataset`
    • Network accessline 94
      curl "https://api.gbif.org/v1/dataset?q=bird+monitoring&type=OCCURRENCE&limit=5"
    • Network accessline 101
      No formal rate limits are enforced on the GBIF API. However, GBIF recommends responsible use patterns. Large data downloads (millions of records) should use the asynchronous download API at `https://api.gbif.org/v1/occurrence/download/reque
    • Network accessline 115
      "limit": 300 } resp = requests.get("https://api.gbif.org/v1/occurrence/search", params=params)
    • Network accessline 116
      } resp = requests.get("https://api.gbif.org/v1/occurrence/search", params=params) data = resp.json()
    • Network accessline 117
      resp = requests.get("https://api.gbif.org/v1/occurrence/search", params=params)
    • Network accessline 136
      for name in names:     resp = requests.get("https://api.gbif.org/v1/species/match", params={"name": name})
    • Network accessline 137
      resp = requests.get("https://api.gbif.org/v1/species/match", params={"name": name})
    • Network accessline 147
      curl -X POST "https://api.gbif.org/v1/occurrence/download/request" \
    • Network accessline 155
      - Official API documentation: https://www.gbif.org/developer/summary
    • Network accessline 156
      - GBIF occurrence search API: https://www.gbif.org/developer/occurrence
    • Network accessline 157
      - GBIF species API: https://www.gbif.org/developer/species
    • Network accessline 158
      - GBIF data use guide: https://www.gbif.org/data-use

    skills/domains/ecology/inaturalist-api/SKILL.md

    • Network accessline 8
      subcategory: "ecology"     keywords: ["ecology", "biodiversity", "taxonomy", "evolutionary biology"]     source: "https://www.inaturalist.org/pages/api+reference"
    • Network accessline 9
      keywords: ["ecology", "biodiversity", "taxonomy", "evolutionary biology"]     source: "https://www.inaturalist.org/pages/api+reference" ---
    • Network accessline 10
      source: "https://www.inaturalist.org/pages/api+reference"
    • Network accessline 27
      For authenticated requests, register an application at https://www.inaturalist.org/oauth/applications and use the OAuth 2.0 flow to obtain an access token.
    • Network accessline 35
      - **URL**: `GET https://api.inaturalist.org/v1/observations`
    • Network accessline 55
      curl "https://api.inaturalist.org/v1/observations?taxon_id=3&quality_grade=research&place_id=1&per_page=10"
    • Network accessline 64
      - **URL**: `GET https://api.inaturalist.org/v1/taxa`
    • Network accessline 78
      curl "https://api.inaturalist.org/v1/taxa?q=monarch+butterfly&rank=species"
    • Network accessline 87
      - **URL**: `GET https://api.inaturalist.org/v1/places`
    • Network accessline 98
      curl "https://api.inaturalist.org/v1/places/autocomplete?q=Yellowstone"
    • Network accessline 105
      The iNaturalist API enforces a rate limit of 100 requests per minute. Exceeding this limit returns HTTP 429 responses. For large-scale data exports, iNaturalist recommends using their export tools at https://www.inaturalist.org/observations
    • Network accessline 123
      resp = requests.get("https://api.inaturalist.org/v1/observations", params=params)
    • Network accessline 147
      resp = requests.get("https://api.inaturalist.org/v1/observations", params=params)
    • Network accessline 164
      # Search for Spotted Lanternfly observations in Pennsylvania curl "https://api.inaturalist.org/v1/observations?taxon_id=325295&place_id=46&quality_grade=research&per_page=50"
    • Network accessline 165
      curl "https://api.inaturalist.org/v1/observations?taxon_id=325295&place_id=46&quality_grade=research&per_page=50"
    • Network accessline 170
      - Official API reference: https://www.inaturalist.org/pages/api+reference
    • Network accessline 171
      - API v1 documentation: https://api.inaturalist.org/v1/docs/
    • Network accessline 172
      - iNaturalist homepage: https://www.inaturalist.org/
    • Network accessline 173
      - Data export tools: https://www.inaturalist.org/observations/export

    skills/domains/economics/fred-api/SKILL.md

    • Network accessline 8
      subcategory: "economics"     keywords: ["microeconomics", "macroeconomics", "econometrics", "development economics"]     source: "https://fred.stlouisfed.org/docs/api/fred/"
    • Network accessline 9
      keywords: ["microeconomics", "macroeconomics", "econometrics", "development economics"]     source: "https://fred.stlouisfed.org/docs/api/fred/"     requires:
    • Network accessline 10
      source: "https://fred.stlouisfed.org/docs/api/fred/"
    • Access to secretsline 12
      [Credential-related source omitted]
    • Network accessline 29
      1. Register for an account at https://fredaccount.stlouisfed.org/login/secure/ 2. Request an API key at https://fredaccount.stlouisfed.org/apikeys 3. Include the key as the `api_key` query parameter in all requests
    • Network accessline 30
      2. Request an API key at https://fredaccount.stlouisfed.org/apikeys
    • Access to secretsline 31
      [Credential-related source omitted]
    • Network accessline 34
      [Credential-related source omitted]
    • Access to secretsline 34
      [Credential-related source omitted]
    • Network accessline 45
      - **URL**: `GET https://api.stlouisfed.org/fred/series`
    • Access to secretsline 51
      [Credential-related source omitted]
    • Network accessline 57
      [Credential-related source omitted]
    • Access to secretsline 57
      [Credential-related source omitted]
    • Network accessline 66
      - **URL**: `GET https://api.stlouisfed.org/fred/series/observations`
    • Access to secretsline 72
      [Credential-related source omitted]
    • Network accessline 82
      [Credential-related source omitted]
    • Access to secretsline 82
      [Credential-related source omitted]
    • Network accessline 91
      - **URL**: `GET https://api.stlouisfed.org/fred/category`
    • Access to secretsline 97
      [Credential-related source omitted]
    • Network accessline 103
      [Credential-related source omitted]
    • Access to secretsline 103
      [Credential-related source omitted]
    • Network accessline 112
      - **URL**: `GET https://api.stlouisfed.org/fred/releases`
    • Access to secretsline 117
      [Credential-related source omitted]
    • Network accessline 123
      [Credential-related source omitted]
    • Access to secretsline 123
      [Credential-related source omitted]
    • Network accessline 130
      The FRED API enforces rate limits that vary by usage. Standard limits allow approximately 120 requests per minute. Exceeding the limit returns HTTP 429 responses. For bulk data retrieval, consider using the FRED Excel add-in or downloading
    • Access to secretsline 143
      [Credential-related source omitted]
    • Network accessline 145
      "observation_start": "2015-01-01" } resp = requests.get("https://api.stlouisfed.org/fred/series/observations", params=params)
    • Network accessline 146
      } resp = requests.get("https://api.stlouisfed.org/fred/series/observations", params=params) data = resp.json()
    • Network accessline 147
      resp = requests.get("https://api.stlouisfed.org/fred/series/observations", params=params)
    • Access to secretsline 162
      [Credential-related source omitted]
    • Network accessline 164
      for sid in series_ids:     resp = requests.get("https://api.stlouisfed.org/fred/series/observations", params={
    • Network accessline 165
      resp = requests.get("https://api.stlouisfed.org/fred/series/observations", params={
    • Access to secretsline 167
      [Credential-related source omitted]
    • Network accessline 181
      [Credential-related source omitted]
    • Access to secretsline 181
      [Credential-related source omitted]
    • Network accessline 186
      - Official API documentation: https://fred.stlouisfed.org/docs/api/fred/
    • Network accessline 187
      - FRED homepage: https://fred.stlouisfed.org/
    • Network accessline 188
      - Series search: https://fred.stlouisfed.org/docs/api/fred/series_search.html
    • Network accessline 189
      - Category tree: https://fred.stlouisfed.org/docs/api/fred/category.html

    skills/domains/economics/imf-data-api-guide/SKILL.md

    • Network accessline 8
      subcategory: "economics"     keywords: ["imf", "economics", "macroeconomics", "indicators", "exchange-rates", "gdp"]     source: "https://datahelp.imf.org/knowledgebase/articles/667681-using-json-restful-web-service"
    • Network accessline 9
      keywords: ["imf", "economics", "macroeconomics", "indicators", "exchange-rates", "gdp"]     source: "https://datahelp.imf.org/knowledgebase/articles/667681-using-json-restful-web-service" ---
    • Network accessline 10
      source: "https://datahelp.imf.org/knowledgebase/articles/667681-using-json-restful-web-service"
    • Network accessline 28
      # No API key needed curl "https://www.imf.org/external/datamapper/api/v1/NGDP_RPCH?periods=2024"
    • Network accessline 29
      curl "https://www.imf.org/external/datamapper/api/v1/NGDP_RPCH?periods=2024"
    • Network accessline 37
      GET https://www.imf.org/external/datamapper/api/v1
    • Dangerous shell operationline 41
      curl -s "https://www.imf.org/external/datamapper/api/v1" | python3 -m json.tool
    • Network accessline 41
      curl -s "https://www.imf.org/external/datamapper/api/v1" | python3 -m json.tool
    • Network accessline 47
      GET https://www.imf.org/external/datamapper/api/v1/indicators
    • Network accessline 53
      GET https://www.imf.org/external/datamapper/api/v1/{indicator}?periods={year}
    • Dangerous shell operationline 66
      curl -s "https://www.imf.org/external/datamapper/api/v1/NGDP_RPCH?periods=2024"    | python3 -m json.tool
    • Network accessline 66
      curl -s "https://www.imf.org/external/datamapper/api/v1/NGDP_RPCH?periods=2024" \
    • Network accessline 75
      GET http://dataservices.imf.org/REST/SDMX_JSON.svc/CompactData/{database}/{dimensions}?startPeriod={start}&endPeriod={end}
    • Dangerous shell operationline 81
      curl -s "http://dataservices.imf.org/REST/SDMX_JSON.svc/CompactData/IFS/M.US+CN.PCPI_IX?startPeriod=2020&endPeriod=2025"    | python3 -m json.tool
    • Network accessline 81
      curl -s "http://dataservices.imf.org/REST/SDMX_JSON.svc/CompactData/IFS/M.US+CN.PCPI_IX?startPeriod=2020&endPeriod=2025" \
    • Network accessline 90
      DATAMAPPER_URL = "https://www.imf.org/external/datamapper/api/v1"
    • Network accessline 96
      if periods:         params["periods"] = ",".join(str(p) for p in periods)     resp = requests.get(url, params=params)
    • Network accessline 97
      params["periods"] = ",".join(str(p) for p in periods)     resp = requests.get(url, params=params)     resp.raise_for_status()
    • Network accessline 98
      resp = requests.get(url, params=params)
    • Network accessline 128
      codes = "+".join(country_codes)     url = (         f"http://dataservices.imf.org/REST/SDMX_JSON.svc/"
    • Network accessline 129
      url = (         f"http://dataservices.imf.org/REST/SDMX_JSON.svc/"         f"CompactData/IFS/A.{codes}.ENDA_XDC_USD_RATE"
    • Network accessline 130
      f"http://dataservices.imf.org/REST/SDMX_JSON.svc/"
    • Network accessline 132
      f"?startPeriod={start_year}&endPeriod={end_year}"     )     resp = requests.get(url)
    • Network accessline 133
      )     resp = requests.get(url)     resp.raise_for_status()
    • Network accessline 134
      resp = requests.get(url)
    • Network accessline 171
      - IMF Data API Documentation: https://datahelp.imf.org/knowledgebase/articles/667681-using-json-restful-web-service
    • Network accessline 172
      - IMF DataMapper: https://www.imf.org/external/datamapper
    • Network accessline 173
      - IMF Data Portal: https://data.imf.org/
    • Network accessline 174
      - IMF World Economic Outlook: https://www.imf.org/en/Publications/WEO

    skills/domains/economics/nber-working-papers-api/SKILL.md

    • Network accessline 8
      subcategory: "economics"     keywords: ["NBER", "working papers", "economics research", "macroeconomics", "economic policy", "recession dating"]     source: "https://www.nber.org/"
    • Network accessline 9
      keywords: ["NBER", "working papers", "economics research", "macroeconomics", "economic policy", "recession dating"]     source: "https://www.nber.org/" ---
    • Network accessline 10
      source: "https://www.nber.org/"
    • Network accessline 24
      # Latest working papers feed curl "https://www.nber.org/papers.rss"
    • Network accessline 25
      curl "https://www.nber.org/papers.rss"
    • Network accessline 27
      # Papers by program curl "https://www.nber.org/programs/ef/papers.rss"  # Economic Fluctuations
    • Network accessline 28
      curl "https://www.nber.org/programs/ef/papers.rss"  # Economic Fluctuations
    • Network accessline 29
      curl "https://www.nber.org/programs/ls/papers.rss"  # Labor Studies
    • Network accessline 30
      curl "https://www.nber.org/programs/io/papers.rss"  # Industrial Organization
    • Network accessline 36
      # Search via NBER website (HTML scraping needed) curl "https://www.nber.org/api/v1/working_page_listing/contentType/working_paper/?page=1&perPage=20&q=inflation+expectations"
    • Network accessline 37
      curl "https://www.nber.org/api/v1/working_page_listing/contentType/working_paper/?page=1&perPage=20&q=inflation+expectations"
    • Network accessline 39
      # Get specific paper metadata curl "https://www.nber.org/api/v1/working_page_listing/contentType/working_paper/?page=1&perPage=1&q=w28104"
    • Network accessline 40
      curl "https://www.nber.org/api/v1/working_page_listing/contentType/working_paper/?page=1&perPage=1&q=w28104"
    • Network accessline 46
      # Macroeconomic history data # Available at: https://data.nber.org/
    • Network accessline 47
      # Available at: https://data.nber.org/
    • Network accessline 49
      # Business cycle dates curl "https://data.nber.org/data/cycles/business_cycle_dates.json"
    • Network accessline 50
      curl "https://data.nber.org/data/cycles/business_cycle_dates.json"
    • Network accessline 52
      # CPS labor data extracts # https://data.nber.org/cps/
    • Network accessline 53
      # https://data.nber.org/cps/
    • Network accessline 87
      """Get latest NBER working papers via RSS."""     if program:         url = f"https://www.nber.org/programs/{program}/papers.rss"
    • Network accessline 88
      if program:         url = f"https://www.nber.org/programs/{program}/papers.rss"     else:
    • Network accessline 89
      url = f"https://www.nber.org/programs/{program}/papers.rss"
    • Network accessline 91
      url = "https://www.nber.org/papers.rss"
    • Network accessline 93
      resp = requests.get(url, timeout=30)
    • Network accessline 109
      per_page: int = 20) -> list:     """Search NBER working papers."""     resp = requests.get(
    • Network accessline 110
      """Search NBER working papers."""     resp = requests.get(         "https://www.nber.org/api/v1/working_page_listing/"
    • Network accessline 111
      resp = requests.get(
    • Network accessline 112
      "https://www.nber.org/api/v1/working_page_listing/"
    • Network accessline 125
      "number": item.get("wp_number", ""),             "date": item.get("date", ""),             "url": f"https://www.nber.org/papers/{item.get('wp_number', '')}",
    • Network accessline 126
      "date": item.get("date", ""),             "url": f"https://www.nber.org/papers/{item.get('wp_number', '')}",             "abstract": item.get("description", "")[:300],
    • Network accessline 127
      "url": f"https://www.nber.org/papers/{item.get('wp_number', '')}",
    • Network accessline 134
      def get_business_cycle_dates() -> list:     """Get NBER official business cycle dates."""     resp = requests.get(
    • Network accessline 135
      """Get NBER official business cycle dates."""     resp = requests.get(         "https://data.nber.org/data/cycles/business_cycle_dates.json",
    • Network accessline 136
      resp = requests.get(
    • Network accessline 137
      "https://data.nber.org/data/cycles/business_cycle_dates.json",
    • Network accessline 174
      - [NBER](https://www.nber.org/)
    • Network accessline 175
      - [NBER Working Papers](https://www.nber.org/papers)
    • Network accessline 176
      - [NBER Data](https://data.nber.org/)
    • Network accessline 177
      - [NBER Programs](https://www.nber.org/programs-projects/programs)

    skills/domains/economics/post-labor-economics/SKILL.md

    • Network accessline 252
      - Frey, C. B. & Osborne, M. A. (2017). The Future of Employment. Technological Forecasting and Social Change, 114, 254-280. - Korinek, A. & Stiglitz, J. E. (2021). Artificial Intelligence, Globalization, and Strategies for Economic Developm
    • Network accessline 254
      - [OECD Future of Work](https://www.oecd.org/future-of-work/) -- Cross-country analysis and policy recommendations

    skills/domains/economics/pricing-psychology-guide/SKILL.md

    • Network accessline 271
      - Rao, V. R. (2009). Handbook of Pricing Research in Marketing. Edward Elgar. - Thomas, M. & Morwitz, V. (2005). Penny Wise and Pound Foolish. JCR, 32(1), 54-64. - [oTree documentation](https://otree.readthedocs.io/) -- Experimental economi
    • Network accessline 273
      - [oTree documentation](https://otree.readthedocs.io/) -- Experimental economics platform

    skills/domains/economics/repec-economics-api/SKILL.md

    • Network accessline 8
      subcategory: "economics"     keywords: ["RePEc", "economics papers", "working papers", "IDEAS", "EconPapers", "economic research"]     source: "https://ideas.repec.org/"
    • Network accessline 9
      keywords: ["RePEc", "economics papers", "working papers", "IDEAS", "EconPapers", "economic research"]     source: "https://ideas.repec.org/" ---
    • Network accessline 10
      source: "https://ideas.repec.org/"
    • Network accessline 24
      # Search economics papers curl "https://ideas.repec.org/cgi-bin/htsearch?q=monetary+policy+inflation&cmd=Search&fmt=json"
    • Network accessline 25
      curl "https://ideas.repec.org/cgi-bin/htsearch?q=monetary+policy+inflation&cmd=Search&fmt=json"
    • Network accessline 27
      # Search specific types # Working papers curl "https://ideas.repec.org/cgi-bin/htsearch?q=fiscal+stimulus&ul=%%2Fp%%2F&fmt=json"
    • Network accessline 29
      curl "https://ideas.repec.org/cgi-bin/htsearch?q=fiscal+stimulus&ul=%%2Fp%%2F&fmt=json"
    • Network accessline 31
      # Journal articles curl "https://ideas.repec.org/cgi-bin/htsearch?q=trade+liberalization&ul=%%2Fa%%2F&fmt=json"
    • Network accessline 32
      curl "https://ideas.repec.org/cgi-bin/htsearch?q=trade+liberalization&ul=%%2Fa%%2F&fmt=json"
    • Network accessline 38
      # Get metadata for a handle curl "https://api.repec.org/handle?handle=RePEc:nbr:nberwo:28104"
    • Network accessline 39
      curl "https://api.repec.org/handle?handle=RePEc:nbr:nberwo:28104"
    • Network accessline 41
      # Author profile by short-id curl "https://api.repec.org/author?short-id=ppi1"
    • Network accessline 42
      curl "https://api.repec.org/author?short-id=ppi1"
    • Network accessline 44
      # List items in a series curl "https://api.repec.org/series?series=RePEc:nbr:nberwo"
    • Network accessline 45
      curl "https://api.repec.org/series?series=RePEc:nbr:nberwo"
    • Network accessline 51
      # Get citations for a paper curl "https://citec.repec.org/api/plain/RePEc:nbr:nberwo:28104"
    • Network accessline 52
      curl "https://citec.repec.org/api/plain/RePEc:nbr:nberwo:28104"
    • Network accessline 60
      # Get download/view statistics curl "https://logec.repec.org/scripts/paperstat.pf?h=RePEc:nbr:nberwo:28104"
    • Network accessline 61
      curl "https://logec.repec.org/scripts/paperstat.pf?h=RePEc:nbr:nberwo:28104"
    • Network accessline 93
      IDEAS_URL = "https://ideas.repec.org/cgi-bin/htsearch"
    • Network accessline 94
      CITEC_URL = "https://citec.repec.org/api/plain"
    • Network accessline 111
      resp = requests.get(IDEAS_URL, params=params, timeout=30)
    • Network accessline 128
      def get_citations(handle: str) -> list:     """Get papers citing a given RePEc handle."""     resp = requests.get(f"{CITEC_URL}/{handle}", timeout=30)
    • Network accessline 129
      """Get papers citing a given RePEc handle."""     resp = requests.get(f"{CITEC_URL}/{handle}", timeout=30)     resp.raise_for_status()
    • Network accessline 130
      resp = requests.get(f"{CITEC_URL}/{handle}", timeout=30)
    • Network accessline 175
      # Top economists curl "https://ideas.repec.org/top/top.person.all.html"
    • Network accessline 176
      curl "https://ideas.repec.org/top/top.person.all.html"
    • Network accessline 178
      # Top institutions curl "https://ideas.repec.org/top/top.inst.all.html"
    • Network accessline 179
      curl "https://ideas.repec.org/top/top.inst.all.html"
    • Network accessline 184
      - [IDEAS/RePEc](https://ideas.repec.org/)
    • Network accessline 185
      - [EconPapers](https://econpapers.repec.org/)
    • Network accessline 186
      - [RePEc Author Service](https://authors.repec.org/)
    • Network accessline 187
      - [CitEc](https://citec.repec.org/)

    skills/domains/economics/world-bank-data-guide/SKILL.md

    • Network accessline 8
      subcategory: "economics"     keywords: ["world-bank", "development", "indicators", "poverty", "economics", "statistics"]     source: "https://datahelpdesk.worldbank.org/knowledgebase/articles/889392-about-the-indicators-api"
    • Network accessline 9
      keywords: ["world-bank", "development", "indicators", "poverty", "economics", "statistics"]     source: "https://datahelpdesk.worldbank.org/knowledgebase/articles/889392-about-the-indicators-api" ---
    • Network accessline 10
      source: "https://datahelpdesk.worldbank.org/knowledgebase/articles/889392-about-the-indicators-api"
    • Network accessline 28
      # No API key needed curl "https://api.worldbank.org/v2/country/US/indicator/NY.GDP.MKTP.CD?format=json&date=2020:2024"
    • Network accessline 29
      curl "https://api.worldbank.org/v2/country/US/indicator/NY.GDP.MKTP.CD?format=json&date=2020:2024"
    • Network accessline 37
      GET https://api.worldbank.org/v2/country/{country_code}/indicator/{indicator_code}?format=json
    • Dangerous shell operationline 60
      curl -s "https://api.worldbank.org/v2/country/BR;RU;IN;CN;ZA/indicator/NY.GDP.PCAP.CD?format=json&date=2019:2023&per_page=100"    | python3 -m json.tool
    • Network accessline 60
      curl -s "https://api.worldbank.org/v2/country/BR;RU;IN;CN;ZA/indicator/NY.GDP.PCAP.CD?format=json&date=2019:2023&per_page=100" \
    • Dangerous shell operationline 67
      curl -s "https://api.worldbank.org/v2/indicator?format=json&per_page=50"    | python3 -m json.tool
    • Network accessline 67
      curl -s "https://api.worldbank.org/v2/indicator?format=json&per_page=50" \
    • Dangerous shell operationline 74
      curl -s "https://api.worldbank.org/v2/topic/8/indicator?format=json&per_page=20"    | python3 -m json.tool
    • Network accessline 74
      curl -s "https://api.worldbank.org/v2/topic/8/indicator?format=json&per_page=20" \
    • Dangerous shell operationline 83
      curl -s "https://api.worldbank.org/v2/country/CN?format=json"    | python3 -m json.tool
    • Network accessline 83
      curl -s "https://api.worldbank.org/v2/country/CN?format=json" \
    • Network accessline 93
      BASE_URL = "https://api.worldbank.org/v2"
    • Network accessline 101
      "per_page": per_page     }     resp = requests.get(url, params=params)
    • Network accessline 102
      }     resp = requests.get(url, params=params)     resp.raise_for_status()
    • Network accessline 103
      resp = requests.get(url, params=params)
    • Network accessline 128
      panel = {}     for ind_code, ind_name in indicators.items():         url = f"https://api.worldbank.org/v2/country/{countries}/indicator/{ind_code}"
    • Network accessline 129
      for ind_code, ind_name in indicators.items():         url = f"https://api.worldbank.org/v2/country/{countries}/indicator/{ind_code}"         params = {"format": "json", "date": years, "per_page": 5000}
    • Network accessline 130
      url = f"https://api.worldbank.org/v2/country/{countries}/indicator/{ind_code}"         params = {"format": "json", "date": years, "per_page": 5000}         resp = requests.get(url, params=params)
    • Network accessline 131
      params = {"format": "json", "date": years, "per_page": 5000}         resp = requests.get(url, params=params)         data = resp.json()
    • Network accessline 132
      resp = requests.get(url, params=params)
    • Network accessline 170
      - **Country groups:** Use aggregate codes like `EUU` (EU), `WLD` (World), `LIC` (Low Income) for pre-computed aggregates - **MRV parameter:** Use `MRV=1` to get the most recent value for each country when the latest year varies - **Bulk dow
    • Network accessline 172
      - **Bulk downloads:** For large-scale analysis, consider the bulk download options at https://data.worldbank.org/
    • Network accessline 176
      - World Bank Indicators API Documentation: https://datahelpdesk.worldbank.org/knowledgebase/articles/889392-about-the-indicators-api
    • Network accessline 177
      - World Bank Data Portal: https://data.worldbank.org/
    • Network accessline 178
      - World Bank Indicator List: https://data.worldbank.org/indicator
    • Network accessline 179
      - World Bank API Query Builder: https://datahelpdesk.worldbank.org/knowledgebase/articles/898581-api-basic-call-structures

    skills/domains/education/academic-study-methods/SKILL.md

    • Network accessline 226
      - Keshav, S. (2007). "How to Read a Paper." *ACM SIGCOMM Computer Communication Review*, 37(3), 83-84. - Brown, P. C., et al. (2014). *Make It Stick: The Science of Successful Learning*. Harvard UP. - [Anki Spaced Repetition Software](https
    • Network accessline 228
      - [Anki Spaced Repetition Software](https://apps.ankiweb.net/)

    skills/domains/education/open-syllabus-api/SKILL.md

    • Network accessline 8
      subcategory: "education"     keywords: ["Open Syllabus", "syllabi analytics", "teaching data", "textbook rankings", "curriculum analysis", "higher education"]     source: "https://opensyllabus.org/"
    • Network accessline 9
      keywords: ["Open Syllabus", "syllabi analytics", "teaching data", "textbook rankings", "curriculum analysis", "higher education"]     source: "https://opensyllabus.org/" ---
    • Network accessline 10
      source: "https://opensyllabus.org/"
    • Network accessline 24
      # The primary interface is the web explorer: # https://explorer.opensyllabus.org/
    • Network accessline 25
      # https://explorer.opensyllabus.org/
    • Network accessline 34
      # API requires institutional subscription # Base URL: https://api.opensyllabus.org/v1/
    • Network accessline 35
      # Base URL: https://api.opensyllabus.org/v1/
    • Network accessline 37
      [Credential-related source omitted]
    • Network accessline 38
      [Credential-related source omitted]
    • Access to secretsline 38
      [Credential-related source omitted]
    • Network accessline 39
      "https://api.opensyllabus.org/v1/titles?query=republic+plato&limit=20"
    • Network accessline 41
      [Credential-related source omitted]
    • Network accessline 42
      [Credential-related source omitted]
    • Access to secretsline 42
      [Credential-related source omitted]
    • Network accessline 43
      "https://api.opensyllabus.org/v1/titles/12345"
    • Network accessline 45
      [Credential-related source omitted]
    • Network accessline 46
      [Credential-related source omitted]
    • Access to secretsline 46
      [Credential-related source omitted]
    • Network accessline 47
      "https://api.opensyllabus.org/v1/titles/12345/co-assigned?limit=20"
    • Network accessline 49
      [Credential-related source omitted]
    • Network accessline 50
      [Credential-related source omitted]
    • Access to secretsline 50
      [Credential-related source omitted]
    • Network accessline 51
      "https://api.opensyllabus.org/v1/rankings?field=Economics&limit=50"
    • Network accessline 80
      BASE_URL = "https://api.opensyllabus.org/v1"
    • Network accessline 94
      resp = requests.get(
    • Network accessline 117
      [Credential-related source omitted]
    • Network accessline 118
      [Credential-related source omitted]
    • Network accessline 119
      resp = requests.get(
    • Network accessline 130
      [Credential-related source omitted]
    • Network accessline 131
      [Credential-related source omitted]
    • Network accessline 132
      resp = requests.get(
    • Network accessline 169
      - [Open Syllabus](https://opensyllabus.org/)
    • Network accessline 170
      - [Open Syllabus Explorer](https://explorer.opensyllabus.org/)

    skills/domains/finance/akshare-finance-data/SKILL.md

    • Network accessline 8
      subcategory: "finance"     keywords: ["akshare", "financial data", "chinese stocks", "market data", "economic indicators", "quantitative finance"]     source: "https://github.com/akfamily/akshare"
    • Network accessline 9
      keywords: ["akshare", "financial data", "chinese stocks", "market data", "economic indicators", "quantitative finance"]     source: "https://github.com/akfamily/akshare" ---
    • Network accessline 10
      source: "https://github.com/akfamily/akshare"
    • Network accessline 205
      - [AkShare Documentation](https://akshare.akfamily.xyz/)
    • Network accessline 206
      - [AkShare GitHub](https://github.com/akfamily/akshare)
    • Network accessline 207
      - [AkShare API Reference](https://akshare.akfamily.xyz/data/stock/stock.html)

    skills/domains/finance/financial-data-analysis/SKILL.md

    • Access to secretsline 61
      [Credential-related source omitted]

    skills/domains/finance/finsight-research-guide/SKILL.md

    • Network accessline 8
      subcategory: "finance"     keywords: ["FinSight", "financial analysis", "deep research", "market analysis", "financial reports", "multi-agent"]     source: "https://github.com/RUC-NLPIR/FinSight"
    • Network accessline 9
      keywords: ["FinSight", "financial analysis", "deep research", "market analysis", "financial reports", "multi-agent"]     source: "https://github.com/RUC-NLPIR/FinSight" ---
    • Network accessline 10
      source: "https://github.com/RUC-NLPIR/FinSight"
    • Network accessline 22
      git clone https://github.com/RUC-NLPIR/FinSight.git
    • Network accessline 112
      - [FinSight GitHub](https://github.com/RUC-NLPIR/FinSight)
    • Network accessline 113
      - [RUC-NLPIR Lab](http://playbigdata.ruc.edu.cn/)

    skills/domains/finance/options-analytics-agent-guide/SKILL.md

    • Network accessline 116
      - [Options Analytics Agent](https://github.com/options-analytics/options-agent)
    • Network accessline 117
      - [QuantLib](https://www.quantlib.org/) — Quantitative finance library

    skills/domains/finance/stata-accounting-research/SKILL.md

    • Network accessline 446
      - Dechow, P. M., Sloan, R. G., & Sweeney, A. P. (1995). Detecting Earnings Management. The Accounting Review, 70(2), 193-225. - Kothari, S. P., Leone, A. J., & Wasley, C. E. (2005). Performance Matched Discretionary Accrual Measures. Journa
    • Network accessline 447
      - Kothari, S. P., Leone, A. J., & Wasley, C. E. (2005). Performance Matched Discretionary Accrual Measures. Journal of Accounting and Economics, 39(1), 163-197. - [WRDS (Wharton Research Data Services)](https://wrds-www.wharton.upenn.edu/)
    • Network accessline 448
      - [WRDS (Wharton Research Data Services)](https://wrds-www.wharton.upenn.edu/) -- Standard data platform for accounting/finance research
    • Network accessline 449
      - [reghdfe documentation](https://github.com/sergiocorreia/reghdfe) -- Fast fixed-effects estimation in STATA

    skills/domains/geoscience/climate-modeling-guide/SKILL.md

    • Network accessline 50
      # Open the Pangeo CMIP6 catalog (cloud-hosted on Google Cloud) url = "https://storage.googleapis.com/cmip6/pangeo-cmip6.json"
    • Network accessline 51
      url = "https://storage.googleapis.com/cmip6/pangeo-cmip6.json"

    skills/domains/geoscience/climate-science-guide/SKILL.md

    • Network accessline 46
      import intake     catalog = intake.open_esm_datastore(         "https://storage.googleapis.com/cmip6/pangeo-cmip6.json"
    • Network accessline 47
      catalog = intake.open_esm_datastore(         "https://storage.googleapis.com/cmip6/pangeo-cmip6.json"     )
    • Network accessline 48
      "https://storage.googleapis.com/cmip6/pangeo-cmip6.json"

    skills/domains/geoscience/pangaea-data-api/SKILL.md

    • Network accessline 8
      subcategory: "geoscience"     keywords: ["PANGAEA", "earth science data", "oceanography", "paleoclimate", "environmental data", "geoscience repository"]     source: "https://www.pangaea.de/"
    • Network accessline 9
      keywords: ["PANGAEA", "earth science data", "oceanography", "paleoclimate", "environmental data", "geoscience repository"]     source: "https://www.pangaea.de/" ---
    • Network accessline 10
      source: "https://www.pangaea.de/"
    • Network accessline 24
      # Search datasets by keyword curl "https://www.pangaea.de/advanced/search.php?q=ocean+temperature&count=20&type=json"
    • Network accessline 25
      curl "https://www.pangaea.de/advanced/search.php?q=ocean+temperature&count=20&type=json"
    • Network accessline 27
      # Search with geographic bounding box curl "https://www.pangaea.de/advanced/search.php?\
    • Network accessline 28
      curl "https://www.pangaea.de/advanced/search.php?\
    • Network accessline 31
      # Filter by parameter (measurement type) curl "https://www.pangaea.de/advanced/search.php?\
    • Network accessline 32
      curl "https://www.pangaea.de/advanced/search.php?\
    • Network accessline 35
      # Filter by date range curl "https://www.pangaea.de/advanced/search.php?\
    • Network accessline 36
      curl "https://www.pangaea.de/advanced/search.php?\
    • Network accessline 43
      # Full-text search via Elasticsearch curl -X POST "https://ws.pangaea.de/es/pangaea/panmd/_search" \
    • Network accessline 44
      curl -X POST "https://ws.pangaea.de/es/pangaea/panmd/_search" \
    • Network accessline 64
      # Get dataset metadata curl "https://doi.pangaea.de/10.1594/PANGAEA.123456?format=metainfo_json"
    • Network accessline 65
      curl "https://doi.pangaea.de/10.1594/PANGAEA.123456?format=metainfo_json"
    • Network accessline 67
      # Download dataset as tab-delimited text curl "https://doi.pangaea.de/10.1594/PANGAEA.123456?format=textfile"
    • Network accessline 68
      curl "https://doi.pangaea.de/10.1594/PANGAEA.123456?format=textfile"
    • Network accessline 70
      # Download as CSV curl "https://doi.pangaea.de/10.1594/PANGAEA.123456?format=csv"
    • Network accessline 71
      curl "https://doi.pangaea.de/10.1594/PANGAEA.123456?format=csv"
    • Network accessline 77
      # List records curl "https://ws.pangaea.de/oai/provider?verb=ListRecords&metadataPrefix=oai_dc"
    • Network accessline 78
      curl "https://ws.pangaea.de/oai/provider?verb=ListRecords&metadataPrefix=oai_dc"
    • Network accessline 80
      # Get specific record curl "https://ws.pangaea.de/oai/provider?verb=GetRecord&identifier=oai:pangaea.de:doi:10.1594/PANGAEA.123456&metadataPrefix=oai_dc"
    • Network accessline 81
      curl "https://ws.pangaea.de/oai/provider?verb=GetRecord&identifier=oai:pangaea.de:doi:10.1594/PANGAEA.123456&metadataPrefix=oai_dc"
    • Network accessline 105
      SEARCH_URL = "https://www.pangaea.de/advanced/search.php"
    • Network accessline 106
      ES_URL = "https://ws.pangaea.de/es/pangaea/panmd/_search"
    • Network accessline 121
      resp = requests.get(SEARCH_URL, params=params, timeout=30)
    • Network accessline 138
      def download_dataset(doi: str) -> pd.DataFrame:     """Download a PANGAEA dataset as a pandas DataFrame."""     url = f"https://doi.pangaea.de/{doi}?format=textfile"
    • Network accessline 139
      """Download a PANGAEA dataset as a pandas DataFrame."""     url = f"https://doi.pangaea.de/{doi}?format=textfile"     resp = requests.get(url, timeout=60)
    • Network accessline 140
      url = f"https://doi.pangaea.de/{doi}?format=textfile"     resp = requests.get(url, timeout=60)     resp.raise_for_status()
    • Network accessline 141
      resp = requests.get(url, timeout=60)
    • Network accessline 194
      - [PANGAEA](https://www.pangaea.de/)
    • Network accessline 195
      - [PANGAEA API](https://wiki.pangaea.de/wiki/PANGAEA_API)
    • Network accessline 196
      - [PANGAEA Elasticsearch](https://wiki.pangaea.de/wiki/Elasticsearch_API)

    skills/domains/geoscience/satellite-remote-sensing/SKILL.md

    • Network accessline 36
      # Search Sentinel-2 imagery via Microsoft Planetary Computer catalog = pystac_client.Client.open(     "https://planetarycomputer.microsoft.com/api/stac/v1",
    • Network accessline 37
      catalog = pystac_client.Client.open(     "https://planetarycomputer.microsoft.com/api/stac/v1",     modifier=planetary_computer.sign_inplace,
    • Network accessline 38
      "https://planetarycomputer.microsoft.com/api/stac/v1",

    skills/domains/humanities/digital-humanities-guide/SKILL.md

    • Network accessline 157
      <TEI xmlns="http://www.tei-c.org/ns/1.0">

    skills/domains/humanities/ethical-philosophy-guide/SKILL.md

    • Network accessline 240
      - [Stanford Encyclopedia of Philosophy](https://plato.stanford.edu/) -- Peer-reviewed reference for all areas of philosophy
    • Network accessline 242
      - Floridi, L. & Cowls, J. (2019). A Unified Framework of Five Principles for AI in Society. Harvard Data Science Review. - Singer, P. (2011). Practical Ethics, 3rd ed. Cambridge UP. - [PhilPapers](https://philpapers.org/) -- Comprehensive i
    • Network accessline 244
      - [PhilPapers](https://philpapers.org/) -- Comprehensive index of philosophy research

    skills/domains/humanities/history-research-guide/SKILL.md

    • Network accessline 256
      - Bloch, M. (1953). The Historian's Craft. Vintage Books. - Tosh, J. (2015). The Pursuit of History: Aims, Methods and New Directions. Routledge, 6th ed. - [Zotero](https://www.zotero.org/) -- Reference management with Chicago style support
    • Network accessline 257
      - Tosh, J. (2015). The Pursuit of History: Aims, Methods and New Directions. Routledge, 6th ed. - [Zotero](https://www.zotero.org/) -- Reference management with Chicago style support - [Internet Archive](https://archive.org/) -- Universal a
    • Network accessline 258
      - [Zotero](https://www.zotero.org/) -- Reference management with Chicago style support
    • Network accessline 259
      - [Internet Archive](https://archive.org/) -- Universal access to human knowledge
    • Network accessline 260
      - [Programming Historian](https://programminghistorian.org/) -- Digital methods tutorials for historians

    skills/domains/humanities/political-history-guide/SKILL.md

    • Network accessline 239
      - Zhao, D. (2015). The Confucian-Legalist State: A New Theory of Chinese History. Oxford UP. - Fukuyama, F. (2011). The Origins of Political Order. Farrar, Straus and Giroux. - [Cambridge History of China](https://www.cambridge.org/core/ser
    • Network accessline 241
      - [Cambridge History of China](https://www.cambridge.org/core/series/cambridge-history-of-china/) -- Standard reference

    skills/domains/law/caselaw-access-api/SKILL.md

    • Network accessline 8
      subcategory: "law"     keywords: ["case law", "legal database", "court opinions", "Harvard law", "judicial data", "legal research"]     source: "https://case.law/"
    • Network accessline 9
      keywords: ["case law", "legal database", "court opinions", "Harvard law", "judicial data", "legal research"]     source: "https://case.law/" ---
    • Network accessline 10
      source: "https://case.law/"
    • Network accessline 24
      https://api.case.law/v1/
    • Network accessline 30
      # Search cases by keyword curl "https://api.case.law/v1/cases/?search=free+speech&decision_date_min=2020-01-01"
    • Network accessline 31
      curl "https://api.case.law/v1/cases/?search=free+speech&decision_date_min=2020-01-01"
    • Network accessline 33
      # Get a specific case by ID curl "https://api.case.law/v1/cases/12345678/"
    • Network accessline 34
      curl "https://api.case.law/v1/cases/12345678/"
    • Network accessline 36
      # Filter by jurisdiction and court curl "https://api.case.law/v1/cases/?jurisdiction=us&court=us-sup-ct&search=miranda+rights"
    • Network accessline 37
      curl "https://api.case.law/v1/cases/?jurisdiction=us&court=us-sup-ct&search=miranda+rights"
    • Network accessline 39
      # Filter by date range curl "https://api.case.law/v1/cases/?decision_date_min=2015-01-01&decision_date_max=2025-12-31"
    • Network accessline 40
      curl "https://api.case.law/v1/cases/?decision_date_min=2015-01-01&decision_date_max=2025-12-31"
    • Network accessline 42
      [Credential-related source omitted]
    • Network accessline 43
      [Credential-related source omitted]
    • Access to secretsline 43
      [Credential-related source omitted]
    • Network accessline 44
      "https://api.case.law/v1/cases/12345678/?full_case=true"
    • Network accessline 65
      # List all courts curl "https://api.case.law/v1/courts/"
    • Network accessline 66
      curl "https://api.case.law/v1/courts/"
    • Network accessline 68
      # List all jurisdictions curl "https://api.case.law/v1/jurisdictions/"
    • Network accessline 69
      curl "https://api.case.law/v1/jurisdictions/"
    • Network accessline 71
      # List all reporters (case report series) curl "https://api.case.law/v1/reporters/"
    • Network accessline 72
      curl "https://api.case.law/v1/reporters/"
    • Network accessline 80
      BASE_URL = "https://api.case.law/v1"
    • Network accessline 91
      resp = requests.get(f"{BASE_URL}/cases/", params=params)
    • Network accessline 118
      # Bulk data available at: # https://case.law/bulk/download/
    • Network accessline 119
      # https://case.law/bulk/download/
    • Network accessline 138
      [Credential-related source omitted]
    • Network accessline 147
      - [CAP API Documentation](https://case.law/api/) - [CAP Bulk Data](https://case.law/bulk/download/)
    • Network accessline 148
      - [CAP Bulk Data](https://case.law/bulk/download/)
    • Network accessline 149
      - [Harvard Library Innovation Lab](https://lil.law.harvard.edu/)

    skills/domains/law/courtlistener-api/SKILL.md

    • Network accessline 8
      subcategory: "law"     keywords: ["law", "case law", "legal theory", "compliance analysis", "jurisprudence"]     source: "https://www.courtlistener.com/api/rest-info/"
    • Network accessline 9
      keywords: ["law", "case law", "legal theory", "compliance analysis", "jurisprudence"]     source: "https://www.courtlistener.com/api/rest-info/" ---
    • Network accessline 10
      source: "https://www.courtlistener.com/api/rest-info/"
    • Network accessline 27
      [Credential-related source omitted]
    • Network accessline 28
      1. Create a free account at https://www.courtlistener.com/
    • Network accessline 34
      # Unauthenticated request curl "https://www.courtlistener.com/api/rest/v4/opinions/?q=first+amendment"
    • Network accessline 35
      curl "https://www.courtlistener.com/api/rest/v4/opinions/?q=first+amendment"
    • Network accessline 37
      [Credential-related source omitted]
    • Network accessline 38
      [Credential-related source omitted]
    • Network accessline 39
      "https://www.courtlistener.com/api/rest/v4/opinions/?q=first+amendment"
    • Network accessline 48
      - **URL**: `GET https://www.courtlistener.com/api/rest/v4/opinions/`
    • Network accessline 64
      curl "https://www.courtlistener.com/api/rest/v4/opinions/?q=privacy+fourth+amendment&court=scotus&ordering=-date_filed"
    • Network accessline 73
      - **URL**: `GET https://www.courtlistener.com/api/rest/v4/dockets/`
    • Network accessline 89
      curl "https://www.courtlistener.com/api/rest/v4/dockets/?q=antitrust&court=scotus&ordering=-date_filed"
    • Network accessline 98
      - **URL**: `GET https://www.courtlistener.com/api/rest/v4/courts/`
    • Network accessline 108
      curl "https://www.courtlistener.com/api/rest/v4/courts/?jurisdiction=F"
    • Network accessline 117
      - **URL**: `GET https://www.courtlistener.com/api/rest/v4/people/`
    • Network accessline 129
      curl "https://www.courtlistener.com/api/rest/v4/people/?q=ginsburg"
    • Network accessline 138
      - **URL**: `GET https://www.courtlistener.com/api/rest/v4/search/`
    • Network accessline 149
      curl "https://www.courtlistener.com/api/rest/v4/search/?q=net+neutrality&type=o"
    • Network accessline 156
      The CourtListener API allows up to 5,000 requests per hour for unauthenticated users. Authenticated users with API tokens receive higher limits. The API returns standard HTTP 429 responses when limits are exceeded. For bulk data access, Cou
    • Network accessline 170
      "page_size": 10 } resp = requests.get("https://www.courtlistener.com/api/rest/v4/opinions/", params=params)
    • Network accessline 171
      } resp = requests.get("https://www.courtlistener.com/api/rest/v4/opinions/", params=params) data = resp.json()
    • Network accessline 172
      resp = requests.get("https://www.courtlistener.com/api/rest/v4/opinions/", params=params)
    • Network accessline 191
      "ordering": "-date_filed" } resp = requests.get("https://www.courtlistener.com/api/rest/v4/search/", params={**params, "type": "o"})
    • Network accessline 192
      } resp = requests.get("https://www.courtlistener.com/api/rest/v4/search/", params={**params, "type": "o"}) results = resp.json()
    • Network accessline 193
      resp = requests.get("https://www.courtlistener.com/api/rest/v4/search/", params={**params, "type": "o"})
    • Network accessline 204
      curl "https://www.courtlistener.com/api/rest/v4/people/?court=scotus&ordering=-date_nominated"
    • Network accessline 209
      - Official API documentation: https://www.courtlistener.com/api/rest-info/
    • Network accessline 210
      - CourtListener homepage: https://www.courtlistener.com/
    • Network accessline 211
      - Bulk data downloads: https://www.courtlistener.com/api/bulk-info/
    • Network accessline 212
      - Free Law Project: https://free.law/
    • Network accessline 213
      - RECAP Archive: https://www.courtlistener.com/recap/

    skills/domains/law/legal-agent-skills-guide/SKILL.md

    • Network accessline 8
      subcategory: "law"     keywords: ["legal AI", "legal automation", "legal research", "agent skills", "contract analysis", "case law"]     source: "https://github.com/lawvable/awesome-legal-skills"
    • Network accessline 9
      keywords: ["legal AI", "legal automation", "legal research", "agent skills", "contract analysis", "case law"]     source: "https://github.com/lawvable/awesome-legal-skills" ---
    • Network accessline 10
      source: "https://github.com/lawvable/awesome-legal-skills"
    • Network accessline 130
      - [awesome-legal-skills](https://github.com/lawvable/awesome-legal-skills)
    • Network accessline 131
      - [CourtListener](https://www.courtlistener.com/) — Free case law
    • Network accessline 132
      - [Caselaw Access Project](https://case.law/)

    skills/domains/law/legal-research-guide/SKILL.md

    • Network accessline 117
      # Using the CourtListener API (free, open-source) BASE_URL = "https://www.courtlistener.com/api/rest/v3"
    • Network accessline 118
      BASE_URL = "https://www.courtlistener.com/api/rest/v3"
    • Network accessline 120
      def search_opinions(query, court="scotus", page_size=20):     """Search case opinions via CourtListener API."""     response = requests.get(
    • Network accessline 121
      """Search case opinions via CourtListener API."""     response = requests.get(         f"{BASE_URL}/search/",
    • Network accessline 122
      response = requests.get(
    • Network accessline 136
      print(f"  Court: {case.get('court', 'N/A')}")         print(f"  Citation: {case.get('citation', ['N/A'])[0] if case.get('citation') else 'N/A'}")         print(f"  URL: https://www.courtlistener.com{case.get('absolute_url', '')}")
    • Network accessline 137
      print(f"  Citation: {case.get('citation', ['N/A'])[0] if case.get('citation') else 'N/A'}")         print(f"  URL: https://www.courtlistener.com{case.get('absolute_url', '')}")     return results
    • Network accessline 138
      print(f"  URL: https://www.courtlistener.com{case.get('absolute_url', '')}")
    • Network accessline 162
      # Get case metadata and citations         resp = requests.get(f"{BASE_URL}/opinions/{case_id}/",
    • Network accessline 163
      resp = requests.get(f"{BASE_URL}/opinions/{case_id}/",

    skills/domains/law/opencontracts-guide/SKILL.md

    • Network accessline 8
      subcategory: "law"     keywords: ["legal documents", "contract annotation", "document versioning", "legal AI", "NLP legal", "MCP"]     source: "https://github.com/Open-Source-Legal/OpenContracts"
    • Network accessline 9
      keywords: ["legal documents", "contract annotation", "document versioning", "legal AI", "NLP legal", "MCP"]     source: "https://github.com/Open-Source-Legal/OpenContracts" ---
    • Network accessline 10
      source: "https://github.com/Open-Source-Legal/OpenContracts"
    • Network accessline 22
      # Docker deployment git clone https://github.com/Open-Source-Legal/OpenContracts.git
    • Network accessline 23
      git clone https://github.com/Open-Source-Legal/OpenContracts.git
    • Network accessline 27
      # Access at http://localhost:3000
    • Network accessline 37
      client = Client("http://localhost:3000")
    • Network accessline 130
      "args": ["@opencontracts/mcp-server"],       "env": {         "OPENCONTRACTS_URL": "http://localhost:3000"
    • Network accessline 131
      "env": {         "OPENCONTRACTS_URL": "http://localhost:3000"       }
    • Network accessline 132
      "OPENCONTRACTS_URL": "http://localhost:3000"
    • Network accessline 167
      - [OpenContracts GitHub](https://github.com/Open-Source-Legal/OpenContracts)
    • Network accessline 168
      - [Legal NLP Resources](https://github.com/thunlp/LegalPapers)

    skills/domains/law/patent-analysis-guide/SKILL.md

    • Network accessline 38
      BASE_URL = "https://ops.epo.org/3.2/rest-services"
    • Network accessline 44
      import base64         credentials = base64.b64encode(f"{key}:{secret}".encode()).decode()         resp = requests.post(
    • Network accessline 45
      credentials = base64.b64encode(f"{key}:{secret}".encode()).decode()         resp = requests.post(             "https://ops.epo.org/3.2/auth/accesstoken",
    • Network accessline 46
      resp = requests.post(
    • Network accessline 47
      "https://ops.epo.org/3.2/auth/accesstoken",
    • Access to secretsline 51
      [Credential-related source omitted]
    • Network accessline 58
      pa="university" AND pd>=2020         """         resp = requests.get(
    • Network accessline 59
      """         resp = requests.get(             f"{self.BASE_URL}/published-data/search",
    • Network accessline 60
      resp = requests.get(

    skills/domains/law/regulatory-compliance-guide/SKILL.md

    • Network accessline 38
      BASE_URL = "https://www.federalregister.gov/api/v1"
    • Network accessline 56
      resp = requests.get(f"{self.BASE_URL}/documents", params=params)
    • Network accessline 74
      def get_document(self, document_number: str) -> dict:         """Retrieve full document details by document number."""         resp = requests.get(
    • Network accessline 75
      """Retrieve full document details by document number."""         resp = requests.get(             f"{self.BASE_URL}/documents/{document_number}.json"
    • Network accessline 76
      resp = requests.get(

    skills/domains/law/uk-legislation-api/SKILL.md

    • Network accessline 8
      subcategory: "law"     keywords: ["UK law", "legislation", "statutory instruments", "legal research", "Parliament", "regulatory analysis"]     source: "https://www.legislation.gov.uk"
    • Network accessline 9
      keywords: ["UK law", "legislation", "statutory instruments", "legal research", "Parliament", "regulatory analysis"]     source: "https://www.legislation.gov.uk" ---
    • Network accessline 10
      source: "https://www.legislation.gov.uk"
    • Network accessline 28
      https://www.legislation.gov.uk/{type}/{year}/{number}
    • Network accessline 49
      # Fetch the Equality Act 2010 — returns structured XML with Dublin Core metadata curl "https://www.legislation.gov.uk/ukpga/2010/15/data.xml"
    • Network accessline 50
      curl "https://www.legislation.gov.uk/ukpga/2010/15/data.xml"
    • Network accessline 51
      # Response: <Legislation DocumentURI="http://www.legislation.gov.uk/ukpga/2010/15"
    • Network accessline 56
      # Fetch Data Protection Act 2018 curl "https://www.legislation.gov.uk/ukpga/2018/12/data.xml"
    • Network accessline 57
      curl "https://www.legislation.gov.uk/ukpga/2018/12/data.xml"
    • Network accessline 61
      # Fetch a Statutory Instrument curl "https://www.legislation.gov.uk/uksi/2020/1374/data.xml"
    • Network accessline 62
      curl "https://www.legislation.gov.uk/uksi/2020/1374/data.xml"
    • Network accessline 69
      # Fetch a single section curl "https://www.legislation.gov.uk/ukpga/2010/15/section/1/data.xml"
    • Network accessline 70
      curl "https://www.legislation.gov.uk/ukpga/2010/15/section/1/data.xml"
    • Network accessline 72
      # Fetch table of contents curl "https://www.legislation.gov.uk/ukpga/2010/15/contents/data.xml"
    • Network accessline 73
      curl "https://www.legislation.gov.uk/ukpga/2010/15/contents/data.xml"
    • Network accessline 75
      # Fetch a specific Part curl "https://www.legislation.gov.uk/ukpga/2010/15/part/1/data.xml"
    • Network accessline 76
      curl "https://www.legislation.gov.uk/ukpga/2010/15/part/1/data.xml"
    • Network accessline 78
      # Fetch a Schedule curl "https://www.legislation.gov.uk/ukpga/2010/15/schedule/1/data.xml"
    • Network accessline 79
      curl "https://www.legislation.gov.uk/ukpga/2010/15/schedule/1/data.xml"
    • Network accessline 85
      # Search by title — returns HTTP 300 with multiple matches curl "https://www.legislation.gov.uk/id?title=equality+act"
    • Network accessline 86
      curl "https://www.legislation.gov.uk/id?title=equality+act"
    • Network accessline 88
      # Browse by type, title keyword, and year curl "https://www.legislation.gov.uk/ukpga?title=data+protection&year=2018"
    • Network accessline 89
      curl "https://www.legislation.gov.uk/ukpga?title=data+protection&year=2018"
    • Network accessline 91
      # List recent Acts via Atom feed curl "https://www.legislation.gov.uk/new/ukpga/data.feed"
    • Network accessline 92
      curl "https://www.legislation.gov.uk/new/ukpga/data.feed"
    • Network accessline 99
      # Changes affecting a specific Act (Atom feed, paginated) curl "https://www.legislation.gov.uk/changes/affected/ukpga/2010/15/data.feed"
    • Network accessline 100
      curl "https://www.legislation.gov.uk/changes/affected/ukpga/2010/15/data.feed"
    • Network accessline 105
      # Changes made BY a specific Act curl "https://www.legislation.gov.uk/changes/affecting/ukpga/2010/15/data.feed"
    • Network accessline 106
      curl "https://www.legislation.gov.uk/changes/affecting/ukpga/2010/15/data.feed"
    • Network accessline 112
      # Legislation as it stood on a specific date curl "https://www.legislation.gov.uk/ukpga/2010/15/2015-01-01/data.xml"
    • Network accessline 113
      curl "https://www.legislation.gov.uk/ukpga/2010/15/2015-01-01/data.xml"
    • Network accessline 115
      # Enacted (original) version curl "https://www.legislation.gov.uk/ukpga/2010/15/enacted/data.xml"
    • Network accessline 116
      curl "https://www.legislation.gov.uk/ukpga/2010/15/enacted/data.xml"
    • Network accessline 145
      BASE = "https://www.legislation.gov.uk"
    • Network accessline 146
      NS = {"leg": "http://www.legislation.gov.uk/namespaces/legislation",
    • Network accessline 147
      "ukm": "http://www.legislation.gov.uk/namespaces/metadata",
    • Network accessline 148
      "dc": "http://purl.org/dc/elements/1.1/",
    • Network accessline 149
      "atom": "http://www.w3.org/2005/Atom"}
    • Network accessline 152
      """Fetch UK legislation metadata and full XML."""     url = f"{BASE}/{leg_type}/{year}/{number}/data.xml"     resp = requests.get(url)
    • Network accessline 153
      url = f"{BASE}/{leg_type}/{year}/{number}/data.xml"     resp = requests.get(url)     resp.raise_for_status()
    • Network accessline 154
      resp = requests.get(url)
    • Network accessline 175
      - [Legislation.gov.uk API Documentation](https://www.legislation.gov.uk/developer)
    • Network accessline 176
      - [CLML Schema Documentation](https://legislation.github.io/clml-schema/)
    • Network accessline 177
      - [Legislation.gov.uk URI Scheme](https://www.legislation.gov.uk/developer/uris)
    • Network accessline 178
      - [The National Archives](https://www.nationalarchives.gov.uk/)
    • Network accessline 179
      - [Atom Feed Specification](https://www.legislation.gov.uk/developer/formats/atom)

    skills/domains/math/lean-theorem-proving-guide/SKILL.md

    • Network accessline 8
      subcategory: "math"     keywords: ["Lean 4", "theorem proving", "formal verification", "LLM math", "proof assistant", "LeanAgent"]     source: "https://github.com/lean-dojo/LeanAgent"
    • Network accessline 9
      keywords: ["Lean 4", "theorem proving", "formal verification", "LLM math", "proof assistant", "LeanAgent"]     source: "https://github.com/lean-dojo/LeanAgent" ---
    • Network accessline 10
      source: "https://github.com/lean-dojo/LeanAgent"
    • Network accessline 137
      - [LeanAgent GitHub](https://github.com/lean-dojo/LeanAgent)
    • Network accessline 138
      - [Lean 4](https://lean-lang.org/)
    • Network accessline 139
      - [Mathlib4](https://leanprover-community.github.io/mathlib4_docs/)
    • Network accessline 140
      - [LeanDojo](https://leandojo.org/)

    skills/domains/math/oeis-api/SKILL.md

    • Network accessline 8
      subcategory: "math"     keywords: ["number theory", "algebra", "probability theory", "applied mathematics"]     source: "https://oeis.org/eishelp1.html"
    • Network accessline 9
      keywords: ["number theory", "algebra", "probability theory", "applied mathematics"]     source: "https://oeis.org/eishelp1.html" ---
    • Network accessline 10
      source: "https://oeis.org/eishelp1.html"
    • Network accessline 33
      - **URL**: `GET https://oeis.org/search`
    • Network accessline 45
      # Search by sequence terms curl "https://oeis.org/search?q=1,1,2,3,5,8,13,21&fmt=json"
    • Network accessline 46
      curl "https://oeis.org/search?q=1,1,2,3,5,8,13,21&fmt=json"
    • Network accessline 48
      # Search by A-number curl "https://oeis.org/search?q=A000045&fmt=json"
    • Network accessline 49
      curl "https://oeis.org/search?q=A000045&fmt=json"
    • Network accessline 51
      # Search by keyword curl "https://oeis.org/search?q=catalan+numbers&fmt=json"
    • Network accessline 52
      curl "https://oeis.org/search?q=catalan+numbers&fmt=json"
    • Network accessline 61
      - **URL**: `GET https://oeis.org/A{number}`
    • Network accessline 72
      # Retrieve the Fibonacci sequence (A000045) curl "https://oeis.org/A000045?fmt=json"
    • Network accessline 73
      curl "https://oeis.org/A000045?fmt=json"
    • Network accessline 75
      # Retrieve the prime numbers (A000040) curl "https://oeis.org/A000040?fmt=json"
    • Network accessline 76
      curl "https://oeis.org/A000040?fmt=json"
    • Network accessline 83
      No formal rate limits are published for the OEIS. However, the service is run by a non-profit organization with limited infrastructure. Users should be respectful and avoid sending more than a few requests per second. For bulk data access,
    • Network accessline 97
      resp = requests.get("https://oeis.org/search", params={"q": unknown_terms, "fmt": "json"})
    • Network accessline 117
      # Get the Catalan numbers (A000108) resp = requests.get("https://oeis.org/A000108", params={"fmt": "json"})
    • Network accessline 118
      resp = requests.get("https://oeis.org/A000108", params={"fmt": "json"})
    • Network accessline 141
      resp = requests.get("https://oeis.org/search", params={"q": "A000045", "fmt": "json"})
    • Network accessline 154
      - Official help and documentation: https://oeis.org/eishelp1.html
    • Network accessline 155
      - OEIS homepage: https://oeis.org/
    • Network accessline 156
      - OEIS Wiki: https://oeis.org/wiki/Welcome
    • Network accessline 157
      - Downloadable data files: https://oeis.org/stripped.gz
    • Network accessline 158
      - OEIS Foundation: https://oeisf.org/

    skills/domains/pharma/madd-drug-discovery-guide/SKILL.md

    • Network accessline 8
      subcategory: "pharma"     keywords: ["drug discovery", "multi-agent", "molecular design", "ADMET", "virtual screening", "pharma AI"]     source: "https://github.com/sb-ai-lab/MADD"
    • Network accessline 9
      keywords: ["drug discovery", "multi-agent", "molecular design", "ADMET", "virtual screening", "pharma AI"]     source: "https://github.com/sb-ai-lab/MADD" ---
    • Network accessline 10
      source: "https://github.com/sb-ai-lab/MADD"
    • Network accessline 151
      - [MADD GitHub](https://github.com/sb-ai-lab/MADD)
    • Network accessline 152
      - [RDKit](https://www.rdkit.org/) — Chemistry toolkit
    • Network accessline 153
      - [AutoDock Vina](https://vina.scripps.edu/) — Molecular docking

    skills/domains/physics/nasa-ads-api/SKILL.md

    • Network accessline 8
      subcategory: "physics"     keywords: ["astrophysics", "observational astronomy", "cosmology", "high energy physics"]     source: "https://ui.adsabs.harvard.edu/help/api/"
    • Network accessline 9
      keywords: ["astrophysics", "observational astronomy", "cosmology", "high energy physics"]     source: "https://ui.adsabs.harvard.edu/help/api/"     requires:
    • Network accessline 10
      source: "https://ui.adsabs.harvard.edu/help/api/"
    • Access to secretsline 12
      [Credential-related source omitted]
    • Network accessline 27
      Authentication is required via a free API token. Register at https://ui.adsabs.harvard.edu/user/settings/token to generate your token. Include it in every request as a header:
    • Network accessline 39
      - **URL**: `GET https://api.adsabs.harvard.edu/v1/search/query`
    • Network accessline 51
      [Credential-related source omitted]
    • Network accessline 52
      "https://api.adsabs.harvard.edu/v1/search/query?q=gravitational+waves&fl=title,author,year,bibcode,citation_count,doi&rows=10&sort=citation_count+desc"
    • Network accessline 58
      - **URL**: `GET https://api.adsabs.harvard.edu/v1/search/query`
    • Network accessline 68
      [Credential-related source omitted]
    • Network accessline 69
      "https://api.adsabs.harvard.edu/v1/search/query?q=author:%22Hawking,+S%22&fl=title,year,bibcode,citation_count&rows=20&sort=citation_count+desc"
    • Network accessline 75
      - **URL**: `GET https://api.adsabs.harvard.edu/v1/search/query`
    • Network accessline 84
      [Credential-related source omitted]
    • Network accessline 85
      "https://api.adsabs.harvard.edu/v1/search/query?q=object:%22Sgr+A*%22&fl=title,author,year,bibcode,citation_count&rows=10&sort=date+desc"
    • Network accessline 91
      - **URL**: `POST https://api.adsabs.harvard.edu/v1/metrics`
    • Network accessline 99
      [Credential-related source omitted]
    • Network accessline 101
      "https://api.adsabs.harvard.edu/v1/metrics" \
    • Network accessline 117
      [Credential-related source omitted]
    • Network accessline 118
      "https://api.adsabs.harvard.edu/v1/search/query?q=dark+energy+AND+year:2023-2026&fl=title,author,year,bibcode,citation_count,doi,abstract&rows=20&sort=citation_count+desc"
    • Network accessline 126
      [Credential-related source omitted]
    • Network accessline 127
      [Credential-related source omitted]
    • Network accessline 128
      "https://api.adsabs.harvard.edu/v1/search/query?q=author:%22Perlmutter,+S%22&fl=title,year,bibcode,citation_count&rows=200&sort=date+desc"
    • Network accessline 130
      [Credential-related source omitted]
    • Network accessline 131
      [Credential-related source omitted]
    • Network accessline 133
      "https://api.adsabs.harvard.edu/v1/metrics" \
    • Network accessline 142
      [Credential-related source omitted]
    • Network accessline 143
      "https://api.adsabs.harvard.edu/v1/search/query?q=object:%22Crab+Nebula%22+AND+year:2024-2026&fl=title,author,year,bibcode,doi&rows=10&sort=date+desc"
    • Network accessline 148
      - Official documentation: https://ui.adsabs.harvard.edu/help/api/
    • Network accessline 149
      - ADS query syntax: https://ui.adsabs.harvard.edu/help/search/
    • Network accessline 150
      - ADS search fields: https://ui.adsabs.harvard.edu/help/search/search-syntax

    skills/domains/social-science/ipums-microdata-api/SKILL.md

    • Network accessline 8
      subcategory: "social-science"     keywords: ["IPUMS", "census data", "microdata", "survey data", "demographics", "social science data"]     source: "https://www.ipums.org/"
    • Network accessline 9
      keywords: ["IPUMS", "census data", "microdata", "survey data", "demographics", "social science data"]     source: "https://www.ipums.org/" ---
    • Network accessline 10
      source: "https://www.ipums.org/"
    • Network accessline 37
      https://api.ipums.org/extracts/
    • Network accessline 43
      # Register at https://www.ipums.org/
    • Access to secretsline 45
      [Credential-related source omitted]
    • Network accessline 51
      # Request a data extract (IPUMS USA example) curl -X POST "https://api.ipums.org/extracts/?collection=usa&version=2" \
    • Network accessline 52
      [Credential-related source omitted]
    • Access to secretsline 52
      [Credential-related source omitted]
    • Access to secretsline 53
      [Credential-related source omitted]
    • Network accessline 74
      [Credential-related source omitted]
    • Access to secretsline 74
      [Credential-related source omitted]
    • Access to secretsline 75
      [Credential-related source omitted]
    • Network accessline 81
      # When status is "completed" curl -O "https://api.ipums.org/extracts/42/download?collection=usa&version=2" \
    • Network accessline 82
      [Credential-related source omitted]
    • Access to secretsline 82
      [Credential-related source omitted]
    • Access to secretsline 83
      [Credential-related source omitted]
    • Network accessline 89
      # List available variables curl "https://api.ipums.org/metadata/usa/variables?version=2" \
    • Network accessline 90
      [Credential-related source omitted]
    • Access to secretsline 90
      [Credential-related source omitted]
    • Access to secretsline 91
      [Credential-related source omitted]
    • Network accessline 93
      # Get variable details curl "https://api.ipums.org/metadata/usa/variables/EDUC?version=2" \
    • Network accessline 94
      [Credential-related source omitted]
    • Access to secretsline 94
      [Credential-related source omitted]
    • Access to secretsline 95
      [Credential-related source omitted]
    • Network accessline 97
      # List available samples curl "https://api.ipums.org/metadata/usa/samples?version=2" \
    • Network accessline 98
      [Credential-related source omitted]
    • Access to secretsline 98
      [Credential-related source omitted]
    • Access to secretsline 99
      [Credential-related source omitted]
    • Network accessline 109
      BASE_URL = "https://api.ipums.org"
    • Access to secretsline 110
      [Credential-related source omitted]
    • Network accessline 127
      resp = requests.post(
    • Network accessline 138
      """Poll until extract is ready, return download URL."""     while True:         resp = requests.get(
    • Network accessline 139
      while True:         resp = requests.get(             f"{BASE_URL}/extracts/{extract_id}"
    • Network accessline 140
      resp = requests.get(
    • Network accessline 157
      def get_variable_info(collection: str, variable: str) -> dict:     """Get metadata about a variable."""     resp = requests.get(
    • Network accessline 158
      """Get metadata about a variable."""     resp = requests.get(         f"{BASE_URL}/metadata/{collection}/variables/{variable}"
    • Network accessline 159
      resp = requests.get(
    • Network accessline 208
      - [IPUMS](https://www.ipums.org/)
    • Network accessline 209
      - [IPUMS API Documentation](https://developer.ipums.org/)
    • Network accessline 210
      - [IPUMS USA](https://usa.ipums.org/)

    skills/domains/social-science/psychology-research-guide/SKILL.md

    • Network accessline 8
      subcategory: "social-science"     keywords: ["psychology", "experimental design", "cognitive science", "psychometrics", "replication", "effect size"]     source: "https://github.com/psych-ds/psych-DS"
    • Network accessline 9
      keywords: ["psychology", "experimental design", "cognitive science", "psychometrics", "replication", "effect size"]     source: "https://github.com/psych-ds/psych-DS" ---
    • Network accessline 10
      source: "https://github.com/psych-ds/psych-DS"
    • Network accessline 266
      - [Open Science Framework (OSF)](https://osf.io/) -- Pre-registration, data sharing, collaboration
    • Network accessline 267
      - Simmons, J. P., Nelson, L. D., & Simonsohn, U. (2011). False-Positive Psychology. Psychological Science, 22(11), 1359-1366. - Cumming, G. (2014). The New Statistics: Why and How. Psychological Science, 25(1), 7-29. - [pingouin](https://pi
    • Network accessline 268
      - Cumming, G. (2014). The New Statistics: Why and How. Psychological Science, 25(1), 7-29. - [pingouin](https://pingouin-stats.org/) -- Python statistical package for psychology - [PsychDS](https://psych-ds.github.io/) -- Data standard for
    • Network accessline 269
      - [pingouin](https://pingouin-stats.org/) -- Python statistical package for psychology
    • Network accessline 270
      - [PsychDS](https://psych-ds.github.io/) -- Data standard for psychology datasets

    skills/domains/social-science/sociology-research-methods/SKILL.md

    • Network accessline 178
      - Geertz, C. (1973). *The Interpretation of Cultures*. Basic Books. - Braun, V., & Clarke, V. (2006). "Using thematic analysis in psychology." *Qualitative Research in Psychology*, 3(2), 77-101. - [ICPSR Data Archive](https://www.icpsr.umic
    • Network accessline 179
      - Braun, V., & Clarke, V. (2006). "Using thematic analysis in psychology." *Qualitative Research in Psychology*, 3(2), 77-101. - [ICPSR Data Archive](https://www.icpsr.umich.edu/) - [GSS Data Explorer](https://gssdataexplorer.norc.org/)
    • Network accessline 180
      - [ICPSR Data Archive](https://www.icpsr.umich.edu/)
    • Network accessline 181
      - [GSS Data Explorer](https://gssdataexplorer.norc.org/)

    skills/literature/discovery/literature-mapping-guide/SKILL.md

    • Network accessline 117
      # Get paper metadata         meta_resp = requests.get(
    • Network accessline 118
      meta_resp = requests.get(
    • Network accessline 119
      f"https://api.semanticscholar.org/graph/v1/paper/{paper_id}",
    • Network accessline 128
      # Get references (backward)         refs_resp = requests.get(
    • Network accessline 129
      refs_resp = requests.get(
    • Network accessline 130
      f"https://api.semanticscholar.org/graph/v1/paper/{paper_id}/references",

    skills/literature/discovery/paper-recommendation-guide/SKILL.md

    • Network accessline 30
      # Find works related to a specific paper via its concepts and citations curl "https://api.openalex.org/works?filter=cites:W2741809807&sort=cited_by_count:desc&per_page=10"
    • Network accessline 31
      curl "https://api.openalex.org/works?filter=cites:W2741809807&sort=cited_by_count:desc&per_page=10"
    • Network accessline 110
      - OpenAlex API: https://api.openalex.org
    • Network accessline 111
      - Connected Papers: https://www.connectedpapers.com
    • Network accessline 112
      - Research Rabbit: https://www.researchrabbitapp.com
    • Network accessline 113
      - Paper Recommendation: https://github.com/pengzhenghao/paper-recommendation
    • Network accessline 114
      - VOSviewer: https://www.vosviewer.com

    skills/literature/discovery/papers-we-love-guide/SKILL.md

    • Network accessline 8
      subcategory: "discovery"     keywords: ["papers we love", "CS papers", "reading groups", "classic papers", "paper recommendations", "curated list"]     source: "https://github.com/papers-we-love/papers-we-love"
    • Network accessline 9
      keywords: ["papers we love", "CS papers", "reading groups", "classic papers", "paper recommendations", "curated list"]     source: "https://github.com/papers-we-love/papers-we-love" ---
    • Network accessline 10
      source: "https://github.com/papers-we-love/papers-we-love"
    • Network accessline 57
      # Clone the repository git clone https://github.com/papers-we-love/papers-we-love.git
    • Network accessline 58
      git clone https://github.com/papers-we-love/papers-we-love.git
    • Network accessline 167
      - [Papers We Love GitHub](https://github.com/papers-we-love/papers-we-love)
    • Network accessline 168
      - [Papers We Love Website](https://paperswelove.org/)
    • Network accessline 169
      - [PWL YouTube Channel](https://www.youtube.com/@PapersWeLove)

    skills/literature/discovery/rss-paper-feeds/SKILL.md

    • Network accessline 23
      | Publisher | Feed URL Pattern | Example | |-----------|-----------------|---------| | Nature | `https://www.nature.com/[journal].rss` | `nature.com/nature.rss` |
    • Network accessline 24
      |-----------|-----------------|---------| | Nature | `https://www.nature.com/[journal].rss` | `nature.com/nature.rss` | | Science | `https://www.science.org/action/showFeed?type=etoc&feed=rss&jc=[code]` | jc=science |
    • Network accessline 25
      | Nature | `https://www.nature.com/[journal].rss` | `nature.com/nature.rss` |
    • Network accessline 26
      | Science | `https://www.science.org/action/showFeed?type=etoc&feed=rss&jc=[code]` | jc=science |
    • Network accessline 27
      | Elsevier | `https://rss.sciencedirect.com/publication/science/[ISSN]` | ISSN 0004-3702 for AI |
    • Network accessline 28
      | Springer | `https://link.springer.com/search.rss?search-within=Journal&facet-journal-id=[id]` | id=10994 |
    • Network accessline 29
      | IEEE | `https://ieeexplore.ieee.org/rss/TOC[journal_number].XML` | |
    • Network accessline 30
      | arXiv | `https://rss.arxiv.org/rss/[category]` | cs.AI, stat.ML |
    • Network accessline 48
      for category in categories:         feed_url = f"https://rss.arxiv.org/rss/{category}"
    • Network accessline 49
      feed_url = f"https://rss.arxiv.org/rss/{category}"
    • Network accessline 108
      work_id: OpenAlex work ID (e.g., 'W2741809807') or DOI     """     headers = {"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"}
    • Network accessline 109
      """     headers = {"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"}     response = requests.get(
    • Network accessline 110
      headers = {"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"}     response = requests.get(         f"https://api.openalex.org/works/{work_id}",
    • Network accessline 111
      response = requests.get(
    • Network accessline 112
      f"https://api.openalex.org/works/{work_id}",
    • Network accessline 117
      # Get recent citing works     citing_resp = requests.get(
    • Network accessline 118
      citing_resp = requests.get(
    • Network accessline 119
      "https://api.openalex.org/works",

    skills/literature/discovery/semantic-paper-radar/SKILL.md

    • Network accessline 39
      # Search works via the OpenAlex API curl "https://api.openalex.org/works?search=attention+mechanisms+for+graph+neural+networks&per_page=20"
    • Network accessline 40
      curl "https://api.openalex.org/works?search=attention+mechanisms+for+graph+neural+networks&per_page=20"
    • Network accessline 140
      - OpenAlex API: https://api.openalex.org
    • Network accessline 141
      - SPECTER2 model: https://huggingface.co/allenai/specter2
    • Network accessline 142
      - ChromaDB: https://www.trychroma.com
    • Network accessline 143
      - ResearchGPT: https://github.com/mukulpatnaik/researchgpt
    • Network accessline 144
      - OpenAlex: https://openalex.org

    skills/literature/discovery/semantic-scholar-recs-guide/SKILL.md

    • Network accessline 27
      Base URL: `https://api.openalex.org`
    • Network accessline 28
      CrossRef URL: `https://api.crossref.org`
    • Network accessline 39
      HEADERS = {"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"}
    • Network accessline 42
      # Get the seed paper's concepts response = requests.get(
    • Network accessline 43
      response = requests.get(
    • Network accessline 44
      f"https://api.openalex.org/works/{WORK_ID}",
    • Network accessline 50
      # Find works sharing the same concepts, sorted by citations for concept_id in concepts:     related = requests.get(
    • Network accessline 51
      for concept_id in concepts:     related = requests.get(         "https://api.openalex.org/works",
    • Network accessline 52
      related = requests.get(
    • Network accessline 53
      "https://api.openalex.org/works",
    • Network accessline 66
      def search_crossref(query, limit=10, sort="is-referenced-by-count"):     """Search CrossRef for papers sorted by citation count."""     resp = requests.get(
    • Network accessline 67
      """Search CrossRef for papers sorted by citation count."""     resp = requests.get(         "https://api.crossref.org/works",
    • Network accessline 68
      resp = requests.get(
    • Network accessline 69
      "https://api.crossref.org/works",
    • Network accessline 70
      params={"query": query, "rows": limit, "sort": sort, "order": "desc"},         headers={"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai; mailto:dev@wentor.ai)"}     )
    • Network accessline 71
      headers={"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai; mailto:dev@wentor.ai)"}
    • Network accessline 90
      response = requests.get(
    • Network accessline 91
      "https://api.openalex.org/works",
    • Network accessline 107
      response = requests.get(
    • Network accessline 108
      f"https://api.openalex.org/works/{work_id}",
    • Network accessline 114
      # Fetch details for referenced works for ref_id in ref_ids[:20]:     ref = requests.get(f"https://api.openalex.org/works/{ref_id.split('/')[-1]}", headers=HEADERS).json()
    • Network accessline 115
      for ref_id in ref_ids[:20]:     ref = requests.get(f"https://api.openalex.org/works/{ref_id.split('/')[-1]}", headers=HEADERS).json()     print(f"  [{ref.get('publication_year')}] {ref.get('title')} ({ref.get('cited_by_count')} cites)")
    • Network accessline 116
      ref = requests.get(f"https://api.openalex.org/works/{ref_id.split('/')[-1]}", headers=HEADERS).json()
    • Network accessline 139
      for seed_id in seed_ids:         # Get concepts from seed paper         paper = requests.get(f"https://api.openalex.org/works/{seed_id}", headers=HEADERS).json()
    • Network accessline 140
      # Get concepts from seed paper         paper = requests.get(f"https://api.openalex.org/works/{seed_id}", headers=HEADERS).json()         concept_ids = [c["id"] for c in paper.get("concepts", [])[:2]]
    • Network accessline 141
      paper = requests.get(f"https://api.openalex.org/works/{seed_id}", headers=HEADERS).json()
    • Network accessline 144
      # Find related works via concepts         for cid in concept_ids:             related = requests.get(
    • Network accessline 145
      for cid in concept_ids:             related = requests.get(                 "https://api.openalex.org/works",
    • Network accessline 146
      related = requests.get(
    • Network accessline 147
      "https://api.openalex.org/works",
    • Network accessline 157
      # Get citing works         citing = requests.get(
    • Network accessline 158
      citing = requests.get(
    • Network accessline 159
      "https://api.openalex.org/works",

    skills/literature/discovery/zotero-arxiv-daily-guide/SKILL.md

    • Network accessline 91
      - GitHub Repository: wentor-research-plugins - arXiv API Documentation: https://info.arxiv.org/help/api
    • Network accessline 92
      - arXiv API Documentation: https://info.arxiv.org/help/api
    • Network accessline 93
      - Zotero Plugin Directory: https://www.zotero.org/support/plugins
    • Network accessline 94
      - arXiv Category Taxonomy: https://arxiv.org/category_taxonomy

    skills/literature/fulltext/arxiv-latex-source/SKILL.md

    • Network accessline 8
      subcategory: "fulltext"     keywords: ["arXiv", "LaTeX source", "paper parsing", "formula extraction", "full text", "preprint"]     source: "https://info.arxiv.org/help/bulk_data_s3.html"
    • Network accessline 9
      keywords: ["arXiv", "LaTeX source", "paper parsing", "formula extraction", "full text", "preprint"]     source: "https://info.arxiv.org/help/bulk_data_s3.html" ---
    • Network accessline 10
      source: "https://info.arxiv.org/help/bulk_data_s3.html"
    • Network accessline 31
      - **URL**: `GET https://arxiv.org/e-print/{arxiv_id}`
    • Network accessline 40
      # Download source archive (response: 200, application/gzip, ~1.3 MB)   curl -sL -o source.tar.gz "https://arxiv.org/e-print/2301.00001"
    • Network accessline 41
      curl -sL -o source.tar.gz "https://arxiv.org/e-print/2301.00001"
    • Network accessline 60
      curl -sL "https://arxiv.org/e-print/{arxiv_id}" -o source.gz
    • Network accessline 68
      - **URL**: `GET https://export.arxiv.org/api/query?id_list={arxiv_id}` - **Response**: Atom XML with `<title>`, `<author>`, `<summary>`, `<category>`, `<published>` - **Example**: `curl -s "https://export.arxiv.org/api/query?id_list=2301.00
    • Network accessline 70
      - **Example**: `curl -s "https://export.arxiv.org/api/query?id_list=2301.00001"`
    • Network accessline 164
      def download_arxiv_source(arxiv_id, delay=1.0):     """Download and extract all .tex files from an arXiv paper's source."""     url = f"https://arxiv.org/e-print/{arxiv_id}"
    • Network accessline 165
      """Download and extract all .tex files from an arXiv paper's source."""     url = f"https://arxiv.org/e-print/{arxiv_id}"     headers = {"User-Agent": "ResearchTool/1.0 (mailto:user@example.com)"}
    • Network accessline 166
      url = f"https://arxiv.org/e-print/{arxiv_id}"     headers = {"User-Agent": "ResearchTool/1.0 (mailto:user@example.com)"}     resp = requests.get(url, headers=headers)
    • Network accessline 167
      headers = {"User-Agent": "ResearchTool/1.0 (mailto:user@example.com)"}     resp = requests.get(url, headers=headers)     resp.raise_for_status()
    • Network accessline 168
      resp = requests.get(url, headers=headers)
    • Network accessline 192
      - arXiv e-print access: https://info.arxiv.org/help/bulk_data_s3.html
    • Network accessline 193
      - arXiv API documentation: https://info.arxiv.org/help/api/index.html
    • Network accessline 194
      - arXiv terms of use: https://info.arxiv.org/help/api/tou.html
    • Network accessline 195
      - arXiv S3 bulk data: https://info.arxiv.org/help/bulk_data_s3.html

    skills/literature/fulltext/bioc-pmc-api/SKILL.md

    • Network accessline 8
      subcategory: "fulltext"     keywords: ["bioc", "pmc", "text mining", "biomedical nlp", "full text", "pubmed central"]     source: "https://www.ncbi.nlm.nih.gov/research/bionlp/APIs/BioC-PMC/"
    • Network accessline 9
      keywords: ["bioc", "pmc", "text mining", "biomedical nlp", "full text", "pubmed central"]     source: "https://www.ncbi.nlm.nih.gov/research/bionlp/APIs/BioC-PMC/" ---
    • Network accessline 10
      source: "https://www.ncbi.nlm.nih.gov/research/bionlp/APIs/BioC-PMC/"
    • Network accessline 24
      https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_json/{PMCID}/unicode
    • Network accessline 30
      # JSON format (recommended for programmatic use) curl "https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_json/PMC6267067/unicode"
    • Network accessline 31
      curl "https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_json/PMC6267067/unicode"
    • Network accessline 33
      # XML format curl "https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_xml/PMC6267067/unicode"
    • Network accessline 34
      curl "https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_xml/PMC6267067/unicode"
    • Network accessline 36
      # ASCII encoding (strips non-ASCII characters) curl "https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_json/PMC6267067/ascii"
    • Network accessline 37
      curl "https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_json/PMC6267067/ascii"
    • Network accessline 43
      # Convert PMID to PMCID first, then query curl "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?ids=29346600&format=json"
    • Network accessline 44
      curl "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?ids=29346600&format=json"
    • Network accessline 100
      def get_bioc_article(pmcid: str, fmt: str = "json") -> dict:     """Fetch a PMC article in BioC format."""     url = f"https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_{fmt}/{pmcid}/unicode"
    • Network accessline 101
      """Fetch a PMC article in BioC format."""     url = f"https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_{fmt}/{pmcid}/unicode"     resp = requests.get(url, timeout=30)
    • Network accessline 102
      url = f"https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_{fmt}/{pmcid}/unicode"     resp = requests.get(url, timeout=30)     resp.raise_for_status()
    • Network accessline 103
      resp = requests.get(url, timeout=30)
    • Network accessline 144
      - [BioC-PMC API Documentation](https://www.ncbi.nlm.nih.gov/research/bionlp/APIs/BioC-PMC/)
    • Network accessline 145
      - [BioC Format Specification](http://bioc.sourceforge.net/)
    • Network accessline 146
      - [PMC Open Access Subset](https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/)

    skills/literature/fulltext/core-api-guide/SKILL.md

    • Network accessline 8
      subcategory: "fulltext"     keywords: ["open-access", "fulltext", "research-papers", "aggregator", "CORE"]     source: "https://core.ac.uk/documentation/api"
    • Network accessline 9
      keywords: ["open-access", "fulltext", "research-papers", "aggregator", "CORE"]     source: "https://core.ac.uk/documentation/api" ---
    • Network accessline 10
      source: "https://core.ac.uk/documentation/api"
    • Network accessline 25
      CORE requires a free API key for all requests. Register at https://core.ac.uk/services/api to obtain one.
    • Access to secretsline 30
      [Credential-related source omitted]
    • Network accessline 36
      [Credential-related source omitted]
    • Access to secretsline 36
      [Credential-related source omitted]
    • Network accessline 37
      "https://api.core.ac.uk/v3/search/works?q=machine+learning"
    • Network accessline 47
      GET https://api.core.ac.uk/v3/search/works?q={query}&limit={n}&offset={n}
    • Dangerous shell operationline 59
      [Credential-related source omitted]
    • Network accessline 59
      [Credential-related source omitted]
    • Access to secretsline 59
      [Credential-related source omitted]
    • Network accessline 60
      "https://api.core.ac.uk/v3/search/works?q=climate+change+adaptation&limit=5" \
    • Access to secretsline 70
      [Credential-related source omitted]
    • Network accessline 74
      "offset": 0 } resp = requests.get("https://api.core.ac.uk/v3/search/works", headers=headers, params=params)
    • Network accessline 75
      } resp = requests.get("https://api.core.ac.uk/v3/search/works", headers=headers, params=params) data = resp.json()
    • Network accessline 76
      resp = requests.get("https://api.core.ac.uk/v3/search/works", headers=headers, params=params)
    • Network accessline 92
      GET https://api.core.ac.uk/v3/works/{core_id}
    • Dangerous shell operationline 96
      [Credential-related source omitted]
    • Network accessline 96
      [Credential-related source omitted]
    • Access to secretsline 96
      [Credential-related source omitted]
    • Network accessline 97
      "https://api.core.ac.uk/v3/works/doi:10.1234/example.doi" \
    • Network accessline 106
      [Credential-related source omitted]
    • Access to secretsline 106
      [Credential-related source omitted]
    • Network accessline 107
      -H "Content-Type: application/json" \   -d '[12345, 67890, 11111]' \   "https://api.core.ac.uk/v3/works"
    • Network accessline 109
      "https://api.core.ac.uk/v3/works"
    • Network accessline 117
      GET https://api.core.ac.uk/v3/data-providers?q={query}
    • Network accessline 141
      - CORE API v3 Documentation: https://core.ac.uk/documentation/api
    • Network accessline 142
      - CORE Dashboard and Key Registration: https://core.ac.uk/services/api
    • Network accessline 143
      - CORE Data Dumps (for bulk access): https://core.ac.uk/documentation/dataset
    • Network accessline 144
      - CORE GitHub: https://github.com/oacore

    skills/literature/fulltext/dataverse-api/SKILL.md

    • Network accessline 8
      subcategory: "fulltext"     keywords: ["Dataverse", "research data", "data repository", "Harvard", "dataset deposit", "data sharing"]     source: "https://dataverse.org/"
    • Network accessline 9
      keywords: ["Dataverse", "research data", "data repository", "Harvard", "dataset deposit", "data sharing"]     source: "https://dataverse.org/" ---
    • Network accessline 10
      source: "https://dataverse.org/"
    • Network accessline 24
      https://dataverse.harvard.edu/api
    • Network accessline 30
      # Search datasets curl "https://dataverse.harvard.edu/api/search?q=climate+change&type=dataset&per_page=20"
    • Network accessline 31
      curl "https://dataverse.harvard.edu/api/search?q=climate+change&type=dataset&per_page=20"
    • Network accessline 33
      # Search files within datasets curl "https://dataverse.harvard.edu/api/search?q=temperature+data&type=file&per_page=20"
    • Network accessline 34
      curl "https://dataverse.harvard.edu/api/search?q=temperature+data&type=file&per_page=20"
    • Network accessline 36
      # Filter by subject curl "https://dataverse.harvard.edu/api/search?q=survey+data&type=dataset&\
    • Network accessline 37
      curl "https://dataverse.harvard.edu/api/search?q=survey+data&type=dataset&\
    • Network accessline 40
      # Filter by publication date curl "https://dataverse.harvard.edu/api/search?q=genomics&type=dataset&\
    • Network accessline 41
      curl "https://dataverse.harvard.edu/api/search?q=genomics&type=dataset&\
    • Network accessline 44
      # Sort by relevance or date curl "https://dataverse.harvard.edu/api/search?q=machine+learning&type=dataset&\
    • Network accessline 45
      curl "https://dataverse.harvard.edu/api/search?q=machine+learning&type=dataset&\
    • Network accessline 52
      # By persistent ID (DOI) curl "https://dataverse.harvard.edu/api/datasets/:persistentId/?persistentId=doi:10.7910/DVN/EXAMPLE"
    • Network accessline 53
      curl "https://dataverse.harvard.edu/api/datasets/:persistentId/?persistentId=doi:10.7910/DVN/EXAMPLE"
    • Network accessline 55
      # By dataset ID curl "https://dataverse.harvard.edu/api/datasets/12345"
    • Network accessline 56
      curl "https://dataverse.harvard.edu/api/datasets/12345"
    • Network accessline 58
      # Get dataset versions curl "https://dataverse.harvard.edu/api/datasets/:persistentId/versions?persistentId=doi:10.7910/DVN/EXAMPLE"
    • Network accessline 59
      curl "https://dataverse.harvard.edu/api/datasets/:persistentId/versions?persistentId=doi:10.7910/DVN/EXAMPLE"
    • Network accessline 65
      # Download a specific file by ID curl -O "https://dataverse.harvard.edu/api/access/datafile/67890"
    • Network accessline 66
      curl -O "https://dataverse.harvard.edu/api/access/datafile/67890"
    • Network accessline 68
      # Download with original format curl -O "https://dataverse.harvard.edu/api/access/datafile/67890?format=original"
    • Network accessline 69
      curl -O "https://dataverse.harvard.edu/api/access/datafile/67890?format=original"
    • Network accessline 71
      # Download all files in a dataset (as zip) curl -O "https://dataverse.harvard.edu/api/access/dataset/:persistentId/?persistentId=doi:10.7910/DVN/EXAMPLE"
    • Network accessline 72
      curl -O "https://dataverse.harvard.edu/api/access/dataset/:persistentId/?persistentId=doi:10.7910/DVN/EXAMPLE"
    • Network accessline 97
      "name": "Global Temperature Dataset 2024",         "type": "dataset",         "url": "https://doi.org/10.7910/DVN/EXAMPLE",
    • Network accessline 98
      "type": "dataset",         "url": "https://doi.org/10.7910/DVN/EXAMPLE",         "global_id": "doi:10.7910/DVN/EXAMPLE",
    • Network accessline 99
      "url": "https://doi.org/10.7910/DVN/EXAMPLE",
    • Network accessline 118
      BASE_URL = "https://dataverse.harvard.edu/api"
    • Network accessline 134
      resp = requests.get(f"{BASE_URL}/search", params=params)
    • Network accessline 152
      def get_dataset_files(doi: str) -> list:     """List files in a dataset."""     resp = requests.get(
    • Network accessline 153
      """List files in a dataset."""     resp = requests.get(         f"{BASE_URL}/datasets/:persistentId/",
    • Network accessline 154
      resp = requests.get(
    • Network accessline 175
      def download_file(file_id: int, output_path: str):     """Download a file from Dataverse."""     resp = requests.get(
    • Network accessline 176
      """Download a file from Dataverse."""     resp = requests.get(         f"{BASE_URL}/access/datafile/{file_id}",
    • Network accessline 177
      resp = requests.get(
    • Network accessline 212
      - [Harvard Dataverse](https://dataverse.harvard.edu/)
    • Network accessline 213
      - [Dataverse API Guide](https://guides.dataverse.org/en/latest/api/)
    • Network accessline 214
      - [Dataverse Project](https://dataverse.org/)

    skills/literature/fulltext/doaj-api/SKILL.md

    • Network accessline 8
      subcategory: "fulltext"     keywords: ["full-text retrieval", "open access", "open access rights", "scholarly database"]     source: "https://doaj.org/api/docs"
    • Network accessline 9
      keywords: ["full-text retrieval", "open access", "open access rights", "scholarly database"]     source: "https://doaj.org/api/docs" ---
    • Network accessline 10
      source: "https://doaj.org/api/docs"
    • Network accessline 25
      No authentication required. The DOAJ API is fully open and free to use. No API key, registration, or email is needed. There are no published rate limits, but users should be respectful and avoid sending excessive concurrent requests. For bu
    • Network accessline 31
      - **URL**: `GET https://doaj.org/api/search/articles/{search_query}`
    • Network accessline 41
      curl "https://doaj.org/api/search/articles/climate+change?page=1&pageSize=10"
    • Network accessline 47
      - **URL**: `GET https://doaj.org/api/search/journals/{search_query}`
    • Network accessline 56
      curl "https://doaj.org/api/search/journals/bioinformatics?page=1&pageSize=5"
    • Network accessline 62
      - **URL**: `GET https://doaj.org/api/search/articles/doi:{doi}`
    • Network accessline 69
      curl "https://doaj.org/api/search/articles/doi:10.1371/journal.pone.0213676"
    • Network accessline 75
      - **URL**: `GET https://doaj.org/api/search/journals/issn:{issn}`
    • Network accessline 82
      curl "https://doaj.org/api/search/journals/issn:1932-6203"
    • Network accessline 97
      curl -s "https://doaj.org/api/search/journals/issn:2045-2322" | jq '{total: .total, title: .results[0].bibjson.title, publisher: .results[0].bibjson.publisher.name, license: .results[0].bibjson.license[0].type}'
    • Network accessline 105
      curl -s "https://doaj.org/api/search/articles/bibjson.subject.term:neuroscience?pageSize=20" | jq '.results[] | {title: .bibjson.title, journal: .bibjson.journal.title, url: .bibjson.link[0].url, year: .bibjson.year}'
    • Network accessline 113
      curl -s "https://doaj.org/api/search/journals/issn:2041-1723" | jq '.results[0].bibjson | {title: .title, has_apc: .apc.has_apc, apc_amount: .apc.max[0].price, currency: .apc.max[0].currency}'
    • Network accessline 118
      - Official documentation: https://doaj.org/api/docs
    • Network accessline 119
      - DOAJ public data dump: https://doaj.org/docs/public-data-dump/
    • Network accessline 120
      - DOAJ journal application criteria: https://doaj.org/apply/guide/

    skills/literature/fulltext/hal-archive-api/SKILL.md

    • Network accessline 8
      subcategory: "fulltext"     keywords: ["HAL", "French research", "open archive", "CNRS", "European research", "institutional repository"]     source: "https://api.archives-ouvertes.fr/"
    • Network accessline 9
      keywords: ["HAL", "French research", "open archive", "CNRS", "European research", "institutional repository"]     source: "https://api.archives-ouvertes.fr/" ---
    • Network accessline 10
      source: "https://api.archives-ouvertes.fr/"
    • Network accessline 24
      # Keyword search curl "https://api.archives-ouvertes.fr/search/?q=machine+learning&rows=20&wt=json"
    • Network accessline 25
      curl "https://api.archives-ouvertes.fr/search/?q=machine+learning&rows=20&wt=json"
    • Network accessline 27
      # Search specific fields curl "https://api.archives-ouvertes.fr/search/?q=title_s:\"deep learning\"&wt=json"
    • Network accessline 28
      curl "https://api.archives-ouvertes.fr/search/?q=title_s:\"deep learning\"&wt=json"
    • Network accessline 30
      # Filter by document type curl "https://api.archives-ouvertes.fr/search/?q=neural+networks&\
    • Network accessline 31
      curl "https://api.archives-ouvertes.fr/search/?q=neural+networks&\
    • Network accessline 34
      # Filter by year and language curl "https://api.archives-ouvertes.fr/search/?q=climate+change&\
    • Network accessline 35
      curl "https://api.archives-ouvertes.fr/search/?q=climate+change&\
    • Network accessline 38
      # Filter by institution curl "https://api.archives-ouvertes.fr/search/?q=robotics&\
    • Network accessline 39
      curl "https://api.archives-ouvertes.fr/search/?q=robotics&\
    • Network accessline 42
      # Return specific fields curl "https://api.archives-ouvertes.fr/search/?q=CRISPR&\
    • Network accessline 43
      curl "https://api.archives-ouvertes.fr/search/?q=CRISPR&\
    • Network accessline 101
      "docType_s": "ART",         "journalTitle_s": "Environmental Modelling",         "uri_s": "https://hal.science/hal-01234567",
    • Network accessline 102
      "journalTitle_s": "Environmental Modelling",         "uri_s": "https://hal.science/hal-01234567",         "files_s": ["https://hal.science/hal-01234567/document"],
    • Network accessline 103
      "uri_s": "https://hal.science/hal-01234567",
    • Network accessline 104
      "files_s": ["https://hal.science/hal-01234567/document"],
    • Network accessline 119
      BASE_URL = "https://api.archives-ouvertes.fr/search/"
    • Network accessline 145
      resp = requests.get(BASE_URL, params=params)
    • Network accessline 182
      "sort": "producedDateY_i desc",     }     resp = requests.get(BASE_URL, params=params)
    • Network accessline 183
      }     resp = requests.get(BASE_URL, params=params)     resp.raise_for_status()
    • Network accessline 184
      resp = requests.get(BASE_URL, params=params)
    • Network accessline 216
      - [HAL Open Archive](https://hal.science/)
    • Network accessline 217
      - [HAL API Documentation](https://api.archives-ouvertes.fr/docs)
    • Network accessline 218
      - [HAL Search Guide](https://doc.archives-ouvertes.fr/en/)

    skills/literature/fulltext/institutional-repository-guide/SKILL.md

    • Network accessline 54
      country: ISO country code (e.g., "US", "GB", "CN")     """     base_url = "https://v2.sherpa.ac.uk/cgi/retrieve"
    • Network accessline 55
      """     base_url = "https://v2.sherpa.ac.uk/cgi/retrieve"     params = "?item-type=repository&format=Json"
    • Network accessline 56
      base_url = "https://v2.sherpa.ac.uk/cgi/retrieve"
    • Network accessline 63
      req = urllib.request.Request(base_url + params)
    • Network accessline 64
      response = urllib.request.urlopen(req)
    • Network accessline 109
      while url:         response = urllib.request.urlopen(url)
    • Network accessline 110
      response = urllib.request.urlopen(url)
    • Network accessline 111
      tree = ET.parse(response)         root = tree.getroot()         ns = {"oai": "http://www.openarchives.org/OAI/2.0/"}
    • Network accessline 113
      ns = {"oai": "http://www.openarchives.org/OAI/2.0/"}
    • Network accessline 208
      - OpenDOAR: https://v2.sherpa.ac.uk/opendoar/
    • Network accessline 209
      - OAI-PMH specification: http://www.openarchives.org/OAI/openarchivesprotocol.html
    • Network accessline 210
      - CORE: https://core.ac.uk
    • Network accessline 211
      - BASE: https://www.base-search.net
    • Network accessline 212
      - DSpace documentation: https://wiki.lyrasis.org/display/DSPACE

    skills/literature/fulltext/open-access-guide/SKILL.md

    • Network accessline 42
      """     email = "researcher@university.edu"  # Required by Unpaywall API     url = f"https://api.unpaywall.org/v2/{doi}?email={email}"
    • Network accessline 44
      url = f"https://api.unpaywall.org/v2/{doi}?email={email}"
    • Network accessline 46
      response = requests.get(url)
    • Access to secretsline 127
      [Credential-related source omitted]
    • Network accessline 133
      [Credential-related source omitted]
    • Access to secretsline 133
      [Credential-related source omitted]
    • Network accessline 135
      [Credential-related source omitted]
    • Access to secretsline 135
      [Credential-related source omitted]
    • Network accessline 137
      response = requests.get(url)

    skills/literature/fulltext/open-access-mining-guide/SKILL.md

    • Network accessline 120
      Parsed article as structured dictionary     """     base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
    • Network accessline 121
      """     base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"     params = {
    • Network accessline 122
      base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
    • Network accessline 129
      response = requests.get(base_url, params=params, timeout=30)

    skills/literature/fulltext/osf-api/SKILL.md

    • Network accessline 8
      subcategory: "fulltext"     keywords: ["OSF", "Open Science Framework", "preprints", "open data", "reproducibility", "preregistration"]     source: "https://osf.io/"
    • Network accessline 9
      keywords: ["OSF", "Open Science Framework", "preprints", "open data", "reproducibility", "preregistration"]     source: "https://osf.io/" ---
    • Network accessline 10
      source: "https://osf.io/"
    • Network accessline 21
      Public read access requires no authentication. For creating or modifying resources, generate a personal access token at https://osf.io/settings/tokens.
    • Network accessline 24
      # Public access (no auth needed) curl "https://api.osf.io/v2/nodes/?filter[title]=reproducibility"
    • Network accessline 25
      curl "https://api.osf.io/v2/nodes/?filter[title]=reproducibility"
    • Network accessline 27
      [Credential-related source omitted]
    • Network accessline 28
      [Credential-related source omitted]
    • Access to secretsline 28
      [Credential-related source omitted]
    • Network accessline 29
      [Credential-related source omitted]
    • Access to secretsline 29
      [Credential-related source omitted]
    • Network accessline 30
      "https://api.osf.io/v2/users/me/"
    • Network accessline 38
      https://api.osf.io/v2
    • Network accessline 44
      # Search across all OSF content curl "https://api.osf.io/v2/search/?q=replication+crisis&page[size]=20"
    • Network accessline 45
      curl "https://api.osf.io/v2/search/?q=replication+crisis&page[size]=20"
    • Network accessline 47
      # Search preprints curl "https://api.osf.io/v2/preprints/?filter[q]=machine+learning&page[size]=20"
    • Network accessline 48
      curl "https://api.osf.io/v2/preprints/?filter[q]=machine+learning&page[size]=20"
    • Network accessline 50
      # Filter by preprint provider curl "https://api.osf.io/v2/preprints/?filter[provider]=psyarxiv&filter[q]=cognitive+bias"
    • Network accessline 51
      curl "https://api.osf.io/v2/preprints/?filter[provider]=psyarxiv&filter[q]=cognitive+bias"
    • Network accessline 53
      # Search registrations (pre-registered studies) curl "https://api.osf.io/v2/registrations/?filter[q]=randomized+controlled+trial"
    • Network accessline 54
      curl "https://api.osf.io/v2/registrations/?filter[q]=randomized+controlled+trial"
    • Network accessline 60
      # Get public projects curl "https://api.osf.io/v2/nodes/?filter[public]=true&filter[q]=neuroimaging"
    • Network accessline 61
      curl "https://api.osf.io/v2/nodes/?filter[public]=true&filter[q]=neuroimaging"
    • Network accessline 63
      # Get project details curl "https://api.osf.io/v2/nodes/{node_id}/"
    • Network accessline 64
      curl "https://api.osf.io/v2/nodes/{node_id}/"
    • Network accessline 66
      # Get project files curl "https://api.osf.io/v2/nodes/{node_id}/files/"
    • Network accessline 67
      curl "https://api.osf.io/v2/nodes/{node_id}/files/"
    • Network accessline 69
      # Get project contributors curl "https://api.osf.io/v2/nodes/{node_id}/contributors/"
    • Network accessline 70
      curl "https://api.osf.io/v2/nodes/{node_id}/contributors/"
    • Network accessline 129
      BASE_URL = "https://api.osf.io/v2"
    • Network accessline 142
      resp = requests.get(f"{BASE_URL}/preprints/", params=params)
    • Network accessline 154
      "date": attrs.get("date_published", "")[:10],             "tags": attrs.get("tags", []),             "url": f"https://osf.io/{item.get('id')}/",
    • Network accessline 155
      "tags": attrs.get("tags", []),             "url": f"https://osf.io/{item.get('id')}/",         })
    • Network accessline 156
      "url": f"https://osf.io/{item.get('id')}/",
    • Network accessline 166
      "page[size]": page_size,     }     resp = requests.get(f"{BASE_URL}/registrations/", params=params)
    • Network accessline 167
      }     resp = requests.get(f"{BASE_URL}/registrations/", params=params)     resp.raise_for_status()
    • Network accessline 168
      resp = requests.get(f"{BASE_URL}/registrations/", params=params)
    • Network accessline 185
      def get_project_files(node_id: str) -> list:     """List files in an OSF project."""     resp = requests.get(f"{BASE_URL}/nodes/{node_id}/files/")
    • Network accessline 186
      """List files in an OSF project."""     resp = requests.get(f"{BASE_URL}/nodes/{node_id}/files/")     resp.raise_for_status()
    • Network accessline 187
      resp = requests.get(f"{BASE_URL}/nodes/{node_id}/files/")
    • Network accessline 232
      - [OSF](https://osf.io/)
    • Network accessline 233
      - [OSF API Documentation](https://developer.osf.io/)
    • Network accessline 234
      - [OSF Preprints](https://osf.io/preprints/)
    • Network accessline 235
      - [OSF Registrations (Preregistration)](https://osf.io/registries/)
    • Network accessline 236
      - [Center for Open Science](https://cos.io/)

    skills/literature/fulltext/pmc-ftp-bulk-download/SKILL.md

    • Network accessline 8
      subcategory: "fulltext"     keywords: ["pmc", "bulk download", "ftp", "text mining", "open access", "pubmed central"]     source: "https://www.ncbi.nlm.nih.gov/pmc/tools/ftp/"
    • Network accessline 9
      keywords: ["pmc", "bulk download", "ftp", "text mining", "open access", "pubmed central"]     source: "https://www.ncbi.nlm.nih.gov/pmc/tools/ftp/" ---
    • Network accessline 10
      source: "https://www.ncbi.nlm.nih.gov/pmc/tools/ftp/"
    • Network accessline 30
      # HTTPS alternative (recommended) # Base: https://ftp.ncbi.nlm.nih.gov/pub/pmc/
    • Network accessline 31
      # Base: https://ftp.ncbi.nlm.nih.gov/pub/pmc/
    • Network accessline 37
      |---------|------|---------|--------| | **OA Commercial** | `/pub/pmc/oa_comm/` | CC BY/CC0 articles (commercial use OK) | .tar.gz packages | | **OA Non-Commercial** | `/pub/pmc/oa_noncomm/` | CC BY-NC articles | .tar.gz packages |
    • Network accessline 38
      | **OA Commercial** | `/pub/pmc/oa_comm/` | CC BY/CC0 articles (commercial use OK) | .tar.gz packages | | **OA Non-Commercial** | `/pub/pmc/oa_noncomm/` | CC BY-NC articles | .tar.gz packages | | **OA Other** | `/pub/pmc/oa_other/` | Other
    • Network accessline 39
      | **OA Non-Commercial** | `/pub/pmc/oa_noncomm/` | CC BY-NC articles | .tar.gz packages |
    • Network accessline 50
      # Download the OA file list (CSV, ~200MB) wget https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_file_list.csv
    • Network accessline 51
      wget https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_file_list.csv
    • Network accessline 67
      def download_article_package(pmcid: str, base_url: str = "https://ftp.ncbi.nlm.nih.gov/pub/pmc"):     """Download and extract a specific PMC article package."""
    • Network accessline 74
      # Download the tar.gz package     resp = requests.get(f"{base_url}/{file_path}", stream=True)
    • Network accessline 75
      resp = requests.get(f"{base_url}/{file_path}", stream=True)
    • Network accessline 94
      # Download the baseline (all current articles) wget -r -np -nH --cut-dirs=3 \
    • Network accessline 95
      wget -r -np -nH --cut-dirs=3 \
    • Network accessline 96
      https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_comm/xml/
    • Network accessline 98
      # Incremental updates (run periodically) wget -r -np -nH --cut-dirs=3 -N \
    • Network accessline 99
      wget -r -np -nH --cut-dirs=3 -N \
    • Network accessline 100
      https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_comm/xml/
    • Network accessline 114
      output = Path(output_dir)     output.mkdir(parents=True, exist_ok=True)     base = "https://ftp.ncbi.nlm.nih.gov/pub/pmc"
    • Network accessline 115
      output.mkdir(parents=True, exist_ok=True)     base = "https://ftp.ncbi.nlm.nih.gov/pub/pmc"     downloaded = 0
    • Network accessline 116
      base = "https://ftp.ncbi.nlm.nih.gov/pub/pmc"
    • Network accessline 134
      resp = requests.get(url, stream=True, timeout=60)
    • Network accessline 149
      # PMID → PMCID → DOI conversion curl "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?ids=29346600&format=json"
    • Network accessline 150
      curl "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?ids=29346600&format=json"
    • Network accessline 152
      # Batch conversion (up to 200 IDs) curl "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?ids=29346600,30266829,31048553&format=json"
    • Network accessline 153
      curl "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?ids=29346600,30266829,31048553&format=json"
    • Network accessline 180
      - [PMC FTP Documentation](https://www.ncbi.nlm.nih.gov/pmc/tools/ftp/)
    • Network accessline 181
      - [PMC Open Access Subset](https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/)
    • Network accessline 182
      - [PMC ID Converter API](https://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/)

    skills/literature/fulltext/pmc-oai-api/SKILL.md

    • Network accessline 8
      subcategory: "fulltext"     keywords: ["full-text retrieval", "open access", "PDF download", "preprint server"]     source: "https://pmc.ncbi.nlm.nih.gov/tools/oai/"
    • Network accessline 9
      keywords: ["full-text retrieval", "open access", "PDF download", "preprint server"]     source: "https://pmc.ncbi.nlm.nih.gov/tools/oai/" ---
    • Network accessline 10
      source: "https://pmc.ncbi.nlm.nih.gov/tools/oai/"
    • Network accessline 33
      - **URL**: `GET https://pmc.ncbi.nlm.nih.gov/api/oai/v1/mh/`
    • Network accessline 48
      # Harvest recent open-access records in Dublin Core format curl "https://pmc.ncbi.nlm.nih.gov/api/oai/v1/mh/?verb=ListRecords&metadataPrefix=oai_dc&from=2024-06-01&until=2024-06-07"
    • Network accessline 49
      curl "https://pmc.ncbi.nlm.nih.gov/api/oai/v1/mh/?verb=ListRecords&metadataPrefix=oai_dc&from=2024-06-01&until=2024-06-07"
    • Network accessline 51
      # Harvest PMC full metadata format curl "https://pmc.ncbi.nlm.nih.gov/api/oai/v1/mh/?verb=ListRecords&metadataPrefix=pmc_fm&from=2024-06-01&until=2024-06-02"
    • Network accessline 52
      curl "https://pmc.ncbi.nlm.nih.gov/api/oai/v1/mh/?verb=ListRecords&metadataPrefix=pmc_fm&from=2024-06-01&until=2024-06-02"
    • Network accessline 61
      - **URL**: `GET https://pmc.ncbi.nlm.nih.gov/api/oai/v1/mh/`
    • Network accessline 73
      curl "https://pmc.ncbi.nlm.nih.gov/api/oai/v1/mh/?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:7096803&metadataPrefix=oai_dc"
    • Network accessline 82
      - **URL**: `GET https://pmc.ncbi.nlm.nih.gov/api/oai/v1/mh/`
    • Network accessline 92
      curl "https://pmc.ncbi.nlm.nih.gov/api/oai/v1/mh/?verb=ListSets"
    • Network accessline 114
      base_url = "https://pmc.ncbi.nlm.nih.gov/api/oai/v1/mh/"
    • Network accessline 122
      all_records = [] while True:     resp = requests.get(base_url, params=params)
    • Network accessline 123
      while True:     resp = requests.get(base_url, params=params)     root = ET.fromstring(resp.text)
    • Network accessline 124
      resp = requests.get(base_url, params=params)
    • Network accessline 126
      ns = {"oai": "http://www.openarchives.org/OAI/2.0/"}
    • Network accessline 149
      url = "https://pmc.ncbi.nlm.nih.gov/api/oai/v1/mh/"
    • Network accessline 156
      resp = requests.get(url, params=params)
    • Network accessline 159
      dc_ns = "http://purl.org/dc/elements/1.1/"
    • Network accessline 160
      oai_ns = "http://www.openarchives.org/OAI/2.0/"
    • Network accessline 175
      curl "https://pmc.ncbi.nlm.nih.gov/api/oai/v1/mh/?verb=ListSets" | head -100
    • Network accessline 180
      - Official PMC OAI documentation: https://pmc.ncbi.nlm.nih.gov/tools/oai/
    • Network accessline 181
      - PMC homepage: https://pmc.ncbi.nlm.nih.gov/
    • Network accessline 182
      - OAI-PMH protocol specification: https://www.openarchives.org/OAI/openarchivesprotocol.html
    • Network accessline 183
      - NCBI usage guidelines: https://www.ncbi.nlm.nih.gov/home/about/policies/
    • Network accessline 184
      - PMC Open Access subset: https://pmc.ncbi.nlm.nih.gov/tools/openftlist/

    skills/literature/fulltext/preprint-servers-guide/SKILL.md

    • Network accessline 60
      # Download arXiv paper PDF programmatically curl -o paper.pdf https://arxiv.org/pdf/2401.12345
    • Network accessline 61
      curl -o paper.pdf https://arxiv.org/pdf/2401.12345
    • Network accessline 63
      # Get metadata via arXiv API curl "http://export.arxiv.org/api/query?id_list=2401.12345"
    • Network accessline 64
      curl "http://export.arxiv.org/api/query?id_list=2401.12345"
    • Network accessline 80
      response = requests.get(
    • Network accessline 81
      "https://api.biorxiv.org/details/biorxiv/2024-01-01/2024-01-31",
    • Network accessline 92
      |---------|-------------|-------------------|--------------------|---------------------| | CC-BY | Yes | Yes | Yes | Yes | | CC-BY-NC | Yes | No | Yes | Yes |
    • Network accessline 93
      | CC-BY | Yes | Yes | Yes | Yes | | CC-BY-NC | Yes | No | Yes | Yes | | CC-BY-ND | Yes | Yes | No | Yes |
    • Network accessline 94
      | CC-BY-NC | Yes | No | Yes | Yes |
    • Network accessline 99
      **Recommendation**: Use CC-BY for maximum openness and compatibility with funder mandates (NIH, Wellcome Trust, ERC). Use CC-BY-NC if you want to restrict commercial reuse.

    skills/literature/fulltext/unpaywall-api/SKILL.md

    • Network accessline 8
      subcategory: "fulltext"     keywords: ["full-text retrieval", "open access", "journal copyright policy", "self-archiving"]     source: "https://unpaywall.org/products/api"
    • Network accessline 9
      keywords: ["full-text retrieval", "open access", "journal copyright policy", "self-archiving"]     source: "https://unpaywall.org/products/api"     requires:
    • Network accessline 10
      source: "https://unpaywall.org/products/api"
    • Network accessline 39
      - **URL**: `GET https://api.unpaywall.org/v2/{doi}`
    • Network accessline 47
      curl "https://api.unpaywall.org/v2/10.1038/nature12373?email=user@example.com"
    • Network accessline 58
      - **URL**: `GET https://api.unpaywall.org/v2/{doi}` (repeated per DOI)
    • Network accessline 66
      # Process multiple DOIs sequentially   for doi in "10.1038/nature12373" "10.1126/science.aaa8685" "10.1016/j.cell.2015.05.002"; do     curl -s "https://api.unpaywall.org/v2/$doi?email=user@example.com" | jq '{doi: .doi, is_oa: .is_oa, oa_st
    • Network accessline 67
      for doi in "10.1038/nature12373" "10.1126/science.aaa8685" "10.1016/j.cell.2015.05.002"; do     curl -s "https://api.unpaywall.org/v2/$doi?email=user@example.com" | jq '{doi: .doi, is_oa: .is_oa, oa_status: .oa_status, best_url: .best_oa_lo
    • Network accessline 68
      curl -s "https://api.unpaywall.org/v2/$doi?email=user@example.com" | jq '{doi: .doi, is_oa: .is_oa, oa_status: .oa_status, best_url: .best_oa_location.url}'
    • Network accessline 76
      For large-scale analyses, Unpaywall provides a complete database snapshot and a weekly data feed, rather than requiring millions of individual API calls. Access is available at https://unpaywall.org/products/data-feed for registered users.
    • Network accessline 89
      curl -s "https://api.unpaywall.org/v2/10.1038/s41586-021-03819-2?email=user@example.com" | jq '{title: .title, is_oa: .is_oa, oa_status: .oa_status, pdf: .best_oa_location.url_for_pdf}'
    • Network accessline 97
      curl -s "https://api.unpaywall.org/v2/10.1145/3292500.3330672?email=user@example.com" | jq '.best_oa_location | {url: .url, pdf: .url_for_pdf, version: .version, license: .license}'
    • Network accessline 105
      # For each publication DOI from the grant curl -s "https://api.unpaywall.org/v2/10.1038/nature12373?email=user@example.com" | jq '{doi: .doi, title: .title, is_oa: .is_oa, oa_status: .oa_status, locations: [.oa_locations[] | {host: .host_ty
    • Network accessline 106
      curl -s "https://api.unpaywall.org/v2/10.1038/nature12373?email=user@example.com" | jq '{doi: .doi, title: .title, is_oa: .is_oa, oa_status: .oa_status, locations: [.oa_locations[] | {host: .host_type, license: .license, version: .version}]
    • Network accessline 111
      - Official documentation: https://unpaywall.org/products/api
    • Network accessline 112
      - Unpaywall data format: https://unpaywall.org/data-format
    • Network accessline 113
      - OurResearch: https://ourresearch.org/

    skills/literature/fulltext/zotero-ai-butler-guide/SKILL.md

    • Network accessline 8
      subcategory: "fulltext"     keywords: ["Zotero", "AI summary", "paper summarization", "LLM", "abstract generation", "reading assistant"]     source: "https://github.com/steven-jianhao-li/zotero-AI-Butler"
    • Network accessline 9
      keywords: ["Zotero", "AI summary", "paper summarization", "LLM", "abstract generation", "reading assistant"]     source: "https://github.com/steven-jianhao-li/zotero-AI-Butler" ---
    • Network accessline 10
      source: "https://github.com/steven-jianhao-li/zotero-AI-Butler"
    • Network accessline 40
      **Option 3: Local (Ollama)** - Provider: Ollama - Endpoint: http://localhost:11434
    • Network accessline 41
      - Provider: Ollama - Endpoint: http://localhost:11434 - Model: llama3.1
    • Network accessline 42
      - Endpoint: http://localhost:11434
    • Network accessline 165
      - [Zotero AI Butler GitHub](https://github.com/steven-jianhao-li/zotero-AI-Butler)
    • Network accessline 166
      - [Zotero Plugin Development](https://www.zotero.org/support/dev/client_coding/plugin_development)

    skills/literature/metadata/academic-paper-summarizer/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["paper summary", "structured extraction", "abstract", "key findings", "research synthesis", "literature review"]     source: "https://github.com/lifan0127/ai-research-assistant"
    • Network accessline 9
      keywords: ["paper summary", "structured extraction", "abstract", "key findings", "research synthesis", "literature review"]     source: "https://github.com/lifan0127/ai-research-assistant" ---
    • Network accessline 10
      source: "https://github.com/lifan0127/ai-research-assistant"
    • Network accessline 99
      - Keshav, S. (2007). "How to Read a Paper." ACM SIGCOMM Computer Communication Review. - Pautasso, M. (2013). "Ten Simple Rules for Writing a Literature Review." PLOS Computational Biology. - AI Research Assistant: https://github.com/lifan0
    • Network accessline 101
      - AI Research Assistant: https://github.com/lifan0127/ai-research-assistant

    skills/literature/metadata/altmetrics-guide/SKILL.md

    • Network accessline 67
      # Look up altmetrics by DOI doi = "10.1038/s41586-021-03819-2" response = requests.get(f"https://api.altmetric.com/v1/doi/{doi}")
    • Network accessline 69
      response = requests.get(f"https://api.altmetric.com/v1/doi/{doi}")
    • Network accessline 91
      # Look up by PubMed ID pmid = "34234348" response = requests.get(f"https://api.altmetric.com/v1/pmid/{pmid}")
    • Network accessline 93
      response = requests.get(f"https://api.altmetric.com/v1/pmid/{pmid}")
    • Network accessline 95
      # Look up by arXiv ID arxiv_id = "2103.14030" response = requests.get(f"https://api.altmetric.com/v1/arxiv/{arxiv_id}")
    • Network accessline 97
      response = requests.get(f"https://api.altmetric.com/v1/arxiv/{arxiv_id}")

    skills/literature/metadata/bibliometrix-guide/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["bibliometrix", "bibliometrics", "science mapping", "R", "citation analysis", "research trends"]     source: "https://github.com/massimoaria/bibliometrix"
    • Network accessline 9
      keywords: ["bibliometrix", "bibliometrics", "science mapping", "R", "citation analysis", "research trends"]     source: "https://github.com/massimoaria/bibliometrix" ---
    • Network accessline 10
      source: "https://github.com/massimoaria/bibliometrix"
    • Network accessline 162
      - [Bibliometrix](https://www.bibliometrix.org/)
    • Network accessline 163
      - [Bibliometrix GitHub](https://github.com/massimoaria/bibliometrix)

    skills/literature/metadata/citation-network-guide/SKILL.md

    • Network accessline 64
      def get_citations(doi, max_results=100):     """Fetch papers that cite a given DOI using OpenAlex."""     work_url = f"https://api.openalex.org/works/doi:{doi}"
    • Network accessline 65
      """Fetch papers that cite a given DOI using OpenAlex."""     work_url = f"https://api.openalex.org/works/doi:{doi}"     resp = requests.get(work_url)
    • Network accessline 66
      work_url = f"https://api.openalex.org/works/doi:{doi}"     resp = requests.get(work_url)     work = resp.json()
    • Network accessline 67
      resp = requests.get(work_url)
    • Network accessline 71
      # Get citing works     citing_url = (         f"https://api.openalex.org/works"
    • Network accessline 72
      citing_url = (         f"https://api.openalex.org/works"         f"?filter=cites:{openalex_id}"
    • Network accessline 73
      f"https://api.openalex.org/works"
    • Network accessline 76
      f"&sort=cited_by_count:desc"     )     citing_resp = requests.get(citing_url)
    • Network accessline 77
      )     citing_resp = requests.get(citing_url)     citing_works = citing_resp.json()['results']
    • Network accessline 78
      citing_resp = requests.get(citing_url)
    • Network accessline 231
      - [OpenAlex API](https://docs.openalex.org/) -- Free, open bibliographic data
    • Network accessline 232
      - [CrossRef API](https://api.crossref.org/) -- DOI resolution and metadata
    • Network accessline 233
      - [VOSviewer](https://www.vosviewer.com/) -- Bibliometric visualization tool
    • Network accessline 234
      - [bibliometrix R package](https://www.bibliometrix.org/) -- Comprehensive bibliometric analysis
    • Network accessline 235
      - [Altmetric](https://www.altmetric.com/) -- Alternative impact metrics
    • Network accessline 236
      - [NetworkX Documentation](https://networkx.org/) -- Python graph analysis library

    skills/literature/metadata/crossref-api/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["DOI resolution", "digital object identifier", "CrossRef", "citation statistics", "citation tracking"]     source: "https://api.crossref.org"
    • Network accessline 9
      keywords: ["DOI resolution", "digital object identifier", "CrossRef", "citation statistics", "citation tracking"]     source: "https://api.crossref.org" ---
    • Network accessline 10
      source: "https://api.crossref.org"
    • Network accessline 28
      https://api.crossref.org/works?mailto=your@email.com
    • Network accessline 37
      - **URL**: `GET https://api.crossref.org/works`
    • Network accessline 52
      curl "https://api.crossref.org/works?query.title=attention+is+all+you+need&rows=5&mailto=user@example.com"
    • Network accessline 58
      - **URL**: `GET https://api.crossref.org/works/{doi}`
    • Network accessline 66
      curl "https://api.crossref.org/works/10.1038/s41586-021-03819-2?mailto=user@example.com"
    • Network accessline 72
      - **URL**: `GET https://api.crossref.org/members`
    • Network accessline 80
      curl "https://api.crossref.org/members?query=springer&rows=5&mailto=user@example.com"
    • Network accessline 86
      - **URL**: `GET https://api.crossref.org/journals`
    • Network accessline 94
      curl "https://api.crossref.org/journals?query=nature+machine+intelligence&rows=5&mailto=user@example.com"
    • Network accessline 109
      # Single DOI resolution with full metadata curl "https://api.crossref.org/works/10.1145/3292500.3330672?mailto=user@example.com"
    • Network accessline 110
      curl "https://api.crossref.org/works/10.1145/3292500.3330672?mailto=user@example.com"
    • Network accessline 118
      curl "https://api.crossref.org/works?filter=from-pub-date:2023,type:journal-article&query=machine+learning&sort=is-referenced-by-count&order=desc&rows=20&mailto=user@example.com"
    • Network accessline 126
      curl "https://api.crossref.org/works/10.1038/s41586-021-03819-2?mailto=user@example.com" | jq '.message["is-referenced-by-count"]'
    • Network accessline 131
      - Official documentation: https://api.crossref.org
    • Network accessline 132
      - API documentation: https://api.crossref.org/swagger-ui/index.html
    • Network accessline 133
      - CrossRef metadata best practices: https://www.crossref.org/documentation/

    skills/literature/metadata/crossref-event-data-api/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["Crossref", "event data", "altmetrics", "social media mentions", "scholarly impact", "web mentions"]     source: "https://www.eventdata.crossref.org/"
    • Network accessline 9
      keywords: ["Crossref", "event data", "altmetrics", "social media mentions", "scholarly impact", "web mentions"]     source: "https://www.eventdata.crossref.org/" ---
    • Network accessline 10
      source: "https://www.eventdata.crossref.org/"
    • Network accessline 24
      https://api.eventdata.crossref.org/v1
    • Network accessline 30
      # Get events for a specific DOI curl "https://api.eventdata.crossref.org/v1/events?obj-id=10.1038/nature14539&rows=20"
    • Network accessline 31
      curl "https://api.eventdata.crossref.org/v1/events?obj-id=10.1038/nature14539&rows=20"
    • Network accessline 33
      # Filter by source curl "https://api.eventdata.crossref.org/v1/events?\
    • Network accessline 34
      curl "https://api.eventdata.crossref.org/v1/events?\
    • Network accessline 37
      # Filter by date range curl "https://api.eventdata.crossref.org/v1/events?\
    • Network accessline 38
      curl "https://api.eventdata.crossref.org/v1/events?\
    • Network accessline 41
      # Get events about a DOI prefix (publisher level) curl "https://api.eventdata.crossref.org/v1/events?obj-id.prefix=10.1371&rows=50"
    • Network accessline 42
      curl "https://api.eventdata.crossref.org/v1/events?obj-id.prefix=10.1371&rows=50"
    • Network accessline 44
      # Events from a specific source curl "https://api.eventdata.crossref.org/v1/events?source=reddit&rows=50"
    • Network accessline 45
      curl "https://api.eventdata.crossref.org/v1/events?source=reddit&rows=50"
    • Network accessline 83
      "events": [       {         "obj_id": "https://doi.org/10.1038/nature14539",
    • Network accessline 84
      {         "obj_id": "https://doi.org/10.1038/nature14539",         "source_id": "wikipedia",
    • Network accessline 85
      "obj_id": "https://doi.org/10.1038/nature14539",
    • Network accessline 86
      "source_id": "wikipedia",         "subj_id": "https://en.wikipedia.org/wiki/Deep_learning",         "relation_type_id": "references",
    • Network accessline 87
      "subj_id": "https://en.wikipedia.org/wiki/Deep_learning",
    • Network accessline 90
      "subj": {           "title": "Deep learning - Wikipedia",           "url": "https://en.wikipedia.org/wiki/Deep_learning"
    • Network accessline 91
      "title": "Deep learning - Wikipedia",           "url": "https://en.wikipedia.org/wiki/Deep_learning"         }
    • Network accessline 92
      "url": "https://en.wikipedia.org/wiki/Deep_learning"
    • Network accessline 107
      BASE_URL = "https://api.eventdata.crossref.org/v1"
    • Network accessline 117
      resp = requests.get(f"{BASE_URL}/events", params=params)
    • Network accessline 181
      - [Crossref Event Data](https://www.eventdata.crossref.org/)
    • Network accessline 182
      - [Event Data API Guide](https://www.eventdata.crossref.org/guide/)
    • Network accessline 183
      - [Event Data User Guide](https://www.crossref.org/services/event-data/)

    skills/literature/metadata/datacite-api/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["DOI resolution", "digital object identifier", "FAIR data principles", "data sharing"]     source: "https://support.datacite.org/docs/api"
    • Network accessline 9
      keywords: ["DOI resolution", "digital object identifier", "FAIR data principles", "data sharing"]     source: "https://support.datacite.org/docs/api" ---
    • Network accessline 10
      source: "https://support.datacite.org/docs/api"
    • Network accessline 31
      - **URL**: `GET https://api.datacite.org/dois`
    • Network accessline 44
      curl "https://api.datacite.org/dois?query=climate+change+dataset&resource-type-id=dataset&page[size]=10&sort=-created"
    • Network accessline 50
      - **URL**: `GET https://api.datacite.org/dois/{doi}`
    • Network accessline 57
      curl "https://api.datacite.org/dois/10.5281/zenodo.3678171"
    • Network accessline 63
      - **URL**: `GET https://api.datacite.org/providers`
    • Network accessline 72
      curl "https://api.datacite.org/providers?query=CERN&page[size]=5"
    • Network accessline 78
      - **URL**: `GET https://api.datacite.org/clients`
    • Network accessline 88
      curl "https://api.datacite.org/clients?query=zenodo&page[size]=5"
    • Network accessline 94
      No published rate limits. DataCite does not enforce strict API quotas for read access. However, the service is operated by a nonprofit organization, so users should implement reasonable request pacing. For large-scale data mining, use the D
    • Network accessline 103
      curl -s "https://api.datacite.org/dois?query=CRISPR+genome+editing&resource-type-id=dataset&page[size]=5&sort=-created" | jq '.data[] | {doi: .attributes.doi, title: .attributes.titles[0].title, year: .attributes.publicationYear, publisher:
    • Network accessline 111
      curl -s "https://api.datacite.org/dois?query=python+machine+learning&resource-type-id=software&page[size]=10" | jq '.data[] | {doi: .attributes.doi, title: .attributes.titles[0].title, year: .attributes.publicationYear}'
    • Network accessline 119
      curl -s "https://api.datacite.org/dois/10.5281/zenodo.3678171" | jq '.data.attributes.relatedIdentifiers[] | select(.relationType == "IsSupplementTo" or .relationType == "IsReferencedBy") | {type: .relationType, id: .relatedIdentifier}'
    • Network accessline 124
      - Official documentation: https://support.datacite.org/docs/api
    • Network accessline 125
      - DataCite Metadata Schema: https://schema.datacite.org/
    • Network accessline 126
      - JSON:API specification: https://jsonapi.org/

    skills/literature/metadata/doi-content-negotiation/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["DOI", "content negotiation", "metadata retrieval", "BibTeX", "citation metadata", "linked data"]     source: "https://citation.crosscite.org/"
    • Network accessline 8
      subcategory: "metadata"     keywords: ["DOI", "content negotiation", "metadata retrieval", "BibTeX", "citation metadata", "linked data"]     source: "https://citation.crosscite.org/"
    • Network accessline 9
      keywords: ["DOI", "content negotiation", "metadata retrieval", "BibTeX", "citation metadata", "linked data"]     source: "https://citation.crosscite.org/" ---
    • Network accessline 9
      keywords: ["DOI", "content negotiation", "metadata retrieval", "BibTeX", "citation metadata", "linked data"]     source: "https://citation.crosscite.org/" ---
    • Network accessline 10
      source: "https://citation.crosscite.org/"
    • Network accessline 10
      source: "https://citation.crosscite.org/"
    • Network accessline 17
      Any DOI can return structured metadata in multiple formats through HTTP content negotiation — simply set the `Accept` header when requesting `https://doi.org/{doi}`. This is the most universal way to get citation metadata, BibTeX entries, J
    • Network accessline 17
      Any DOI can return structured metadata in multiple formats through HTTP content negotiation — simply set the `Accept` header when requesting `https://doi.org/{doi}`. This is the most universal way to get citation metadata, BibTeX entries, J
    • Network accessline 24
      # Get JSON citation metadata (Citeproc JSON) curl -LH "Accept: application/vnd.citationstyles.csl+json" \
    • Network accessline 24
      # Get JSON citation metadata (Citeproc JSON) curl -LH "Accept: application/vnd.citationstyles.csl+json" \
    • Network accessline 25
      curl -LH "Accept: application/vnd.citationstyles.csl+json" \
    • Network accessline 25
      curl -LH "Accept: application/vnd.citationstyles.csl+json" \
    • Network accessline 26
      "https://doi.org/10.1038/nature14539"
    • Network accessline 26
      "https://doi.org/10.1038/nature14539"
    • Network accessline 28
      # Get BibTeX curl -LH "Accept: application/x-bibtex" \
    • Network accessline 28
      # Get BibTeX curl -LH "Accept: application/x-bibtex" \
    • Network accessline 29
      curl -LH "Accept: application/x-bibtex" \
    • Network accessline 29
      curl -LH "Accept: application/x-bibtex" \
    • Network accessline 30
      "https://doi.org/10.1038/nature14539"
    • Network accessline 30
      "https://doi.org/10.1038/nature14539"
    • Network accessline 32
      # Get RIS format curl -LH "Accept: application/x-research-info-systems" \
    • Network accessline 32
      # Get RIS format curl -LH "Accept: application/x-research-info-systems" \
    • Network accessline 33
      curl -LH "Accept: application/x-research-info-systems" \
    • Network accessline 33
      curl -LH "Accept: application/x-research-info-systems" \
    • Network accessline 34
      "https://doi.org/10.1038/nature14539"
    • Network accessline 34
      "https://doi.org/10.1038/nature14539"
    • Network accessline 36
      # Get formatted citation (APA style) curl -LH "Accept: text/x-bibliography; style=apa" \
    • Network accessline 36
      # Get formatted citation (APA style) curl -LH "Accept: text/x-bibliography; style=apa" \
    • Network accessline 37
      curl -LH "Accept: text/x-bibliography; style=apa" \
    • Network accessline 37
      curl -LH "Accept: text/x-bibliography; style=apa" \
    • Network accessline 38
      "https://doi.org/10.1038/nature14539"
    • Network accessline 38
      "https://doi.org/10.1038/nature14539"
    • Network accessline 40
      # Get formatted citation (Chicago style) curl -LH "Accept: text/x-bibliography; style=chicago-author-date" \
    • Network accessline 40
      # Get formatted citation (Chicago style) curl -LH "Accept: text/x-bibliography; style=chicago-author-date" \
    • Network accessline 41
      curl -LH "Accept: text/x-bibliography; style=chicago-author-date" \
    • Network accessline 41
      curl -LH "Accept: text/x-bibliography; style=chicago-author-date" \
    • Network accessline 42
      "https://doi.org/10.1038/nature14539"
    • Network accessline 42
      "https://doi.org/10.1038/nature14539"
    • Network accessline 103
      "publisher": "Springer Science and Business Media LLC",   "ISSN": ["0028-0836", "1476-4687"],   "URL": "http://dx.doi.org/10.1038/nature14539",
    • Network accessline 103
      "publisher": "Springer Science and Business Media LLC",   "ISSN": ["0028-0836", "1476-4687"],   "URL": "http://dx.doi.org/10.1038/nature14539",
    • Network accessline 104
      "ISSN": ["0028-0836", "1476-4687"],   "URL": "http://dx.doi.org/10.1038/nature14539",   "abstract": "Deep learning allows computational models..."
    • Network accessline 104
      "ISSN": ["0028-0836", "1476-4687"],   "URL": "http://dx.doi.org/10.1038/nature14539",   "abstract": "Deep learning allows computational models..."
    • Network accessline 105
      "URL": "http://dx.doi.org/10.1038/nature14539",
    • Network accessline 105
      "URL": "http://dx.doi.org/10.1038/nature14539",
    • Network accessline 116
      def get_metadata(doi: str) -> dict:     """Get structured metadata for a DOI."""     resp = requests.get(
    • Network accessline 116
      def get_metadata(doi: str) -> dict:     """Get structured metadata for a DOI."""     resp = requests.get(
    • Network accessline 117
      """Get structured metadata for a DOI."""     resp = requests.get(         f"https://doi.org/{doi}",
    • Network accessline 117
      """Get structured metadata for a DOI."""     resp = requests.get(         f"https://doi.org/{doi}",
    • Network accessline 118
      resp = requests.get(
    • Network accessline 118
      resp = requests.get(
    • Network accessline 119
      f"https://doi.org/{doi}",
    • Network accessline 119
      f"https://doi.org/{doi}",
    • Network accessline 127
      def get_bibtex(doi: str) -> str:     """Get BibTeX entry for a DOI."""     resp = requests.get(
    • Network accessline 127
      def get_bibtex(doi: str) -> str:     """Get BibTeX entry for a DOI."""     resp = requests.get(
    • Network accessline 128
      """Get BibTeX entry for a DOI."""     resp = requests.get(         f"https://doi.org/{doi}",
    • Network accessline 128
      """Get BibTeX entry for a DOI."""     resp = requests.get(         f"https://doi.org/{doi}",
    • Network accessline 129
      resp = requests.get(
    • Network accessline 129
      resp = requests.get(
    • Network accessline 130
      f"https://doi.org/{doi}",
    • Network accessline 130
      f"https://doi.org/{doi}",
    • Network accessline 139
      style: str = "apa") -> str:     """Get a formatted citation string."""     resp = requests.get(
    • Network accessline 139
      style: str = "apa") -> str:     """Get a formatted citation string."""     resp = requests.get(
    • Network accessline 140
      """Get a formatted citation string."""     resp = requests.get(         f"https://doi.org/{doi}",
    • Network accessline 140
      """Get a formatted citation string."""     resp = requests.get(         f"https://doi.org/{doi}",
    • Network accessline 141
      resp = requests.get(
    • Network accessline 141
      resp = requests.get(
    • Network accessline 142
      f"https://doi.org/{doi}",
    • Network accessline 142
      f"https://doi.org/{doi}",
    • Network accessline 200
      - [DOI Content Negotiation](https://citation.crosscite.org/docs.html)
    • Network accessline 200
      - [DOI Content Negotiation](https://citation.crosscite.org/docs.html)
    • Network accessline 201
      - [Crossref Content Negotiation](https://www.crossref.org/documentation/retrieve-metadata/content-negotiation/)
    • Network accessline 201
      - [Crossref Content Negotiation](https://www.crossref.org/documentation/retrieve-metadata/content-negotiation/)
    • Network accessline 202
      - [CSL Style Repository](https://github.com/citation-style-language/styles)
    • Network accessline 202
      - [CSL Style Repository](https://github.com/citation-style-language/styles)

    skills/literature/metadata/doi-resolution-guide/SKILL.md

    • Network accessline 21
      The DOI resolver endpoint is `https://doi.org/{doi}` or equivalently `https://dx.doi.org/{doi}`.
    • Network accessline 21
      The DOI resolver endpoint is `https://doi.org/{doi}` or equivalently `https://dx.doi.org/{doi}`.
    • Network accessline 40
      curl -LH "Accept: application/vnd.citationstyles.csl+json" \
    • Network accessline 40
      curl -LH "Accept: application/vnd.citationstyles.csl+json" \
    • Network accessline 41
      https://doi.org/10.1038/s41586-021-03819-2
    • Network accessline 41
      https://doi.org/10.1038/s41586-021-03819-2
    • Network accessline 47
      doi = "10.1038/s41586-021-03819-2" headers = {"Accept": "application/vnd.citationstyles.csl+json"} response = requests.get(f"https://doi.org/{doi}", headers=headers, allow_redirects=True)
    • Network accessline 47
      doi = "10.1038/s41586-021-03819-2" headers = {"Accept": "application/vnd.citationstyles.csl+json"} response = requests.get(f"https://doi.org/{doi}", headers=headers, allow_redirects=True)
    • Network accessline 49
      response = requests.get(f"https://doi.org/{doi}", headers=headers, allow_redirects=True)
    • Network accessline 49
      response = requests.get(f"https://doi.org/{doi}", headers=headers, allow_redirects=True)
    • Network accessline 62
      # APA format curl -LH "Accept: text/x-bibliography; style=apa" \
    • Network accessline 62
      # APA format curl -LH "Accept: text/x-bibliography; style=apa" \
    • Network accessline 63
      curl -LH "Accept: text/x-bibliography; style=apa" \
    • Network accessline 63
      curl -LH "Accept: text/x-bibliography; style=apa" \
    • Network accessline 64
      https://doi.org/10.1038/s41586-021-03819-2
    • Network accessline 64
      https://doi.org/10.1038/s41586-021-03819-2
    • Network accessline 66
      # Chicago format curl -LH "Accept: text/x-bibliography; style=chicago-author-date" \
    • Network accessline 66
      # Chicago format curl -LH "Accept: text/x-bibliography; style=chicago-author-date" \
    • Network accessline 67
      curl -LH "Accept: text/x-bibliography; style=chicago-author-date" \
    • Network accessline 67
      curl -LH "Accept: text/x-bibliography; style=chicago-author-date" \
    • Network accessline 68
      https://doi.org/10.1038/s41586-021-03819-2
    • Network accessline 68
      https://doi.org/10.1038/s41586-021-03819-2
    • Network accessline 70
      # Harvard format curl -LH "Accept: text/x-bibliography; style=harvard-cite-them-right" \
    • Network accessline 70
      # Harvard format curl -LH "Accept: text/x-bibliography; style=harvard-cite-them-right" \
    • Network accessline 71
      curl -LH "Accept: text/x-bibliography; style=harvard-cite-them-right" \
    • Network accessline 71
      curl -LH "Accept: text/x-bibliography; style=harvard-cite-them-right" \
    • Network accessline 72
      https://doi.org/10.1038/s41586-021-03819-2
    • Network accessline 72
      https://doi.org/10.1038/s41586-021-03819-2
    • Network accessline 78
      curl -LH "Accept: application/x-bibtex" \
    • Network accessline 78
      curl -LH "Accept: application/x-bibtex" \
    • Network accessline 79
      https://doi.org/10.1038/s41586-021-03819-2
    • Network accessline 79
      https://doi.org/10.1038/s41586-021-03819-2
    • Network accessline 105
      doi = "10.1038/s41586-021-03819-2" response = requests.get(
    • Network accessline 105
      doi = "10.1038/s41586-021-03819-2" response = requests.get(
    • Network accessline 106
      response = requests.get(
    • Network accessline 106
      response = requests.get(
    • Network accessline 107
      f"https://api.crossref.org/works/{doi}",
    • Network accessline 107
      f"https://api.crossref.org/works/{doi}",
    • Network accessline 128
      results = [] for doi in dois:     resp = requests.get(
    • Network accessline 128
      results = [] for doi in dois:     resp = requests.get(
    • Network accessline 129
      for doi in dois:     resp = requests.get(         f"https://api.crossref.org/works/{doi}",
    • Network accessline 129
      for doi in dois:     resp = requests.get(         f"https://api.crossref.org/works/{doi}",
    • Network accessline 130
      resp = requests.get(
    • Network accessline 130
      resp = requests.get(
    • Network accessline 131
      f"https://api.crossref.org/works/{doi}",
    • Network accessline 131
      f"https://api.crossref.org/works/{doi}",
    • Network accessline 156
      # Examples normalize_doi("https://doi.org/10.1038/s41586-021-03819-2")  # 10.1038/s41586-021-03819-2
    • Network accessline 156
      # Examples normalize_doi("https://doi.org/10.1038/s41586-021-03819-2")  # 10.1038/s41586-021-03819-2
    • Network accessline 157
      normalize_doi("https://doi.org/10.1038/s41586-021-03819-2")  # 10.1038/s41586-021-03819-2
    • Network accessline 157
      normalize_doi("https://doi.org/10.1038/s41586-021-03819-2")  # 10.1038/s41586-021-03819-2
    • Network accessline 164
      - **Polite pool**: CrossRef provides faster responses to requests with a `User-Agent` header that includes a `mailto:` contact. This is their "polite pool" with higher rate limits. - **OpenAlex alternative**: OpenAlex (https://api.openalex.
    • Network accessline 164
      - **Polite pool**: CrossRef provides faster responses to requests with a `User-Agent` header that includes a `mailto:` contact. This is their "polite pool" with higher rate limits. - **OpenAlex alternative**: OpenAlex (https://api.openalex.
    • Network accessline 165
      - **OpenAlex alternative**: OpenAlex (https://api.openalex.org/works/doi:10.xxx/yyy) provides similar metadata for free, with richer entity linking. - **Handle redirects**: Always use `allow_redirects=True` (or `-L` in curl) as DOIs redirec
    • Network accessline 165
      - **OpenAlex alternative**: OpenAlex (https://api.openalex.org/works/doi:10.xxx/yyy) provides similar metadata for free, with richer entity linking. - **Handle redirects**: Always use `allow_redirects=True` (or `-L` in curl) as DOIs redirec

    skills/literature/metadata/h-index-guide/SKILL.md

    • Network accessline 96
      # Using the OpenAlex API to get journal/source information journal_name = "Nature" response = requests.get(
    • Network accessline 97
      journal_name = "Nature" response = requests.get(     "https://api.openalex.org/sources",
    • Network accessline 98
      response = requests.get(
    • Network accessline 99
      "https://api.openalex.org/sources",
    • Network accessline 121
      # OpenAlex provides h-index directly in author profiles author_name = "Geoffrey Hinton" response = requests.get(
    • Network accessline 122
      author_name = "Geoffrey Hinton" response = requests.get(     "https://api.openalex.org/authors",
    • Network accessline 123
      response = requests.get(
    • Network accessline 124
      "https://api.openalex.org/authors",

    skills/literature/metadata/opencitations-api/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["citation statistics", "citation tracking", "citation analysis", "bibliometrics", "citation network"]     source: "https://opencitations.net/index/api/v1"
    • Network accessline 9
      keywords: ["citation statistics", "citation tracking", "citation analysis", "bibliometrics", "citation network"]     source: "https://opencitations.net/index/api/v1" ---
    • Network accessline 10
      source: "https://opencitations.net/index/api/v1"
    • Network accessline 25
      No authentication required. The OpenCitations API is fully open and free. No API key, registration, or email is needed. There are no published rate limits, but users should implement reasonable request pacing for large-scale queries. For bu
    • Network accessline 31
      - **URL**: `GET https://api.opencitations.net/index/v1/citations/{doi}`
    • Network accessline 39
      curl "https://api.opencitations.net/index/v1/citations/10.1038/nature12373"
    • Network accessline 52
      - **URL**: `GET https://api.opencitations.net/index/v1/references/{doi}`
    • Network accessline 59
      curl "https://api.opencitations.net/index/v1/references/10.1038/nature12373"
    • Network accessline 65
      - **URL**: `GET https://api.opencitations.net/index/v1/metadata/{doi}`
    • Network accessline 72
      curl "https://api.opencitations.net/index/v1/metadata/10.1038/nature12373"
    • Network accessline 78
      - **URL**: `GET https://api.opencitations.net/index/v1/citation-count/{doi}`
    • Network accessline 85
      curl "https://api.opencitations.net/index/v1/citation-count/10.1038/nature12373"
    • Network accessline 100
      # Get all papers citing the target paper curl -s "https://api.opencitations.net/index/v1/citations/10.1145/3292500.3330672" | jq '.[].citing'
    • Network accessline 101
      curl -s "https://api.opencitations.net/index/v1/citations/10.1145/3292500.3330672" | jq '.[].citing'
    • Network accessline 103
      # Get all papers referenced by the target paper curl -s "https://api.opencitations.net/index/v1/references/10.1145/3292500.3330672" | jq '.[].cited'
    • Network accessline 104
      curl -s "https://api.opencitations.net/index/v1/references/10.1145/3292500.3330672" | jq '.[].cited'
    • Network accessline 112
      curl -s "https://api.opencitations.net/index/v1/citations/10.1038/nature12373" | jq '[.[] | select(.author_sc == "no")] | length'
    • Network accessline 120
      # Multiple DOIs separated by double underscore curl -s "https://api.opencitations.net/index/v1/metadata/10.1038/nature12373__10.1126/science.aaa8685__10.1016/j.cell.2015.05.002" | jq '.[] | {doi: .doi, title: .title, citations: .citation_co
    • Network accessline 121
      curl -s "https://api.opencitations.net/index/v1/metadata/10.1038/nature12373__10.1126/science.aaa8685__10.1016/j.cell.2015.05.002" | jq '.[] | {doi: .doi, title: .title, citations: .citation_count}'
    • Network accessline 126
      - Official documentation: https://opencitations.net/index/api/v1 - OpenCitations data model: https://opencitations.net/model - COCI dataset download: https://opencitations.net/download
    • Network accessline 127
      - OpenCitations data model: https://opencitations.net/model
    • Network accessline 128
      - COCI dataset download: https://opencitations.net/download

    skills/literature/metadata/orcid-api/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["researcher ID", "ORCID", "academic identity", "academic metrics"]     source: "https://info.orcid.org/documentation/api-tutorial/"
    • Network accessline 8
      subcategory: "metadata"     keywords: ["researcher ID", "ORCID", "academic identity", "academic metrics"]     source: "https://info.orcid.org/documentation/api-tutorial/"
    • Network accessline 9
      keywords: ["researcher ID", "ORCID", "academic identity", "academic metrics"]     source: "https://info.orcid.org/documentation/api-tutorial/"     requires:
    • Network accessline 9
      keywords: ["researcher ID", "ORCID", "academic identity", "academic metrics"]     source: "https://info.orcid.org/documentation/api-tutorial/"     requires:
    • Network accessline 10
      source: "https://info.orcid.org/documentation/api-tutorial/"
    • Network accessline 10
      source: "https://info.orcid.org/documentation/api-tutorial/"
    • Access to secretsline 12
      [Credential-related source omitted]
    • Access to secretsline 12
      [Credential-related source omitted]
    • Network accessline 27
      [Credential-related source omitted]
    • Network accessline 27
      [Credential-related source omitted]
    • Network accessline 30
      [Credential-related source omitted]
    • Network accessline 30
      [Credential-related source omitted]
    • Access to secretsline 30
      [Credential-related source omitted]
    • Access to secretsline 30
      [Credential-related source omitted]
    • Access to secretsline 33
      [Credential-related source omitted]
    • Access to secretsline 33
      [Credential-related source omitted]
    • Access to secretsline 41
      [Credential-related source omitted]
    • Access to secretsline 41
      [Credential-related source omitted]
    • Network accessline 50
      - **URL**: `GET https://pub.orcid.org/v3.0/{orcid-id}/record`
    • Network accessline 50
      - **URL**: `GET https://pub.orcid.org/v3.0/{orcid-id}/record`
    • Network accessline 58
      [Credential-related source omitted]
    • Network accessline 58
      [Credential-related source omitted]
    • Network accessline 60
      "https://pub.orcid.org/v3.0/0000-0002-1825-0097/record"
    • Network accessline 60
      "https://pub.orcid.org/v3.0/0000-0002-1825-0097/record"
    • Network accessline 66
      - **URL**: `GET https://pub.orcid.org/v3.0/{orcid-id}/works`
    • Network accessline 66
      - **URL**: `GET https://pub.orcid.org/v3.0/{orcid-id}/works`
    • Network accessline 73
      [Credential-related source omitted]
    • Network accessline 73
      [Credential-related source omitted]
    • Network accessline 75
      "https://pub.orcid.org/v3.0/0000-0002-1825-0097/works"
    • Network accessline 75
      "https://pub.orcid.org/v3.0/0000-0002-1825-0097/works"
    • Network accessline 81
      - **URL**: `GET https://pub.orcid.org/v3.0/search`
    • Network accessline 81
      - **URL**: `GET https://pub.orcid.org/v3.0/search`
    • Network accessline 90
      [Credential-related source omitted]
    • Network accessline 90
      [Credential-related source omitted]
    • Network accessline 92
      "https://pub.orcid.org/v3.0/search?q=family-name:Hinton+AND+affiliation-org-name:Toronto&rows=10"
    • Network accessline 92
      "https://pub.orcid.org/v3.0/search?q=family-name:Hinton+AND+affiliation-org-name:Toronto&rows=10"
    • Network accessline 107
      [Credential-related source omitted]
    • Network accessline 107
      [Credential-related source omitted]
    • Network accessline 109
      "https://pub.orcid.org/v3.0/0000-0001-5109-3700/person"
    • Network accessline 109
      "https://pub.orcid.org/v3.0/0000-0001-5109-3700/person"
    • Network accessline 117
      [Credential-related source omitted]
    • Network accessline 117
      [Credential-related source omitted]
    • Network accessline 119
      "https://pub.orcid.org/v3.0/0000-0002-1825-0097/works" | jq '.group[].work-summary[0] | {title: .title.title.value, doi: (.["external-ids"]["external-id"][] | select(.["external-id-type"] == "doi") | .["external-id-value"])}'
    • Network accessline 119
      "https://pub.orcid.org/v3.0/0000-0002-1825-0097/works" | jq '.group[].work-summary[0] | {title: .title.title.value, doi: (.["external-ids"]["external-id"][] | select(.["external-id-type"] == "doi") | .["external-id-value"])}'
    • Network accessline 127
      [Credential-related source omitted]
    • Network accessline 127
      [Credential-related source omitted]
    • Network accessline 129
      "https://pub.orcid.org/v3.0/search?q=affiliation-org-name:Stanford+AND+current-institution-affiliation-name:Stanford&rows=50"
    • Network accessline 129
      "https://pub.orcid.org/v3.0/search?q=affiliation-org-name:Stanford+AND+current-institution-affiliation-name:Stanford&rows=50"
    • Network accessline 134
      - Official documentation: https://info.orcid.org/documentation/api-tutorial/
    • Network accessline 134
      - Official documentation: https://info.orcid.org/documentation/api-tutorial/
    • Network accessline 135
      - API reference: https://pub.orcid.org/v3.0/
    • Network accessline 135
      - API reference: https://pub.orcid.org/v3.0/
    • Network accessline 136
      - ORCID integration guide: https://info.orcid.org/documentation/integration-guide/
    • Network accessline 136
      - ORCID integration guide: https://info.orcid.org/documentation/integration-guide/

    skills/literature/metadata/orcid-integration-guide/SKILL.md

    • Network accessline 146
      orcid_id: The ORCID iD (e.g., '0000-0002-1825-0097')     """     url = f"https://pub.orcid.org/v3.0/{orcid_id}/works"
    • Network accessline 146
      orcid_id: The ORCID iD (e.g., '0000-0002-1825-0097')     """     url = f"https://pub.orcid.org/v3.0/{orcid_id}/works"
    • Network accessline 147
      """     url = f"https://pub.orcid.org/v3.0/{orcid_id}/works"     req = urllib.request.Request(url, headers={
    • Network accessline 147
      """     url = f"https://pub.orcid.org/v3.0/{orcid_id}/works"     req = urllib.request.Request(url, headers={
    • Network accessline 148
      url = f"https://pub.orcid.org/v3.0/{orcid_id}/works"     req = urllib.request.Request(url, headers={         "Accept": "application/json"
    • Network accessline 148
      url = f"https://pub.orcid.org/v3.0/{orcid_id}/works"     req = urllib.request.Request(url, headers={         "Accept": "application/json"
    • Network accessline 149
      req = urllib.request.Request(url, headers={
    • Network accessline 149
      req = urllib.request.Request(url, headers={
    • Network accessline 150
      "Accept": "application/json"     })     response = urllib.request.urlopen(req)
    • Network accessline 150
      "Accept": "application/json"     })     response = urllib.request.urlopen(req)
    • Network accessline 151
      })     response = urllib.request.urlopen(req)     data = json.loads(response.read())
    • Network accessline 151
      })     response = urllib.request.urlopen(req)     data = json.loads(response.read())
    • Network accessline 152
      response = urllib.request.urlopen(req)
    • Network accessline 152
      response = urllib.request.urlopen(req)
    • Network accessline 176
      - Include peer review activity (via Publons/Web of Science integration) - Use your ORCID iD in email signatures, CVs, and personal websites - Format as a full URL: https://orcid.org/0000-0002-1825-0097
    • Network accessline 176
      - Include peer review activity (via Publons/Web of Science integration) - Use your ORCID iD in email signatures, CVs, and personal websites - Format as a full URL: https://orcid.org/0000-0002-1825-0097
    • Network accessline 178
      - Format as a full URL: https://orcid.org/0000-0002-1825-0097
    • Network accessline 178
      - Format as a full URL: https://orcid.org/0000-0002-1825-0097

    skills/literature/metadata/orkg-api/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["knowledge graph", "research data", "structured research", "ORKG", "research contributions", "scholarly graph"]     source: "https://orkg.org/"
    • Network accessline 9
      keywords: ["knowledge graph", "research data", "structured research", "ORKG", "research contributions", "scholarly graph"]     source: "https://orkg.org/" ---
    • Network accessline 10
      source: "https://orkg.org/"
    • Network accessline 24
      https://orkg.org/api/
    • Network accessline 30
      # Search papers in ORKG curl "https://orkg.org/api/papers?q=climate+change+adaptation&size=20"
    • Network accessline 31
      curl "https://orkg.org/api/papers?q=climate+change+adaptation&size=20"
    • Network accessline 33
      # Get paper details by ID curl "https://orkg.org/api/papers/R12345"
    • Network accessline 34
      curl "https://orkg.org/api/papers/R12345"
    • Network accessline 40
      # Search any resource (papers, predicates, comparisons) curl "https://orkg.org/api/resources?q=machine+learning&size=20"
    • Network accessline 41
      curl "https://orkg.org/api/resources?q=machine+learning&size=20"
    • Network accessline 43
      # Filter by class curl "https://orkg.org/api/resources?q=BERT&exact=false&classes=Paper"
    • Network accessline 44
      curl "https://orkg.org/api/resources?q=BERT&exact=false&classes=Paper"
    • Network accessline 52
      # List comparisons curl "https://orkg.org/api/comparisons?size=10"
    • Network accessline 53
      curl "https://orkg.org/api/comparisons?size=10"
    • Network accessline 55
      # Get a specific comparison curl "https://orkg.org/api/comparisons/R54321"
    • Network accessline 56
      curl "https://orkg.org/api/comparisons/R54321"
    • Network accessline 58
      # Search comparisons curl "https://orkg.org/api/comparisons?q=sentiment+analysis"
    • Network accessline 59
      curl "https://orkg.org/api/comparisons?q=sentiment+analysis"
    • Network accessline 65
      # Get contributions of a paper curl "https://orkg.org/api/papers/R12345/contributions"
    • Network accessline 66
      curl "https://orkg.org/api/papers/R12345/contributions"
    • Network accessline 80
      BASE_URL = "https://orkg.org/api"
    • Network accessline 82
      def search_orkg_papers(query: str, size: int = 20) -> list:     """Search papers in the Open Research Knowledge Graph."""     resp = requests.get(f"{BASE_URL}/papers", params={"q": query, "size": size})
    • Network accessline 83
      """Search papers in the Open Research Knowledge Graph."""     resp = requests.get(f"{BASE_URL}/papers", params={"q": query, "size": size})     resp.raise_for_status()
    • Network accessline 84
      resp = requests.get(f"{BASE_URL}/papers", params={"q": query, "size": size})
    • Network accessline 98
      def get_paper_contributions(paper_id: str) -> dict:     """Get structured research contributions for a paper."""     resp = requests.get(f"{BASE_URL}/papers/{paper_id}/contributions")
    • Network accessline 99
      """Get structured research contributions for a paper."""     resp = requests.get(f"{BASE_URL}/papers/{paper_id}/contributions")     resp.raise_for_status()
    • Network accessline 100
      resp = requests.get(f"{BASE_URL}/papers/{paper_id}/contributions")
    • Network accessline 104
      def search_comparisons(topic: str) -> list:     """Find structured paper comparisons on a topic."""     resp = requests.get(f"{BASE_URL}/comparisons", params={"q": topic, "size": 10})
    • Network accessline 105
      """Find structured paper comparisons on a topic."""     resp = requests.get(f"{BASE_URL}/comparisons", params={"q": topic, "size": 10})     resp.raise_for_status()
    • Network accessline 106
      resp = requests.get(f"{BASE_URL}/comparisons", params={"q": topic, "size": 10})
    • Network accessline 150
      - [ORKG Website](https://orkg.org/)
    • Network accessline 151
      - [ORKG API Documentation](https://orkg.org/api/)
    • Network accessline 152
      - [ORKG Help Center](https://orkg.org/help-center)

    skills/literature/metadata/plumx-metrics-api/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["PlumX", "altmetrics", "research impact", "social media metrics", "usage statistics", "scholarly metrics"]     source: "https://plumanalytics.com/"
    • Network accessline 9
      keywords: ["PlumX", "altmetrics", "research impact", "social media metrics", "usage statistics", "scholarly metrics"]     source: "https://plumanalytics.com/" ---
    • Network accessline 10
      source: "https://plumanalytics.com/"
    • Network accessline 34
      https://api.elsevier.com/analytics/plumx/
    • Network accessline 40
      [Credential-related source omitted]
    • Access to secretsline 40
      [Credential-related source omitted]
    • Network accessline 41
      "https://api.elsevier.com/analytics/plumx/doi/10.1038/nature14539"
    • Network accessline 47
      [Credential-related source omitted]
    • Network accessline 48
      [Credential-related source omitted]
    • Access to secretsline 48
      [Credential-related source omitted]
    • Network accessline 49
      "https://api.elsevier.com/analytics/plumx/pmid/25428114"
    • Network accessline 51
      [Credential-related source omitted]
    • Network accessline 52
      [Credential-related source omitted]
    • Access to secretsline 52
      [Credential-related source omitted]
    • Network accessline 53
      "https://api.elsevier.com/analytics/plumx/isbn/9780262035613"
    • Network accessline 55
      [Credential-related source omitted]
    • Network accessline 56
      [Credential-related source omitted]
    • Access to secretsline 56
      [Credential-related source omitted]
    • Network accessline 57
      "https://api.elsevier.com/analytics/plumx/scopusId/84920765826"
    • Network accessline 117
      [Credential-related source omitted]
    • Access to secretsline 117
      [Credential-related source omitted]
    • Network accessline 118
      BASE_URL = "https://api.elsevier.com/analytics/plumx"
    • Access to secretsline 119
      [Credential-related source omitted]
    • Network accessline 122
      def get_plumx_metrics(doi: str) -> dict:     """Get PlumX metrics for a paper by DOI."""     resp = requests.get(
    • Network accessline 123
      """Get PlumX metrics for a paper by DOI."""     resp = requests.get(         f"{BASE_URL}/doi/{doi}",
    • Network accessline 124
      resp = requests.get(
    • Network accessline 186
      - [PlumX Metrics](https://plumanalytics.com/learn/about-metrics/)
    • Network accessline 187
      - [Elsevier Developer Portal](https://dev.elsevier.com/)
    • Network accessline 188
      - [PlumX API Documentation](https://dev.elsevier.com/documentation/PlumXMetricsAPI.wadl)

    skills/literature/metadata/ror-organization-api/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["ROR", "research organizations", "institution registry", "affiliation", "organization identifiers", "ISNI"]     source: "https://ror.org/"
    • Network accessline 9
      keywords: ["ROR", "research organizations", "institution registry", "affiliation", "organization identifiers", "ISNI"]     source: "https://ror.org/" ---
    • Network accessline 10
      source: "https://ror.org/"
    • Network accessline 24
      https://api.ror.org/v2
    • Network accessline 30
      # Text search curl "https://api.ror.org/v2/organizations?query=MIT"
    • Network accessline 31
      curl "https://api.ror.org/v2/organizations?query=MIT"
    • Network accessline 33
      # Affiliation matching (fuzzy match for messy affiliation strings) curl "https://api.ror.org/v2/organizations?affiliation=Dept+of+CS,+Massachusetts+Inst+of+Technology"
    • Network accessline 34
      curl "https://api.ror.org/v2/organizations?affiliation=Dept+of+CS,+Massachusetts+Inst+of+Technology"
    • Network accessline 36
      # Filter by country curl "https://api.ror.org/v2/organizations?query=university&filter=locations.geonames_details.country_code:US"
    • Network accessline 37
      curl "https://api.ror.org/v2/organizations?query=university&filter=locations.geonames_details.country_code:US"
    • Network accessline 39
      # Filter by organization type curl "https://api.ror.org/v2/organizations?query=research&filter=types:facility"
    • Network accessline 40
      curl "https://api.ror.org/v2/organizations?query=research&filter=types:facility"
    • Network accessline 46
      # Retrieve full record curl "https://api.ror.org/v2/organizations/https://ror.org/042nb2s44"
    • Network accessline 47
      curl "https://api.ror.org/v2/organizations/https://ror.org/042nb2s44"
    • Network accessline 49
      # Also works with just the ID portion curl "https://api.ror.org/v2/organizations/042nb2s44"
    • Network accessline 50
      curl "https://api.ror.org/v2/organizations/042nb2s44"
    • Network accessline 80
      "items": [     {       "id": "https://ror.org/042nb2s44",
    • Network accessline 81
      {       "id": "https://ror.org/042nb2s44",       "names": [
    • Network accessline 82
      "id": "https://ror.org/042nb2s44",
    • Network accessline 100
      {"type": "wikidata", "all": ["Q49108"]}       ],       "links": [{"type": "website", "value": "https://www.mit.edu/"}],
    • Network accessline 101
      ],       "links": [{"type": "website", "value": "https://www.mit.edu/"}],       "relationships": [
    • Network accessline 102
      "links": [{"type": "website", "value": "https://www.mit.edu/"}],
    • Network accessline 103
      "relationships": [         {"id": "https://ror.org/01a8ajp77", "label": "Lincoln Laboratory", "type": "child"}       ],
    • Network accessline 104
      {"id": "https://ror.org/01a8ajp77", "label": "Lincoln Laboratory", "type": "child"}
    • Network accessline 118
      BASE_URL = "https://api.ror.org/v2/organizations"
    • Network accessline 135
      resp = requests.get(BASE_URL, params=params)
    • Network accessline 162
      def match_affiliation(affiliation_string: str) -> dict:     """Disambiguate a messy affiliation string to a ROR record."""     resp = requests.get(
    • Network accessline 163
      """Disambiguate a messy affiliation string to a ROR record."""     resp = requests.get(         BASE_URL,
    • Network accessline 164
      resp = requests.get(
    • Network accessline 175
      def get_organization(ror_id: str) -> dict:     """Get full ROR record for an organization."""     resp = requests.get(f"{BASE_URL}/{ror_id}")
    • Network accessline 176
      """Get full ROR record for an organization."""     resp = requests.get(f"{BASE_URL}/{ror_id}")     resp.raise_for_status()
    • Network accessline 177
      resp = requests.get(f"{BASE_URL}/{ror_id}")
    • Network accessline 206
      - [ROR](https://ror.org/)
    • Network accessline 207
      - [ROR API Documentation](https://ror.readme.io/)
    • Network accessline 208
      - [ROR Data Dump](https://doi.org/10.5281/zenodo.6347574)

    skills/literature/metadata/sophosia-reference-guide/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["reference manager", "PDF viewer", "Markdown notes", "Excalidraw", "paper organization", "open source"]     source: "https://github.com/sophosia/sophosia"
    • Network accessline 9
      keywords: ["reference manager", "PDF viewer", "Markdown notes", "Excalidraw", "paper organization", "open source"]     source: "https://github.com/sophosia/sophosia" ---
    • Network accessline 10
      source: "https://github.com/sophosia/sophosia"
    • Network accessline 22
      # Download from GitHub releases (Windows/macOS/Linux) # Or build from source: git clone https://github.com/sophosia/sophosia.git
    • Network accessline 23
      # Or build from source: git clone https://github.com/sophosia/sophosia.git cd sophosia
    • Network accessline 24
      git clone https://github.com/sophosia/sophosia.git
    • Network accessline 109
      - [Sophosia GitHub](https://github.com/sophosia/sophosia)
    • Network accessline 110
      - [Excalidraw](https://excalidraw.com/)

    skills/literature/metadata/viaf-authority-api/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["VIAF", "authority control", "author disambiguation", "name authority", "OCLC", "library catalog"]     source: "https://viaf.org/"
    • Network accessline 9
      keywords: ["VIAF", "authority control", "author disambiguation", "name authority", "OCLC", "library catalog"]     source: "https://viaf.org/" ---
    • Network accessline 10
      source: "https://viaf.org/"
    • Network accessline 24
      https://viaf.org
    • Network accessline 30
      # Search by name (AutoSuggest) curl "https://viaf.org/viaf/AutoSuggest?query=einstein+albert"
    • Network accessline 31
      curl "https://viaf.org/viaf/AutoSuggest?query=einstein+albert"
    • Network accessline 33
      # Search via SRU (structured query) curl "https://viaf.org/viaf/search?query=local.personalNames+all+\"hinton+geoffrey\"&\
    • Network accessline 34
      curl "https://viaf.org/viaf/search?query=local.personalNames+all+\"hinton+geoffrey\"&\
    • Network accessline 37
      # Search corporate names curl "https://viaf.org/viaf/search?query=local.corporateNames+all+\"MIT\"&\
    • Network accessline 38
      curl "https://viaf.org/viaf/search?query=local.corporateNames+all+\"MIT\"&\
    • Network accessline 45
      # JSON format curl "https://viaf.org/viaf/75121530/viaf.json"
    • Network accessline 46
      curl "https://viaf.org/viaf/75121530/viaf.json"
    • Network accessline 48
      # Linked data formats curl -H "Accept: application/json" "https://viaf.org/viaf/75121530"
    • Network accessline 49
      curl -H "Accept: application/json" "https://viaf.org/viaf/75121530"
    • Network accessline 51
      # Cluster data (all linked identities) curl "https://viaf.org/viaf/75121530/justlinks.json"
    • Network accessline 52
      curl "https://viaf.org/viaf/75121530/justlinks.json"
    • Network accessline 58
      # Look up by Library of Congress ID curl "https://viaf.org/viaf/lccn/n79021164/viaf.json"
    • Network accessline 59
      curl "https://viaf.org/viaf/lccn/n79021164/viaf.json"
    • Network accessline 61
      # Look up by ISNI curl "https://viaf.org/viaf/isni/0000000121174331/viaf.json"
    • Network accessline 62
      curl "https://viaf.org/viaf/isni/0000000121174331/viaf.json"
    • Network accessline 64
      # Look up by ORCID curl "https://viaf.org/viaf/sourceID/ORCID|0000-0002-1825-0097/viaf.json"
    • Network accessline 65
      curl "https://viaf.org/viaf/sourceID/ORCID|0000-0002-1825-0097/viaf.json"
    • Network accessline 67
      # Look up by Wikidata QID curl "https://viaf.org/viaf/sourceID/WKP|Q937/viaf.json"
    • Network accessline 68
      curl "https://viaf.org/viaf/sourceID/WKP|Q937/viaf.json"
    • Network accessline 119
      BASE_URL = "https://viaf.org/viaf"
    • Network accessline 122
      def search_person(name: str, limit: int = 10) -> list:     """Search VIAF for personal name authorities."""     resp = requests.get(
    • Network accessline 123
      """Search VIAF for personal name authorities."""     resp = requests.get(         f"{BASE_URL}/AutoSuggest",
    • Network accessline 124
      resp = requests.get(
    • Network accessline 142
      def get_authority(viaf_id: str) -> dict:     """Get full VIAF authority record."""     resp = requests.get(f"{BASE_URL}/{viaf_id}/viaf.json")
    • Network accessline 143
      """Get full VIAF authority record."""     resp = requests.get(f"{BASE_URL}/{viaf_id}/viaf.json")     resp.raise_for_status()
    • Network accessline 144
      resp = requests.get(f"{BASE_URL}/{viaf_id}/viaf.json")
    • Network accessline 172
      def resolve_by_orcid(orcid: str) -> dict:     """Resolve ORCID to VIAF authority record."""     resp = requests.get(
    • Network accessline 173
      """Resolve ORCID to VIAF authority record."""     resp = requests.get(         f"{BASE_URL}/sourceID/ORCID|{orcid}/viaf.json"
    • Network accessline 174
      resp = requests.get(
    • Network accessline 207
      - [VIAF](https://viaf.org/)
    • Network accessline 208
      - [VIAF API Documentation](https://www.oclc.org/developer/api/oclc-apis/viaf.en.html)
    • Network accessline 209
      - [VIAF Guidelines](https://www.oclc.org/research/activities/viaf.html)

    skills/literature/metadata/wikidata-api-guide/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["wikidata", "sparql", "linked-data", "metadata", "knowledge-graph", "scholarly"]     source: "https://www.wikidata.org/wiki/Wikidata:SPARQL_query_service"
    • Network accessline 9
      keywords: ["wikidata", "sparql", "linked-data", "metadata", "knowledge-graph", "scholarly"]     source: "https://www.wikidata.org/wiki/Wikidata:SPARQL_query_service" ---
    • Network accessline 10
      source: "https://www.wikidata.org/wiki/Wikidata:SPARQL_query_service"
    • Network accessline 28
      # No API key needed -- set a descriptive User-Agent header as courtesy curl -G "https://query.wikidata.org/sparql" \
    • Network accessline 29
      curl -G "https://query.wikidata.org/sparql" \
    • Network accessline 40
      GET https://query.wikidata.org/sparql?query={SPARQL}&format=json
    • Network accessline 50
      curl -G "https://query.wikidata.org/sparql" \
    • Network accessline 81
      SPARQL_URL = "https://query.wikidata.org/sparql"
    • Network accessline 87
      def query_wikidata(sparql_query):     """Execute a SPARQL query against Wikidata."""     resp = requests.get(
    • Network accessline 88
      """Execute a SPARQL query against Wikidata."""     resp = requests.get(         SPARQL_URL,
    • Network accessline 89
      resp = requests.get(
    • Network accessline 153
      - Wikidata SPARQL Query Service: https://query.wikidata.org/
    • Network accessline 154
      - Wikidata SPARQL Tutorial: https://www.wikidata.org/wiki/Wikidata:SPARQL_tutorial
    • Network accessline 155
      - Wikidata Properties for Scholarly Articles: https://www.wikidata.org/wiki/Wikidata:WikiProject_Source_MetaData
    • Network accessline 156
      - Wikidata REST API: https://www.wikidata.org/wiki/Wikidata:REST_API

    skills/literature/metadata/zoplicate-dedup-guide/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["Zotero", "deduplication", "duplicate detection", "library cleanup", "metadata merge"]     source: "https://github.com/ChenglongMa/zoplicate"
    • Network accessline 9
      keywords: ["Zotero", "deduplication", "duplicate detection", "library cleanup", "metadata merge"]     source: "https://github.com/ChenglongMa/zoplicate" ---
    • Network accessline 10
      source: "https://github.com/ChenglongMa/zoplicate"
    • Network accessline 146
      - [Zoplicate GitHub](https://github.com/ChenglongMa/zoplicate)
    • Network accessline 147
      - [Zotero Duplicate Detection](https://www.zotero.org/support/duplicate_detection)

    skills/literature/metadata/zotero-actions-tags-guide/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["Zotero", "automation", "tags", "workflow", "actions", "productivity"]     source: "https://github.com/windingwind/zotero-actions-tags"
    • Network accessline 9
      keywords: ["Zotero", "automation", "tags", "workflow", "actions", "productivity"]     source: "https://github.com/windingwind/zotero-actions-tags" ---
    • Network accessline 10
      source: "https://github.com/windingwind/zotero-actions-tags"
    • Network accessline 210
      - [Zotero Actions & Tags GitHub](https://github.com/windingwind/zotero-actions-tags)
    • Network accessline 211
      - [Zotero JavaScript API](https://www.zotero.org/support/dev/client_coding/javascript_api)
    • Network accessline 212
      - [Zotero Plugin Development](https://www.zotero.org/support/dev/client_coding/plugin_development)

    skills/literature/metadata/zotmoov-guide/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["Zotero", "file management", "attachment", "auto-move", "organization", "linked files"]     source: "https://github.com/wileyyugioh/zotmoov"
    • Network accessline 9
      keywords: ["Zotero", "file management", "attachment", "auto-move", "organization", "linked files"]     source: "https://github.com/wileyyugioh/zotmoov" ---
    • Network accessline 10
      source: "https://github.com/wileyyugioh/zotmoov"
    • Network accessline 119
      - [ZotMoov GitHub](https://github.com/wileyyugioh/zotmoov)
    • Network accessline 120
      - [Zotero Linked Files](https://www.zotero.org/support/attaching_files)

    skills/literature/metadata/zutilo-guide/SKILL.md

    • Network accessline 8
      subcategory: "metadata"     keywords: ["Zotero", "shortcuts", "batch editing", "utility", "productivity", "copy paste"]     source: "https://github.com/wshanks/Zutilo"
    • Network accessline 9
      keywords: ["Zotero", "shortcuts", "batch editing", "utility", "productivity", "copy paste"]     source: "https://github.com/wshanks/Zutilo" ---
    • Network accessline 10
      source: "https://github.com/wshanks/Zutilo"
    • Network accessline 139
      - [Zutilo GitHub](https://github.com/wshanks/Zutilo)
    • Network accessline 140
      - [Zotero Keyboard Shortcuts](https://www.zotero.org/support/kb)

    skills/literature/search/arxiv-api/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["academic database search", "literature search", "scholarly database", "semantic search", "preprint server"]     source: "https://info.arxiv.org/help/api/"
    • Network accessline 9
      keywords: ["academic database search", "literature search", "scholarly database", "semantic search", "preprint server"]     source: "https://info.arxiv.org/help/api/" ---
    • Network accessline 10
      source: "https://info.arxiv.org/help/api/"
    • Network accessline 40
      - **URL**: `GET http://export.arxiv.org/api/query`
    • Network accessline 52
      curl "http://export.arxiv.org/api/query?search_query=au:hinton+AND+ti:deep+learning&start=0&max_results=5&sortBy=submittedDate&sortOrder=descending"
    • Network accessline 58
      - **URL**: `GET http://export.arxiv.org/api/query`
    • Network accessline 66
      curl "http://export.arxiv.org/api/query?id_list=2301.07041&max_results=1"
    • Network accessline 81
      curl "http://export.arxiv.org/api/query?search_query=cat:cs.AI+AND+submittedDate:[202603010000+TO+202603092359]&sortBy=submittedDate&sortOrder=descending&max_results=50"
    • Network accessline 89
      curl "http://export.arxiv.org/api/query?search_query=(ti:transformer+OR+abs:transformer)+AND+cat:cs.CL&max_results=20&sortBy=relevance"
    • Network accessline 97
      curl "http://export.arxiv.org/api/query?id_list=2301.07041,2302.13971,2303.08774&max_results=3"
    • Network accessline 102
      - Official documentation: https://info.arxiv.org/help/api/
    • Network accessline 103
      - arXiv API user manual: https://info.arxiv.org/help/api/user-manual.html
    • Network accessline 104
      - arXiv bulk data access: https://info.arxiv.org/help/bulk_data.html

    skills/literature/search/arxiv-batch-reporting/SKILL.md

    • Network accessline 131
      - arXiv API documentation: https://info.arxiv.org/help/api/index.html
    • Network accessline 132
      - arXiv category taxonomy: https://arxiv.org/category_taxonomy

    skills/literature/search/arxiv-cli-tools/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["arxiv", "command line", "paper download", "preprint search", "batch download", "literature retrieval"]     source: "https://pypi.org/project/arxiv-cli-tools/"
    • Network accessline 9
      keywords: ["arxiv", "command line", "paper download", "preprint search", "batch download", "literature retrieval"]     source: "https://pypi.org/project/arxiv-cli-tools/" ---
    • Network accessline 10
      source: "https://pypi.org/project/arxiv-cli-tools/"
    • Network accessline 156
      # Get BibTeX for a specific paper curl -s "https://arxiv.org/bibtex/1706.03762"
    • Network accessline 157
      curl -s "https://arxiv.org/bibtex/1706.03762"
    • Network accessline 163
      - For bulk downloads, add delays between requests - The CLI tool respects rate limits by default - See [arXiv API Terms of Use](https://info.arxiv.org/help/api/tou.html)
    • Network accessline 165
      - See [arXiv API Terms of Use](https://info.arxiv.org/help/api/tou.html)
    • Network accessline 169
      - [arxiv-cli-tools on PyPI](https://pypi.org/project/arxiv-cli-tools/)
    • Network accessline 170
      - [arxiv Python Client](https://github.com/lukasschwab/arxiv.py)
    • Network accessline 171
      - [arXiv API Documentation](https://info.arxiv.org/help/api/)
    • Network accessline 172
      - [arXiv Category Taxonomy](https://arxiv.org/category_taxonomy)

    skills/literature/search/arxiv-paper-processor/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["arxiv", "paper processing", "PDF parsing", "metadata extraction", "preprint analysis", "research pipeline"]     source: "https://github.com/tatsu-lab/gpt_paper_assistant"
    • Network accessline 9
      keywords: ["arxiv", "paper processing", "PDF parsing", "metadata extraction", "preprint analysis", "research pipeline"]     source: "https://github.com/tatsu-lab/gpt_paper_assistant" ---
    • Network accessline 10
      source: "https://github.com/tatsu-lab/gpt_paper_assistant"
    • Network accessline 33
      # Fetch metadata via Atom feed arxiv_id = "2301.07041" url = f"http://export.arxiv.org/api/query?id_list={arxiv_id}"
    • Network accessline 34
      arxiv_id = "2301.07041" url = f"http://export.arxiv.org/api/query?id_list={arxiv_id}" response = urllib.request.urlopen(url)
    • Network accessline 35
      url = f"http://export.arxiv.org/api/query?id_list={arxiv_id}" response = urllib.request.urlopen(url) feed = feedparser.parse(response.read())
    • Network accessline 36
      response = urllib.request.urlopen(url)
    • Network accessline 51
      # Download LaTeX source (typically a .tar.gz) wget https://arxiv.org/e-print/2301.07041 -O paper_source.tar.gz
    • Network accessline 52
      wget https://arxiv.org/e-print/2301.07041 -O paper_source.tar.gz
    • Network accessline 77
      # Process a PDF curl -X POST "http://localhost:8070/api/processFulltextDocument" \
    • Network accessline 78
      curl -X POST "http://localhost:8070/api/processFulltextDocument" \
    • Network accessline 138
      - arXiv API: https://info.arxiv.org/help/api/index.html
    • Network accessline 139
      - GROBID: https://github.com/kermitt2/grobid
    • Network accessline 140
      - GPT Paper Assistant: https://github.com/tatsu-lab/gpt_paper_assistant
    • Network accessline 141
      - arXiv bulk data access: https://info.arxiv.org/help/bulk_data/index.html

    skills/literature/search/baidu-scholar-guide/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["baidu scholar", "chinese literature", "academic search", "CNKI", "bilingual research", "chinese journals"]     source: "https://xueshu.baidu.com"
    • Network accessline 9
      keywords: ["baidu scholar", "chinese literature", "academic search", "CNKI", "bilingual research", "chinese journals"]     source: "https://xueshu.baidu.com" ---
    • Network accessline 10
      source: "https://xueshu.baidu.com"
    • Network accessline 27
      Navigate to `https://xueshu.baidu.com` and enter your search terms. Baidu Scholar supports both Chinese and English queries. For bilingual research, run parallel searches:
    • Network accessline 107
      - Baidu Scholar: https://xueshu.baidu.com
    • Network accessline 108
      - CNKI: https://www.cnki.net
    • Network accessline 109
      - ChinaXiv: https://chinaxiv.org
    • Network accessline 110
      - GB/T 7714-2015 citation standard: https://std.samr.gov.cn

    skills/literature/search/base-academic-search/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["BASE", "academic search", "open access", "Bielefeld", "OAI-PMH", "repository aggregator"]     source: "https://www.base-search.net/"
    • Network accessline 9
      keywords: ["BASE", "academic search", "open access", "Bielefeld", "OAI-PMH", "repository aggregator"]     source: "https://www.base-search.net/" ---
    • Network accessline 10
      source: "https://www.base-search.net/"
    • Network accessline 24
      https://api.base-search.net/cgi-bin/BaseHttpSearchInterface.fcgi
    • Network accessline 30
      # Basic keyword search (JSON response) curl "https://api.base-search.net/cgi-bin/BaseHttpSearchInterface.fcgi?\
    • Network accessline 31
      curl "https://api.base-search.net/cgi-bin/BaseHttpSearchInterface.fcgi?\
    • Network accessline 34
      # Search with field filters curl "https://api.base-search.net/cgi-bin/BaseHttpSearchInterface.fcgi?\
    • Network accessline 35
      curl "https://api.base-search.net/cgi-bin/BaseHttpSearchInterface.fcgi?\
    • Network accessline 38
      # Filter by document type and year curl "https://api.base-search.net/cgi-bin/BaseHttpSearchInterface.fcgi?\
    • Network accessline 39
      curl "https://api.base-search.net/cgi-bin/BaseHttpSearchInterface.fcgi?\
    • Network accessline 42
      # Open access only curl "https://api.base-search.net/cgi-bin/BaseHttpSearchInterface.fcgi?\
    • Network accessline 43
      curl "https://api.base-search.net/cgi-bin/BaseHttpSearchInterface.fcgi?\
    • Network accessline 98
      "dcsubject": ["machine learning", "attention mechanism"],         "dcdescription": "The dominant sequence transduction models...",         "dcidentifier": "https://arxiv.org/abs/1706.03762",
    • Network accessline 99
      "dcdescription": "The dominant sequence transduction models...",         "dcidentifier": "https://arxiv.org/abs/1706.03762",         "dcsource": "arXiv.org",
    • Network accessline 100
      "dcidentifier": "https://arxiv.org/abs/1706.03762",
    • Network accessline 118
      BASE_URL = "https://api.base-search.net/cgi-bin/BaseHttpSearchInterface.fcgi"
    • Network accessline 138
      resp = requests.get(BASE_URL, params=params)
    • Network accessline 194
      - [BASE Search Engine](https://www.base-search.net/)
    • Network accessline 195
      - [BASE API Documentation](https://www.base-search.net/about/en/about_develop.php)
    • Network accessline 196
      - [BASE Content Providers](https://www.base-search.net/about/en/about_sources.php)

    skills/literature/search/biorxiv-api/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["preprint server", "literature search", "academic database search", "full-text retrieval"]     source: "https://api.biorxiv.org/"
    • Network accessline 9
      keywords: ["preprint server", "literature search", "academic database search", "full-text retrieval"]     source: "https://api.biorxiv.org/" ---
    • Network accessline 10
      source: "https://api.biorxiv.org/"
    • Network accessline 33
      - **URL**: `GET https://api.biorxiv.org/details/{server}/{interval}/{cursor}`
    • Network accessline 45
      curl "https://api.biorxiv.org/details/biorxiv/2024-01-01/2024-01-31/0"
    • Network accessline 54
      - **URL**: `GET https://api.biorxiv.org/pubs/{server}/{interval}/{cursor}`
    • Network accessline 66
      curl "https://api.biorxiv.org/pubs/biorxiv/2024-01-01/2024-06-30/0"
    • Network accessline 82
      # Fetch recent neuroscience preprints curl "https://api.biorxiv.org/details/biorxiv/2024-06-01/2024-06-07/0" \
    • Network accessline 83
      curl "https://api.biorxiv.org/details/biorxiv/2024-06-01/2024-06-07/0" \
    • Network accessline 92
      # Check publication status for recent preprints curl "https://api.biorxiv.org/pubs/biorxiv/2024-01-01/2024-06-30/0" \
    • Network accessline 93
      curl "https://api.biorxiv.org/pubs/biorxiv/2024-01-01/2024-06-30/0" \
    • Network accessline 104
      base = "https://api.biorxiv.org/details/biorxiv/2024-06-01/2024-06-07"
    • Network accessline 108
      while True:     resp = requests.get(f"{base}/{cursor}").json()
    • Network accessline 109
      resp = requests.get(f"{base}/{cursor}").json()
    • Network accessline 121
      - Official documentation: https://api.biorxiv.org/
    • Network accessline 122
      - bioRxiv homepage: https://www.biorxiv.org/
    • Network accessline 123
      - medRxiv API (same structure): https://api.biorxiv.org/ (use `medrxiv` as server parameter)

    skills/literature/search/chatpaper-guide/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["arxiv", "paper-summarization", "literature-search", "chatgpt", "research-acceleration"]     source: "https://github.com/kaixindelele/ChatPaper"
    • Network accessline 9
      keywords: ["arxiv", "paper-summarization", "literature-search", "chatgpt", "research-acceleration"]     source: "https://github.com/kaixindelele/ChatPaper" ---
    • Network accessline 10
      source: "https://github.com/kaixindelele/ChatPaper"
    • Network accessline 28
      git clone https://github.com/kaixindelele/ChatPaper.git
    • Access to secretsline 37
      [Credential-related source omitted]
    • Network accessline 120
      - ChatPaper repository: https://github.com/kaixindelele/ChatPaper
    • Network accessline 121
      - arXiv API documentation: https://info.arxiv.org/help/api/

    skills/literature/search/citation-chaining-guide/SKILL.md

    • Network accessline 43
      HEADERS = {"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"}
    • Network accessline 45
      def get_references(work_id):     """Get all references of a paper via OpenAlex."""     url = f"https://api.openalex.org/works/{work_id}"
    • Network accessline 46
      """Get all references of a paper via OpenAlex."""     url = f"https://api.openalex.org/works/{work_id}"     response = requests.get(url, headers=HEADERS)
    • Network accessline 47
      url = f"https://api.openalex.org/works/{work_id}"     response = requests.get(url, headers=HEADERS)     paper = response.json()
    • Network accessline 48
      response = requests.get(url, headers=HEADERS)
    • Network accessline 52
      references = []     for ref_id in ref_ids:         ref = requests.get(f"https://api.openalex.org/works/{ref_id.split('/')[-1]}", headers=HEADERS).json()
    • Network accessline 53
      for ref_id in ref_ids:         ref = requests.get(f"https://api.openalex.org/works/{ref_id.split('/')[-1]}", headers=HEADERS).json()         if ref.get("title"):
    • Network accessline 54
      ref = requests.get(f"https://api.openalex.org/works/{ref_id.split('/')[-1]}", headers=HEADERS).json()
    • Network accessline 77
      page = 1     while len(all_citations) < limit:         response = requests.get(
    • Network accessline 78
      while len(all_citations) < limit:         response = requests.get(             "https://api.openalex.org/works",
    • Network accessline 79
      response = requests.get(
    • Network accessline 80
      "https://api.openalex.org/works",

    skills/literature/search/citeseerx-api/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["CiteSeerX", "computer science", "citation index", "academic search", "CS literature", "autonomous citation"]     source: "https://citeseerx.ist.psu.edu/"
    • Network accessline 9
      keywords: ["CiteSeerX", "computer science", "citation index", "academic search", "CS literature", "autonomous citation"]     source: "https://citeseerx.ist.psu.edu/" ---
    • Network accessline 10
      source: "https://citeseerx.ist.psu.edu/"
    • Network accessline 24
      https://citeseerx.ist.psu.edu/api
    • Network accessline 30
      # Keyword search curl "https://citeseerx.ist.psu.edu/api/search?q=graph+neural+networks&start=0&rows=20"
    • Network accessline 31
      curl "https://citeseerx.ist.psu.edu/api/search?q=graph+neural+networks&start=0&rows=20"
    • Network accessline 33
      # Search by title curl "https://citeseerx.ist.psu.edu/api/search?q=title:attention+is+all+you+need"
    • Network accessline 34
      curl "https://citeseerx.ist.psu.edu/api/search?q=title:attention+is+all+you+need"
    • Network accessline 36
      # Search by author curl "https://citeseerx.ist.psu.edu/api/search?q=author:hinton&rows=25"
    • Network accessline 37
      curl "https://citeseerx.ist.psu.edu/api/search?q=author:hinton&rows=25"
    • Network accessline 39
      # Filter by year curl "https://citeseerx.ist.psu.edu/api/search?q=federated+learning&year=2024"
    • Network accessline 40
      curl "https://citeseerx.ist.psu.edu/api/search?q=federated+learning&year=2024"
    • Network accessline 42
      # Sort by citation count curl "https://citeseerx.ist.psu.edu/api/search?q=reinforcement+learning&sort=citationCount+desc"
    • Network accessline 43
      curl "https://citeseerx.ist.psu.edu/api/search?q=reinforcement+learning&sort=citationCount+desc"
    • Network accessline 49
      # Get document metadata curl "https://citeseerx.ist.psu.edu/api/document?doi=10.1.1.123.456"
    • Network accessline 50
      curl "https://citeseerx.ist.psu.edu/api/document?doi=10.1.1.123.456"
    • Network accessline 52
      # Get citations for a document curl "https://citeseerx.ist.psu.edu/api/citations?doi=10.1.1.123.456"
    • Network accessline 53
      curl "https://citeseerx.ist.psu.edu/api/citations?doi=10.1.1.123.456"
    • Network accessline 55
      # Get citing documents curl "https://citeseerx.ist.psu.edu/api/citedby?doi=10.1.1.123.456"
    • Network accessline 56
      curl "https://citeseerx.ist.psu.edu/api/citedby?doi=10.1.1.123.456"
    • Network accessline 83
      "venue": "AI Open",         "citationCount": 3500,         "url": "https://citeseerx.ist.psu.edu/doc/10.1.1.123.456"
    • Network accessline 84
      "citationCount": 3500,         "url": "https://citeseerx.ist.psu.edu/doc/10.1.1.123.456"       }
    • Network accessline 85
      "url": "https://citeseerx.ist.psu.edu/doc/10.1.1.123.456"
    • Network accessline 97
      BASE_URL = "https://citeseerx.ist.psu.edu/api"
    • Network accessline 111
      resp = requests.get(f"{BASE_URL}/search", params=params, timeout=30)
    • Network accessline 130
      def get_citations(doc_id: str) -> list:     """Get papers cited by a document."""     resp = requests.get(
    • Network accessline 131
      """Get papers cited by a document."""     resp = requests.get(         f"{BASE_URL}/citations",
    • Network accessline 132
      resp = requests.get(
    • Network accessline 141
      def get_cited_by(doc_id: str) -> list:     """Get papers that cite a document."""     resp = requests.get(
    • Network accessline 142
      """Get papers that cite a document."""     resp = requests.get(         f"{BASE_URL}/citedby",
    • Network accessline 143
      resp = requests.get(
    • Network accessline 181
      - [CiteSeerX](https://citeseerx.ist.psu.edu/)
    • Network accessline 182
      - [CiteSeerX Documentation](https://citeseerx.ist.psu.edu/about)

    skills/literature/search/database-comparison-guide/SKILL.md

    • Network accessline 37
      # arXiv API query for recent ML papers curl "http://export.arxiv.org/api/query?search_query=cat:cs.LG+AND+ti:transformer&start=0&max_results=25&sortBy=submittedDate&sortOrder=descending"
    • Network accessline 38
      curl "http://export.arxiv.org/api/query?search_query=cat:cs.LG+AND+ti:transformer&start=0&max_results=25&sortBy=submittedDate&sortOrder=descending"
    • Network accessline 44
      # PubMed E-utilities search with MeSH curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=%22machine+learning%22[MeSH]+AND+%22drug+discovery%22[MeSH]&retmax=50&sort=date"
    • Network accessline 45
      curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=%22machine+learning%22[MeSH]+AND+%22drug+discovery%22[MeSH]&retmax=50&sort=date"

    skills/literature/search/deep-literature-search/SKILL.md

    • Network accessline 146
      - PRISMA 2020 Statement: https://www.prisma-statement.org
    • Network accessline 147
      - Cochrane Handbook, Ch. 4 (Searching for studies): https://training.cochrane.org/handbook

    skills/literature/search/eric-education-api/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["ERIC", "education research", "IES", "pedagogy", "teaching", "educational technology"]     source: "https://eric.ed.gov/"
    • Network accessline 9
      keywords: ["ERIC", "education research", "IES", "pedagogy", "teaching", "educational technology"]     source: "https://eric.ed.gov/" ---
    • Network accessline 10
      source: "https://eric.ed.gov/"
    • Network accessline 24
      https://api.ies.ed.gov/eric/
    • Network accessline 30
      # Basic keyword search curl "https://api.ies.ed.gov/eric/?search=online+learning&format=json&rows=20"
    • Network accessline 31
      curl "https://api.ies.ed.gov/eric/?search=online+learning&format=json&rows=20"
    • Network accessline 33
      # Search in specific fields curl "https://api.ies.ed.gov/eric/?search=title:\"blended learning\"&format=json"
    • Network accessline 34
      curl "https://api.ies.ed.gov/eric/?search=title:\"blended learning\"&format=json"
    • Network accessline 36
      # Filter by publication date curl "https://api.ies.ed.gov/eric/?search=STEM+education&start=0&rows=25&\
    • Network accessline 37
      curl "https://api.ies.ed.gov/eric/?search=STEM+education&start=0&rows=25&\
    • Network accessline 40
      # Filter by publication type curl "https://api.ies.ed.gov/eric/?search=formative+assessment&\
    • Network accessline 41
      curl "https://api.ies.ed.gov/eric/?search=formative+assessment&\
    • Network accessline 44
      # Filter by descriptor (ERIC thesaurus term) curl "https://api.ies.ed.gov/eric/?search=descriptor:\"Higher Education\"&format=json"
    • Network accessline 45
      curl "https://api.ies.ed.gov/eric/?search=descriptor:\"Higher Education\"&format=json"
    • Network accessline 47
      # Peer-reviewed only curl "https://api.ies.ed.gov/eric/?search=metacognition&peerreviewed=true&format=json"
    • Network accessline 48
      curl "https://api.ies.ed.gov/eric/?search=metacognition&peerreviewed=true&format=json"
    • Network accessline 106
      "educationlevel": ["Higher Education"],         "peerreviewed": "T",         "url": "https://eric.ed.gov/?id=EJ1389012",
    • Network accessline 107
      "peerreviewed": "T",         "url": "https://eric.ed.gov/?id=EJ1389012",         "publicationtype": "Journal Articles",
    • Network accessline 108
      "url": "https://eric.ed.gov/?id=EJ1389012",
    • Network accessline 122
      BASE_URL = "https://api.ies.ed.gov/eric/"
    • Network accessline 142
      resp = requests.get(BASE_URL, params=params)
    • Network accessline 197
      - [ERIC Website](https://eric.ed.gov/)
    • Network accessline 198
      - [ERIC API Guide](https://eric.ed.gov/pdf/ERIC_API.pdf)
    • Network accessline 199
      - [ERIC Thesaurus](https://eric.ed.gov/thesaurus)

    skills/literature/search/europe-pmc-api/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["academic database search", "literature search", "citation tracking", "field-specific search"]     source: "https://europepmc.org/RestfulWebService"
    • Network accessline 9
      keywords: ["academic database search", "literature search", "citation tracking", "field-specific search"]     source: "https://europepmc.org/RestfulWebService" ---
    • Network accessline 10
      source: "https://europepmc.org/RestfulWebService"
    • Network accessline 31
      - **URL**: `GET https://www.ebi.ac.uk/europepmc/webservices/rest/search`
    • Network accessline 44
      curl "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=CRISPR+AND+cancer&format=json&resultType=core&pageSize=10&sort=CITED+desc"
    • Network accessline 50
      - **URL**: `GET https://www.ebi.ac.uk/europepmc/webservices/rest/{source}/{id}/citations`
    • Network accessline 61
      curl "https://www.ebi.ac.uk/europepmc/webservices/rest/MED/33116299/citations?format=json&pageSize=10"
    • Network accessline 67
      - **URL**: `GET https://www.ebi.ac.uk/europepmc/webservices/rest/{source}/{id}/references`
    • Network accessline 78
      curl "https://www.ebi.ac.uk/europepmc/webservices/rest/MED/33116299/references?format=json&pageSize=50"
    • Network accessline 93
      curl -s "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=(TITLE:immunotherapy+AND+TITLE:melanoma)+AND+(PUB_YEAR:[2022+TO+2026])&format=json&resultType=core&pageSize=25&sort=CITED+desc" | jq '.resultList.result[] | {title: .tit
    • Network accessline 101
      curl -s "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=(SRC:PPR)+AND+large+language+models+AND+biology&format=json&pageSize=10" | jq '.resultList.result[] | {title: .title, source: .source, year: .pubYear, doi: .doi}'
    • Network accessline 109
      # Get papers that cite the target curl -s "https://www.ebi.ac.uk/europepmc/webservices/rest/MED/33116299/citations?format=json&pageSize=50" | jq '.citationList.citation | length'
    • Network accessline 110
      curl -s "https://www.ebi.ac.uk/europepmc/webservices/rest/MED/33116299/citations?format=json&pageSize=50" | jq '.citationList.citation | length'
    • Network accessline 112
      # Get papers referenced by the target curl -s "https://www.ebi.ac.uk/europepmc/webservices/rest/MED/33116299/references?format=json&pageSize=100" | jq '.referenceList.reference | length'
    • Network accessline 113
      curl -s "https://www.ebi.ac.uk/europepmc/webservices/rest/MED/33116299/references?format=json&pageSize=100" | jq '.referenceList.reference | length'
    • Network accessline 118
      - Official documentation: https://europepmc.org/RestfulWebService
    • Network accessline 119
      - Europe PMC search syntax: https://europepmc.org/searchsyntax
    • Network accessline 120
      - Europe PMC annotations API: https://europepmc.org/AnnotationsApi

    skills/literature/search/findpapers-guide/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["Findpapers", "multi-database search", "systematic review", "arXiv", "PubMed", "Scopus", "IEEE"]     source: "https://github.com/jonatasgrosman/findpapers"
    • Network accessline 9
      keywords: ["Findpapers", "multi-database search", "systematic review", "arXiv", "PubMed", "Scopus", "IEEE"]     source: "https://github.com/jonatasgrosman/findpapers" ---
    • Network accessline 10
      source: "https://github.com/jonatasgrosman/findpapers"
    • Access to secretsline 111
      [Credential-related source omitted]
    • Access to secretsline 112
      [Credential-related source omitted]
    • Network accessline 175
      - [Findpapers GitHub](https://github.com/jonatasgrosman/findpapers)
    • Network accessline 176
      - [Findpapers PyPI](https://pypi.org/project/findpapers/)

    skills/literature/search/ieee-xplore-api/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["ieee", "engineering literature", "computer science", "technical standards", "conference papers", "xplore"]     source: "https://developer.ieee.org/"
    • Network accessline 9
      keywords: ["ieee", "engineering literature", "computer science", "technical standards", "conference papers", "xplore"]     source: "https://developer.ieee.org/" ---
    • Network accessline 10
      source: "https://developer.ieee.org/"
    • Network accessline 24
      https://ieeexploreapi.ieee.org/api/v1/search/articles
    • Network accessline 30
      # Basic keyword search curl "https://ieeexploreapi.ieee.org/api/v1/search/articles?\
    • Network accessline 31
      [Credential-related source omitted]
    • Access to secretsline 31
      [Credential-related source omitted]
    • Access to secretsline 32
      [Credential-related source omitted]
    • Network accessline 36
      # Search with filters curl "https://ieeexploreapi.ieee.org/api/v1/search/articles?\
    • Network accessline 37
      [Credential-related source omitted]
    • Access to secretsline 37
      [Credential-related source omitted]
    • Access to secretsline 38
      [Credential-related source omitted]
    • Network accessline 82
      # Look up up to 25 DOIs at once curl "https://ieeexploreapi.ieee.org/api/v1/search/articles?\
    • Network accessline 83
      [Credential-related source omitted]
    • Access to secretsline 83
      [Credential-related source omitted]
    • Access to secretsline 84
      [Credential-related source omitted]
    • Network accessline 108
      "end_page": "110",       "citing_paper_count": 15,       "pdf_url": "https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=12345",
    • Network accessline 109
      "citing_paper_count": 15,       "pdf_url": "https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=12345",       "html_url": "https://ieeexplore.ieee.org/document/12345"
    • Network accessline 110
      "pdf_url": "https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=12345",
    • Network accessline 111
      "html_url": "https://ieeexplore.ieee.org/document/12345"
    • Network accessline 123
      [Credential-related source omitted]
    • Access to secretsline 123
      [Credential-related source omitted]
    • Network accessline 124
      BASE_URL = "https://ieeexploreapi.ieee.org/api/v1/search/articles"
    • Access to secretsline 130
      [Credential-related source omitted]
    • Network accessline 141
      resp = requests.get(BASE_URL, params=params)
    • Network accessline 175
      - [IEEE Xplore API Portal](https://developer.ieee.org/)
    • Network accessline 176
      - [API Documentation](https://developer.ieee.org/docs)
    • Network accessline 177
      - [IEEE Xplore Digital Library](https://ieeexplore.ieee.org/)

    skills/literature/search/lens-scholarly-api/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["Lens.org", "patent search", "scholarly search", "citation linking", "innovation", "prior art"]     source: "https://www.lens.org/"
    • Network accessline 9
      keywords: ["Lens.org", "patent search", "scholarly search", "citation linking", "innovation", "prior art"]     source: "https://www.lens.org/" ---
    • Network accessline 10
      source: "https://www.lens.org/"
    • Network accessline 22
      # Register at https://www.lens.org/lens/user/subscriptions
    • Network accessline 32
      # POST-based search curl -X POST "https://api.lens.org/scholarly/search" \
    • Network accessline 33
      [Credential-related source omitted]
    • Access to secretsline 33
      [Credential-related source omitted]
    • Access to secretsline 34
      [Credential-related source omitted]
    • Network accessline 45
      # Boolean query curl -X POST "https://api.lens.org/scholarly/search" \
    • Network accessline 46
      [Credential-related source omitted]
    • Access to secretsline 46
      [Credential-related source omitted]
    • Access to secretsline 47
      [Credential-related source omitted]
    • Network accessline 68
      [Credential-related source omitted]
    • Access to secretsline 68
      [Credential-related source omitted]
    • Access to secretsline 69
      [Credential-related source omitted]
    • Network accessline 106
      [Credential-related source omitted]
    • Access to secretsline 106
      [Credential-related source omitted]
    • Network accessline 107
      BASE_URL = "https://api.lens.org"
    • Network accessline 132
      resp = requests.post(
    • Network accessline 171
      resp = requests.post(
    • Network accessline 209
      - [Lens.org](https://www.lens.org/)
    • Network accessline 210
      - [Lens API Documentation](https://docs.api.lens.org/)
    • Network accessline 211
      - [Lens Scholarly Search](https://www.lens.org/lens/search/scholar/list)

    skills/literature/search/open-library-api/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["Open Library", "book search", "ISBN lookup", "Internet Archive", "book metadata", "digital library"]     source: "https://openlibrary.org/"
    • Network accessline 9
      keywords: ["Open Library", "book search", "ISBN lookup", "Internet Archive", "book metadata", "digital library"]     source: "https://openlibrary.org/" ---
    • Network accessline 10
      source: "https://openlibrary.org/"
    • Network accessline 24
      # Full-text search curl "https://openlibrary.org/search.json?q=machine+learning&limit=20"
    • Network accessline 25
      curl "https://openlibrary.org/search.json?q=machine+learning&limit=20"
    • Network accessline 27
      # Search by title curl "https://openlibrary.org/search.json?title=deep+learning&limit=10"
    • Network accessline 28
      curl "https://openlibrary.org/search.json?title=deep+learning&limit=10"
    • Network accessline 30
      # Search by author curl "https://openlibrary.org/search.json?author=goodfellow&title=deep+learning"
    • Network accessline 31
      curl "https://openlibrary.org/search.json?author=goodfellow&title=deep+learning"
    • Network accessline 33
      # Filter by subject curl "https://openlibrary.org/search.json?q=statistics&subject=data+analysis"
    • Network accessline 34
      curl "https://openlibrary.org/search.json?q=statistics&subject=data+analysis"
    • Network accessline 36
      # Filter by publication year curl "https://openlibrary.org/search.json?q=artificial+intelligence&first_publish_year=2020"
    • Network accessline 37
      curl "https://openlibrary.org/search.json?q=artificial+intelligence&first_publish_year=2020"
    • Network accessline 39
      # Sort by edition count curl "https://openlibrary.org/search.json?q=calculus&sort=editions"
    • Network accessline 40
      curl "https://openlibrary.org/search.json?q=calculus&sort=editions"
    • Network accessline 46
      # Get work (canonical book entity) curl "https://openlibrary.org/works/OL45804W.json"
    • Network accessline 47
      curl "https://openlibrary.org/works/OL45804W.json"
    • Network accessline 49
      # Get edition curl "https://openlibrary.org/books/OL7353617M.json"
    • Network accessline 50
      curl "https://openlibrary.org/books/OL7353617M.json"
    • Network accessline 52
      # Get by ISBN curl "https://openlibrary.org/isbn/9780262035613.json"
    • Network accessline 53
      curl "https://openlibrary.org/isbn/9780262035613.json"
    • Network accessline 55
      # Bibliographic data via Books API curl "https://openlibrary.org/api/books?bibkeys=ISBN:9780262035613&format=json&jscmd=data"
    • Network accessline 56
      curl "https://openlibrary.org/api/books?bibkeys=ISBN:9780262035613&format=json&jscmd=data"
    • Network accessline 62
      # By ISBN (S/M/L sizes) https://covers.openlibrary.org/b/isbn/9780262035613-M.jpg
    • Network accessline 63
      https://covers.openlibrary.org/b/isbn/9780262035613-M.jpg
    • Network accessline 65
      # By OLID https://covers.openlibrary.org/b/olid/OL7353617M-L.jpg
    • Network accessline 66
      https://covers.openlibrary.org/b/olid/OL7353617M-L.jpg
    • Network accessline 72
      # Get author curl "https://openlibrary.org/authors/OL34184A.json"
    • Network accessline 73
      curl "https://openlibrary.org/authors/OL34184A.json"
    • Network accessline 75
      # Search authors curl "https://openlibrary.org/search/authors.json?q=hinton"
    • Network accessline 76
      curl "https://openlibrary.org/search/authors.json?q=hinton"
    • Network accessline 78
      # Author's works curl "https://openlibrary.org/authors/OL34184A/works.json?limit=20"
    • Network accessline 79
      curl "https://openlibrary.org/authors/OL34184A/works.json?limit=20"
    • Network accessline 124
      BASE_URL = "https://openlibrary.org"
    • Network accessline 134
      resp = requests.get(f"{BASE_URL}/search.json", params=params)
    • Network accessline 154
      def get_by_isbn(isbn: str) -> dict:     """Look up a book by ISBN."""     resp = requests.get(
    • Network accessline 155
      """Look up a book by ISBN."""     resp = requests.get(         f"{BASE_URL}/api/books",
    • Network accessline 156
      resp = requests.get(
    • Network accessline 169
      def get_author_works(author_key: str, limit: int = 20) -> list:     """Get works by an author."""     resp = requests.get(
    • Network accessline 170
      """Get works by an author."""     resp = requests.get(         f"{BASE_URL}/authors/{author_key}/works.json",
    • Network accessline 171
      resp = requests.get(
    • Network accessline 194
      - [Open Library](https://openlibrary.org/)
    • Network accessline 195
      - [Open Library API](https://openlibrary.org/developers/api)
    • Network accessline 196
      - [Open Library Data Dumps](https://openlibrary.org/developers/dumps)

    skills/literature/search/open-semantic-search-guide/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["semantic search", "text mining", "self-hosted", "Solr", "NLP", "entity extraction"]     source: "https://github.com/opensemanticsearch/open-semantic-search"
    • Network accessline 9
      keywords: ["semantic search", "text mining", "self-hosted", "Solr", "NLP", "entity extraction"]     source: "https://github.com/opensemanticsearch/open-semantic-search" ---
    • Network accessline 10
      source: "https://github.com/opensemanticsearch/open-semantic-search"
    • Network accessline 22
      # Docker deployment (recommended) git clone https://github.com/opensemanticsearch/open-semantic-search.git
    • Network accessline 23
      git clone https://github.com/opensemanticsearch/open-semantic-search.git
    • Network accessline 27
      # Access web UI at http://localhost:8080
    • Network accessline 28
      # Admin panel at http://localhost:8080/admin
    • Network accessline 53
      # Index a directory of papers curl -X POST "http://localhost:8080/api/index" \
    • Network accessline 54
      curl -X POST "http://localhost:8080/api/index" \
    • Network accessline 58
      # Index single file curl -X POST "http://localhost:8080/api/index" \
    • Network accessline 59
      curl -X POST "http://localhost:8080/api/index" \
    • Network accessline 95
      SEARCH_URL = "http://localhost:8080/api/search"
    • Network accessline 111
      resp = requests.get(SEARCH_URL, params=params)
    • Network accessline 161
      def get_entity_network(entity, depth=2):     """Get co-occurring entities for a given entity."""     resp = requests.get(
    • Network accessline 162
      """Get co-occurring entities for a given entity."""     resp = requests.get(         f"{SEARCH_URL}/graph",
    • Network accessline 163
      resp = requests.get(
    • Network accessline 188
      - [Open Semantic Search GitHub](https://github.com/opensemanticsearch/open-semantic-search)
    • Network accessline 189
      - [Apache Solr](https://solr.apache.org/)
    • Network accessline 190
      - [Apache Tika](https://tika.apache.org/)

    skills/literature/search/openaire-api/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["openaire", "european research", "open science", "EU funding", "research outputs", "open access"]     source: "https://develop.openaire.eu/"
    • Network accessline 9
      keywords: ["openaire", "european research", "open science", "EU funding", "research outputs", "open access"]     source: "https://develop.openaire.eu/" ---
    • Network accessline 10
      source: "https://develop.openaire.eu/"
    • Network accessline 24
      https://api.openaire.eu
    • Network accessline 30
      # Search by keywords curl "https://api.openaire.eu/search/publications?keywords=climate+change+adaptation&format=json&size=10"
    • Network accessline 31
      curl "https://api.openaire.eu/search/publications?keywords=climate+change+adaptation&format=json&size=10"
    • Network accessline 33
      # Filter by open access curl "https://api.openaire.eu/search/publications?keywords=machine+learning&openaccessonly=true&format=json"
    • Network accessline 34
      curl "https://api.openaire.eu/search/publications?keywords=machine+learning&openaccessonly=true&format=json"
    • Network accessline 36
      # Filter by date curl "https://api.openaire.eu/search/publications?keywords=CRISPR&fromDateAccepted=2023-01-01&toDateAccepted=2026-12-31&format=json"
    • Network accessline 37
      curl "https://api.openaire.eu/search/publications?keywords=CRISPR&fromDateAccepted=2023-01-01&toDateAccepted=2026-12-31&format=json"
    • Network accessline 39
      # Filter by EU project curl "https://api.openaire.eu/search/publications?projectID=corda__h2020::123456&format=json"
    • Network accessline 40
      curl "https://api.openaire.eu/search/publications?projectID=corda__h2020::123456&format=json"
    • Network accessline 42
      # Search by DOI curl "https://api.openaire.eu/search/publications?doi=10.1038/s41586-023-05881-4&format=json"
    • Network accessline 43
      curl "https://api.openaire.eu/search/publications?doi=10.1038/s41586-023-05881-4&format=json"
    • Network accessline 49
      # Find research datasets curl "https://api.openaire.eu/search/datasets?keywords=genomics+sequencing&format=json&size=20"
    • Network accessline 50
      curl "https://api.openaire.eu/search/datasets?keywords=genomics+sequencing&format=json&size=20"
    • Network accessline 52
      # Open access datasets only curl "https://api.openaire.eu/search/datasets?keywords=ocean+temperature&openaccessonly=true&format=json"
    • Network accessline 53
      curl "https://api.openaire.eu/search/datasets?keywords=ocean+temperature&openaccessonly=true&format=json"
    • Network accessline 59
      # Search EU-funded projects curl "https://api.openaire.eu/search/projects?keywords=artificial+intelligence&funder=EC&format=json"
    • Network accessline 60
      curl "https://api.openaire.eu/search/projects?keywords=artificial+intelligence&funder=EC&format=json"
    • Network accessline 62
      # Horizon 2020 projects curl "https://api.openaire.eu/search/projects?keywords=renewable+energy&fundingStream=H2020&format=json"
    • Network accessline 63
      curl "https://api.openaire.eu/search/projects?keywords=renewable+energy&fundingStream=H2020&format=json"
    • Network accessline 65
      # Horizon Europe projects curl "https://api.openaire.eu/search/projects?keywords=quantum+computing&fundingStream=HE&format=json"
    • Network accessline 66
      curl "https://api.openaire.eu/search/projects?keywords=quantum+computing&fundingStream=HE&format=json"
    • Network accessline 90
      BASE_URL = "https://api.openaire.eu"
    • Network accessline 105
      resp = requests.get(f"{BASE_URL}/search/publications", params=params)
    • Network accessline 139
      - [OpenAIRE API Documentation](https://develop.openaire.eu/)
    • Network accessline 140
      - [OpenAIRE Graph](https://graph.openaire.eu/)
    • Network accessline 141
      - [OpenAIRE EXPLORE Portal](https://explore.openaire.eu/)

    skills/literature/search/openalex-api/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["academic database search", "literature search", "citation statistics", "academic metrics", "bibliometrics"]     source: "https://docs.openalex.org/"
    • Network accessline 9
      keywords: ["academic database search", "literature search", "citation statistics", "academic metrics", "bibliometrics"]     source: "https://docs.openalex.org/" ---
    • Network accessline 10
      source: "https://docs.openalex.org/"
    • Network accessline 28
      https://api.openalex.org/works?mailto=your@email.com
    • Network accessline 37
      - **URL**: `GET https://api.openalex.org/works`
    • Network accessline 49
      curl "https://api.openalex.org/works?search=large+language+models&filter=publication_year:2024&sort=cited_by_count:desc&per_page=10&mailto=user@example.com"
    • Network accessline 55
      - **URL**: `GET https://api.openalex.org/authors`
    • Network accessline 65
      curl "https://api.openalex.org/authors?search=Geoffrey+Hinton&mailto=user@example.com"
    • Network accessline 71
      - **URL**: `GET https://api.openalex.org/institutions`
    • Network accessline 81
      curl "https://api.openalex.org/institutions?search=MIT&mailto=user@example.com"
    • Network accessline 87
      - **URL**: `GET https://api.openalex.org/concepts`
    • Network accessline 96
      curl "https://api.openalex.org/concepts?filter=level:0&per_page=50&mailto=user@example.com"
    • Network accessline 111
      curl "https://api.openalex.org/works?filter=cites:W2741809807&sort=cited_by_count:desc&per_page=25&mailto=user@example.com"
    • Network accessline 119
      curl "https://api.openalex.org/works?filter=institutions.id:I136199984,publication_year:2024&group_by=open_access.is_oa&mailto=user@example.com"
    • Network accessline 127
      curl "https://api.openalex.org/concepts/C41008148?mailto=user@example.com"
    • Network accessline 132
      - Official documentation: https://docs.openalex.org/
    • Network accessline 133
      - OpenAlex data model: https://docs.openalex.org/about-the-data
    • Network accessline 134
      - API filters reference: https://docs.openalex.org/how-to-use-the-api/get-lists-of-entities/filter-entity-lists

    skills/literature/search/plos-open-access-api/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["PLOS", "open access", "biomedical", "Solr search", "full text", "peer reviewed"]     source: "https://api.plos.org/"
    • Network accessline 9
      keywords: ["PLOS", "open access", "biomedical", "Solr search", "full text", "peer reviewed"]     source: "https://api.plos.org/" ---
    • Network accessline 10
      source: "https://api.plos.org/"
    • Network accessline 24
      https://api.plos.org/search
    • Network accessline 30
      # Basic keyword search curl "https://api.plos.org/search?q=CRISPR+gene+editing&rows=20&wt=json"
    • Network accessline 31
      curl "https://api.plos.org/search?q=CRISPR+gene+editing&rows=20&wt=json"
    • Network accessline 33
      # Search in specific fields curl "https://api.plos.org/search?q=title:\"machine learning\"+AND+abstract:biomarker&wt=json"
    • Network accessline 34
      curl "https://api.plos.org/search?q=title:\"machine learning\"+AND+abstract:biomarker&wt=json"
    • Network accessline 36
      # Filter by journal curl "https://api.plos.org/search?q=microbiome&fq=journal:\"PLOS ONE\"&wt=json"
    • Network accessline 37
      curl "https://api.plos.org/search?q=microbiome&fq=journal:\"PLOS ONE\"&wt=json"
    • Network accessline 39
      # Filter by date range curl "https://api.plos.org/search?q=COVID-19+vaccine&\
    • Network accessline 40
      curl "https://api.plos.org/search?q=COVID-19+vaccine&\
    • Network accessline 43
      # Filter by article type curl "https://api.plos.org/search?q=climate+change&fq=article_type:\"Research Article\"&wt=json"
    • Network accessline 44
      curl "https://api.plos.org/search?q=climate+change&fq=article_type:\"Research Article\"&wt=json"
    • Network accessline 46
      # Return specific fields only curl "https://api.plos.org/search?q=deep+learning&fl=id,title,author,publication_date,score&wt=json"
    • Network accessline 47
      curl "https://api.plos.org/search?q=deep+learning&fl=id,title,author,publication_date,score&wt=json"
    • Network accessline 106
      BASE_URL = "https://api.plos.org/search"
    • Network accessline 131
      resp = requests.get(BASE_URL, params=params)
    • Network accessline 155
      "wt": "json",     }     resp = requests.get(BASE_URL, params=params)
    • Network accessline 156
      }     resp = requests.get(BASE_URL, params=params)     resp.raise_for_status()
    • Network accessline 157
      resp = requests.get(BASE_URL, params=params)
    • Network accessline 201
      - [PLOS API Documentation](https://api.plos.org/)
    • Network accessline 202
      - [PLOS Search Tips](https://journals.plos.org/plosone/s/search)
    • Network accessline 203
      - [Solr Query Syntax](https://solr.apache.org/guide/solr/latest/query-guide/standard-query-parser.html)

    skills/literature/search/pubmed-api/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["academic database search", "literature search", "scholarly database", "field-specific search"]     source: "https://www.ncbi.nlm.nih.gov/books/NBK25501/"
    • Network accessline 9
      keywords: ["academic database search", "literature search", "scholarly database", "field-specific search"]     source: "https://www.ncbi.nlm.nih.gov/books/NBK25501/" ---
    • Network accessline 10
      source: "https://www.ncbi.nlm.nih.gov/books/NBK25501/"
    • Network accessline 25
      No authentication required for basic usage (3 requests/second). For higher rate limits (10 requests/second), register for a free API key at https://www.ncbi.nlm.nih.gov/account/ and include it in requests:
    • Access to secretsline 28
      [Credential-related source omitted]
    • Network accessline 37
      - **URL**: `GET https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi`
    • Network accessline 53
      curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CRISPR+AND+cancer[Title]&retmax=10&retmode=json&sort=pub_date"
    • Network accessline 59
      - **URL**: `GET https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi`
    • Network accessline 71
      curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=33116299,34735795&rettype=abstract&retmode=xml"
    • Network accessline 77
      - **URL**: `GET https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi`
    • Network accessline 87
      curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=33116299&retmode=json&version=2.0"
    • Network accessline 102
      # Search for clinical trials on diabetes treatment from the last 2 years curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=diabetes[MeSH]+AND+treatment[Title]+AND+clinical+trial[Publication+Type]&mindate=2024/0
    • Network accessline 103
      curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=diabetes[MeSH]+AND+treatment[Title]+AND+clinical+trial[Publication+Type]&mindate=2024/01/01&maxdate=2026/03/09&datetype=pdat&retmax=100&retmode=json"
    • Network accessline 111
      # Step 1: Search and store results curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=machine+learning+AND+radiology&retmax=0&usehistory=y&retmode=json"
    • Network accessline 112
      curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=machine+learning+AND+radiology&retmax=0&usehistory=y&retmode=json"
    • Network accessline 114
      # Step 2: Fetch records using WebEnv and query_key from step 1 curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&WebEnv=WEBENV_VALUE&query_key=1&retmax=50&rettype=abstract&retmode=xml"
    • Network accessline 115
      curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&WebEnv=WEBENV_VALUE&query_key=1&retmax=50&rettype=abstract&retmode=xml"
    • Network accessline 123
      curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=33116299,34735795,35363452&retmode=json&version=2.0"
    • Network accessline 128
      - Official documentation: https://www.ncbi.nlm.nih.gov/books/NBK25501/
    • Network accessline 129
      - E-utilities quick start: https://www.ncbi.nlm.nih.gov/books/NBK25500/
    • Network accessline 130
      - PubMed search help: https://pubmed.ncbi.nlm.nih.gov/help/

    skills/literature/search/scielo-api/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["SciELO", "Latin America", "open access journals", "developing countries", "Brazilian research", "Spanish research"]     source: "https://wiki.scielo.org/"
    • Network accessline 9
      keywords: ["SciELO", "Latin America", "open access journals", "developing countries", "Brazilian research", "Spanish research"]     source: "https://wiki.scielo.org/" ---
    • Network accessline 10
      source: "https://wiki.scielo.org/"
    • Network accessline 26
      # Search articles by keyword curl "https://articlemeta.scielo.org/api/v1/article/?collection=scl&q=machine+learning"
    • Network accessline 27
      curl "https://articlemeta.scielo.org/api/v1/article/?collection=scl&q=machine+learning"
    • Network accessline 29
      # Get article by PID (SciELO identifier) curl "https://articlemeta.scielo.org/api/v1/article/?code=S0100-204X2024000100001"
    • Network accessline 30
      curl "https://articlemeta.scielo.org/api/v1/article/?code=S0100-204X2024000100001"
    • Network accessline 32
      # Filter by collection (country) curl "https://articlemeta.scielo.org/api/v1/article/?collection=esp&q=climate+change"
    • Network accessline 33
      curl "https://articlemeta.scielo.org/api/v1/article/?collection=esp&q=climate+change"
    • Network accessline 35
      # Filter by journal ISSN curl "https://articlemeta.scielo.org/api/v1/article/?issn=0100-204X&from_date=2024-01-01"
    • Network accessline 36
      curl "https://articlemeta.scielo.org/api/v1/article/?issn=0100-204X&from_date=2024-01-01"
    • Network accessline 57
      # List journals in a collection curl "https://articlemeta.scielo.org/api/v1/journal/?collection=scl"
    • Network accessline 58
      curl "https://articlemeta.scielo.org/api/v1/journal/?collection=scl"
    • Network accessline 60
      # Get journal by ISSN curl "https://articlemeta.scielo.org/api/v1/journal/?issn=0100-204X"
    • Network accessline 61
      curl "https://articlemeta.scielo.org/api/v1/journal/?issn=0100-204X"
    • Network accessline 63
      # Journal indicators curl "https://analytics.scielo.org/api/v1/journal/?issn=0100-204X"
    • Network accessline 64
      curl "https://analytics.scielo.org/api/v1/journal/?issn=0100-204X"
    • Network accessline 72
      # Full-text search curl "https://search.scielo.org/?q=biodiversity+conservation&format=json&count=20"
    • Network accessline 73
      curl "https://search.scielo.org/?q=biodiversity+conservation&format=json&count=20"
    • Network accessline 75
      # Filter by subject area curl "https://search.scielo.org/?q=neural+networks&filter[subject_area]=Computer+Science&format=json"
    • Network accessline 76
      curl "https://search.scielo.org/?q=neural+networks&filter[subject_area]=Computer+Science&format=json"
    • Network accessline 78
      # Filter by year range curl "https://search.scielo.org/?q=CRISPR&filter[year_cluster]=2023-2026&format=json"
    • Network accessline 79
      curl "https://search.scielo.org/?q=CRISPR&filter[year_cluster]=2023-2026&format=json"
    • Network accessline 81
      # Filter by language curl "https://search.scielo.org/?q=epidemiology&filter[la]=en&format=json"
    • Network accessline 82
      curl "https://search.scielo.org/?q=epidemiology&filter[la]=en&format=json"
    • Network accessline 103
      ARTICLE_API = "https://articlemeta.scielo.org/api/v1"
    • Network accessline 104
      SEARCH_API = "https://search.scielo.org"
    • Network accessline 114
      resp = requests.get(f"{SEARCH_API}/", params=params)
    • Network accessline 126
      "pid": doc.get("pid", ""),             "language": doc.get("la", []),             "url": f"https://scielo.org/article/{doc.get('pid', '')}",
    • Network accessline 127
      "language": doc.get("la", []),             "url": f"https://scielo.org/article/{doc.get('pid', '')}",         })
    • Network accessline 128
      "url": f"https://scielo.org/article/{doc.get('pid', '')}",
    • Network accessline 133
      def get_article(pid: str) -> dict:     """Get full article metadata by SciELO PID."""     resp = requests.get(
    • Network accessline 134
      """Get full article metadata by SciELO PID."""     resp = requests.get(         f"{ARTICLE_API}/article/",
    • Network accessline 135
      resp = requests.get(
    • Network accessline 143
      def list_journals(collection: str = "scl") -> list:     """List journals in a SciELO collection."""     resp = requests.get(
    • Network accessline 144
      """List journals in a SciELO collection."""     resp = requests.get(         f"{ARTICLE_API}/journal/",
    • Network accessline 145
      resp = requests.get(
    • Network accessline 179
      - [SciELO](https://scielo.org/)
    • Network accessline 180
      - [SciELO Analytics](https://analytics.scielo.org/)
    • Network accessline 181
      - [ArticleMeta API](https://articlemeta.scielo.org/)
    • Network accessline 182
      - [SciELO Developer Wiki](https://wiki.scielo.org/)

    skills/literature/search/semantic-scholar-api/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["academic database search", "semantic search", "AI-powered literature search", "citation analysis", "citation network"]     source: "https://api.openalex.org/"
    • Network accessline 9
      keywords: ["academic database search", "semantic search", "AI-powered literature search", "citation analysis", "citation network"]     source: "https://api.openalex.org/" ---
    • Network accessline 10
      source: "https://api.openalex.org/"
    • Network accessline 29
      User-Agent: ResearchPlugins/1.0 (https://wentor.ai)
    • Network accessline 34
      User-Agent: ResearchPlugins/1.0 (https://wentor.ai; mailto:dev@wentor.ai)
    • Network accessline 41
      - **URL**: `GET https://api.openalex.org/works`
    • Network accessline 52
      curl "https://api.openalex.org/works?search=attention+is+all+you+need&per_page=5"
    • Network accessline 58
      - **URL**: `GET https://api.openalex.org/works/{id}`
    • Network accessline 65
      curl "https://api.openalex.org/works/W2741809807"
    • Network accessline 71
      - **URL**: `GET https://api.openalex.org/authors`
    • Network accessline 80
      curl "https://api.openalex.org/authors?search=Yoshua+Bengio&per_page=5"
    • Network accessline 86
      - **URL**: `GET https://api.crossref.org/works/{doi}`
    • Network accessline 93
      curl "https://api.crossref.org/works/10.18653/v1/N19-1423"
    • Network accessline 110
      # Get paper details curl "https://api.openalex.org/works/W2741809807"
    • Network accessline 111
      curl "https://api.openalex.org/works/W2741809807"
    • Network accessline 113
      # Get works citing this paper, sorted by citation count curl "https://api.openalex.org/works?filter=cites:W2741809807&sort=cited_by_count:desc&per_page=20"
    • Network accessline 114
      curl "https://api.openalex.org/works?filter=cites:W2741809807&sort=cited_by_count:desc&per_page=20"
    • Network accessline 122
      curl "https://api.openalex.org/works?search=graph+neural+networks&sort=cited_by_count:desc&per_page=20"
    • Network accessline 130
      curl "https://api.crossref.org/works?query=graph+neural+networks&sort=is-referenced-by-count&order=desc&rows=20"
    • Network accessline 135
      - OpenAlex documentation: https://docs.openalex.org/
    • Network accessline 136
      - CrossRef API documentation: https://api.crossref.org/swagger-ui/index.html
    • Network accessline 137
      - OpenAlex source: https://github.com/ourresearch/openalex-guts

    skills/literature/search/share-research-api/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["SHARE", "open access", "research notification", "COS", "repository aggregator", "preprints"]     source: "https://share.osf.io/"
    • Network accessline 9
      keywords: ["SHARE", "open access", "research notification", "COS", "repository aggregator", "preprints"]     source: "https://share.osf.io/" ---
    • Network accessline 10
      source: "https://share.osf.io/"
    • Network accessline 24
      https://share.osf.io/api/v2
    • Network accessline 30
      # Text search across all sources curl "https://share.osf.io/api/v2/search/creativeworks/?q=climate+change&page[size]=20"
    • Network accessline 31
      curl "https://share.osf.io/api/v2/search/creativeworks/?q=climate+change&page[size]=20"
    • Network accessline 33
      # Filter by type curl "https://share.osf.io/api/v2/search/creativeworks/?q=neural+networks&filter[type]=preprint"
    • Network accessline 34
      curl "https://share.osf.io/api/v2/search/creativeworks/?q=neural+networks&filter[type]=preprint"
    • Network accessline 36
      # Filter by source curl "https://share.osf.io/api/v2/search/creativeworks/?q=genomics&filter[sources]=PubMed+Central"
    • Network accessline 37
      curl "https://share.osf.io/api/v2/search/creativeworks/?q=genomics&filter[sources]=PubMed+Central"
    • Network accessline 39
      # Filter by date curl "https://share.osf.io/api/v2/search/creativeworks/?q=COVID-19&filter[date][gte]=2024-01-01"
    • Network accessline 40
      curl "https://share.osf.io/api/v2/search/creativeworks/?q=COVID-19&filter[date][gte]=2024-01-01"
    • Network accessline 42
      # Filter by tag/subject curl "https://share.osf.io/api/v2/search/creativeworks/?q=machine+learning&filter[tags]=deep+learning"
    • Network accessline 43
      curl "https://share.osf.io/api/v2/search/creativeworks/?q=machine+learning&filter[tags]=deep+learning"
    • Network accessline 76
      BASE_URL = "https://share.osf.io/api/v2"
    • Network accessline 92
      resp = requests.get(
    • Network accessline 127
      - [SHARE](https://share.osf.io/)
    • Network accessline 128
      - [SHARE API Documentation](https://share.osf.io/api/v2/)
    • Network accessline 129
      - [Center for Open Science](https://cos.io/)

    skills/literature/search/worldcat-search-api/SKILL.md

    • Network accessline 8
      subcategory: "search"     keywords: ["worldcat", "library catalog", "OCLC", "book search", "holdings", "interlibrary loan"]     source: "https://developer.api.oclc.org/"
    • Network accessline 9
      keywords: ["worldcat", "library catalog", "OCLC", "book search", "holdings", "interlibrary loan"]     source: "https://developer.api.oclc.org/" ---
    • Network accessline 10
      source: "https://developer.api.oclc.org/"
    • Network accessline 22
      # Register at https://platform.worldcat.org/
    • Network accessline 25
      # OAuth 2.0 client credentials flow curl -X POST "https://oauth.oclc.org/token" \
    • Network accessline 26
      [Credential-related source omitted]
    • Access to secretsline 26
      [Credential-related source omitted]
    • Access to secretsline 27
      [Credential-related source omitted]
    • Network accessline 36
      https://www.worldcat.org/api/search/
    • Network accessline 42
      [Credential-related source omitted]
    • Network accessline 43
      [Credential-related source omitted]
    • Network accessline 44
      "https://www.worldcat.org/api/search?q=machine+learning&limit=25"
    • Network accessline 46
      [Credential-related source omitted]
    • Network accessline 47
      [Credential-related source omitted]
    • Network accessline 48
      "https://www.worldcat.org/api/search?q=ti:attention+is+all+you+need"
    • Network accessline 50
      [Credential-related source omitted]
    • Network accessline 51
      [Credential-related source omitted]
    • Network accessline 52
      "https://www.worldcat.org/api/search?q=au:hinton+geoffrey"
    • Network accessline 54
      [Credential-related source omitted]
    • Network accessline 55
      [Credential-related source omitted]
    • Network accessline 56
      "https://www.worldcat.org/api/search?q=bn:9780262035613"
    • Network accessline 58
      [Credential-related source omitted]
    • Network accessline 59
      [Credential-related source omitted]
    • Network accessline 60
      "https://www.worldcat.org/api/search?q=su:artificial+intelligence+AND+yr:2020-2026&itemType=book"
    • Network accessline 93
      [Credential-related source omitted]
    • Network accessline 94
      "https://www.worldcat.org/api/search/brief-bibs/{oclc_number}"
    • Network accessline 100
      [Credential-related source omitted]
    • Network accessline 101
      [Credential-related source omitted]
    • Network accessline 102
      "https://www.worldcat.org/api/search/brief-bibs/{oclc_number}/holdings?lat=42.36&lon=-71.06&distance=50"
    • Network accessline 136
      [Credential-related source omitted]
    • Access to secretsline 136
      [Credential-related source omitted]
    • Access to secretsline 137
      [Credential-related source omitted]
    • Network accessline 138
      BASE_URL = "https://www.worldcat.org/api/search"
    • Network accessline 141
      def get_token() -> str:     """Obtain OAuth token from OCLC."""     resp = requests.post(
    • Network accessline 142
      """Obtain OAuth token from OCLC."""     resp = requests.post(         "https://oauth.oclc.org/token",
    • Network accessline 143
      resp = requests.post(
    • Network accessline 144
      "https://oauth.oclc.org/token",
    • Access to secretsline 145
      [Credential-related source omitted]
    • Access to secretsline 149
      [Credential-related source omitted]
    • Network accessline 160
      resp = requests.get(
    • Network accessline 186
      [Credential-related source omitted]
    • Network accessline 187
      [Credential-related source omitted]
    • Network accessline 188
      resp = requests.get(
    • Network accessline 222
      - [WorldCat Search API Documentation](https://developer.api.oclc.org/)
    • Network accessline 223
      - [OCLC Developer Network](https://platform.worldcat.org/)
    • Network accessline 224
      - [WorldCat.org](https://www.worldcat.org/)

    skills/research/automation/ai-scientist-v2-guide/SKILL.md

    • Network accessline 8
      subcategory: "automation"     keywords: ["scientific-discovery", "automation", "tree-search", "paper-generation", "experiment-design", "sakana-ai"]     source: "https://github.com/SakanaAI/AI-Scientist-v2"
    • Network accessline 9
      keywords: ["scientific-discovery", "automation", "tree-search", "paper-generation", "experiment-design", "sakana-ai"]     source: "https://github.com/SakanaAI/AI-Scientist-v2" ---
    • Network accessline 10
      source: "https://github.com/SakanaAI/AI-Scientist-v2"
    • Network accessline 26
      # Clone the repository git clone https://github.com/SakanaAI/AI-Scientist-v2.git
    • Network accessline 27
      git clone https://github.com/SakanaAI/AI-Scientist-v2.git
    • Access to secretsline 44
      [Credential-related source omitted]
    • Access to secretsline 46
      [Credential-related source omitted]
    • Dangerous shell operationline 53
      sudo apt-get install texlive-full
    • Network accessline 281
      - Repository: https://github.com/SakanaAI/AI-Scientist-v2
    • Network accessline 282
      - Original AI Scientist paper: https://arxiv.org/abs/2408.06292
    • Network accessline 283
      - Sakana AI: https://sakana.ai/
    • Network accessline 284
      - AI Scientist v1: https://github.com/SakanaAI/AI-Scientist

    skills/research/automation/aim-experiment-guide/SKILL.md

    • Network accessline 8
      subcategory: "automation"     keywords: ["experiment-tracking", "visualization", "mlops", "reproducibility", "metrics", "hyperparameters"]     source: "https://github.com/aimhubio/aim"
    • Network accessline 9
      keywords: ["experiment-tracking", "visualization", "mlops", "reproducibility", "metrics", "hyperparameters"]     source: "https://github.com/aimhubio/aim" ---
    • Network accessline 10
      source: "https://github.com/aimhubio/aim"
    • Network accessline 44
      The dashboard becomes available at `http://localhost:43800`, providing interactive visualizations of all tracked experiments.
    • Network accessline 231
      - Aim repository: https://github.com/aimhubio/aim
    • Network accessline 232
      - Aim documentation: https://aimstack.readthedocs.io/

    skills/research/automation/claude-academic-workflow-guide/SKILL.md

    • Network accessline 8
      subcategory: "automation"     keywords: ["Claude Code", "academic workflow", "LaTeX", "Beamer", "R", "multi-agent review"]     source: "https://github.com/pedrohcgs/claude-code-my-workflow"
    • Network accessline 9
      keywords: ["Claude Code", "academic workflow", "LaTeX", "Beamer", "R", "multi-agent review"]     source: "https://github.com/pedrohcgs/claude-code-my-workflow" ---
    • Network accessline 10
      source: "https://github.com/pedrohcgs/claude-code-my-workflow"
    • Network accessline 200
      - [claude-code-my-workflow](https://github.com/pedrohcgs/claude-code-my-workflow)
    • Network accessline 201
      - [Metropolis Beamer Theme](https://github.com/matze/mtheme)
    • Network accessline 202
      - [modelsummary](https://modelsummary.com/)

    skills/research/automation/data-collection-automation/SKILL.md

    • Network accessline 37
      [Credential-related source omitted]
    • Access to secretsline 37
      [Credential-related source omitted]
    • Access to secretsline 38
      [Credential-related source omitted]
    • Network accessline 39
      base_url = f"https://{data_center}.qualtrics.com/API/v3"
    • Network accessline 52
      req = urllib.request.Request(
    • Network accessline 55
      headers=headers     )     response = json.loads(urllib.request.urlopen(req).read())
    • Network accessline 56
      )     response = json.loads(urllib.request.urlopen(req).read())     progress_id = response["result"]["progressId"]
    • Network accessline 57
      response = json.loads(urllib.request.urlopen(req).read())
    • Network accessline 62
      while status == "inProgress":         time.sleep(2)         req = urllib.request.Request(
    • Network accessline 63
      time.sleep(2)         req = urllib.request.Request(             f"{base_url}/surveys/{survey_id}/export-responses/{progress_id}",
    • Network accessline 64
      req = urllib.request.Request(
    • Network accessline 66
      headers=headers         )         check = json.loads(urllib.request.urlopen(req).read())
    • Network accessline 67
      )         check = json.loads(urllib.request.urlopen(req).read())         status = check["result"]["status"]
    • Network accessline 68
      check = json.loads(urllib.request.urlopen(req).read())
    • Network accessline 73
      # Step 3: Download file     req = urllib.request.Request(
    • Network accessline 74
      req = urllib.request.Request(
    • Network accessline 76
      headers=headers     )     file_data = urllib.request.urlopen(req).read()
    • Network accessline 78
      file_data = urllib.request.urlopen(req).read()
    • Access to secretsline 98
      [Credential-related source omitted]
    • Network accessline 110
      encoded = urllib.parse.urlencode(data).encode("utf-8")     req = urllib.request.Request(api_url, data=encoded)
    • Network accessline 111
      req = urllib.request.Request(api_url, data=encoded)
    • Network accessline 112
      response = urllib.request.urlopen(req)

    skills/research/automation/datagen-research-guide/SKILL.md

    • Network accessline 2
      name: datagen-research-guide description: "AI-driven multi-agent research assistant for end-to-end studies" source: https://github.com/DATAGEN-AI/DATAGEN
    • Network accessline 3
      description: "AI-driven multi-agent research assistant for end-to-end studies" source: https://github.com/DATAGEN-AI/DATAGEN metadata:
    • Network accessline 4
      source: https://github.com/DATAGEN-AI/DATAGEN

    skills/research/automation/kedro-pipeline-guide/SKILL.md

    • Network accessline 8
      subcategory: "automation"     keywords: ["pipeline", "reproducibility", "data-science", "workflow", "automation", "mlops"]     source: "https://github.com/kedro-org/kedro"
    • Network accessline 9
      keywords: ["pipeline", "reproducibility", "data-science", "workflow", "automation", "mlops"]     source: "https://github.com/kedro-org/kedro" ---
    • Network accessline 10
      source: "https://github.com/kedro-org/kedro"
    • Network accessline 213
      - Kedro repository: https://github.com/kedro-org/kedro
    • Network accessline 214
      - Kedro documentation: https://docs.kedro.org/
    • Network accessline 215
      - Kedro-Viz for pipeline visualization: https://github.com/kedro-org/kedro-viz

    skills/research/automation/mle-agent-guide/SKILL.md

    • Network accessline 2
      name: mle-agent-guide description: "Intelligent companion for ML engineering with arXiv integration" source: https://github.com/MLSys-Tools/MLE-agent
    • Network accessline 3
      description: "Intelligent companion for ML engineering with arXiv integration" source: https://github.com/MLSys-Tools/MLE-agent metadata:
    • Network accessline 4
      source: https://github.com/MLSys-Tools/MLE-agent

    skills/research/automation/paper-to-agent-guide/SKILL.md

    • Network accessline 2
      name: paper-to-agent-guide description: "Transform research papers into interactive AI agents for exploration" source: https://github.com/paper2agent/Paper2Agent
    • Network accessline 3
      description: "Transform research papers into interactive AI agents for exploration" source: https://github.com/paper2agent/Paper2Agent metadata:
    • Network accessline 4
      source: https://github.com/paper2agent/Paper2Agent

    skills/research/automation/rd-agent-guide/SKILL.md

    • Network accessline 8
      subcategory: "automation"     keywords: ["r-and-d", "microsoft", "automation", "model-development", "data-science", "experiment-automation"]     source: "https://github.com/microsoft/RD-Agent"
    • Network accessline 9
      keywords: ["r-and-d", "microsoft", "automation", "model-development", "data-science", "experiment-automation"]     source: "https://github.com/microsoft/RD-Agent" ---
    • Network accessline 10
      source: "https://github.com/microsoft/RD-Agent"
    • Network accessline 26
      # Clone the repository git clone https://github.com/microsoft/RD-Agent.git
    • Network accessline 27
      git clone https://github.com/microsoft/RD-Agent.git
    • Access to secretsline 41
      [Credential-related source omitted]
    • Access to secretsline 45
      [Credential-related source omitted]
    • Network accessline 243
      - Repository: https://github.com/microsoft/RD-Agent
    • Network accessline 244
      - Microsoft Research blog post: https://www.microsoft.com/en-us/research/project/rd-agent/
    • Network accessline 245
      - Qlib quantitative platform: https://github.com/microsoft/qlib
    • Network accessline 246
      - Documentation: https://microsoft.github.io/RD-Agent/

    skills/research/automation/research-workflow-automation/SKILL.md

    • Network accessline 50
      url = lambda wildcards: config["datasets"][wildcards.dataset]["url"]     shell:         "curl -L {params.url} -o {output}"
    • Network accessline 52
      "curl -L {params.url} -o {output}"
    • Dangerous shell operationline 135
      rm -rf data/cleaned/ results/ paper/*.pdf paper/*.aux paper/*.log

    skills/research/deep-research/deep-searcher-guide/SKILL.md

    • Network accessline 8
      subcategory: "deep-research"     keywords: ["deep-search", "private-data", "milvus", "vector-search", "rag", "document-retrieval"]     source: "https://github.com/zilliztech/deep-searcher"
    • Network accessline 9
      keywords: ["deep-search", "private-data", "milvus", "vector-search", "rag", "document-retrieval"]     source: "https://github.com/zilliztech/deep-searcher" ---
    • Network accessline 10
      source: "https://github.com/zilliztech/deep-searcher"
    • Network accessline 29
      # Or clone for development git clone https://github.com/zilliztech/deep-searcher.git
    • Network accessline 30
      git clone https://github.com/zilliztech/deep-searcher.git
    • Network accessline 50
      [Credential-related source omitted]
    • Access to secretsline 50
      [Credential-related source omitted]
    • Network accessline 52
      export OLLAMA_BASE_URL=http://localhost:11434
    • Access to secretsline 200
      [Credential-related source omitted]
    • Network accessline 233
      # Query via REST API curl -X POST http://localhost:8000/research \
    • Network accessline 234
      curl -X POST http://localhost:8000/research \
    • Network accessline 250
      - Repository: https://github.com/zilliztech/deep-searcher
    • Network accessline 251
      - Milvus vector database: https://milvus.io/
    • Network accessline 252
      - Zilliz Cloud (managed Milvus): https://zilliz.com/
    • Network accessline 253
      - Milvus documentation: https://milvus.io/docs/

    skills/research/deep-research/gpt-researcher-guide/SKILL.md

    • Network accessline 8
      subcategory: "deep-research"     keywords: ["deep-research", "autonomous-agent", "web-search", "report-generation", "literature-review"]     source: "https://github.com/assafelovic/gpt-researcher"
    • Network accessline 9
      keywords: ["deep-research", "autonomous-agent", "web-search", "report-generation", "literature-review"]     source: "https://github.com/assafelovic/gpt-researcher" ---
    • Network accessline 10
      source: "https://github.com/assafelovic/gpt-researcher"
    • Network accessline 29
      # Or clone for development git clone https://github.com/assafelovic/gpt-researcher.git
    • Network accessline 30
      git clone https://github.com/assafelovic/gpt-researcher.git
    • Access to secretsline 39
      [Credential-related source omitted]
    • Access to secretsline 41
      [Credential-related source omitted]
    • Access to secretsline 44
      [Credential-related source omitted]
    • Access to secretsline 46
      [Credential-related source omitted]
    • Network accessline 53
      # Use local LLM via Ollama export OPENAI_BASE_URL=http://localhost:11434/v1
    • Network accessline 54
      export OPENAI_BASE_URL=http://localhost:11434/v1
    • Network accessline 59
      # Use local search via SearXNG export SEARX_URL=http://localhost:8888
    • Network accessline 60
      export SEARX_URL=http://localhost:8888
    • Network accessline 141
      query="CRISPR gene editing safety profiles",     source_urls=[         "https://pubmed.ncbi.nlm.nih.gov/",
    • Network accessline 142
      source_urls=[         "https://pubmed.ncbi.nlm.nih.gov/",         "https://www.nature.com/",
    • Network accessline 143
      "https://pubmed.ncbi.nlm.nih.gov/",
    • Network accessline 144
      "https://www.nature.com/",
    • Network accessline 145
      "https://www.science.org/",
    • Network accessline 188
      - Repository: https://github.com/assafelovic/gpt-researcher
    • Network accessline 189
      - Documentation: https://docs.gptr.dev/
    • Network accessline 190
      - Tavily Search API: https://tavily.com/
    • Network accessline 191
      - Research paper: https://arxiv.org/abs/2305.04091

    skills/research/deep-research/khoj-research-guide/SKILL.md

    • Network accessline 8
      subcategory: "deep-research"     keywords: ["second-brain", "knowledge-management", "document-analysis", "rag", "self-hosted", "research-assistant"]     source: "https://github.com/khoj-ai/khoj"
    • Network accessline 9
      keywords: ["second-brain", "knowledge-management", "document-analysis", "rag", "self-hosted", "research-assistant"]     source: "https://github.com/khoj-ai/khoj" ---
    • Network accessline 10
      source: "https://github.com/khoj-ai/khoj"
    • Network accessline 44
      After starting Khoj, configure it through the web interface at `http://localhost:42110/config`:
    • Network accessline 52
      [Credential-related source omitted]
    • Access to secretsline 52
      [Credential-related source omitted]
    • Network accessline 54
      export OLLAMA_HOST=http://localhost:11434
    • Network accessline 61
      - **Web interface**: Full-featured browser UI at `http://localhost:42110`
    • Network accessline 68
      # Install the Obsidian plugin # In Obsidian: Settings > Community Plugins > Search "Khoj" # Configure server URL: http://localhost:42110
    • Network accessline 70
      # Configure server URL: http://localhost:42110
    • Network accessline 92
      # Add a document directory requests.post("http://localhost:42110/api/config/data/source", json={
    • Network accessline 93
      requests.post("http://localhost:42110/api/config/data/source", json={
    • Network accessline 106
      # Trigger deep research via the API response = requests.post("http://localhost:42110/api/chat", json={
    • Network accessline 107
      response = requests.post("http://localhost:42110/api/chat", json={
    • Network accessline 140
      # Create a research agent that monitors new papers requests.post("http://localhost:42110/api/agents", json={
    • Network accessline 141
      requests.post("http://localhost:42110/api/agents", json={
    • Network accessline 197
      - Repository: https://github.com/khoj-ai/khoj
    • Network accessline 198
      - Documentation: https://docs.khoj.dev/
    • Network accessline 199
      - Obsidian plugin: https://github.com/khoj-ai/khoj/tree/master/src/interface/obsidian
    • Network accessline 200
      - Self-hosting guide: https://docs.khoj.dev/get-started/setup/

    skills/research/deep-research/kosmos-scientist-guide/SKILL.md

    • Network accessline 8
      subcategory: "deep-research"     keywords: ["AI Scientist", "autonomous discovery", "Claude Code", "research automation", "scientific method", "experiment"]     source: "https://github.com/jimmc414/Kosmos"
    • Network accessline 9
      keywords: ["AI Scientist", "autonomous discovery", "Claude Code", "research automation", "scientific method", "experiment"]     source: "https://github.com/jimmc414/Kosmos" ---
    • Network accessline 10
      source: "https://github.com/jimmc414/Kosmos"
    • Network accessline 183
      - [Kosmos GitHub](https://github.com/jimmc414/Kosmos)
    • Network accessline 184
      - [The AI Scientist](https://arxiv.org/abs/2408.06292)
    • Network accessline 185
      - [Claude Code](https://docs.anthropic.com/en/docs/claude-code)

    skills/research/deep-research/llm-scientific-discovery-guide/SKILL.md

    • Network accessline 8
      subcategory: "deep-research"     keywords: ["LLM agents", "scientific discovery", "biomedical AI", "drug discovery", "hypothesis generation", "lab automation"]     source: "https://github.com/zjlrock777/Awesome-LLM-Agents-Scientific-Discove
    • Network accessline 9
      keywords: ["LLM agents", "scientific discovery", "biomedical AI", "drug discovery", "hypothesis generation", "lab automation"]     source: "https://github.com/zjlrock777/Awesome-LLM-Agents-Scientific-Discovery" ---
    • Network accessline 10
      source: "https://github.com/zjlrock777/Awesome-LLM-Agents-Scientific-Discovery"
    • Network accessline 176
      - [Awesome-LLM-Agents-Scientific-Discovery](https://github.com/zjlrock777/Awesome-LLM-Agents-Scientific-Discovery)
    • Network accessline 177
      - [The AI Scientist](https://arxiv.org/abs/2408.06292)
    • Network accessline 178
      - [ChemCrow](https://arxiv.org/abs/2304.05376)

    skills/research/deep-research/local-deep-research-guide/SKILL.md

    • Network accessline 8
      subcategory: "deep-research"     keywords: ["local-llm", "deep-research", "multi-source", "ollama", "privacy", "academic-search"]     source: "https://github.com/LearningCircuit/local-deep-research"
    • Network accessline 9
      keywords: ["local-llm", "deep-research", "multi-source", "ollama", "privacy", "academic-search"]     source: "https://github.com/LearningCircuit/local-deep-research" ---
    • Network accessline 10
      source: "https://github.com/LearningCircuit/local-deep-research"
    • Network accessline 29
      # Or clone for development git clone https://github.com/LearningCircuit/local-deep-research.git
    • Network accessline 30
      git clone https://github.com/LearningCircuit/local-deep-research.git
    • Network accessline 40
      # Option 1: Local LLM via Ollama (fully private) # First, install Ollama: https://ollama.com/
    • Network accessline 41
      # First, install Ollama: https://ollama.com/
    • Network accessline 46
      # Option 2: Local LLM via LM Studio export LDR_LLM_PROVIDER=lmstudio export LDR_LLM_BASE_URL=http://localhost:1234/v1
    • Network accessline 48
      export LDR_LLM_BASE_URL=http://localhost:1234/v1
    • Access to secretsline 52
      [Credential-related source omitted]
    • Access to secretsline 57
      [Credential-related source omitted]
    • Access to secretsline 67
      [Credential-related source omitted]
    • Network accessline 69
      [Credential-related source omitted]
    • Access to secretsline 69
      [Credential-related source omitted]
    • Network accessline 71
      export SEARX_URL=http://localhost:8888  # Self-hosted SearXNG
    • Access to secretsline 74
      [Credential-related source omitted]
    • Network accessline 238
      export LDR_LLM_PROVIDER=ollama export LDR_LLM_MODEL=llama3.1:70b export SEARX_URL=http://localhost:8888
    • Network accessline 239
      export LDR_LLM_MODEL=llama3.1:70b export SEARX_URL=http://localhost:8888 export LDR_SEARCH_SOURCES=searxng,arxiv,pubmed,wikipedia
    • Network accessline 240
      export SEARX_URL=http://localhost:8888
    • Network accessline 249
      - Repository: https://github.com/LearningCircuit/local-deep-research
    • Network accessline 250
      - Ollama: https://ollama.com/
    • Network accessline 251
      - SearXNG: https://github.com/searxng/searxng
    • Network accessline 252
      - OpenAlex API: https://api.openalex.org/
    • Network accessline 253
      - arXiv API: https://info.arxiv.org/help/api/

    skills/research/deep-research/open-researcher-guide/SKILL.md

    • Network accessline 8
      subcategory: "deep-research"     keywords: ["OpenResearcher", "deep research", "research trajectory", "open pipeline", "literature synthesis", "LLM research"]     source: "https://github.com/GAIR-NLP/OpenResearcher"
    • Network accessline 9
      keywords: ["OpenResearcher", "deep research", "research trajectory", "open pipeline", "literature synthesis", "LLM research"]     source: "https://github.com/GAIR-NLP/OpenResearcher" ---
    • Network accessline 10
      source: "https://github.com/GAIR-NLP/OpenResearcher"
    • Network accessline 137
      - [OpenResearcher GitHub](https://github.com/GAIR-NLP/OpenResearcher)
    • Network accessline 138
      - [GAIR-NLP Lab](https://github.com/GAIR-NLP)

    skills/research/deep-research/tongyi-deep-research-guide/SKILL.md

    • Network accessline 8
      subcategory: "deep-research"     keywords: ["deep-research", "alibaba", "tongyi", "agentic-rag", "scholarly-search", "open-source"]     source: "https://github.com/Alibaba-NLP/DeepResearch"
    • Network accessline 9
      keywords: ["deep-research", "alibaba", "tongyi", "agentic-rag", "scholarly-search", "open-source"]     source: "https://github.com/Alibaba-NLP/DeepResearch" ---
    • Network accessline 10
      source: "https://github.com/Alibaba-NLP/DeepResearch"
    • Network accessline 26
      # Clone the repository git clone https://github.com/Alibaba-NLP/DeepResearch.git
    • Network accessline 27
      git clone https://github.com/Alibaba-NLP/DeepResearch.git
    • Access to secretsline 43
      [Credential-related source omitted]
    • Access to secretsline 48
      [Credential-related source omitted]
    • Network accessline 55
      # Use local models export LLM_BASE_URL=http://localhost:11434/v1
    • Network accessline 56
      export LLM_BASE_URL=http://localhost:11434/v1
    • Access to secretsline 58
      [Credential-related source omitted]
    • Network accessline 214
      - Repository: https://github.com/Alibaba-NLP/DeepResearch
    • Network accessline 215
      - Qwen model family: https://github.com/QwenLM/Qwen
    • Network accessline 216
      - Alibaba NLP group: https://github.com/Alibaba-NLP
    • Network accessline 217
      - OpenAlex API: https://api.openalex.org/

    skills/research/funding/eu-horizon-guide/SKILL.md

    • Network accessline 57
      1. Funding and Tenders Portal (primary source):    https://ec.europa.eu/info/funding-tenders/opportunities/portal/
    • Network accessline 58
      https://ec.europa.eu/info/funding-tenders/opportunities/portal/

    skills/research/funding/figshare-api/SKILL.md

    • Network accessline 8
      subcategory: "funding"     keywords: ["open data", "data sharing", "data archiving", "FAIR data principles", "open source code"]     source: "https://docs.figshare.com/"
    • Network accessline 9
      keywords: ["open data", "data sharing", "data archiving", "FAIR data principles", "open source code"]     source: "https://docs.figshare.com/"     requires:
    • Network accessline 10
      source: "https://docs.figshare.com/"
    • Access to secretsline 12
      [Credential-related source omitted]
    • Network accessline 29
      1. Log in to Figshare at https://figshare.com/
    • Network accessline 35
      [Credential-related source omitted]
    • Network accessline 46
      - **URL**: `GET https://api.figshare.com/v2/articles`
    • Network accessline 62
      curl -X POST "https://api.figshare.com/v2/articles/search" \
    • Network accessline 73
      - **URL**: `GET https://api.figshare.com/v2/articles/{article_id}`
    • Network accessline 83
      # Get a specific dataset by ID curl "https://api.figshare.com/v2/articles/12345678"
    • Network accessline 84
      curl "https://api.figshare.com/v2/articles/12345678"
    • Network accessline 86
      # List files in a dataset curl "https://api.figshare.com/v2/articles/12345678/files"
    • Network accessline 87
      curl "https://api.figshare.com/v2/articles/12345678/files"
    • Network accessline 94
      Rate limits vary based on authentication status and endpoint. Authenticated requests generally allow up to 100 requests per minute. Unauthenticated requests are limited to approximately 10 requests per minute. The API returns HTTP 429 with
    • Network accessline 113
      resp = requests.post("https://api.figshare.com/v2/articles/search", json=payload)
    • Access to secretsline 130
      [Credential-related source omitted]
    • Network accessline 139
      "categories": [69]  # Genetics category } resp = requests.post("https://api.figshare.com/v2/account/articles",
    • Network accessline 140
      } resp = requests.post("https://api.figshare.com/v2/account/articles",                      headers=headers, json=article_data)
    • Network accessline 141
      resp = requests.post("https://api.figshare.com/v2/account/articles",
    • Network accessline 145
      # Step 2: Upload file article = requests.get(article_url, headers=headers).json()
    • Network accessline 146
      article = requests.get(article_url, headers=headers).json()
    • Network accessline 155
      curl "https://api.figshare.com/v2/oai?verb=ListRecords&metadataPrefix=oai_dc&set=institution_123"
    • Network accessline 160
      - Official API documentation: https://docs.figshare.com/
    • Network accessline 161
      - Figshare homepage: https://figshare.com/
    • Network accessline 162
      - API endpoint reference: https://docs.figshare.com/#figshare_documentation_api_description
    • Network accessline 163
      - OAI-PMH endpoint: https://docs.figshare.com/#oai_pmh

    skills/research/funding/nih-reporter-api-guide/SKILL.md

    • Network accessline 8
      subcategory: "funding"     keywords: ["nih", "grants", "biomedical", "funding", "reporter", "health-research"]     source: "https://api.reporter.nih.gov/"
    • Network accessline 9
      keywords: ["nih", "grants", "biomedical", "funding", "reporter", "health-research"]     source: "https://api.reporter.nih.gov/" ---
    • Network accessline 10
      source: "https://api.reporter.nih.gov/"
    • Network accessline 28
      # No API key needed curl -X POST "https://api.reporter.nih.gov/v2/projects/search" \
    • Network accessline 29
      curl -X POST "https://api.reporter.nih.gov/v2/projects/search" \
    • Network accessline 41
      POST https://api.reporter.nih.gov/v2/projects/search
    • Network accessline 57
      curl -s -X POST "https://api.reporter.nih.gov/v2/projects/search" \
    • Network accessline 78
      POST https://api.reporter.nih.gov/v2/publications/search
    • Network accessline 82
      curl -s -X POST "https://api.reporter.nih.gov/v2/publications/search" \
    • Network accessline 98
      API_URL = "https://api.reporter.nih.gov/v2/projects/search"
    • Network accessline 117
      resp = requests.post(API_URL, json=payload)
    • Network accessline 163
      - NIH RePORTER API v2 Documentation: https://api.reporter.nih.gov/
    • Network accessline 164
      - NIH RePORTER Web Interface: https://reporter.nih.gov/
    • Network accessline 165
      - NIH Activity Codes (Grant Mechanisms): https://grants.nih.gov/grants/funding/ac_search_results.htm
    • Network accessline 166
      - NIH Institutes and Centers: https://www.nih.gov/institutes-nih/list-nih-institutes-centers-offices

    skills/research/funding/nsf-award-api-guide/SKILL.md

    • Network accessline 8
      subcategory: "funding"     keywords: ["nsf", "grants", "funding", "awards", "national-science-foundation"]     source: "https://www.research.gov/common/webapi/awardapisearch-v1.htm"
    • Network accessline 9
      keywords: ["nsf", "grants", "funding", "awards", "national-science-foundation"]     source: "https://www.research.gov/common/webapi/awardapisearch-v1.htm" ---
    • Network accessline 10
      source: "https://www.research.gov/common/webapi/awardapisearch-v1.htm"
    • Network accessline 28
      # No API key needed -- just make the request curl "https://api.nsf.gov/services/v1/awards.json?keyword=quantum+computing"
    • Network accessline 29
      curl "https://api.nsf.gov/services/v1/awards.json?keyword=quantum+computing"
    • Network accessline 37
      GET https://api.nsf.gov/services/v1/awards.json?{params}
    • Dangerous shell operationline 53
      curl -s "https://api.nsf.gov/services/v1/awards.json? keyword=machine+learning& awardeeName=Massachusetts+Institute+of+Technology& printFields=id,title,piFirstName,piLastName,startDate,awardeeName,fundsObligatedAmt,abstractText& offset=1" |
    • Network accessline 53
      curl -s "https://api.nsf.gov/services/v1/awards.json?\
    • Dangerous shell operationline 65
      curl -s "https://api.nsf.gov/services/v1/awards/2345678.json? printFields=id,title,piFirstName,piLastName,startDate,expDate,awardeeName,fundsObligatedAmt,abstractText"    | python3 -m json.tool
    • Network accessline 65
      curl -s "https://api.nsf.gov/services/v1/awards/2345678.json?\
    • Network accessline 76
      base_url = "https://api.nsf.gov/services/v1/awards.json"
    • Network accessline 89
      "offset": offset         }         resp = requests.get(base_url, params=params)
    • Network accessline 90
      }         resp = requests.get(base_url, params=params)         data = resp.json()
    • Network accessline 91
      resp = requests.get(base_url, params=params)
    • Network accessline 125
      - **Date formats:** Use MM/DD/YYYY format strictly - **Pagination:** The API uses 1-based offset; increment by 25 for each page - **Large datasets:** For bulk analysis, consider using the NSF data download at https://www.nsf.gov/awardsearch
    • Network accessline 127
      - **Large datasets:** For bulk analysis, consider using the NSF data download at https://www.nsf.gov/awardsearch/download.jsp
    • Network accessline 131
      - NSF Award Search API Documentation: https://www.research.gov/common/webapi/awardapisearch-v1.htm - NSF Award Search Web Interface: https://www.nsf.gov/awardsearch/ - NSF Data Downloads: https://www.nsf.gov/awardsearch/download.jsp
    • Network accessline 132
      - NSF Award Search Web Interface: https://www.nsf.gov/awardsearch/
    • Network accessline 133
      - NSF Data Downloads: https://www.nsf.gov/awardsearch/download.jsp

    skills/research/funding/zenodo-api/SKILL.md

    • Network accessline 8
      subcategory: "funding"     keywords: ["open data", "data sharing", "data archiving", "FAIR data principles"]     source: "https://developers.zenodo.org/"
    • Network accessline 9
      keywords: ["open data", "data sharing", "data archiving", "FAIR data principles"]     source: "https://developers.zenodo.org/"     requires:
    • Network accessline 10
      source: "https://developers.zenodo.org/"
    • Access to secretsline 12
      [Credential-related source omitted]
    • Network accessline 29
      1. Create an account at https://zenodo.org/
    • Access to secretsline 32
      [Credential-related source omitted]
    • Network accessline 35
      [Credential-related source omitted]
    • Network accessline 36
      [Credential-related source omitted]
    • Access to secretsline 36
      [Credential-related source omitted]
    • Network accessline 38
      [Credential-related source omitted]
    • Network accessline 39
      [Credential-related source omitted]
    • Network accessline 50
      - **URL**: `GET https://zenodo.org/api/records`
    • Network accessline 65
      curl "https://zenodo.org/api/records?q=climate+change&type=dataset&sort=mostrecent&size=5"
    • Network accessline 74
      - **URL**: `GET https://zenodo.org/api/deposit/depositions`
    • Access to secretsline 79
      [Credential-related source omitted]
    • Network accessline 87
      [Credential-related source omitted]
    • Network accessline 88
      [Credential-related source omitted]
    • Access to secretsline 88
      [Credential-related source omitted]
    • Network accessline 90
      [Credential-related source omitted]
    • Network accessline 91
      [Credential-related source omitted]
    • Access to secretsline 91
      [Credential-related source omitted]
    • Network accessline 115
      "size": 20 } resp = requests.get("https://zenodo.org/api/records", params=params)
    • Network accessline 116
      } resp = requests.get("https://zenodo.org/api/records", params=params) data = resp.json()
    • Network accessline 117
      resp = requests.get("https://zenodo.org/api/records", params=params)
    • Access to secretsline 132
      [Credential-related source omitted]
    • Network accessline 135
      # Step 1: Create empty deposition dep = requests.post("https://zenodo.org/api/deposit/depositions",
    • Network accessline 136
      dep = requests.post("https://zenodo.org/api/deposit/depositions",
    • Network accessline 140
      bucket_url = dep["links"]["bucket"] with open("analysis_code.zip", "rb") as f:     requests.put(f"{bucket_url}/analysis_code.zip",
    • Network accessline 141
      [Credential-related source omitted]
    • Network accessline 142
      requests.put(f"{bucket_url}/analysis_code.zip",
    • Network accessline 153
      } } requests.put(f"https://zenodo.org/api/deposit/depositions/{dep['id']}",
    • Network accessline 154
      } requests.put(f"https://zenodo.org/api/deposit/depositions/{dep['id']}",              headers=headers, json=metadata)
    • Network accessline 155
      requests.put(f"https://zenodo.org/api/deposit/depositions/{dep['id']}",
    • Network accessline 156
      [Credential-related source omitted]
    • Network accessline 157
      requests.post(f"https://zenodo.org/api/deposit/depositions/{dep['id']}/actions/publish",
    • Network accessline 166
      curl "https://zenodo.org/api/records?communities=astronomy&size=100&sort=mostrecent"
    • Network accessline 171
      - Official API documentation: https://developers.zenodo.org/
    • Network accessline 172
      - Zenodo homepage: https://zenodo.org/
    • Network accessline 173
      - GitHub integration guide: https://guides.github.com/activities/citable-code/
    • Network accessline 174
      - DataCite Metadata Schema: https://schema.datacite.org/

    skills/research/methodology/claude-scientific-guide/SKILL.md

    • Network accessline 2
      name: claude-scientific-guide description: "Ready-to-use agent skills for scientific research and engineering" source: https://github.com/zyphlar/claude-scientific-skills
    • Network accessline 3
      description: "Ready-to-use agent skills for scientific research and engineering" source: https://github.com/zyphlar/claude-scientific-skills metadata:
    • Network accessline 4
      source: https://github.com/zyphlar/claude-scientific-skills

    skills/research/methodology/grad-school-guide/SKILL.md

    • Network accessline 8
      subcategory: "methodology"     keywords: ["research question formulation", "hypothesis formulation", "theoretical framework", "conceptual model"]     source: "https://github.com/poloclub/awesome-grad-school"
    • Network accessline 9
      keywords: ["research question formulation", "hypothesis formulation", "theoretical framework", "conceptual model"]     source: "https://github.com/poloclub/awesome-grad-school" ---
    • Network accessline 10
      source: "https://github.com/poloclub/awesome-grad-school"
    • Network accessline 178
      - [awesome-grad-school](https://github.com/poloclub/awesome-grad-school) -- Curated grad school advice (450+ stars)
    • Network accessline 179
      - [A Survival Guide to a PhD](http://karpathy.github.io/2016/09/07/phd/) -- Andrej Karpathy
    • Network accessline 180
      - [Modest Advice for New Graduate Students](https://stearnslab.yale.edu/modest-advice) -- Stephen Stearns, Yale
    • Network accessline 181
      - [De-Mystifying Good Research](https://bigaidream.gitbooks.io/tech-blog/content/2014/de-mystifying-good-research.html) -- Fei-Fei Li
    • Network accessline 182
      - [How to Write a Great Research Paper](https://www.microsoft.com/en-us/research/academic-program/write-great-research-paper/) -- Simon Peyton Jones

    skills/research/methodology/parsifal-slr-guide/SKILL.md

    • Network accessline 8
      subcategory: "methodology"     keywords: ["Parsifal", "systematic review", "SLR", "review protocol", "PICO", "research methodology"]     source: "https://github.com/vitorfs/parsifal"
    • Network accessline 9
      keywords: ["Parsifal", "systematic review", "SLR", "review protocol", "PICO", "research methodology"]     source: "https://github.com/vitorfs/parsifal" ---
    • Network accessline 10
      source: "https://github.com/vitorfs/parsifal"
    • Network accessline 133
      git clone https://github.com/vitorfs/parsifal.git
    • Network accessline 136
      python manage.py migrate python manage.py runserver # Access at http://localhost:8000
    • Network accessline 138
      # Access at http://localhost:8000
    • Network accessline 151
      - [Parsifal](https://github.com/vitorfs/parsifal)
    • Network accessline 152
      - Kitchenham, B. & Charters, S. (2007). "Guidelines for performing Systematic Literature Reviews in Software Engineering." - [PRISMA Statement](http://www.prisma-statement.org/) - [PROSPERO Registry](https://www.crd.york.ac.uk/prospero/)
    • Network accessline 153
      - [PRISMA Statement](http://www.prisma-statement.org/)
    • Network accessline 154
      - [PROSPERO Registry](https://www.crd.york.ac.uk/prospero/)

    skills/research/methodology/research-paper-kb/SKILL.md

    • Network accessline 260
      - Obsidian knowledge management: https://obsidian.md
    • Network accessline 261
      - Zettlekasten method: https://zettelkasten.de/introduction
    • Network accessline 262
      - Notion for research: https://www.notion.so/templates/research
    • Network accessline 263
      - YAML specification: https://yaml.org/spec/1.2.2/

    skills/research/methodology/research-town-guide/SKILL.md

    • Network accessline 259
      - Research Town: wentor-research-plugins - The AI Scientist (Sakana AI): https://github.com/SakanaAI/AI-Scientist
    • Network accessline 260
      - The AI Scientist (Sakana AI): https://github.com/SakanaAI/AI-Scientist
    • Network accessline 261
      - AutoGen multi-agent framework: https://github.com/microsoft/autogen
    • Network accessline 262
      - CrewAI agent framework: https://github.com/joaomdmoura/crewAI

    skills/research/methodology/scientify-idea-generation/SKILL.md

    • Network accessline 105
      mkdir -p $WORKSPACE/papers/{arxiv_id} curl -L "https://arxiv.org/src/{arxiv_id}" | tar -xz -C $WORKSPACE/papers/{arxiv_id}
    • Network accessline 106
      curl -L "https://arxiv.org/src/{arxiv_id}" | tar -xz -C $WORKSPACE/papers/{arxiv_id}

    skills/research/methodology/slr-automation-guide/SKILL.md

    • Network accessline 8
      subcategory: "methodology"     keywords: ["systematic review", "SLR", "automation", "screening", "PRISMA", "evidence synthesis"]     source: "https://github.com/asreview/asreview"
    • Network accessline 9
      keywords: ["systematic review", "SLR", "automation", "screening", "PRISMA", "evidence synthesis"]     source: "https://github.com/asreview/asreview" ---
    • Network accessline 10
      source: "https://github.com/asreview/asreview"
    • Network accessline 232
      - [ASReview](https://asreview.nl/) — Active learning for systematic reviews
    • Network accessline 233
      - [PRISMA 2020](http://www.prisma-statement.org/) — Reporting guidelines
    • Network accessline 234
      - [Cochrane Handbook](https://training.cochrane.org/handbook)
    • Network accessline 235
      - [Rayyan](https://www.rayyan.ai/) — Collaborative screening platform

    skills/research/paper-review/latte-review-guide/SKILL.md

    • Network accessline 8
      subcategory: "paper-review"     keywords: ["LatteReview", "systematic review", "literature screening", "AI review", "title screening", "PRISMA"]     source: "https://github.com/PouriaRouzrokh/LatteReview"
    • Network accessline 9
      keywords: ["LatteReview", "systematic review", "literature screening", "AI review", "title screening", "PRISMA"]     source: "https://github.com/PouriaRouzrokh/LatteReview" ---
    • Network accessline 10
      source: "https://github.com/PouriaRouzrokh/LatteReview"
    • Network accessline 143
      llm_provider="ollama",     model="llama3",     base_url="http://localhost:11434",
    • Network accessline 144
      model="llama3",     base_url="http://localhost:11434", )
    • Network accessline 145
      base_url="http://localhost:11434",
    • Network accessline 173
      - [LatteReview GitHub](https://github.com/PouriaRouzrokh/LatteReview)
    • Network accessline 174
      - [LatteReview Documentation](https://lattereview.readthedocs.io/)

    skills/research/paper-review/paper-critique-framework/SKILL.md

    • Network accessline 178
      - Smith, R. (2006). "Peer review: a flawed process at the heart of science and journals." *Journal of the Royal Society of Medicine*, 99(4), 178-182. - [NeurIPS Reviewer Guidelines](https://neurips.cc/Conferences/2025/ReviewerGuidelines)
    • Network accessline 179
      - [NeurIPS Reviewer Guidelines](https://neurips.cc/Conferences/2025/ReviewerGuidelines)
    • Network accessline 180
      - [ACL Reviewer Tutorial](https://aclrollingreview.org/reviewertutorial)

    skills/tools/code-exec/google-colab-guide/SKILL.md

    • Network accessline 8
      subcategory: "code-exec"     keywords: ["Google Colab", "Jupyter", "GPU", "machine learning", "Python", "cloud computing"]     source: "https://colab.research.google.com"
    • Network accessline 9
      keywords: ["Google Colab", "Jupyter", "GPU", "machine learning", "Python", "cloud computing"]     source: "https://colab.research.google.com" ---
    • Network accessline 10
      source: "https://colab.research.google.com"
    • Network accessline 67
      # From URL !wget -q https://example.com/dataset.zip -O /content/dataset.zip
    • Network accessline 68
      !wget -q https://example.com/dataset.zip -O /content/dataset.zip
    • Network accessline 186
      # Install from GitHub !pip install -q git+https://github.com/huggingface/peft.git
    • Network accessline 187
      !pip install -q git+https://github.com/huggingface/peft.git
    • Network accessline 259
      # Clone a research repository !git clone https://github.com/user/research-repo.git /content/repo
    • Network accessline 260
      !git clone https://github.com/user/research-repo.git /content/repo
    • Network accessline 273
      - Google Colab documentation: https://colab.research.google.com/notebooks/intro.ipynb
    • Network accessline 274
      - Colab resource limits FAQ: https://research.google.com/colaboratory/faq.html
    • Network accessline 275
      - PyTorch on Colab: https://pytorch.org/tutorials/beginner/colab
    • Network accessline 276
      - Hugging Face + Colab: https://huggingface.co/docs/transformers/notebooks

    skills/tools/code-exec/jupyter-notebook-guide/SKILL.md

    • Network accessline 169
      # Then open http://localhost:8888 in your local browser

    skills/tools/code-exec/kaggle-api-guide/SKILL.md

    • Network accessline 8
      subcategory: "code-exec"     keywords: ["kaggle", "datasets", "competitions", "notebooks", "data-science", "machine-learning"]     source: "https://www.kaggle.com/docs/api"
    • Network accessline 9
      keywords: ["kaggle", "datasets", "competitions", "notebooks", "data-science", "machine-learning"]     source: "https://www.kaggle.com/docs/api" ---
    • Network accessline 10
      source: "https://www.kaggle.com/docs/api"
    • Network accessline 25
      A free Kaggle API token is required. Generate one from your Kaggle account settings at https://www.kaggle.com/settings.
    • Access to secretsline 41
      [Credential-related source omitted]
    • Network accessline 212
      - Kaggle API Documentation: https://www.kaggle.com/docs/api
    • Network accessline 213
      - Kaggle API GitHub Repository: https://github.com/Kaggle/kaggle-api
    • Network accessline 214
      - Kaggle Datasets: https://www.kaggle.com/datasets
    • Network accessline 215
      - Kaggle Competitions: https://www.kaggle.com/competitions
    • Network accessline 216
      - Kaggle Notebooks: https://www.kaggle.com/code

    skills/tools/code-exec/overleaf-cli-guide/SKILL.md

    • Network accessline 8
      subcategory: "code-exec"     keywords: ["Overleaf", "LaTeX", "CLI", "sync", "git", "collaboration", "academic writing"]     source: "https://github.com/overleaf/overleaf"
    • Network accessline 9
      keywords: ["Overleaf", "LaTeX", "CLI", "sync", "git", "collaboration", "academic writing"]     source: "https://github.com/overleaf/overleaf" ---
    • Network accessline 10
      source: "https://github.com/overleaf/overleaf"
    • Network accessline 32
      # Clone your Overleaf project (requires paid plan) git clone https://git.overleaf.com/YOUR_PROJECT_ID my-paper
    • Network accessline 33
      git clone https://git.overleaf.com/YOUR_PROJECT_ID my-paper
    • Network accessline 36
      # The remote is already configured git remote -v # origin  https://git.overleaf.com/YOUR_PROJECT_ID (fetch)
    • Network accessline 37
      git remote -v # origin  https://git.overleaf.com/YOUR_PROJECT_ID (fetch) # origin  https://git.overleaf.com/YOUR_PROJECT_ID (push)
    • Network accessline 38
      # origin  https://git.overleaf.com/YOUR_PROJECT_ID (fetch)
    • Network accessline 39
      # origin  https://git.overleaf.com/YOUR_PROJECT_ID (push)
    • Network accessline 133
      # Export from Zotero using Better BibTeX     subprocess.run([         "curl", "-s",
    • Network accessline 134
      subprocess.run([         "curl", "-s",         f"http://localhost:23119/better-bibtex/export/library?/"
    • Network accessline 135
      "curl", "-s",         f"http://localhost:23119/better-bibtex/export/library?/"         f"{zotero_lib_id}/library.biblatex",
    • Network accessline 136
      f"http://localhost:23119/better-bibtex/export/library?/"
    • Network accessline 276
      - Overleaf Git bridge documentation: https://www.overleaf.com/learn/how-to/Git_integration
    • Network accessline 277
      - overleaf-sync: https://github.com/moritzgloeckl/overleaf-sync
    • Network accessline 278
      - LaTeX Workshop (VS Code): https://github.com/James-Yu/LaTeX-Workshop
    • Network accessline 279
      - latexmk documentation: https://mg.readthedocs.io/latexmk.html

    skills/tools/code-exec/python-reproducibility-guide/SKILL.md

    • Access to secretsline 179
      [Credential-related source omitted]
    • Dangerous shell operationline 211
      RUN apt-get update && apt-get install -y      build-essential      git      && rm -rf /var/lib/apt/lists/*
    • Dangerous shell operationline 214
      && rm -rf /var/lib/apt/lists/*
    • Dangerous shell operationline 290
      rm -rf data/processed/ outputs/

    skills/tools/code-exec/r-reproducibility-guide/SKILL.md

    • Dangerous shell operationline 201
      rm -rf output/figures/* output/manuscript.pdf data/processed/*

    skills/tools/code-exec/sandbox-execution-guide/SKILL.md

    • Dangerous shell operationline 34
      RUN apt-get update && apt-get install -y --no-install-recommends      build-essential      gfortran      libopenblas-dev      && rm -rf /var/lib/apt/lists/*
    • Dangerous shell operationline 38
      && rm -rf /var/lib/apt/lists/*
    • Network accessline 149
      # shell.nix for a research project { pkgs ? import (fetchTarball {     url = "https://github.com/NixOS/nixpkgs/archive/nixos-23.11.tar.gz";
    • Network accessline 150
      { pkgs ? import (fetchTarball {     url = "https://github.com/NixOS/nixpkgs/archive/nixos-23.11.tar.gz";   }) {} }:
    • Network accessline 151
      url = "https://github.com/NixOS/nixpkgs/archive/nixos-23.11.tar.gz";

    skills/tools/diagram/code-flow-visualizer/SKILL.md

    • Network accessline 8
      subcategory: "diagram"     keywords: ["code visualization", "flowchart", "Mermaid", "Python", "control flow", "AST"]     source: "https://github.com/mermaid-js/mermaid"
    • Network accessline 9
      keywords: ["code visualization", "flowchart", "Mermaid", "Python", "control flow", "AST"]     source: "https://github.com/mermaid-js/mermaid" ---
    • Network accessline 10
      source: "https://github.com/mermaid-js/mermaid"
    • Network accessline 194
      - Mermaid flowchart syntax: https://mermaid.js.org/syntax/flowchart.html
    • Network accessline 195
      - Python AST module: https://docs.python.org/3/library/ast.html
    • Network accessline 196
      - TypeScript Compiler API: https://github.com/microsoft/TypeScript/wiki/Using-the-Compiler-API
    • Network accessline 197
      - Code2Flow (related tool): https://github.com/scottrogowski/code2flow

    skills/tools/diagram/excalidraw-diagram-guide/SKILL.md

    • Network accessline 8
      subcategory: "diagram"     keywords: ["Excalidraw", "diagram", "whiteboard", "hand-drawn", "sketch", "visual"]     source: "https://github.com/excalidraw/excalidraw"
    • Network accessline 9
      keywords: ["Excalidraw", "diagram", "whiteboard", "hand-drawn", "sketch", "visual"]     source: "https://github.com/excalidraw/excalidraw" ---
    • Network accessline 10
      source: "https://github.com/excalidraw/excalidraw"
    • Network accessline 105
      <iframe   src="https://excalidraw.com/#json=YOUR_ENCODED_DATA"
    • Network accessline 106
      src="https://excalidraw.com/#json=YOUR_ENCODED_DATA"
    • Network accessline 168
      - Excalidraw open-source repository: https://github.com/excalidraw/excalidraw
    • Network accessline 169
      - Excalidraw libraries (pre-made shapes): https://libraries.excalidraw.com
    • Network accessline 170
      - Excalidraw file format specification: https://docs.excalidraw.com

    skills/tools/diagram/json-data-visualizer/SKILL.md

    • Network accessline 8
      subcategory: "diagram"     keywords: ["JSON visualization", "data structure diagram", "tree visualization", "API response viewer", "schema explorer"]     source: "https://github.com/AykutSarac/jsoncrack.com"
    • Network accessline 9
      keywords: ["JSON visualization", "data structure diagram", "tree visualization", "API response viewer", "schema explorer"]     source: "https://github.com/AykutSarac/jsoncrack.com" ---
    • Network accessline 10
      source: "https://github.com/AykutSarac/jsoncrack.com"
    • Network accessline 32
      # Clone the repository git clone https://github.com/AykutSarac/jsoncrack.com.git
    • Network accessline 33
      git clone https://github.com/AykutSarac/jsoncrack.com.git
    • Network accessline 56
      # Access at http://localhost:8888
    • Network accessline 147
      # Fetch metadata from CrossRef API response = requests.get(
    • Network accessline 148
      response = requests.get(
    • Network accessline 149
      "https://api.crossref.org/works/10.1038/nature12373"
    • Network accessline 192
      <iframe   src="https://jsoncrack.internal.lab/widget"
    • Network accessline 193
      src="https://jsoncrack.internal.lab/widget"
    • Network accessline 267
      - JSON Crack website: https://jsoncrack.com
    • Network accessline 268
      - JSON Crack GitHub: https://github.com/AykutSarac/jsoncrack.com
    • Network accessline 269
      - JSON Crack React embed: https://www.npmjs.com/package/jsoncrack-react

    skills/tools/diagram/kroki-diagram-api/SKILL.md

    • Network accessline 8
      subcategory: "diagram"     keywords: ["Kroki", "diagram generation", "text-to-diagram", "Graphviz", "PlantUML", "Mermaid"]     source: "https://kroki.io/"
    • Network accessline 9
      keywords: ["Kroki", "diagram generation", "text-to-diagram", "Graphviz", "PlantUML", "Mermaid"]     source: "https://kroki.io/" ---
    • Network accessline 10
      source: "https://kroki.io/"
    • Network accessline 24
      # Graphviz DOT diagram curl "https://kroki.io/graphviz/svg/digraph{A->B->C}" -o diagram.svg
    • Network accessline 25
      curl "https://kroki.io/graphviz/svg/digraph{A->B->C}" -o diagram.svg
    • Network accessline 27
      # Mermaid diagram (base64-encoded) echo "graph TD; A-->B; B-->C;" | base64 | \   curl "https://kroki.io/mermaid/svg/$(cat -)" -o diagram.svg
    • Network accessline 28
      echo "graph TD; A-->B; B-->C;" | base64 |    curl "https://kroki.io/mermaid/svg/$(cat -)" -o diagram.svg
    • Network accessline 29
      curl "https://kroki.io/mermaid/svg/$(cat -)" -o diagram.svg
    • Network accessline 35
      # PlantUML sequence diagram curl -X POST "https://kroki.io/plantuml/svg" \
    • Network accessline 36
      curl -X POST "https://kroki.io/plantuml/svg" \
    • Network accessline 43
      # Mermaid flowchart curl -X POST "https://kroki.io/mermaid/svg" \
    • Network accessline 44
      curl -X POST "https://kroki.io/mermaid/svg" \
    • Network accessline 53
      # Graphviz curl -X POST "https://kroki.io/graphviz/svg" \
    • Network accessline 54
      curl -X POST "https://kroki.io/graphviz/svg" \
    • Network accessline 61
      # D2 diagram curl -X POST "https://kroki.io/d2/svg" \
    • Network accessline 62
      curl -X POST "https://kroki.io/d2/svg" \
    • Network accessline 73
      https://kroki.io/{diagram_type}/{output_format}/{encoded_source}
    • Network accessline 75
      # Or POST to: https://kroki.io/{diagram_type}/{output_format}
    • Network accessline 76
      https://kroki.io/{diagram_type}/{output_format}
    • Network accessline 115
      KROKI_URL = "https://kroki.io"
    • Network accessline 119
      output_format: str = "svg") -> bytes:     """Render a text diagram to image via Kroki."""     resp = requests.post(
    • Network accessline 120
      """Render a text diagram to image via Kroki."""     resp = requests.post(         f"{KROKI_URL}/{diagram_type}/{output_format}",
    • Network accessline 121
      resp = requests.post(
    • Network accessline 191
      # Then use http://localhost:8000 instead of https://kroki.io
    • Network accessline 196
      - [Kroki](https://kroki.io/)
    • Network accessline 197
      - [Kroki Documentation](https://docs.kroki.io/)
    • Network accessline 198
      - [Kroki GitHub](https://github.com/yuzutech/kroki)

    skills/tools/diagram/mermaid-architect-guide/SKILL.md

    • Network accessline 8
      subcategory: "diagram"     keywords: ["Mermaid", "architecture", "system design", "C4 model", "diagram", "hand-drawn"]     source: "https://github.com/mermaid-js/mermaid"
    • Network accessline 9
      keywords: ["Mermaid", "architecture", "system design", "C4 model", "diagram", "hand-drawn"]     source: "https://github.com/mermaid-js/mermaid" ---
    • Network accessline 10
      source: "https://github.com/mermaid-js/mermaid"
    • Network accessline 216
      - Mermaid official documentation: https://mermaid.js.org
    • Network accessline 217
      - C4 model specification: https://c4model.com
    • Network accessline 218
      - Mermaid CLI (mmdc): https://github.com/mermaid-js/mermaid-cli
    • Network accessline 219
      - Mermaid Live Editor: https://mermaid.live

    skills/tools/diagram/mermaid-diagram-guide/SKILL.md

    • Network accessline 260
      - **Export as SVG for papers.** SVG scales perfectly and produces crisp output at any size. - **Version-control your diagrams.** Since Mermaid is text, it diffs cleanly in Git. - **Test in the live editor.** Use [mermaid.live](https://merma
    • Network accessline 262
      - **Test in the live editor.** Use [mermaid.live](https://mermaid.live/) to iterate quickly before committing.
    • Network accessline 266
      - [Mermaid Documentation](https://mermaid.js.org/) -- Official reference
    • Network accessline 267
      - [Mermaid Live Editor](https://mermaid.live/) -- Interactive diagram editor
    • Network accessline 268
      - [Mermaid CLI](https://github.com/mermaid-js/mermaid-cli) -- Command-line rendering tool
    • Network accessline 269
      - [GitHub Mermaid Support](https://github.blog/2022-02-14-include-diagrams-markdown-files-mermaid/) -- Native rendering in GitHub

    skills/tools/diagram/plantuml-guide/SKILL.md

    • Network accessline 379
      server = plantuml.PlantUML(url="http://www.plantuml.com/plantuml/svg/")

    skills/tools/diagram/tldraw-whiteboard-guide/SKILL.md

    • Network accessline 8
      subcategory: "diagram"     keywords: ["whiteboard", "infinite canvas", "diagram SDK", "collaborative drawing", "research diagrams", "visual thinking"]     source: "https://github.com/tldraw/tldraw"
    • Network accessline 9
      keywords: ["whiteboard", "infinite canvas", "diagram SDK", "collaborative drawing", "research diagrams", "visual thinking"]     source: "https://github.com/tldraw/tldraw" ---
    • Network accessline 10
      source: "https://github.com/tldraw/tldraw"
    • Network accessline 32
      # Clone and run locally git clone https://github.com/tldraw/tldraw.git
    • Network accessline 33
      git clone https://github.com/tldraw/tldraw.git
    • Network accessline 38
      # Access at http://localhost:5420
    • Network accessline 394
      - tldraw official site: https://tldraw.com
    • Network accessline 395
      - tldraw GitHub repository: https://github.com/tldraw/tldraw
    • Network accessline 396
      - tldraw SDK documentation: https://tldraw.dev
    • Network accessline 397
      - tldraw examples: https://github.com/tldraw/tldraw/tree/main/apps/examples

    skills/tools/document/anystyle-api/SKILL.md

    • Network accessline 8
      subcategory: "document"     keywords: ["PDF parsing", "document chunking", "format conversion", "PDF extraction"]     source: "https://anystyle.io/"
    • Network accessline 9
      keywords: ["PDF parsing", "document chunking", "format conversion", "PDF extraction"]     source: "https://anystyle.io/" ---
    • Network accessline 10
      source: "https://anystyle.io/"
    • Network accessline 25
      No authentication required. The AnyStyle web service is freely accessible without any API key, token, or registration. The service can be used via the web interface at https://anystyle.io/ or through its API endpoint. For heavy usage or pri
    • Network accessline 33
      - **URL**: `POST https://anystyle.io/parse`
    • Network accessline 44
      # Parse a single citation curl -X POST "https://anystyle.io/parse" \
    • Network accessline 45
      curl -X POST "https://anystyle.io/parse" \
    • Network accessline 49
      # Parse multiple citations (one per line) curl -X POST "https://anystyle.io/parse" \
    • Network accessline 50
      curl -X POST "https://anystyle.io/parse" \
    • Network accessline 98
      resp = requests.post(
    • Network accessline 99
      "https://anystyle.io/parse",
    • Network accessline 121
      def parse_references(raw_text):     """Parse raw citation text into structured records."""     resp = requests.post(
    • Network accessline 122
      """Parse raw citation text into structured records."""     resp = requests.post(         "https://anystyle.io/parse",
    • Network accessline 123
      resp = requests.post(
    • Network accessline 124
      "https://anystyle.io/parse",
    • Network accessline 154
      resp = requests.post(
    • Network accessline 155
      "https://anystyle.io/parse",
    • Network accessline 195
      - AnyStyle web service: https://anystyle.io/
    • Network accessline 196
      - AnyStyle GitHub repository: https://github.com/inukshuk/anystyle
    • Network accessline 197
      - AnyStyle Ruby gem: https://rubygems.org/gems/anystyle
    • Network accessline 198
      - AnyStyle CLI documentation: https://github.com/inukshuk/anystyle-cli
    • Network accessline 199
      - CSL (Citation Style Language): https://citationstyles.org/

    skills/tools/document/docsgpt-guide/SKILL.md

    • Network accessline 8
      subcategory: "document"     keywords: ["document-analysis", "knowledge-base", "rag", "private-ai", "enterprise-search", "question-answering"]     source: "https://github.com/arc53/DocsGPT"
    • Network accessline 9
      keywords: ["document-analysis", "knowledge-base", "rag", "private-ai", "enterprise-search", "question-answering"]     source: "https://github.com/arc53/DocsGPT" ---
    • Network accessline 10
      source: "https://github.com/arc53/DocsGPT"
    • Network accessline 28
      git clone https://github.com/arc53/DocsGPT.git
    • Access to secretsline 32
      [Credential-related source omitted]
    • Access to secretsline 40
      [Credential-related source omitted]
    • Network accessline 42
      # Or use a local model via Ollama LLM_NAME=ollama OLLAMA_API_BASE=http://localhost:11434
    • Network accessline 43
      LLM_NAME=ollama OLLAMA_API_BASE=http://localhost:11434 MODEL_NAME=llama3
    • Network accessline 44
      OLLAMA_API_BASE=http://localhost:11434
    • Network accessline 54
      The web interface becomes available at `http://localhost:5173`. For production deployments behind a reverse proxy, configure the appropriate `VITE_API_HOST` environment variable.
    • Network accessline 69
      # Upload documents via the API curl -X POST http://localhost:7091/api/upload \
    • Network accessline 70
      curl -X POST http://localhost:7091/api/upload \
    • Network accessline 80
      # Query your document collection via API curl -X POST http://localhost:7091/api/answer \
    • Network accessline 81
      curl -X POST http://localhost:7091/api/answer \
    • Network accessline 128
      - DocsGPT repository: https://github.com/arc53/DocsGPT
    • Network accessline 129
      - DocsGPT documentation: https://docs.docsgpt.cloud/

    skills/tools/document/grobid-pdf-parsing/SKILL.md

    • Network accessline 8
      subcategory: "document"     keywords: ["PDF parsing", "PDF extraction", "document chunking", "format conversion"]     source: "https://github.com/kermitt2/grobid"
    • Network accessline 9
      keywords: ["PDF parsing", "PDF extraction", "document chunking", "format conversion"]     source: "https://github.com/kermitt2/grobid" ---
    • Network accessline 10
      source: "https://github.com/kermitt2/grobid"
    • Network accessline 37
      # GROBID is now running at http://localhost:8070
    • Network accessline 38
      # Web console: http://localhost:8070/console
    • Network accessline 44
      git clone https://github.com/kermitt2/grobid.git
    • Network accessline 55
      # Process a single PDF and get TEI XML curl -v --form input=@paper.pdf \
    • Network accessline 56
      curl -v --form input=@paper.pdf \
    • Network accessline 57
      http://localhost:8070/api/processFulltextDocument \
    • Network accessline 60
      # With options curl -v --form input=@paper.pdf \
    • Network accessline 61
      curl -v --form input=@paper.pdf \
    • Network accessline 63
      --form consolidateCitations=1 \   --form includeRawCitations=1 \   http://localhost:8070/api/processFulltextDocument \
    • Network accessline 64
      --form includeRawCitations=1 \   http://localhost:8070/api/processFulltextDocument \   -o paper.tei.xml
    • Network accessline 65
      http://localhost:8070/api/processFulltextDocument \
    • Network accessline 85
      class GrobidClient:     def __init__(self, base_url='http://localhost:8070'):
    • Network accessline 86
      def __init__(self, base_url='http://localhost:8070'):
    • Network accessline 96
      'consolidateCitations': '1' if consolidate_citations else '0',         }         response = requests.post(url, files=files, data=data)
    • Network accessline 97
      }         response = requests.post(url, files=files, data=data)         response.raise_for_status()
    • Network accessline 98
      response = requests.post(url, files=files, data=data)
    • Network accessline 104
      url = f'{self.base_url}/api/processHeaderDocument'         files = {'input': open(pdf_path, 'rb')}         response = requests.post(url, files=files)
    • Network accessline 105
      files = {'input': open(pdf_path, 'rb')}         response = requests.post(url, files=files)         response.raise_for_status()
    • Network accessline 106
      response = requests.post(url, files=files)
    • Network accessline 111
      """Check if GROBID server is running."""         try:             resp = requests.get(f'{self.base_url}/api/isalive')
    • Network accessline 112
      try:             resp = requests.get(f'{self.base_url}/api/isalive')             return resp.status_code == 200
    • Network accessline 113
      resp = requests.get(f'{self.base_url}/api/isalive')
    • Network accessline 133
      def parse_tei_metadata(tei_xml):     """Extract title, authors, abstract from TEI XML."""     ns = {'tei': 'http://www.tei-c.org/ns/1.0'}
    • Network accessline 134
      """Extract title, authors, abstract from TEI XML."""     ns = {'tei': 'http://www.tei-c.org/ns/1.0'}     root = etree.fromstring(tei_xml.encode('utf-8'))
    • Network accessline 135
      ns = {'tei': 'http://www.tei-c.org/ns/1.0'}
    • Network accessline 169
      def parse_tei_sections(tei_xml):     """Extract structured sections from TEI XML body."""     ns = {'tei': 'http://www.tei-c.org/ns/1.0'}
    • Network accessline 170
      """Extract structured sections from TEI XML body."""     ns = {'tei': 'http://www.tei-c.org/ns/1.0'}     root = etree.fromstring(tei_xml.encode('utf-8'))
    • Network accessline 171
      ns = {'tei': 'http://www.tei-c.org/ns/1.0'}
    • Network accessline 194
      def parse_tei_references(tei_xml):     """Extract structured references from TEI XML."""     ns = {'tei': 'http://www.tei-c.org/ns/1.0'}
    • Network accessline 195
      """Extract structured references from TEI XML."""     ns = {'tei': 'http://www.tei-c.org/ns/1.0'}     root = etree.fromstring(tei_xml.encode('utf-8'))
    • Network accessline 196
      ns = {'tei': 'http://www.tei-c.org/ns/1.0'}
    • Network accessline 199
      refs = []     for bib in root.findall('.//tei:listBibl/tei:biblStruct', ns):         ref = {'id': bib.get('{http://www.w3.org/XML/1998/namespace}id', '')}
    • Network accessline 201
      ref = {'id': bib.get('{http://www.w3.org/XML/1998/namespace}id', '')}
    • Network accessline 290
      - [GROBID Documentation](https://grobid.readthedocs.io/) -- Official documentation
    • Network accessline 291
      - [GROBID GitHub](https://github.com/kermitt2/grobid) -- Source code
    • Network accessline 292
      - [TEI Guidelines](https://tei-c.org/release/doc/tei-p5-doc/en/html/) -- TEI XML standard
    • Network accessline 293
      - [grobid-client-python](https://github.com/kermitt2/grobid_client_python) -- Official Python client
    • Network accessline 294
      - [Science Parse](https://github.com/allenai/science-parse) -- Allen AI alternative parser

    skills/tools/document/large-document-reader/SKILL.md

    • Network accessline 199
      - pdfplumber: https://github.com/jsvine/pdfplumber
    • Network accessline 200
      - python-docx: https://python-docx.readthedocs.io
    • Network accessline 201
      - ebooklib: https://github.com/aerkalov/ebooklib
    • Network accessline 202
      - PyMuPDF (fitz): https://pymupdf.readthedocs.io

    skills/tools/document/paper-parse-guide/SKILL.md

    • Network accessline 31
      | Local PDF | Direct file path | Best quality, no network needed | | DOI | Resolve via CrossRef/Unpaywall | Auto-fetches open access version | | arXiv ID | `https://arxiv.org/pdf/{id}` | Always available |
    • Network accessline 32
      | DOI | Resolve via CrossRef/Unpaywall | Auto-fetches open access version | | arXiv ID | `https://arxiv.org/pdf/{id}` | Always available | | URL | Direct download | May require institutional access |
    • Network accessline 33
      | arXiv ID | `https://arxiv.org/pdf/{id}` | Always available | | URL | Direct download | May require institutional access | | OpenAlex ID | OpenAlex API + OA link | Includes metadata |
    • Network accessline 83
      # Parse a paper curl -X POST "http://localhost:8070/api/processFulltextDocument" \
    • Network accessline 84
      curl -X POST "http://localhost:8070/api/processFulltextDocument" \
    • Network accessline 239
      - GROBID: https://github.com/kermitt2/grobid
    • Network accessline 240
      - PyMuPDF: https://pymupdf.readthedocs.io
    • Network accessline 241
      - OpenAlex API: https://api.openalex.org
    • Network accessline 242
      - Unpaywall API: https://unpaywall.org/products/api
    • Network accessline 243
      - S. Keshav, "How to Read a Paper" (2007): http://ccr.sigcomm.org/online/files/p83-keshavA.pdf

    skills/tools/document/pdf-extraction-guide/SKILL.md

    • Network accessline 167
      def parse_with_grobid(pdf_path, grobid_url="http://localhost:8070"):
    • Network accessline 168
      """Parse a paper PDF using GROBID."""     with open(pdf_path, "rb") as f:         response = requests.post(
    • Network accessline 169
      with open(pdf_path, "rb") as f:         response = requests.post(             f"{grobid_url}/api/processFulltextDocument",
    • Network accessline 170
      response = requests.post(
    • Network accessline 184
      tei_xml = parse_with_grobid("paper.pdf") root = etree.fromstring(tei_xml.encode()) ns = {"tei": "http://www.tei-c.org/ns/1.0"}
    • Network accessline 186
      ns = {"tei": "http://www.tei-c.org/ns/1.0"}

    skills/tools/document/zotero-addon-market-guide/SKILL.md

    • Network accessline 8
      subcategory: "document"     keywords: ["Zotero", "plugin marketplace", "add-ons", "plugin discovery", "extension manager"]     source: "https://github.com/syt2/zotero-addons"
    • Network accessline 9
      keywords: ["Zotero", "plugin marketplace", "add-ons", "plugin discovery", "extension manager"]     source: "https://github.com/syt2/zotero-addons" ---
    • Network accessline 10
      source: "https://github.com/syt2/zotero-addons"
    • Network accessline 106
      - [Zotero Add-ons GitHub](https://github.com/syt2/zotero-addons)
    • Network accessline 107
      - [Zotero Plugin Template](https://github.com/windingwind/zotero-plugin-template)
    • Network accessline 108
      - [Zotero 7 Plugin Development](https://www.zotero.org/support/dev/client_coding/plugin_development)

    skills/tools/document/zotero-night-theme-guide/SKILL.md

    • Network accessline 8
      subcategory: "document"     keywords: ["Zotero", "dark mode", "theme", "night mode", "UI customization", "eye comfort"]     source: "https://github.com/tefkah/zotero-night"
    • Network accessline 9
      keywords: ["Zotero", "dark mode", "theme", "night mode", "UI customization", "eye comfort"]     source: "https://github.com/tefkah/zotero-night" ---
    • Network accessline 10
      source: "https://github.com/tefkah/zotero-night"
    • Network accessline 141
      - [Zotero Night GitHub](https://github.com/tefkah/zotero-night)
    • Network accessline 142
      - [Zotero 7 Theming](https://www.zotero.org/support/preferences)

    skills/tools/document/zotero-style-guide/SKILL.md

    • Network accessline 8
      subcategory: "document"     keywords: ["Zotero", "styling", "UI customization", "reading progress", "tags", "columns"]     source: "https://github.com/MuiseDestiny/zotero-style"
    • Network accessline 9
      keywords: ["Zotero", "styling", "UI customization", "reading progress", "tags", "columns"]     source: "https://github.com/MuiseDestiny/zotero-style" ---
    • Network accessline 10
      source: "https://github.com/MuiseDestiny/zotero-style"
    • Network accessline 215
      - [Zotero Style GitHub](https://github.com/MuiseDestiny/zotero-style)
    • Network accessline 216
      - [Zotero Plugin Development](https://www.zotero.org/support/dev/client_coding/plugin_development)
    • Network accessline 217
      - [Zotero Styles Gallery](https://www.zotero.org/styles)

    skills/tools/knowledge-graph/citation-network-builder/SKILL.md

    • Network accessline 72
      records["doi"]         .str.lower()         .str.replace("https://doi.org/", "", regex=False)
    • Network accessline 73
      .str.lower()         .str.replace("https://doi.org/", "", regex=False)         .str.replace("http://dx.doi.org/", "", regex=False)
    • Network accessline 74
      .str.replace("https://doi.org/", "", regex=False)
    • Network accessline 75
      .str.replace("http://dx.doi.org/", "", regex=False)

    skills/tools/knowledge-graph/concept-map-generator/SKILL.md

    • Network accessline 215
      # CXL is an XML format specific to CmapTools     header = '<?xml version="1.0" encoding="UTF-8"?>\n'     header += '<cmap xmlns="http://cmap.ihmc.us/xml/cmap/">\n'
    • Network accessline 217
      header += '<cmap xmlns="http://cmap.ihmc.us/xml/cmap/">\n'

    skills/tools/knowledge-graph/graphiti-guide/SKILL.md

    • Network accessline 8
      subcategory: "knowledge-graph"     keywords: ["knowledge-graph", "ai-agents", "temporal-graphs", "neo4j", "memory", "entity-extraction"]     source: "https://github.com/getzep/graphiti"
    • Network accessline 9
      keywords: ["knowledge-graph", "ai-agents", "temporal-graphs", "neo4j", "memory", "entity-extraction"]     source: "https://github.com/getzep/graphiti" ---
    • Network accessline 10
      source: "https://github.com/getzep/graphiti"
    • Access to secretsline 48
      [Credential-related source omitted]
    • Network accessline 196
      Access the Neo4j browser at `http://localhost:7474` to visually explore your knowledge graph. Use Cypher queries for advanced exploration:
    • Network accessline 216
      - Graphiti repository: https://github.com/getzep/graphiti
    • Network accessline 217
      - Zep documentation: https://docs.getzep.com/
    • Network accessline 218
      - Neo4j graph database: https://neo4j.com/

    skills/tools/knowledge-graph/knowledge-graph-construction/SKILL.md

    • Network accessline 302
      - [Neo4j Documentation](https://neo4j.com/docs/) -- Graph database
    • Network accessline 303
      - [NetworkX Documentation](https://networkx.org/) -- Python graph library
    • Network accessline 304
      - [OpenAlex API](https://docs.openalex.org/) -- Open bibliographic data
    • Network accessline 305
      - [LlamaIndex Knowledge Graph Guide](https://docs.llamaindex.ai/) -- KG-RAG integration
    • Network accessline 306
      - [Graphiti](https://github.com/getzep/graphiti) -- Temporal knowledge graph library

    skills/tools/knowledge-graph/notero-zotero-notion-guide/SKILL.md

    • Network accessline 8
      subcategory: "knowledge-graph"     keywords: ["Zotero", "Notion", "sync", "reference management", "knowledge base", "annotations"]     source: "https://github.com/dvanoni/notero"
    • Network accessline 9
      keywords: ["Zotero", "Notion", "sync", "reference management", "knowledge base", "annotations"]     source: "https://github.com/dvanoni/notero" ---
    • Network accessline 10
      source: "https://github.com/dvanoni/notero"
    • Network accessline 185
      - [Notero GitHub](https://github.com/dvanoni/notero)
    • Network accessline 186
      - [Notion API](https://developers.notion.com/)
    • Network accessline 187
      - [Zotero Plugin Development](https://www.zotero.org/support/dev/)

    skills/tools/knowledge-graph/ontology-design-guide/SKILL.md

    • Network accessline 136
      @prefix : <http://example.org/research#> .
    • Network accessline 137
      @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
    • Network accessline 138
      @prefix owl: <http://www.w3.org/2002/07/owl#> .

    skills/tools/knowledge-graph/openspg-guide/SKILL.md

    • Network accessline 8
      subcategory: "knowledge-graph"     keywords: ["OpenSPG", "knowledge graph", "SPG", "KAG", "Ant Group", "semantic reasoning"]     source: "https://github.com/OpenSPG/openspg"
    • Network accessline 9
      keywords: ["OpenSPG", "knowledge graph", "SPG", "KAG", "Ant Group", "semantic reasoning"]     source: "https://github.com/OpenSPG/openspg" ---
    • Network accessline 10
      source: "https://github.com/OpenSPG/openspg"
    • Network accessline 22
      # Docker deployment git clone https://github.com/OpenSPG/openspg.git
    • Network accessline 23
      git clone https://github.com/OpenSPG/openspg.git
    • Network accessline 30
      # Access KG Studio at http://localhost:8887
    • Network accessline 208
      - [OpenSPG GitHub](https://github.com/OpenSPG/openspg)
    • Network accessline 209
      - [KAG Framework](https://github.com/OpenSPG/KAG)
    • Network accessline 210
      - [SPG White Paper](https://arxiv.org/abs/2302.09560)

    skills/tools/knowledge-graph/zotero-markdb-connect-guide/SKILL.md

    • Network accessline 8
      subcategory: "knowledge-graph"     keywords: ["Zotero", "Obsidian", "Logseq", "markdown", "PKM", "literature notes"]     source: "https://github.com/daeh/zotero-markdb-connect"
    • Network accessline 9
      keywords: ["Zotero", "Obsidian", "Logseq", "markdown", "PKM", "literature notes"]     source: "https://github.com/daeh/zotero-markdb-connect" ---
    • Network accessline 10
      source: "https://github.com/daeh/zotero-markdb-connect"
    • Network accessline 63
      **Year:** {{year}} **Venue:** {{publicationTitle}} **DOI:** [{{doi}}](https://doi.org/{{doi}})
    • Network accessline 65
      **DOI:** [{{doi}}](https://doi.org/{{doi}})
    • Network accessline 160
      - [MarkDB-Connect GitHub](https://github.com/daeh/zotero-markdb-connect)
    • Network accessline 161
      - [Obsidian](https://obsidian.md/)
    • Network accessline 162
      - [Logseq](https://logseq.com/)

    skills/tools/ocr-translate/latex-ocr-guide/SKILL.md

    • Network accessline 36
      # Or install from GitHub for latest version pip install git+https://github.com/lukas-blecher/LaTeX-OCR.git
    • Network accessline 37
      pip install git+https://github.com/lukas-blecher/LaTeX-OCR.git
    • Network accessline 172
      response = requests.post(
    • Network accessline 173
      'https://api.mathpix.com/v3/text',

    skills/tools/ocr-translate/latex-translation-guide/SKILL.md

    • Network accessline 8
      subcategory: "ocr-translate"     keywords: ["LaTeX translation", "document translation", "multilingual", "math preservation", "academic translation"]     source: "https://github.com/SUSYUSTC/MathTranslate"
    • Network accessline 9
      keywords: ["LaTeX translation", "document translation", "multilingual", "math preservation", "academic translation"]     source: "https://github.com/SUSYUSTC/MathTranslate" ---
    • Network accessline 10
      source: "https://github.com/SUSYUSTC/MathTranslate"
    • Network accessline 174
      - [LaTeXTrans](https://github.com/SUSYUSTC/MathTranslate)
    • Network accessline 175
      - [PDFMathTranslate](https://github.com/Byaidu/PDFMathTranslate)
    • Network accessline 176
      - [arXiv LaTeX Cleaner](https://github.com/google-research/arxiv-latex-cleaner)

    skills/tools/ocr-translate/pdf-math-translate-guide/SKILL.md

    • Network accessline 8
      subcategory: "ocr-translate"     keywords: ["pdf-translation", "math-formatting", "scientific-papers", "multilingual", "latex-preservation"]     source: "https://github.com/Byaidu/PDFMathTranslate"
    • Network accessline 9
      keywords: ["pdf-translation", "math-formatting", "scientific-papers", "multilingual", "latex-preservation"]     source: "https://github.com/Byaidu/PDFMathTranslate" ---
    • Network accessline 10
      source: "https://github.com/Byaidu/PDFMathTranslate"
    • Access to secretsline 41
      [Credential-related source omitted]
    • Access to secretsline 48
      [Credential-related source omitted]
    • Network accessline 139
      - PDFMathTranslate repository: https://github.com/Byaidu/PDFMathTranslate
    • Network accessline 140
      - PyPI package: https://pypi.org/project/pdf2zh/

    skills/tools/ocr-translate/zotero-pdf-translate-guide/SKILL.md

    • Network accessline 8
      subcategory: "ocr-translate"     keywords: ["zotero", "pdf-translate", "multilingual", "annotation", "academic-translation"]     source: "https://github.com/windingwind/zotero-pdf-translate"
    • Network accessline 9
      keywords: ["zotero", "pdf-translate", "multilingual", "annotation", "academic-translation"]     source: "https://github.com/windingwind/zotero-pdf-translate" ---
    • Network accessline 10
      source: "https://github.com/windingwind/zotero-pdf-translate"
    • Network accessline 27
      1. Download the latest `.xpi` file from the GitHub releases page at https://github.com/windingwind/zotero-pdf-translate/releases
    • Access to secretsline 36
      [Credential-related source omitted]
    • Access to secretsline 37
      [Credential-related source omitted]
    • Access to secretsline 38
      [Credential-related source omitted]
    • Network accessline 92
      - GitHub Repository: https://github.com/windingwind/zotero-pdf-translate
    • Network accessline 93
      - Zotero Plugin Directory: https://www.zotero.org/support/plugins
    • Network accessline 94
      - Zotero Forums Translation Discussion: https://forums.zotero.org
    • Network accessline 95
      - DeepL API Documentation: https://www.deepl.com/docs-api

    skills/tools/ocr-translate/zotero-pdf2zh-guide/SKILL.md

    • Network accessline 2
      name: zotero-pdf2zh-guide description: "PDF Chinese translation plugin for Zotero reference manager" source: https://github.com/guaguastandup/zotero-pdf2zh
    • Network accessline 3
      description: "PDF Chinese translation plugin for Zotero reference manager" source: https://github.com/guaguastandup/zotero-pdf2zh metadata:
    • Network accessline 4
      source: https://github.com/guaguastandup/zotero-pdf2zh

    skills/tools/scraping/academic-web-scraping/SKILL.md

    • Network accessline 43
      class OpenAlexClient:     BASE_URL = "https://api.openalex.org"
    • Network accessline 44
      BASE_URL = "https://api.openalex.org"
    • Network accessline 46
      def __init__(self, email):         self.session = requests.Session()
    • Network accessline 47
      self.session = requests.Session()
    • Access to secretsline 110
      [Credential-related source omitted]
    • Network accessline 172
      response = requests.get(url, headers=headers, timeout=30)
    • Network accessline 226
      1. **Check for an API first.** Most academic platforms have one. 2. **Read robots.txt.** `https://example.com/robots.txt` specifies what is allowed.
    • Network accessline 227
      2. **Read robots.txt.** `https://example.com/robots.txt` specifies what is allowed.
    • Network accessline 320
      - [OpenAlex API Documentation](https://docs.openalex.org/) -- Open bibliographic data API
    • Network accessline 321
      - [CrossRef API](https://api.crossref.org/) -- DOI resolution and metadata
    • Network accessline 322
      - [BeautifulSoup Documentation](https://www.crummy.com/software/BeautifulSoup/bs4/doc/) -- HTML parsing
    • Network accessline 323
      - [Scrapy Documentation](https://docs.scrapy.org/) -- Web scraping framework
    • Network accessline 324
      - [Playwright Documentation](https://playwright.dev/python/) -- Browser automation
    • Network accessline 325
      - [Web Scraping Ethics](https://towardsdatascience.com/ethics-in-web-scraping-b96b18136f01) -- Ethical considerations

    skills/tools/scraping/dataset-finder-guide/SKILL.md

    • Network accessline 114
      def search_google_datasets(query, num_results=10):     """Search Google Dataset Search and extract results."""     url = f"https://datasetsearch.research.google.com/search"
    • Network accessline 115
      """Search Google Dataset Search and extract results."""     url = f"https://datasetsearch.research.google.com/search"     params = {"query": query, "docid": ""}
    • Network accessline 116
      url = f"https://datasetsearch.research.google.com/search"
    • Network accessline 129
      def search_zenodo(query, resource_type="dataset", size=10):     """Search Zenodo for research datasets."""     url = "https://zenodo.org/api/records"
    • Network accessline 130
      """Search Zenodo for research datasets."""     url = "https://zenodo.org/api/records"     params = {
    • Network accessline 131
      url = "https://zenodo.org/api/records"
    • Network accessline 137
      "access_right": "open"     }     response = requests.get(url, params=params)
    • Network accessline 138
      }     response = requests.get(url, params=params)     results = response.json()
    • Network accessline 139
      response = requests.get(url, params=params)
    • Network accessline 170
      | CC-BY 4.0 | Yes | Yes | Yes | | CC-BY-SA 4.0 | Yes | Yes (share-alike) | Yes | | CC-BY-NC 4.0 | No | Yes | Yes |
    • Network accessline 171
      | CC-BY-SA 4.0 | Yes | Yes (share-alike) | Yes | | CC-BY-NC 4.0 | No | Yes | Yes | | ODC-ODbL | Yes | Yes (share-alike) | Yes |
    • Network accessline 172
      | CC-BY-NC 4.0 | No | Yes | Yes |
    • Network accessline 220
      DATASETS = {     "main_dataset": {         "url": "https://zenodo.org/record/12345/files/data.csv",
    • Network accessline 221
      "main_dataset": {         "url": "https://zenodo.org/record/12345/files/data.csv",         "sha256": "abc123...",
    • Network accessline 222
      "url": "https://zenodo.org/record/12345/files/data.csv",
    • Network accessline 236
      path.parent.mkdir(parents=True, exist_ok=True)     print(f"Downloading {name}...")     response = requests.get(info["url"])
    • Network accessline 237
      print(f"Downloading {name}...")     response = requests.get(info["url"])     path.write_bytes(response.content)
    • Network accessline 238
      response = requests.get(info["url"])
    • Network accessline 249
      - Kaggle API documentation: https://github.com/Kaggle/kaggle-api
    • Network accessline 250
      - Hugging Face Datasets: https://huggingface.co/docs/datasets
    • Network accessline 251
      - Zenodo API: https://developers.zenodo.org
    • Network accessline 252
      - Google Dataset Search: https://datasetsearch.research.google.com
    • Network accessline 253
      - Gebru et al., "Datasheets for Datasets" (2021): https://arxiv.org/abs/1803.09010

    skills/tools/scraping/easy-spider-guide/SKILL.md

    • Network accessline 8
      subcategory: "scraping"     keywords: ["web scraping", "visual crawler", "no-code scraping", "data collection", "research data", "web automation"]     source: "https://github.com/NaiboWang/EasySpider"
    • Network accessline 9
      keywords: ["web scraping", "visual crawler", "no-code scraping", "data collection", "research data", "web automation"]     source: "https://github.com/NaiboWang/EasySpider" ---
    • Network accessline 10
      source: "https://github.com/NaiboWang/EasySpider"
    • Network accessline 28
      # Download the latest release for your platform from GitHub releases # https://github.com/NaiboWang/EasySpider/releases
    • Network accessline 29
      # https://github.com/NaiboWang/EasySpider/releases
    • Network accessline 37
      # Or run from source git clone https://github.com/NaiboWang/EasySpider.git
    • Network accessline 38
      git clone https://github.com/NaiboWang/EasySpider.git
    • Network accessline 247
      - EasySpider GitHub repository: https://github.com/NaiboWang/EasySpider
    • Network accessline 248
      - EasySpider documentation: https://github.com/NaiboWang/EasySpider/wiki
    • Network accessline 249
      - EasySpider video tutorials: https://github.com/NaiboWang/EasySpider#tutorials
    • Network accessline 250
      - Web scraping ethics in research: https://doi.org/10.1177/2053951720943006

    skills/tools/scraping/repository-harvesting-guide/SKILL.md

    • Network accessline 40
      Transport: HTTP GET or POST Response format: XML Base URL example: https://arxiv.org/oai2
    • Network accessline 42
      Base URL example: https://arxiv.org/oai2
    • Network accessline 96
      OAI_NS = "http://www.openarchives.org/OAI/2.0/"
    • Network accessline 97
      DC_NS = "http://purl.org/dc/elements/1.1/"
    • Network accessline 128
      while True:         response = requests.get(base_url, params=params, timeout=30)
    • Network accessline 129
      response = requests.get(base_url, params=params, timeout=30)
    • Network accessline 297
      arXiv:          https://export.arxiv.org/oai2
    • Network accessline 298
      PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi
    • Network accessline 299
      Europeana:      https://oai.europeana.eu/oai
    • Network accessline 300
      HAL (France):   https://api.archives-ouvertes.fr/oai/hal
    • Network accessline 301
      DBLP:           https://dblp.org/oai
    • Network accessline 302
      CiteSeerX:      https://citeseerx.ist.psu.edu/oai2
    • Network accessline 304
      To find more endpoints:   - OpenDOAR directory: https://v2.sherpa.ac.uk/opendoar/
    • Network accessline 305
      - OpenDOAR directory: https://v2.sherpa.ac.uk/opendoar/

    skills/tools/scraping/web-scraping-ethics-guide/SKILL.md

    • Network accessline 63
      Args:         base_url: The website's base URL (e.g., 'https://example.com')
    • Network accessline 64
      base_url: The website's base URL (e.g., 'https://example.com')
    • Network accessline 127
      for i, url in enumerate(urls):         try:             req = urllib.request.Request(url, headers={
    • Network accessline 128
      try:             req = urllib.request.Request(url, headers={                 "User-Agent": user_agent,
    • Network accessline 129
      req = urllib.request.Request(url, headers={
    • Network accessline 134
      response = urllib.request.urlopen(req, timeout=30)

    skills/writing/citation/academic-citation-manager/SKILL.md

    • Network accessline 32
      def get_bibtex_from_doi(doi):     """Retrieve BibTeX entry from a DOI via CrossRef."""     url = f"https://doi.org/{doi}"
    • Network accessline 33
      """Retrieve BibTeX entry from a DOI via CrossRef."""     url = f"https://doi.org/{doi}"     headers = {"Accept": "application/x-bibtex"}
    • Network accessline 34
      url = f"https://doi.org/{doi}"     headers = {"Accept": "application/x-bibtex"}     response = requests.get(url, headers=headers, allow_redirects=True)
    • Network accessline 35
      headers = {"Accept": "application/x-bibtex"}     response = requests.get(url, headers=headers, allow_redirects=True)     if response.status_code == 200:
    • Network accessline 36
      response = requests.get(url, headers=headers, allow_redirects=True)
    • Network accessline 58
      def get_citation_from_openalex(work_id):     """Retrieve citation data from OpenAlex API."""     url = f"https://api.openalex.org/works/{work_id}"
    • Network accessline 59
      """Retrieve citation data from OpenAlex API."""     url = f"https://api.openalex.org/works/{work_id}"     headers = {"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"}
    • Network accessline 60
      url = f"https://api.openalex.org/works/{work_id}"     headers = {"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"}     response = requests.get(url, headers=headers)
    • Network accessline 61
      headers = {"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"}     response = requests.get(url, headers=headers)     if response.status_code == 200:
    • Network accessline 62
      response = requests.get(url, headers=headers)
    • Network accessline 92
      """Retrieve BibTeX from arXiv."""     import feedparser     url = f"http://export.arxiv.org/api/query?id_list={arxiv_id}"
    • Network accessline 93
      import feedparser     url = f"http://export.arxiv.org/api/query?id_list={arxiv_id}"     feed = feedparser.parse(url)
    • Network accessline 94
      url = f"http://export.arxiv.org/api/query?id_list={arxiv_id}"
    • Network accessline 104
      year={{{year}}},   journal={{arXiv preprint arXiv:{arxiv_id}}},   url={{https://arxiv.org/abs/{arxiv_id}}}
    • Network accessline 105
      journal={{arXiv preprint arXiv:{arxiv_id}}},   url={{https://arxiv.org/abs/{arxiv_id}}} }}"""
    • Network accessline 106
      url={{https://arxiv.org/abs/{arxiv_id}}}
    • Network accessline 137
      citation += "."     if doi:         citation += f" https://doi.org/{doi}"
    • Network accessline 139
      citation += f" https://doi.org/{doi}"
    • Network accessline 184
      **APA 7th:** Jumper, J., Evans, R., & Pritzel, A. (2021). Highly accurate protein structure prediction with AlphaFold. *Nature*, *596*, 583-589. https://doi.org/10.1038/s41586-021-03819-2
    • Network accessline 185
      Jumper, J., Evans, R., & Pritzel, A. (2021). Highly accurate protein structure prediction with AlphaFold. *Nature*, *596*, 583-589. https://doi.org/10.1038/s41586-021-03819-2
    • Network accessline 251
      def validate_citation(doi):     """Validate a citation against CrossRef metadata."""     url = f"https://api.crossref.org/works/{doi}"
    • Network accessline 252
      """Validate a citation against CrossRef metadata."""     url = f"https://api.crossref.org/works/{doi}"     response = requests.get(url)
    • Network accessline 253
      url = f"https://api.crossref.org/works/{doi}"     response = requests.get(url)     if response.status_code != 200:
    • Network accessline 254
      response = requests.get(url)
    • Network accessline 313
      - CrossRef API: https://api.crossref.org
    • Network accessline 314
      - OpenAlex API: https://api.openalex.org
    • Network accessline 315
      - APA 7th Edition Manual: https://apastyle.apa.org/products/publication-manual-7th-edition
    • Network accessline 316
      - BibTeX documentation: http://www.bibtex.org
    • Network accessline 317
      - CSL styles repository: https://github.com/citation-style-language/styles

    skills/writing/citation/bibtex-management-guide/SKILL.md

    • Network accessline 177
      if 'doi' in fields:         doi = fields['doi']         doi = doi.replace('https://doi.org/', '')
    • Network accessline 178
      doi = fields['doi']         doi = doi.replace('https://doi.org/', '')         doi = doi.replace('http://dx.doi.org/', '')
    • Network accessline 179
      doi = doi.replace('https://doi.org/', '')
    • Network accessline 180
      doi = doi.replace('http://dx.doi.org/', '')
    • Network accessline 199
      Retrieve a complete BibTeX entry from a DOI using CrossRef.     """     url = f"https://doi.org/{doi}"
    • Network accessline 200
      """     url = f"https://doi.org/{doi}"     headers = {'Accept': 'application/x-bibtex'}
    • Network accessline 201
      url = f"https://doi.org/{doi}"     headers = {'Accept': 'application/x-bibtex'}     response = requests.get(url, headers=headers, allow_redirects=True)
    • Network accessline 203
      response = requests.get(url, headers=headers, allow_redirects=True)

    skills/writing/citation/citation-assistant-skill/SKILL.md

    • Network accessline 8
      subcategory: "citation"     keywords: ["citation assistant", "OpenAlex", "Claude Code skill", "reference lookup", "academic citation"]     source: "https://github.com/ZhangNy301/citation-assistant"
    • Network accessline 9
      keywords: ["citation assistant", "OpenAlex", "Claude Code skill", "reference lookup", "academic citation"]     source: "https://github.com/ZhangNy301/citation-assistant" ---
    • Network accessline 10
      source: "https://github.com/ZhangNy301/citation-assistant"
    • Network accessline 35
      OA_API = "https://api.openalex.org"
    • Network accessline 37
      def search_papers(query, limit=5):     """Search OpenAlex for papers."""     resp = requests.get(
    • Network accessline 38
      """Search OpenAlex for papers."""     resp = requests.get(         f"{OA_API}/works",
    • Network accessline 39
      resp = requests.get(
    • Network accessline 43
      "per_page": limit,         },         headers={"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"},
    • Network accessline 44
      },         headers={"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"},     )
    • Network accessline 45
      headers={"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"},
    • Network accessline 60
      def get_bibtex(doi):     """Get BibTeX for a paper via CrossRef DOI resolution."""     resp = requests.get(
    • Network accessline 61
      """Get BibTeX for a paper via CrossRef DOI resolution."""     resp = requests.get(         f"https://api.crossref.org/works/{doi}",
    • Network accessline 62
      resp = requests.get(
    • Network accessline 63
      f"https://api.crossref.org/works/{doi}",
    • Network accessline 64
      headers={"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai; mailto:dev@wentor.ai)"},
    • Network accessline 98
      def get_citing_works(openalex_id, limit=10):     """Get papers that cite this work via OpenAlex."""     resp = requests.get(
    • Network accessline 99
      """Get papers that cite this work via OpenAlex."""     resp = requests.get(         f"{OA_API}/works",
    • Network accessline 100
      resp = requests.get(
    • Network accessline 105
      "sort": "cited_by_count:desc",         },         headers={"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"},
    • Network accessline 106
      },         headers={"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"},     )
    • Network accessline 107
      headers={"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"},
    • Network accessline 124
      """Find papers related to a given paper via OpenAlex."""     # Get the paper's concepts, then search for similar works     resp = requests.get(
    • Network accessline 125
      # Get the paper's concepts, then search for similar works     resp = requests.get(         f"{OA_API}/works/{openalex_id}",
    • Network accessline 126
      resp = requests.get(
    • Network accessline 127
      f"{OA_API}/works/{openalex_id}",         headers={"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"},     )
    • Network accessline 128
      headers={"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"},
    • Network accessline 133
      related_resp = requests.get(
    • Network accessline 138
      "sort": "cited_by_count:desc",         },         headers={"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"},
    • Network accessline 139
      },         headers={"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"},     )
    • Network accessline 140
      headers={"User-Agent": "ResearchPlugins/1.0 (https://wentor.ai)"},
    • Network accessline 177
      if doi and doi not in seen_ids:                 seen_ids.add(doi)                 bibtex = get_bibtex(doi.replace("https://doi.org/", ""))
    • Network accessline 179
      bibtex = get_bibtex(doi.replace("https://doi.org/", ""))
    • Network accessline 204
      - [Citation Assistant GitHub](https://github.com/ZhangNy301/citation-assistant)
    • Network accessline 205
      - [OpenAlex API](https://api.openalex.org/)
    • Network accessline 206
      - [CrossRef API](https://api.crossref.org/)

    skills/writing/citation/citation-style-guide/SKILL.md

    • Network accessline 49
      Smith, J. A., & Jones, B. C. (2023). Title of the article in sentence     case. Journal Name in Title Case, 45(2), 123-145.     https://doi.org/10.1234/example
    • Network accessline 51
      https://doi.org/10.1234/example
    • Network accessline 53
      # Book Williams, R. T. (2022). Title of the book in sentence case (3rd ed.).     Publisher Name. https://doi.org/10.1234/example
    • Network accessline 55
      Publisher Name. https://doi.org/10.1234/example
    • Network accessline 57
      # Chapter in edited book Chen, L. (2023). Chapter title. In A. Editor & B. Editor (Eds.),     Book title (pp. 50-75). Publisher. https://doi.org/10.1234/example
    • Network accessline 59
      Book title (pp. 50-75). Publisher. https://doi.org/10.1234/example
    • Network accessline 62
      Lee, S., & Park, J. (2023). Paper title. In Proceedings of the 2023     Conference Name (pp. 100-110). Publisher.     https://doi.org/10.1234/example
    • Network accessline 64
      https://doi.org/10.1234/example
    • Network accessline 66
      # Webpage National Institutes of Health. (2023, March 15). Page title.     https://www.nih.gov/example
    • Network accessline 68
      https://www.nih.gov/example
    • Network accessline 70
      # Preprint Garcia, M. (2023). Title of preprint. arXiv.     https://doi.org/10.48550/arXiv.2301.12345
    • Network accessline 72
      https://doi.org/10.48550/arXiv.2301.12345
    • Network accessline 74
      # Dataset Johnson, K. (2023). Dataset title (Version 2.0) [Data set]. Repository.     https://doi.org/10.1234/example
    • Network accessline 76
      https://doi.org/10.1234/example
    • Network accessline 95
      Smith, John A., and Beth C. Jones. "Article Title in Title Case."     Journal Name, vol. 45, no. 2, 2023, pp. 123-45.     https://doi.org/10.1234/example.
    • Network accessline 97
      https://doi.org/10.1234/example.
    • Network accessline 139
      # Online source [4] Author, "Page title," Website, date. [Online]. Available:     https://www.example.com
    • Network accessline 141
      https://www.example.com
    • Network accessline 158
      <?xml version="1.0" encoding="utf-8"?> <style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0">
    • Network accessline 159
      <style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0">
    • Network accessline 160
      <info>     <title>Custom Style</title>     <id>http://www.example.com/custom-style</id>
    • Network accessline 161
      <title>Custom Style</title>     <id>http://www.example.com/custom-style</id>   </info>
    • Network accessline 162
      <id>http://www.example.com/custom-style</id>

    skills/writing/citation/jabref-reference-guide/SKILL.md

    • Network accessline 8
      subcategory: "citation"     keywords: ["jabref", "bibtex", "biblatex", "reference-manager", "latex", "bibliography"]     source: "https://github.com/JabRef/jabref"
    • Network accessline 9
      keywords: ["jabref", "bibtex", "biblatex", "reference-manager", "latex", "bibliography"]     source: "https://github.com/JabRef/jabref" ---
    • Network accessline 10
      source: "https://github.com/JabRef/jabref"
    • Network accessline 27
      **Direct Download**: 1. Visit https://www.jabref.org and download the installer for your platform
    • Network accessline 28
      1. Visit https://www.jabref.org and download the installer for your platform
    • Dangerous shell operationline 34
      - Linux (Snap): `sudo snap install jabref`
    • Network accessline 123
      - Official Website: https://www.jabref.org
    • Network accessline 124
      - GitHub Repository: https://github.com/JabRef/jabref
    • Network accessline 125
      - JabRef User Documentation: https://docs.jabref.org
    • Network accessline 126
      - JabRef Blog: https://blog.jabref.org
    • Network accessline 127
      - CTAN BibTeX Documentation: https://ctan.org/pkg/bibtex

    skills/writing/citation/jasminum-zotero-guide/SKILL.md

    • Network accessline 8
      subcategory: "citation"     keywords: ["zotero", "cnki", "chinese-academic", "jasminum", "metadata", "bibliography"]     source: "https://github.com/l0o0/jasminum"
    • Network accessline 9
      keywords: ["zotero", "cnki", "chinese-academic", "jasminum", "metadata", "bibliography"]     source: "https://github.com/l0o0/jasminum" ---
    • Network accessline 10
      source: "https://github.com/l0o0/jasminum"
    • Network accessline 27
      1. Download the latest `.xpi` file from https://github.com/l0o0/jasminum/releases
    • Network accessline 99
      - GitHub Repository: https://github.com/l0o0/jasminum
    • Network accessline 100
      - CNKI (China National Knowledge Infrastructure): https://www.cnki.net
    • Network accessline 101
      - Zotero Plugin Directory: https://www.zotero.org/support/plugins
    • Network accessline 102
      - GB/T 7714 Citation Standard: https://std.samr.gov.cn
    • Network accessline 103
      - Zotero Chinese User Community: https://zotero-chinese.com

    skills/writing/citation/mendeley-api/SKILL.md

    • Network accessline 24
      # 1. Register app at https://dev.elsevier.com/ # 2. Get access token via client credentials (for catalog search) curl -X POST "https://api.mendeley.com/oauth/token" \
    • Network accessline 25
      # 2. Get access token via client credentials (for catalog search) curl -X POST "https://api.mendeley.com/oauth/token" \   -d "grant_type=client_credentials" \
    • Network accessline 26
      [Credential-related source omitted]
    • Access to secretsline 26
      [Credential-related source omitted]
    • Access to secretsline 30
      [Credential-related source omitted]
    • Access to secretsline 32
      [Credential-related source omitted]
    • Network accessline 40
      https://api.mendeley.com
    • Network accessline 48
      [Credential-related source omitted]
    • Network accessline 49
      [Credential-related source omitted]
    • Network accessline 50
      "https://api.mendeley.com/catalog?query=deep+learning+NLP&limit=20"
    • Network accessline 52
      [Credential-related source omitted]
    • Network accessline 53
      [Credential-related source omitted]
    • Network accessline 54
      "https://api.mendeley.com/catalog?doi=10.1038/nature14539"
    • Network accessline 56
      [Credential-related source omitted]
    • Network accessline 57
      [Credential-related source omitted]
    • Network accessline 58
      "https://api.mendeley.com/catalog?title=attention+is+all+you+need"
    • Network accessline 64
      [Credential-related source omitted]
    • Network accessline 65
      [Credential-related source omitted]
    • Network accessline 66
      "https://api.mendeley.com/documents?limit=50&sort=created&order=desc"
    • Network accessline 68
      [Credential-related source omitted]
    • Network accessline 69
      [Credential-related source omitted]
    • Network accessline 70
      "https://api.mendeley.com/documents/{doc_id}"
    • Network accessline 72
      [Credential-related source omitted]
    • Network accessline 73
      [Credential-related source omitted]
    • Network accessline 74
      -H "Content-Type: application/vnd.mendeley-document.1+json" \   -d '{"title":"My Paper","type":"journal","year":2025,"authors":[{"first_name":"A","last_name":"B"}]}' \   "https://api.mendeley.com/documents"
    • Network accessline 76
      "https://api.mendeley.com/documents"
    • Network accessline 82
      [Credential-related source omitted]
    • Network accessline 83
      [Credential-related source omitted]
    • Network accessline 84
      "https://api.mendeley.com/folders"
    • Network accessline 86
      [Credential-related source omitted]
    • Network accessline 87
      [Credential-related source omitted]
    • Network accessline 88
      "https://api.mendeley.com/documents?group_id={group_id}"
    • Network accessline 94
      [Credential-related source omitted]
    • Network accessline 95
      [Credential-related source omitted]
    • Network accessline 96
      "https://api.mendeley.com/annotations?document_id={doc_id}"
    • Network accessline 131
      "abstract": "The dominant sequence transduction models...",   "reader_count": 15432,   "link": "https://www.mendeley.com/catalogue/..."
    • Network accessline 132
      "reader_count": 15432,   "link": "https://www.mendeley.com/catalogue/..." }
    • Network accessline 133
      "link": "https://www.mendeley.com/catalogue/..."
    • Network accessline 143
      [Credential-related source omitted]
    • Access to secretsline 143
      [Credential-related source omitted]
    • Network accessline 144
      [Credential-related source omitted]
    • Access to secretsline 144
      [Credential-related source omitted]
    • Network accessline 145
      TOKEN_URL = "https://api.mendeley.com/oauth/token"
    • Network accessline 146
      BASE_URL = "https://api.mendeley.com"
    • Network accessline 149
      def get_token() -> str:     """Obtain access token via client credentials."""     resp = requests.post(TOKEN_URL, data={
    • Network accessline 150
      """Obtain access token via client credentials."""     resp = requests.post(TOKEN_URL, data={         "grant_type": "client_credentials",
    • Network accessline 151
      resp = requests.post(TOKEN_URL, data={
    • Access to secretsline 155
      [Credential-related source omitted]
    • Access to secretsline 158
      [Credential-related source omitted]
    • Network accessline 169
      resp = requests.get(
    • Network accessline 191
      [Credential-related source omitted]
    • Network accessline 192
      [Credential-related source omitted]
    • Network accessline 193
      resp = requests.get(
    • Network accessline 229
      - [Mendeley API Documentation](wentor-research-plugins) - [Mendeley Developer Portal](https://dev.elsevier.com/)
    • Network accessline 230
      - [Mendeley Developer Portal](https://dev.elsevier.com/)
    • Network accessline 231
      - [Mendeley API Reference](https://api.mendeley.com/apidocs/)

    skills/writing/citation/obsidian-citation-guide/SKILL.md

    • Network accessline 2
      name: obsidian-citation-guide description: "Citation plugin for Obsidian note-taking with BibTeX support" source: https://github.com/hans/obsidian-citation-plugin
    • Network accessline 3
      description: "Citation plugin for Obsidian note-taking with BibTeX support" source: https://github.com/hans/obsidian-citation-plugin metadata:
    • Network accessline 4
      source: https://github.com/hans/obsidian-citation-plugin

    skills/writing/citation/obsidian-zotero-guide/SKILL.md

    • Network accessline 2
      name: obsidian-zotero-guide description: "Insert citations and notes from Zotero into Obsidian knowledge bases" source: https://github.com/mgmeyers/obsidian-zotero-integration
    • Network accessline 3
      description: "Insert citations and notes from Zotero into Obsidian knowledge bases" source: https://github.com/mgmeyers/obsidian-zotero-integration metadata:
    • Network accessline 4
      source: https://github.com/mgmeyers/obsidian-zotero-integration

    skills/writing/citation/onecite-reference-guide/SKILL.md

    • Network accessline 8
      subcategory: "citation"     keywords: ["OneCite", "reference formatting", "citation parser", "BibTeX", "metadata completion", "MCP"]     source: "https://github.com/HzaCode/OneCite"
    • Network accessline 9
      keywords: ["OneCite", "reference formatting", "citation parser", "BibTeX", "metadata completion", "MCP"]     source: "https://github.com/HzaCode/OneCite" ---
    • Network accessline 10
      source: "https://github.com/HzaCode/OneCite"
    • Network accessline 166
      - [OneCite GitHub](https://github.com/HzaCode/OneCite)
    • Network accessline 167
      - [CrossRef API](https://api.crossref.org/)
    • Network accessline 168
      - [Citation Style Language](https://citationstyles.org/)

    skills/writing/citation/papersgpt-zotero-guide/SKILL.md

    • Network accessline 2
      name: papersgpt-zotero-guide description: "AI plugin for Zotero with ChatGPT, Claude, and DeepSeek support" source: https://github.com/papersgpt/papersgpt-for-zotero
    • Network accessline 3
      description: "AI plugin for Zotero with ChatGPT, Claude, and DeepSeek support" source: https://github.com/papersgpt/papersgpt-for-zotero metadata:
    • Network accessline 4
      source: https://github.com/papersgpt/papersgpt-for-zotero

    skills/writing/citation/papis-cli-guide/SKILL.md

    • Network accessline 8
      subcategory: "citation"     keywords: ["papis", "cli", "bibliography", "document-manager", "terminal", "command-line"]     source: "https://github.com/papis/papis"
    • Network accessline 9
      keywords: ["papis", "cli", "bibliography", "document-manager", "terminal", "command-line"]     source: "https://github.com/papis/papis" ---
    • Network accessline 10
      source: "https://github.com/papis/papis"
    • Dangerous shell operationline 118
      papis rm "old paper 2015"
    • Network accessline 210
      - GitHub Repository: https://github.com/papis/papis
    • Network accessline 211
      - Papis Documentation: https://papis.readthedocs.io
    • Network accessline 212
      - Papis Wiki: https://github.com/papis/papis/wiki
    • Network accessline 213
      - PyPI Package: https://pypi.org/project/papis

    skills/writing/citation/zotero-api/SKILL.md

    • Network accessline 8
      subcategory: "citation"     keywords: ["reference management", "citation management", "bibliography organization", "literature import"]     source: "https://www.zotero.org/support/dev/web_api/v3/basics"
    • Network accessline 9
      keywords: ["reference management", "citation management", "bibliography organization", "literature import"]     source: "https://www.zotero.org/support/dev/web_api/v3/basics" ---
    • Network accessline 10
      source: "https://www.zotero.org/support/dev/web_api/v3/basics"
    • Network accessline 27
      1. Log in to your Zotero account at https://www.zotero.org/
    • Network accessline 28
      2. Navigate to https://www.zotero.org/settings/keys
    • Network accessline 33
      [Credential-related source omitted]
    • Network accessline 34
      [Credential-related source omitted]
    • Access to secretsline 34
      [Credential-related source omitted]
    • Network accessline 36
      # Public group library (no auth needed) curl "https://api.zotero.org/groups/GROUP_ID/items"
    • Network accessline 37
      curl "https://api.zotero.org/groups/GROUP_ID/items"
    • Network accessline 40
      Your user ID can be found at https://www.zotero.org/settings/keys alongside your API key settings.
    • Network accessline 48
      - **URL**: `GET https://api.zotero.org/users/{userID}/items`
    • Network accessline 67
      [Credential-related source omitted]
    • Network accessline 68
      [Credential-related source omitted]
    • Network accessline 69
      "https://api.zotero.org/users/12345/items?itemType=journalArticle&tag=machine+learning&format=json"
    • Network accessline 71
      [Credential-related source omitted]
    • Network accessline 72
      [Credential-related source omitted]
    • Network accessline 73
      "https://api.zotero.org/users/12345/items?q=neural+networks&format=json"
    • Network accessline 82
      - **URL**: `GET https://api.zotero.org/groups/{groupID}/items`
    • Network accessline 99
      # List items in a public group library curl "https://api.zotero.org/groups/67890/items?format=json&limit=50"
    • Network accessline 100
      curl "https://api.zotero.org/groups/67890/items?format=json&limit=50"
    • Network accessline 102
      # Get formatted bibliography from a group curl "https://api.zotero.org/groups/67890/items?format=bib&style=apa"
    • Network accessline 103
      curl "https://api.zotero.org/groups/67890/items?format=bib&style=apa"
    • Network accessline 123
      # Get items formatted as APA bibliography resp = requests.get(
    • Network accessline 124
      resp = requests.get(
    • Network accessline 125
      "https://api.zotero.org/users/12345/collections/ABCDEF/items",
    • Network accessline 142
      resp = requests.get(
    • Network accessline 143
      "https://api.zotero.org/users/12345/items",
    • Network accessline 167
      resp = requests.get(
    • Network accessline 168
      "https://api.zotero.org/users/12345/items",
    • Network accessline 184
      - Official Web API documentation: https://www.zotero.org/support/dev/web_api/v3/basics
    • Network accessline 185
      - API key management: https://www.zotero.org/settings/keys
    • Network accessline 186
      - Item types and fields: https://api.zotero.org/itemTypes
    • Network accessline 187
      - Zotero homepage: https://www.zotero.org/
    • Network accessline 188
      - Citation styles: https://www.zotero.org/styles

    skills/writing/citation/zotero-better-bibtex-guide/SKILL.md

    • Network accessline 8
      subcategory: "citation"     keywords: ["zotero", "bibtex", "latex", "citation-keys", "better-bibtex", "bibliography"]     source: "https://github.com/retorquere/zotero-better-bibtex"
    • Network accessline 9
      keywords: ["zotero", "bibtex", "latex", "citation-keys", "better-bibtex", "bibliography"]     source: "https://github.com/retorquere/zotero-better-bibtex" ---
    • Network accessline 10
      source: "https://github.com/retorquere/zotero-better-bibtex"
    • Network accessline 27
      1. Download the latest `.xpi` file from https://github.com/retorquere/zotero-better-bibtex/releases
    • Network accessline 72
      **Pull Export via HTTP**: BBT runs a local HTTP server that serves your bibliography on demand. Configure your LaTeX build system to pull the latest `.bib` file from `http://127.0.0.1:23119/better-bibtex/export/collection?...` before each c
    • Network accessline 104
      - GitHub Repository: https://github.com/retorquere/zotero-better-bibtex
    • Network accessline 105
      - BBT Documentation: https://retorque.re/zotero-better-bibtex/
    • Network accessline 106
      - Citation Key Formulas: https://retorque.re/zotero-better-bibtex/citing/
    • Network accessline 107
      - Zotero Plugin Directory: https://www.zotero.org/support/plugins

    skills/writing/citation/zotero-better-notes-guide/SKILL.md

    • Network accessline 8
      subcategory: "citation"     keywords: ["zotero", "note-taking", "better-notes", "research-notes", "knowledge-management"]     source: "https://github.com/windingwind/zotero-better-notes"
    • Network accessline 9
      keywords: ["zotero", "note-taking", "better-notes", "research-notes", "knowledge-management"]     source: "https://github.com/windingwind/zotero-better-notes" ---
    • Network accessline 10
      source: "https://github.com/windingwind/zotero-better-notes"
    • Network accessline 27
      1. Download the latest `.xpi` release from https://github.com/windingwind/zotero-better-notes/releases
    • Network accessline 118
      - GitHub Repository: https://github.com/windingwind/zotero-better-notes
    • Network accessline 119
      - Better Notes Documentation: https://github.com/windingwind/zotero-better-notes/wiki
    • Network accessline 120
      - Zotero Plugin Directory: https://www.zotero.org/support/plugins
    • Network accessline 121
      - Zettelkasten Method for Researchers: https://zettelkasten.de/introduction

    skills/writing/citation/zotero-gpt-guide/SKILL.md

    • Network accessline 8
      subcategory: "citation"     keywords: ["zotero", "gpt", "ai-assistant", "research-ai", "paper-analysis"]     source: "https://github.com/MuiseDestiny/zotero-gpt"
    • Network accessline 9
      keywords: ["zotero", "gpt", "ai-assistant", "research-ai", "paper-analysis"]     source: "https://github.com/MuiseDestiny/zotero-gpt" ---
    • Network accessline 10
      source: "https://github.com/MuiseDestiny/zotero-gpt"
    • Network accessline 27
      1. Download the latest `.xpi` file from https://github.com/MuiseDestiny/zotero-gpt/releases
    • Access to secretsline 36
      [Credential-related source omitted]
    • Access to secretsline 37
      [Credential-related source omitted]
    • Access to secretsline 38
      [Credential-related source omitted]
    • Network accessline 108
      - GitHub Repository: https://github.com/MuiseDestiny/zotero-gpt
    • Network accessline 109
      - Zotero Plugin Directory: https://www.zotero.org/support/plugins
    • Network accessline 110
      - OpenAI API Documentation: https://platform.openai.com/docs
    • Network accessline 111
      - Responsible AI Use in Research: https://www.nature.com/articles/d41586-023-00056-7

    skills/writing/citation/zotero-mcp-guide/SKILL.md

    • Network accessline 8
      subcategory: "citation"     keywords: ["zotero", "mcp", "claude", "ai-assistant", "model-context-protocol"]     source: "https://github.com/54yyyu/zotero-mcp"
    • Network accessline 9
      keywords: ["zotero", "mcp", "claude", "ai-assistant", "model-context-protocol"]     source: "https://github.com/54yyyu/zotero-mcp" ---
    • Network accessline 10
      source: "https://github.com/54yyyu/zotero-mcp"
    • Network accessline 35
      # Clone the repository git clone https://github.com/54yyyu/zotero-mcp.git
    • Network accessline 36
      git clone https://github.com/54yyyu/zotero-mcp.git
    • Network accessline 161
      - GitHub Repository: https://github.com/54yyyu/zotero-mcp
    • Network accessline 162
      - Model Context Protocol Specification: https://modelcontextprotocol.io
    • Network accessline 163
      - Zotero Local API Documentation: https://www.zotero.org/support/dev/web_api/v3/basics
    • Network accessline 164
      - Claude Desktop MCP Configuration: https://docs.anthropic.com/en/docs/claude-desktop

    skills/writing/citation/zotero-mdnotes-guide/SKILL.md

    • Network accessline 2
      name: zotero-mdnotes-guide description: "Export Zotero items and annotations to Markdown note files" source: https://github.com/argenos/zotero-mdnotes
    • Network accessline 3
      description: "Export Zotero items and annotations to Markdown note files" source: https://github.com/argenos/zotero-mdnotes metadata:
    • Network accessline 4
      source: https://github.com/argenos/zotero-mdnotes

    skills/writing/citation/zotero-reference-guide/SKILL.md

    • Network accessline 2
      name: zotero-reference-guide description: "PDF references add-on for enriching Zotero library metadata" source: https://github.com/MuiseDestiny/zotero-reference
    • Network accessline 3
      description: "PDF references add-on for enriching Zotero library metadata" source: https://github.com/MuiseDestiny/zotero-reference metadata:
    • Network accessline 4
      source: https://github.com/MuiseDestiny/zotero-reference

    skills/writing/citation/zotero-scholar-guide/SKILL.md

    • Network accessline 8
      subcategory: "citation"     keywords: ["zotero", "reference manager", "citation management", "API", "metadata", "bibliography", "paper organization"]     source: "https://github.com/zotero/zotero"
    • Network accessline 9
      keywords: ["zotero", "reference manager", "citation management", "API", "metadata", "bibliography", "paper organization"]     source: "https://github.com/zotero/zotero" ---
    • Network accessline 10
      source: "https://github.com/zotero/zotero"
    • Network accessline 27
      1. Log in to your Zotero account at https://www.zotero.org
    • Network accessline 28
      2. Navigate to Settings > Feeds/API (https://www.zotero.org/settings/keys)
    • Access to secretsline 38
      [Credential-related source omitted]
    • Network accessline 45
      [Credential-related source omitted]
    • Dangerous shell operationline 46
      [Credential-related source omitted]
    • Network accessline 46
      [Credential-related source omitted]
    • Access to secretsline 46
      [Credential-related source omitted]
    • Network accessline 47
      "https://api.zotero.org/users/$ZOTERO_USER_ID/items?limit=5&format=json" \
    • Network accessline 63
      [Credential-related source omitted]
    • Access to secretsline 63
      [Credential-related source omitted]
    • Network accessline 64
      [Credential-related source omitted]
    • Access to secretsline 64
      [Credential-related source omitted]
    • Network accessline 65
      BASE_URL = f"https://api.zotero.org/users/{USER_ID}"
    • Access to secretsline 67
      [Credential-related source omitted]
    • Network accessline 72
      """Resolve DOI metadata and add to Zotero."""     # Step 1: Get metadata from DOI via Crossref     cr_resp = requests.get(
    • Network accessline 73
      # Step 1: Get metadata from DOI via Crossref     cr_resp = requests.get(         f"https://api.crossref.org/works/{doi}",
    • Network accessline 74
      cr_resp = requests.get(
    • Network accessline 75
      f"https://api.crossref.org/works/{doi}",
    • Network accessline 89
      "abstractNote": cr_data.get("abstract", ""),         "DOI": doi,         "url": f"https://doi.org/{doi}",
    • Network accessline 90
      "DOI": doi,         "url": f"https://doi.org/{doi}",         "date": cr_data.get("published-print", {}).get("date-parts", [[""]])[0][0],
    • Network accessline 91
      "url": f"https://doi.org/{doi}",
    • Network accessline 100
      # Step 3: POST to Zotero     resp = requests.post(
    • Network accessline 101
      resp = requests.post(
    • Network accessline 126
      """Fetch arXiv metadata and add to Zotero."""     feed = feedparser.parse(         f"http://export.arxiv.org/api/query?id_list={arxiv_id}"
    • Network accessline 127
      feed = feedparser.parse(         f"http://export.arxiv.org/api/query?id_list={arxiv_id}"     )
    • Network accessline 128
      f"http://export.arxiv.org/api/query?id_list={arxiv_id}"
    • Network accessline 152
      resp = requests.post(
    • Network accessline 184
      resp = requests.post(
    • Network accessline 201
      "parentCollection": parent_key or False     }     resp = requests.post(
    • Network accessline 202
      }     resp = requests.post(         f"{BASE_URL}/collections",
    • Network accessline 203
      resp = requests.post(
    • Network accessline 226
      """     # Fetch all items     items = requests.get(
    • Network accessline 227
      # Fetch all items     items = requests.get(         f"{BASE_URL}/items?limit=100&format=json",
    • Network accessline 228
      items = requests.get(
    • Network accessline 243
      if len(new_tags) > len(item["data"].get("tags", [])):             requests.patch(
    • Network accessline 244
      requests.patch(
    • Network accessline 263
      [Credential-related source omitted]
    • Network accessline 264
      [Credential-related source omitted]
    • Access to secretsline 264
      [Credential-related source omitted]
    • Network accessline 265
      "https://api.zotero.org/users/$ZOTERO_USER_ID/items?format=bibtex&limit=100" \
    • Network accessline 268
      [Credential-related source omitted]
    • Network accessline 269
      [Credential-related source omitted]
    • Access to secretsline 269
      [Credential-related source omitted]
    • Network accessline 270
      "https://api.zotero.org/users/$ZOTERO_USER_ID/collections/ABCD1234/items?format=csljson" \
    • Network accessline 273
      [Credential-related source omitted]
    • Network accessline 274
      [Credential-related source omitted]
    • Access to secretsline 274
      [Credential-related source omitted]
    • Network accessline 275
      "https://api.zotero.org/users/$ZOTERO_USER_ID/items?format=ris&limit=100" \
    • Network accessline 282
      [Credential-related source omitted]
    • Network accessline 283
      [Credential-related source omitted]
    • Access to secretsline 283
      [Credential-related source omitted]
    • Network accessline 285
      "https://api.zotero.org/users/$ZOTERO_USER_ID/items?format=bib&style=apa&limit=50"
    • Network accessline 290
      - Zotero Web API v3 documentation: https://www.zotero.org/support/dev/web_api/v3/start
    • Network accessline 291
      - Zotero source code: https://github.com/zotero/zotero
    • Network accessline 292
      - pyzotero (Python library): https://github.com/urschrei/pyzotero
    • Network accessline 293
      - Crossref API: https://api.crossref.org
    • Network accessline 294
      - Zotero Better BibTeX plugin: https://retorque.re/zotero-better-bibtex/

    skills/writing/citation/zotfile-attachment-guide/SKILL.md

    • Network accessline 8
      subcategory: "citation"     keywords: ["zotero", "zotfile", "attachment", "pdf-management", "file-organization", "sync"]     source: "https://github.com/jlegewie/zotfile"
    • Network accessline 9
      keywords: ["zotero", "zotfile", "attachment", "pdf-management", "file-organization", "sync"]     source: "https://github.com/jlegewie/zotfile" ---
    • Network accessline 10
      source: "https://github.com/jlegewie/zotfile"
    • Network accessline 15
      **WARNING: ZotFile is NOT compatible with Zotero 7.** For Zotero 7, use the built-in attachment management or the [Attanger](https://github.com/MuiseDestiny/zotero-attanger) plugin as a replacement.
    • Network accessline 29
      1. Download the latest `.xpi` file from https://github.com/jlegewie/zotfile/releases
    • Network accessline 139
      - GitHub Repository: https://github.com/jlegewie/zotfile
    • Network accessline 140
      - ZotFile Documentation: http://zotfile.com
    • Network accessline 141
      - Zotero Plugin Directory: https://www.zotero.org/support/plugins
    • Network accessline 142
      - Zotero File Management Guide: https://www.zotero.org/support/attaching_files

    skills/writing/composition/ml-paper-writing/SKILL.md

    • Network accessline 8
      subcategory: "composition"     keywords: ["machine learning", "NeurIPS", "ICML", "ICLR", "AI paper", "deep learning", "conference paper"]     source: "https://github.com/karpathy/arxiv-sanity-lite"
    • Network accessline 9
      keywords: ["machine learning", "NeurIPS", "ICML", "ICLR", "AI paper", "deep learning", "conference paper"]     source: "https://github.com/karpathy/arxiv-sanity-lite" ---
    • Network accessline 10
      source: "https://github.com/karpathy/arxiv-sanity-lite"
    • Network accessline 159
      - NeurIPS 2025 Call for Papers and Reviewer Guidelines: https://neurips.cc
    • Network accessline 160
      - ICML Author Instructions: https://icml.cc
    • Network accessline 161
      - ICLR Submission Guidelines: https://iclr.cc
    • Network accessline 162
      - Karpathy's arXiv Sanity: https://github.com/karpathy/arxiv-sanity-lite

    skills/writing/composition/research-paper-writer/SKILL.md

    • Network accessline 223
      - [IEEE Author Tools](https://journals.ieeeauthorcenter.ieee.org/)
    • Network accessline 224
      - [ACM Primary Article Templates](https://www.acm.org/publications/proceedings-template)
    • Network accessline 225
      - [ACM CCS Tree](https://dl.acm.org/ccs)
    • Network accessline 226
      - [Booktabs Package Documentation](https://ctan.org/pkg/booktabs)

    skills/writing/composition/scientific-writing-guide/SKILL.md

    • Network accessline 8
      subcategory: "composition"     keywords: ["scientific writing", "academic writing", "writing tools", "manuscript preparation", "AI writing workflow", "prose quality"]     source: "https://github.com/writing-resources/awesome-scientific-writ
    • Network accessline 9
      keywords: ["scientific writing", "academic writing", "writing tools", "manuscript preparation", "AI writing workflow", "prose quality"]     source: "https://github.com/writing-resources/awesome-scientific-writing" ---
    • Network accessline 10
      source: "https://github.com/writing-resources/awesome-scientific-writing"
    • Network accessline 217
      - [awesome-scientific-writing](https://github.com/writing-resources/awesome-scientific-writing) -- Curated list of tools and resources (920+ stars)
    • Network accessline 218
      - [How to Write a Great Research Paper](https://www.microsoft.com/en-us/research/academic-program/write-great-research-paper/) -- Simon Peyton Jones, Microsoft Research
    • Network accessline 219
      - [The Science of Scientific Writing](https://www.americanscientist.org/blog/the-long-view/the-science-of-scientific-writing) -- Gopen and Swan, American Scientist
    • Network accessline 220
      - [Improving Your Scientific Writing](https://lijunsun.github.io/files/ScientificWritingV39.pdf) -- Lijun Sun, McGill University
    • Network accessline 221
      - [Three Sins of Authors in CS and Math](http://www.cs.cmu.edu/~jrs/sins.html) -- Jonathan Shewchuk, UC Berkeley

    skills/writing/latex/academic-writing-latex/SKILL.md

    • Network accessline 23
      | Publisher | Template Source | Document Class | |-----------|----------------|---------------| | IEEE | [ieee.org/conferences](https://www.ieee.org/conferences/publishing/templates.html) | `IEEEtran` |
    • Network accessline 24
      |-----------|----------------|---------------| | IEEE | [ieee.org/conferences](https://www.ieee.org/conferences/publishing/templates.html) | `IEEEtran` | | ACM | [acm.org/publications](https://www.acm.org/publications/proceedings-template)
    • Network accessline 25
      | IEEE | [ieee.org/conferences](https://www.ieee.org/conferences/publishing/templates.html) | `IEEEtran` |
    • Network accessline 26
      | ACM | [acm.org/publications](https://www.acm.org/publications/proceedings-template) | `acmart` |
    • Network accessline 27
      | Springer | LNCS template package | `llncs` | | Elsevier | [elsarticle](https://www.elsevier.com/researcher/author/policies-and-guidelines/latex-instructions) | `elsarticle` | | Nature | Author submission guidelines | `nature` |
    • Network accessline 28
      | Elsevier | [elsarticle](https://www.elsevier.com/researcher/author/policies-and-guidelines/latex-instructions) | `elsarticle` |
    • Network accessline 30
      | APS/AIP | [REVTeX](https://journals.aps.org/revtex) | `revtex4-2` |
    • Network accessline 282
      - [Overleaf Documentation](https://www.overleaf.com/learn)
    • Network accessline 283
      - [LaTeX Wikibook](https://en.wikibooks.org/wiki/LaTeX)
    • Network accessline 284
      - [CTAN Package Repository](https://ctan.org/)
    • Network accessline 285
      - [BibTeX Entry Types](https://www.bibtex.com/e/entry-types/)

    skills/writing/latex/latex-drawing-collection/SKILL.md

    • Network accessline 2
      name: latex-drawing-collection description: "LaTeX drawing examples for Bayesian networks, tensors, and diagrams" source: https://github.com/xinychen/awesome-latex-drawing
    • Network accessline 3
      description: "LaTeX drawing examples for Bayesian networks, tensors, and diagrams" source: https://github.com/xinychen/awesome-latex-drawing metadata:
    • Network accessline 4
      source: https://github.com/xinychen/awesome-latex-drawing

    skills/writing/latex/latex-drawing-guide/SKILL.md

    • Network accessline 8
      subcategory: "latex"     keywords: ["LaTeX typesetting", "LaTeX figure insertion", "LaTeX custom style", "scientific figure creation"]     source: "https://github.com/xinychen/awesome-latex-drawing"
    • Network accessline 9
      keywords: ["LaTeX typesetting", "LaTeX figure insertion", "LaTeX custom style", "scientific figure creation"]     source: "https://github.com/xinychen/awesome-latex-drawing" ---
    • Network accessline 10
      source: "https://github.com/xinychen/awesome-latex-drawing"
    • Network accessline 230
      - [awesome-latex-drawing](https://github.com/xinychen/awesome-latex-drawing) -- 30+ LaTeX drawing examples (2,000+ stars)
    • Network accessline 231
      - [TikZ and PGF Manual](https://tikz.dev/) -- Official documentation
    • Network accessline 232
      - [PGFPlots Manual](https://pgfplots.net/) -- Data visualization in LaTeX
    • Network accessline 233
      - [TikZ Examples](https://texample.net/tikz/examples/) -- Community gallery
    • Network accessline 234
      - [LaTeX Drawing Tutorial](https://www.overleaf.com/learn/latex/TikZ_package) -- Overleaf tutorial

    skills/writing/latex/latex-ecosystem-guide/SKILL.md

    • Network accessline 8
      subcategory: "latex"     keywords: ["LaTeX typesetting", "LaTeX template", "LaTeX package management", "online LaTeX editor"]     source: "https://github.com/egeerardyn/awesome-LaTeX"
    • Network accessline 9
      keywords: ["LaTeX typesetting", "LaTeX template", "LaTeX package management", "online LaTeX editor"]     source: "https://github.com/egeerardyn/awesome-LaTeX" ---
    • Network accessline 10
      source: "https://github.com/egeerardyn/awesome-LaTeX"
    • Network accessline 236
      - [awesome-LaTeX](https://github.com/egeerardyn/awesome-LaTeX) -- Curated list of LaTeX resources (1,600+ stars)
    • Network accessline 237
      - [CTAN](https://ctan.org/) -- Comprehensive TeX Archive Network
    • Network accessline 238
      - [LaTeX Wikibook](https://en.wikibooks.org/wiki/LaTeX) -- Community-maintained reference
    • Network accessline 239
      - [Overleaf Documentation](https://www.overleaf.com/learn) -- Tutorials and templates
    • Network accessline 240
      - [LaTeX Workshop for VS Code](https://github.com/James-Yu/LaTeX-Workshop) -- VS Code extension

    skills/writing/latex/latex-templates-collection/SKILL.md

    • Network accessline 2
      name: latex-templates-collection description: "Collection of LaTeX templates for papers, presentations, and CVs" source: https://github.com/deedydas/latex-templates
    • Network accessline 3
      description: "Collection of LaTeX templates for papers, presentations, and CVs" source: https://github.com/deedydas/latex-templates metadata:
    • Network accessline 4
      source: https://github.com/deedydas/latex-templates

    skills/writing/latex/md-to-pdf-academic/SKILL.md

    • Network accessline 8
      subcategory: "latex"     keywords: ["markdown", "PDF", "pandoc", "LaTeX rendering", "document conversion", "academic formatting"]     source: "https://github.com/Wandmalfarbe/pandoc-latex-template"
    • Network accessline 9
      keywords: ["markdown", "PDF", "pandoc", "LaTeX rendering", "document conversion", "academic formatting"]     source: "https://github.com/Wandmalfarbe/pandoc-latex-template" ---
    • Network accessline 10
      source: "https://github.com/Wandmalfarbe/pandoc-latex-template"
    • Dangerous shell operationline 35
      sudo tlmgr install collection-fontsrecommended latexmk
    • Dangerous shell operationline 38
      sudo apt-get install pandoc texlive-full
    • Network accessline 65
      # Download Eisvogel template mkdir -p ~/.pandoc/templates wget https://github.com/Wandmalfarbe/pandoc-latex-template/releases/latest/download/Eisvogel.tar.gz
    • Network accessline 66
      mkdir -p ~/.pandoc/templates wget https://github.com/Wandmalfarbe/pandoc-latex-template/releases/latest/download/Eisvogel.tar.gz tar -xzf Eisvogel.tar.gz -C ~/.pandoc/templates/
    • Network accessline 67
      wget https://github.com/Wandmalfarbe/pandoc-latex-template/releases/latest/download/Eisvogel.tar.gz
    • Dangerous shell operationline 192
      rm -f $(PAPER).pdf $(PAPER).docx $(PAPER).html
    • Network accessline 227
      - Pandoc User's Guide: https://pandoc.org/MANUAL.html
    • Network accessline 228
      - Eisvogel LaTeX Template: https://github.com/Wandmalfarbe/pandoc-latex-template
    • Network accessline 229
      - pandoc-crossref: https://github.com/lierdakil/pandoc-crossref
    • Network accessline 230
      - Pandoc citations: https://pandoc.org/MANUAL.html#citations

    skills/writing/latex/overleaf-collaboration-guide/SKILL.md

    • Network accessline 144
      # Clone your Overleaf project via git git clone https://git.overleaf.com/YOUR_PROJECT_ID my-paper
    • Network accessline 145
      git clone https://git.overleaf.com/YOUR_PROJECT_ID my-paper

    skills/writing/latex/tex-render-guide/SKILL.md

    • Network accessline 187
      # Using the codecogs API (free for reasonable usage) # URL-encode your LaTeX and fetch the image curl "https://latex.codecogs.com/png.image?\dpi{300}\bg{white}\int_{0}^{1}x^2\,dx" \
    • Network accessline 188
      # URL-encode your LaTeX and fetch the image curl "https://latex.codecogs.com/png.image?\dpi{300}\bg{white}\int_{0}^{1}x^2\,dx" \   -o equation.png
    • Network accessline 189
      curl "https://latex.codecogs.com/png.image?\dpi{300}\bg{white}\int_{0}^{1}x^2\,dx" \
    • Network accessline 192
      # SVG variant: curl "https://latex.codecogs.com/svg.image?\int_{0}^{1}x^2\,dx" \
    • Network accessline 193
      curl "https://latex.codecogs.com/svg.image?\int_{0}^{1}x^2\,dx" \
    • Network accessline 238
      - KaTeX: https://katex.org
    • Network accessline 239
      - MathJax: https://www.mathjax.org
    • Network accessline 240
      - dvipng documentation: https://ctan.org/pkg/dvipng
    • Network accessline 241
      - dvisvgm: https://dvisvgm.de
    • Network accessline 243
      - CodeCogs equation editor: https://latex.codecogs.com

    skills/writing/polish/academic-writing-refiner/SKILL.md

    • Network accessline 8
      subcategory: "polish"     keywords: ["academic English grammar check", "readability improvement", "academic writing style", "Chinglish correction"]     source: "https://github.com/SYSUSELab/academic-writing-guide"
    • Network accessline 9
      keywords: ["academic English grammar check", "readability improvement", "academic writing style", "Chinglish correction"]     source: "https://github.com/SYSUSELab/academic-writing-guide" ---
    • Network accessline 10
      source: "https://github.com/SYSUSELab/academic-writing-guide"
    • Network accessline 140
      - [academic-writing-guide](https://github.com/SYSUSELab/academic-writing-guide) -- Writing checklist and tutorials (327+ stars)
    • Network accessline 141
      - [Common Errors in Technical Writing](https://www.cs.columbia.edu/~hgs/etc/writing-bugs.html) -- Henning Schulzrinne, Columbia University
    • Network accessline 142
      - [Writefull](https://writefull.com/) -- AI writing assistant trained on published papers
    • Network accessline 143
      - [LanguageTool](https://languagetool.org/) -- Open-source grammar checker

    skills/writing/polish/chinese-text-humanizer/SKILL.md

    • Network accessline 138
      - 中国社会科学院语言研究所 (2016). *现代汉语词典* (第7版). 商务印书馆. - 毕飞宇 (2017). *小说课*. 人民文学出版社. (关于汉语写作节奏的参考) - [中国知网写作规范](https://www.cnki.net/)
    • Network accessline 140
      - [中国知网写作规范](https://www.cnki.net/)

    skills/writing/polish/grammar-checker-guide/SKILL.md

    • Network accessline 62
      [Credential-related source omitted]
    • Access to secretsline 62
      [Credential-related source omitted]
    • Network accessline 63
      "LANGUAGETOOL_URL",         "https://api.languagetool.org/v2/check"     )
    • Network accessline 64
      "https://api.languagetool.org/v2/check"
    • Network accessline 74
      req = urllib.request.Request(api_url, data=data)
    • Network accessline 75
      response = urllib.request.urlopen(req)

    skills/writing/polish/paper-polish-guide/SKILL.md

    • Network accessline 158
      - Strunk, W. & White, E.B. "The Elements of Style" - Zobel, J. "Writing for Computer Science" (Springer) - Chktex LaTeX linter: https://www.nongnu.org/chktex/
    • Network accessline 160
      - Chktex LaTeX linter: https://www.nongnu.org/chktex/

    skills/writing/templates/arxiv-preprint-template/SKILL.md

    • Network accessline 8
      subcategory: "templates"     keywords: ["arXiv", "preprint", "NIPS style", "LaTeX template", "NeurIPS", "manuscript"]     source: "https://github.com/kourgeorge/arxiv-style"
    • Network accessline 9
      keywords: ["arXiv", "preprint", "NIPS style", "LaTeX template", "NeurIPS", "manuscript"]     source: "https://github.com/kourgeorge/arxiv-style" ---
    • Network accessline 10
      source: "https://github.com/kourgeorge/arxiv-style"
    • Network accessline 22
      git clone https://github.com/kourgeorge/arxiv-style.git
    • Network accessline 182
      - [arxiv-style GitHub](https://github.com/kourgeorge/arxiv-style)
    • Network accessline 183
      - [arXiv Submission Guide](https://info.arxiv.org/help/submit/index.html)
    • Network accessline 184
      - [arXiv LaTeX Cleaner](https://github.com/google-research/arxiv-latex-cleaner)

    skills/writing/templates/elegant-paper-template/SKILL.md

    • Network accessline 8
      subcategory: "templates"     keywords: ["ElegantPaper", "LaTeX template", "working paper", "technical report", "elegant design", "academic paper"]     source: "https://github.com/ElegantLaTeX/ElegantPaper"
    • Network accessline 9
      keywords: ["ElegantPaper", "LaTeX template", "working paper", "technical report", "elegant design", "academic paper"]     source: "https://github.com/ElegantLaTeX/ElegantPaper" ---
    • Network accessline 10
      source: "https://github.com/ElegantLaTeX/ElegantPaper"
    • Network accessline 22
      # Download template git clone https://github.com/ElegantLaTeX/ElegantPaper.git
    • Network accessline 23
      git clone https://github.com/ElegantLaTeX/ElegantPaper.git
    • Network accessline 139
      - [ElegantPaper GitHub](https://github.com/ElegantLaTeX/ElegantPaper)
    • Network accessline 140
      - [ElegantLaTeX](https://elegantlatex.org/)
    • Network accessline 141
      - [ElegantPaper Documentation](https://github.com/ElegantLaTeX/ElegantPaper/blob/master/elegantpaper-en.pdf)

    skills/writing/templates/graphical-abstract-guide/SKILL.md

    • Network accessline 8
      subcategory: "templates"     keywords: ["graphical abstract", "SVG", "paper submission", "visual summary", "journal figure", "scientific illustration"]     source: "https://github.com/jgraph/drawio"
    • Network accessline 9
      keywords: ["graphical abstract", "SVG", "paper submission", "visual summary", "journal figure", "scientific illustration"]     source: "https://github.com/jgraph/drawio" ---
    • Network accessline 10
      source: "https://github.com/jgraph/drawio"
    • Network accessline 93
      1. Open https://app.diagrams.net
    • Dangerous shell operationline 104
      sudo apt install inkscape     # Ubuntu
    • Network accessline 179
      - Draw.io: https://app.diagrams.net
    • Network accessline 180
      - Inkscape: https://inkscape.org
    • Network accessline 181
      - Elsevier Graphical Abstract Guidelines: https://www.elsevier.com/authors/tools-and-resources/graphical-abstracts
    • Network accessline 182
      - ACS Author Guidelines: https://pubs.acs.org/page/4authors/submission/graphics.html

    skills/writing/templates/novathesis-guide/SKILL.md

    • Network accessline 2
      name: novathesis-guide description: "LaTeX thesis template supporting multiple universities and formats" source: https://github.com/joaomlourenco/novathesis
    • Network accessline 3
      description: "LaTeX thesis template supporting multiple universities and formats" source: https://github.com/joaomlourenco/novathesis metadata:
    • Network accessline 4
      source: https://github.com/joaomlourenco/novathesis

    skills/writing/templates/scientific-article-pdf/SKILL.md

    • Network accessline 31
      # IEEE conference and journal templates # Download from: https://www.ieee.org/conferences/publishing/templates.html
    • Network accessline 32
      # Download from: https://www.ieee.org/conferences/publishing/templates.html
    • Network accessline 34
      wget https://www.ieee.org/content/dam/ieee-org/ieee/web/org/pubs/conference-latex-template_10-17-19.zip
    • Network accessline 39
      # ACM Primary Article Template # Download from: https://www.acm.org/publications/proceedings-template
    • Network accessline 40
      # Download from: https://www.acm.org/publications/proceedings-template
    • Network accessline 48
      # Download from: https://www.springer.com/gp/computer-science/lncs/conference-proceedings-guidelines
    • Network accessline 55
      # Elsevier article template # Download from: https://www.elsevier.com/authors/policies-and-guidelines/latex-instructions
    • Network accessline 56
      # Download from: https://www.elsevier.com/authors/policies-and-guidelines/latex-instructions
    • Network accessline 64
      # NeurIPS: https://neurips.cc/Conferences/2026/PaperInformation/StyleFiles
    • Network accessline 65
      # ICML: https://icml.cc/Conferences/2026/StyleAuthorInstructions
    • Dangerous shell operationline 218
      rm -f *.aux *.bbl *.blg *.log *.out *.toc *.fls *.fdb_latexmk
    • Network accessline 257
      - IEEE LaTeX templates: https://www.ieee.org/conferences/publishing/templates.html
    • Network accessline 258
      - ACM acmart class: https://www.acm.org/publications/proceedings-template
    • Network accessline 259
      - Springer LNCS: https://www.springer.com/gp/computer-science/lncs
    • Network accessline 260
      - Elsevier elsarticle: https://www.elsevier.com/authors/policies-and-guidelines/latex-instructions
    • Network accessline 261
      - LaTeX Wikibook: https://en.wikibooks.org/wiki/LaTeX

    skills/writing/templates/sjtuthesis-guide/SKILL.md

    • Network accessline 8
      subcategory: "templates"     keywords: ["latex", "thesis", "sjtu", "template", "academic-writing", "shanghai-jiaotong"]     source: "https://github.com/sjtug/SJTUThesis"
    • Network accessline 9
      keywords: ["latex", "thesis", "sjtu", "template", "academic-writing", "shanghai-jiaotong"]     source: "https://github.com/sjtug/SJTUThesis" ---
    • Network accessline 10
      source: "https://github.com/sjtug/SJTUThesis"
    • Dangerous shell operationline 32
      sudo apt-get install texlive-full
    • Network accessline 40
      git clone https://github.com/sjtug/SJTUThesis.git
    • Network accessline 194
      - SJTUThesis repository: https://github.com/sjtug/SJTUThesis
    • Network accessline 195
      - SJTU graduate school formatting guidelines - SJTUG user group: https://sjtug.org/ - LaTeX workshop materials from SJTUG
    • Network accessline 196
      - SJTUG user group: https://sjtug.org/

    skills/writing/templates/thesis-writing-guide/SKILL.md

    • Network accessline 8
      subcategory: "templates"     keywords: ["thesis template", "dissertation formatting", "journal formatting requirements", "page limit"]     source: "https://github.com/awesome-thesis/awesome-thesis"
    • Network accessline 9
      keywords: ["thesis template", "dissertation formatting", "journal formatting requirements", "page limit"]     source: "https://github.com/awesome-thesis/awesome-thesis" ---
    • Network accessline 10
      source: "https://github.com/awesome-thesis/awesome-thesis"
    • Network accessline 216
      - [awesome-thesis](https://github.com/awesome-thesis/awesome-thesis) -- Practical thesis tips (626+ stars)
    • Network accessline 217
      - [How to Write a Thesis](https://www.ldeo.columbia.edu/~martins/sen_res/how_to_thesis.html) -- Columbia University guide
    • Network accessline 218
      - [Dissertate Template](https://github.com/suchow/Dissertate) -- Harvard multi-school LaTeX template
    • Network accessline 219
      - [latexdiff](https://ctan.org/pkg/latexdiff) -- Visual diff tool for LaTeX documents
    • Network accessline 220
      - [Overleaf Thesis Templates](https://www.overleaf.com/latex/templates/tagged/thesis) -- Gallery of institutional templates

    skills/writing/templates/thuthesis-guide/SKILL.md

    • Network accessline 8
      subcategory: "templates"     keywords: ["latex", "thesis", "tsinghua", "template", "academic-writing", "typesetting"]     source: "https://github.com/tuna/thuthesis"
    • Network accessline 9
      keywords: ["latex", "thesis", "tsinghua", "template", "academic-writing", "typesetting"]     source: "https://github.com/tuna/thuthesis" ---
    • Network accessline 10
      source: "https://github.com/tuna/thuthesis"
    • Dangerous shell operationline 34
      sudo apt-get install texlive-full
    • Network accessline 42
      git clone https://github.com/tuna/thuthesis.git
    • Network accessline 178
      - ThuThesis repository: https://github.com/tuna/thuthesis
    • Network accessline 179
      - CTAN package page: https://ctan.org/pkg/thuthesis
    • Network accessline 181
      - TUNA association: https://tuna.moe/

    How the signals fit together

    Facts from a static read of the files at the pinned commit. They describe what the code does, not why.

    Some files could not be read; the facts below still hold.

    Signal confidence: 500 facts

    and 450 more

    Only the first 500 facts are listed.

    Works with

    Agent compatibility, from the files in this repository
    AgentStatusEvidenceInstall to
    Claude CodeCompatibleStandard SKILL.md skills/analysis/dataviz/SKILL.md.claude/skills/<skill-name>/
    CodexCompatibleStandard SKILL.md skills/analysis/dataviz/SKILL.md.agents/skills/<skill-name>/
    CursorCompatibleStandard SKILL.md skills/analysis/dataviz/SKILL.md.cursor/skills/<skill-name>/
    Gemini CLICompatibleStandard SKILL.md skills/analysis/dataviz/SKILL.md.gemini/skills/<skill-name>/
    GitHub CopilotCompatibleStandard SKILL.md skills/analysis/dataviz/SKILL.md.github/skills/<skill-name>/
    OpenCodeCompatibleStandard SKILL.md skills/analysis/dataviz/SKILL.md.opencode/skills/<skill-name>/
    • Native The repository ships a manifest, folder or frontmatter field for this agent.
    • Compatible A standard SKILL.md that this agent can read.
    • Unknown No evidence either way.

    Derived automatically from paths, manifests and frontmatter. Not tested on each agent.

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