Individual skill
tooluniverse-microbiome-research
Microbiome research using MGnify, GTDB, ENA, OLS (ENVO biomes), EuropePMC, BacDive (strain phenotypes), MediaDive (growth media recipes), and GMrepo (gut microbiome disease-association counts). Covers study discovery, taxonomic profiling, host-microbe interaction analysis, biome-by-condition queries, strain culturing requirements, and phenotype/disease prevalence lookups. Use for microbiome study selection, organism-environment associations, clinical-microbiome literature review, and "how do I grow this organism" / "how prevalent is this species in condition X" questions. Distinct from analytical workflow (use tooluniverse-metagenomics-analysis for that).
plugins/tooluniverse/skills/tooluniverse-microbiome-research/SKILL.md
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# Microbiome Research with ToolUniverse
Comprehensive microbiome analysis using MGnify (EBI metagenomics), GTDB (genome taxonomy), ENA (sequencing data), OLS (ontology lookup for ENVO biomes), and EuropePMC (literature).
## Core Tools
| Tool | Purpose | Auth |
|------|---------|------|
| **MGnify_search_studies** | Find metagenomics studies by biome/keyword | None |
| **MGnify_get_study_detail** | Study metadata, abstract, sample counts | None |
| **MGnify_list_analyses** | List taxonomic/functional analysis outputs for a study | None |
| **MGnify_get_taxonomy** | Taxonomic composition from an analysis | None |
| **MGnify_get_go_terms** | GO functional annotations from an analysis | None |
| **MGnify_get_interpro** | InterPro protein domain annotations | None |