google-deepmind/science-skills

.licenses/alphafold_database_fetch_and_analyze_LICENSE.txt does not already     exist in the workspace root directory then (1) prominently notify the user     to check the terms at https://alphafold.ebi.ac.uk/, then (2) create the file

exist in the workspace root directory then (1) prominently notify the user     to check the terms at https://alphafold.ebi.ac.uk/, then (2) create the file     recording the notification text and timestamp.

to check the terms at https://alphafold.ebi.ac.uk/, then (2) create the file

-   The user only has a protein name, gene name, or amino acid sequence (no     UniProt ID) — ask them to look up the ID on     [UniProt](https://www.uniprot.org).

UniProt ID) — ask them to look up the ID on     [UniProt](https://www.uniprot.org). -   The user wants to search for structural homologs (use **Foldseek**).

[UniProt](https://www.uniprot.org).

@ARTICLE{Varadi2022,   ABSTRACT = {The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) is an openly accessible, extensive database of high-accuracy protein-structure predictions. Powered by AlphaFold v2.0 of

ABSTRACT = {The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) is an openly accessible, extensive database of high-accuracy protein-structure predictions. Powered by AlphaFold v2.0 of DeepMind, it has enabl

AUTHOR = {Varadi, Mihaly and Anyango, Stephen and Deshpande, Mandar and Nair, Sreenath and Natassia, Cindy and Yordanova, Galabina and Yuan, David and Stroe, Oana and Wood, Gemma and Laydon, Agata and Žídek, Augustin and Green, Tim and Tuny

URL = {https://doi.org/10.1093/nar/gkab1061},

DATE = {2022-01},   DOI = {10.1093/nar/gkab1061},   EPRINT = {https://academic.oup.com/nar/article-pdf/50/D1/D439/43502749/gkab1061.pdf},

DOI = {10.1093/nar/gkab1061},   EPRINT = {https://academic.oup.com/nar/article-pdf/50/D1/D439/43502749/gkab1061.pdf},   ISSN = {0305-1048},

EPRINT = {https://academic.oup.com/nar/article-pdf/50/D1/D439/43502749/gkab1061.pdf},

@ARTICLE{Varadi2024,   ABSTRACT = {The AlphaFold Database Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) has significantly impacted structural biology by amassing over 214 million predicted protein structures, expand

ABSTRACT = {The AlphaFold Database Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) has significantly impacted structural biology by amassing over 214 million predicted protein structures, expanding from the initial 30

AUTHOR = {Varadi, Mihaly and Bertoni, Damian and Magana, Paulyna and Paramval, Urmila and Pidruchna, Ivanna and Radhakrishnan, Malarvizhi and Tsenkov, Maxim and Nair, Sreenath and Mirdita, Milot and Yeo, Jingi and Kovalevskiy, Oleg and Tuny

URL = {https://doi.org/10.1093/nar/gkad1011},

DATE = {2024-01},   DOI = {10.1093/nar/gkad1011},   EPRINT = {https://academic.oup.com/nar/article-pdf/52/D1/D368/55039845/gkad1011.pdf},

DOI = {10.1093/nar/gkad1011},   EPRINT = {https://academic.oup.com/nar/article-pdf/52/D1/D368/55039845/gkad1011.pdf},   ISSN = {0305-1048},

EPRINT = {https://academic.oup.com/nar/article-pdf/52/D1/D368/55039845/gkad1011.pdf},

ABSTRACT = {Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort1--4, the structures of around 100,000 unique proteins have b

AUTHOR = {Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf and Tunyasuvunakool, Kathryn and Bates, Russ and Žídek, Augustin and Potapenko, Anna and Bridgland, Alex and Meyer, 

URL = {https://doi.org/10.1038/s41586-021-03819-2},

ABSTRACT = {Protein structures can provide invaluable information, both for reasoning about biological processes and for enabling interventions such as structure-based drug development or targeted mutagenesis. After decades of effort, 17{\%

AUTHOR = {Tunyasuvunakool, Kathryn and Adler, Jonas and Wu, Zachary and Green, Tim and Zielinski, Michal and Žídek, Augustin and Bridgland, Alex and Cowie, Andrew and Meyer, Clemens and Laydon, Agata and Velankar, Sameer and Kleywegt, Gerar

URL = {https://doi.org/10.1038/s41586-021-03828-1},

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

CLIENT = http_client.HttpClient("https://alphafold.ebi.ac.uk", qps=1.0)

uniprot_id = uniprot_id.strip().upper()   api_url = f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}"

api_url = f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}"

Construct and validate deep-links for the AlphaGenome Atlas web application (`https://deepmind.google.com/science/alphagenome/atlas`).

(`https://deepmind.google.com/science/alphagenome/atlas`).

Base URL: `https://deepmind.google.com/science/alphagenome/atlas`

> presenting, discussing, or scoring genetic variants, you **MUST always provide > clickable deep-links to the > [AlphaGenome Atlas](https://deepmind.google.com/science/alphagenome/atlas)**.

> clickable deep-links to the > [AlphaGenome Atlas](https://deepmind.google.com/science/alphagenome/atlas)**. > Use `scripts/alphagenome_atlas_links.py` to automate link and table

> [AlphaGenome Atlas](https://deepmind.google.com/science/alphagenome/atlas)**.

*   **Route**:     `https://deepmind.google.com/science/alphagenome/atlas/track-predictions`

`https://deepmind.google.com/science/alphagenome/atlas/track-predictions`

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

Constructs validated deep-links and multi-modality Ref vs. Alt track predictions for the AlphaGenome Atlas web application (https://deepmind.google.com/science/alphagenome/atlas).

(https://deepmind.google.com/science/alphagenome/atlas).

BASE_ATLAS_URL = "https://deepmind.google.com/science/alphagenome/atlas"

[Credential-related source omitted]

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" the 'credentials' skill for the safe credentials protocol,\n     or"         " register for an API key at"         " https://deepmind.google.com/science/alphagenome/.\n",

" register for an API key at"         " https://deepmind.google.com/science/alphagenome/.\n",         file=sys.stderr,

" https://deepmind.google.com/science/alphagenome/.\n",

[Credential-related source omitted]

GTF_URL = (     "https://storage.googleapis.com/alphagenome/reference/gencode/"

"https://storage.googleapis.com/alphagenome/reference/gencode/"

[Credential-related source omitted]

.licenses/alphagenome_single_variant_analysis_LICENSE.txt does not already     exist in the workspace root directory then (1) prominently notify the user     to check the terms at https://deepmind.google.com/science/alphagenome/, then

exist in the workspace root directory then (1) prominently notify the user     to check the terms at https://deepmind.google.com/science/alphagenome/, then     (2) create the file recording the notification text and timestamp.

to check the terms at https://deepmind.google.com/science/alphagenome/, then

[Credential-related source omitted]

You can register for a key at https://deepmind.google.com/science/alphagenome/.

[Credential-related source omitted]

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instructions in [Prerequisites](#prerequisites). -   **Registry Authentication Error (401)**: If `uv` fails with 401 Unauthorized     for a private registry, set `UV_INDEX_URL=https://pypi.org/simple` before

-   **Registry Authentication Error (401)**: If `uv` fails with 401 Unauthorized     for a private registry, set `UV_INDEX_URL=https://pypi.org/simple` before     running the script.

for a private registry, set `UV_INDEX_URL=https://pypi.org/simple` before

[Credential-related source omitted]

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gtf = pd.read_feather(     'https://storage.googleapis.com/alphagenome/reference/gencode/'

'https://storage.googleapis.com/alphagenome/reference/gencode/'

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

[Credential-related source omitted]

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Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

[Credential-related source omitted]

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Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

[Credential-related source omitted]

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Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

GTF_URL = (     'https://storage.googleapis.com/alphagenome/reference/gencode/'

'https://storage.googleapis.com/alphagenome/reference/gencode/'

[Credential-related source omitted]

[Credential-related source omitted]

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

[Credential-related source omitted]

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

GTF_URL = (     'https://storage.googleapis.com/alphagenome/reference/gencode/'

'https://storage.googleapis.com/alphagenome/reference/gencode/'

[Credential-related source omitted]

[Credential-related source omitted]

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Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

GTF_URL = (     'https://storage.googleapis.com/alphagenome/reference/gencode/'

'https://storage.googleapis.com/alphagenome/reference/gencode/'

[Credential-related source omitted]

[Credential-related source omitted]

[Credential-related source omitted]

[Credential-related source omitted]

[Credential-related source omitted]

[Credential-related source omitted]

[Credential-related source omitted]

[Credential-related source omitted]

[Credential-related source omitted]

> single variant query, a ranked candidate table, or a genomic region scan), you > **MUST always provide a clickable deep-link to the > [AlphaGenome Atlas](https://deepmind.google.com/science/alphagenome/atlas)**

> **MUST always provide a clickable deep-link to the > [AlphaGenome Atlas](https://deepmind.google.com/science/alphagenome/atlas)** > for each variant.

> [AlphaGenome Atlas](https://deepmind.google.com/science/alphagenome/atlas)**

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

_ATLAS_TRACK_PREDICTIONS_URL = (     'https://deepmind.google.com/science/alphagenome/atlas/track-predictions'

'https://deepmind.google.com/science/alphagenome/atlas/track-predictions'

[Credential-related source omitted]

[Credential-related source omitted]

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with pysam.VariantFile(output_path, 'w', header=vcf_in.header) as vcf_out:       for record in vcf_in.fetch():

for record in vcf_in.fetch():

GTF_URL = (     'https://storage.googleapis.com/alphagenome/reference/gencode/'

'https://storage.googleapis.com/alphagenome/reference/gencode/'

[Credential-related source omitted]

[Credential-related source omitted]

already exist in the workspace root directory then (1) prominently notify     the user to check the terms at     https://chembl.gitbook.io/chembl-interface-documentation/about, then (2)

the user to check the terms at     https://chembl.gitbook.io/chembl-interface-documentation/about, then (2)     create the file recording the notification text and timestamp.

https://chembl.gitbook.io/chembl-interface-documentation/about, then (2)

Base URL: `https://www.ebi.ac.uk/chembl/api/data`

@ARTICLE{Zdrazil2024,   ABSTRACT = {ChEMBL (https://www.ebi.ac.uk/chembl/) is a manually curated, high-quality, large-scale, open, FAIR and Global Core Biodata Resource of bioactive molecules with drug-like properties, previously described 

ABSTRACT = {ChEMBL (https://www.ebi.ac.uk/chembl/) is a manually curated, high-quality, large-scale, open, FAIR and Global Core Biodata Resource of bioactive molecules with drug-like properties, previously described in the 2012, 2014, 2017 

AUTHOR = {Zdrazil, Barbara and Felix, Eloy and Hunter, Fiona and Manners, Emma J and Blackshaw, James and Corbett, Sybilla and de Veij, Marleen and Ioannidis, Harris and Lopez, David Mendez and Mosquera, Juan F and Magarinos, Maria Paula an

URL = {https://doi.org/10.1093/nar/gkad1004},

DATE = {2024-01},   DOI = {10.1093/nar/gkad1004},   EPRINT = {https://academic.oup.com/nar/article-pdf/52/D1/D1180/55040046/gkad1004.pdf},

DOI = {10.1093/nar/gkad1004},   EPRINT = {https://academic.oup.com/nar/article-pdf/52/D1/D1180/55040046/gkad1004.pdf},   ISSN = {0305-1048},

EPRINT = {https://academic.oup.com/nar/article-pdf/52/D1/D1180/55040046/gkad1004.pdf},

@ARTICLE{Davies2015,   ABSTRACT = {ChEMBL is now a well-established resource in the fields of drug discovery and medicinal chemistry research. The ChEMBL database curates and stores standardized bioactivity, molecule, target and drug data e

ABSTRACT = {ChEMBL is now a well-established resource in the fields of drug discovery and medicinal chemistry research. The ChEMBL database curates and stores standardized bioactivity, molecule, target and drug data extracted from multiple 

AUTHOR = {Davies, Mark and Nowotka, Michał and Papadatos, George and Dedman, Nathan and Gaulton, Anna and Atkinson, Francis and Bellis, Louisa and Overington, John P.},   URL = {https://doi.org/10.1093/nar/gkv352},   DATE = {2015-07},

URL = {https://doi.org/10.1093/nar/gkv352},

DATE = {2015-07},   DOI = {10.1093/nar/gkv352},   EPRINT = {https://academic.oup.com/nar/article-pdf/43/W1/W612/17435802/gkv352.pdf},

DOI = {10.1093/nar/gkv352},   EPRINT = {https://academic.oup.com/nar/article-pdf/43/W1/W612/17435802/gkv352.pdf},   ISSN = {0305-1048},

EPRINT = {https://academic.oup.com/nar/article-pdf/43/W1/W612/17435802/gkv352.pdf},

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

BASE_URL = "https://www.ebi.ac.uk/chembl/api/data"

data["_license_notice"] = (         "Data from the ChEMBL Database. Please review the licensing terms at"         " https://www.ebi.ac.uk/chembl/"

"Data from the ChEMBL Database. Please review the licensing terms at"         " https://www.ebi.ac.uk/chembl/"     )

" https://www.ebi.ac.uk/chembl/"

2.  **User Notification**: If .licenses/clinical_trials_database_LICENSE.txt     does not already exist in the workspace root directory then (1) prominently     notify the user to check the terms at https://clinicaltrials.gov/, then (2)

does not already exist in the workspace root directory then (1) prominently     notify the user to check the terms at https://clinicaltrials.gov/, then (2)     create the file recording the notification text and timestamp.

notify the user to check the terms at https://clinicaltrials.gov/, then (2)

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

BASE_URL = "https://clinicaltrials.gov/api/v2"

2.  **User Notification**: If .licenses/clinvar_database_LICENSE.txt does not     already exist in the workspace root directory then (1) prominently notify     the user to check the terms at https://www.ncbi.nlm.nih.gov/clinvar/, then

already exist in the workspace root directory then (1) prominently notify     the user to check the terms at https://www.ncbi.nlm.nih.gov/clinvar/, then     (2) create the file recording the notification text and timestamp.

the user to check the terms at https://www.ncbi.nlm.nih.gov/clinvar/, then

[Credential-related source omitted]

requests/second. The skill works without it, but a key is recommended if the     user plans many queries or encounters a 429 error. You can register for a     key for free at https://www.ncbi.nlm.nih.gov/account/settings/. You **MUST**

user plans many queries or encounters a 429 error. You can register for a     key for free at https://www.ncbi.nlm.nih.gov/account/settings/. You **MUST**     use the safe credentials protocol in the `credentials` skill to check for

key for free at https://www.ncbi.nlm.nih.gov/account/settings/. You **MUST**

[Credential-related source omitted]

You can register for a key for free at https://www.ncbi.nlm.nih.gov/account/settings/. You **MUST** use the safe

https://www.ncbi.nlm.nih.gov/account/settings/. You **MUST** use the safe

[Credential-related source omitted]

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

BASE_URL = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/'

[Credential-related source omitted]

[Credential-related source omitted]

[Credential-related source omitted]

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[Credential-related source omitted]

[Credential-related source omitted]

try:       resp = self.client.fetch(full_url, timeout=DEFAULT_TIMEOUT_SECONDS)

resp = self.client.fetch(full_url, timeout=DEFAULT_TIMEOUT_SECONDS)

' INSTRUCTION: Pause execution and inform the user that an NCBI API'             ' Key is required to increase the rate limit, providing the URL'             ' https://www.ncbi.nlm.nih.gov/clinvar/docs/api_http/ for'

' Key is required to increase the rate limit, providing the URL'             ' https://www.ncbi.nlm.nih.gov/clinvar/docs/api_http/ for'             ' instructions on how to obtain one. The user will need to set the'

' https://www.ncbi.nlm.nih.gov/clinvar/docs/api_http/ for'

[Credential-related source omitted]

[Credential-related source omitted]

[Credential-related source omitted]

[Credential-related source omitted]

[Credential-related source omitted]

2.  **User Notification**: If .licenses/dbsnp_database_LICENSE.txt does not     already exist in the workspace root directory then (1) prominently notify     the user to check the terms at https://www.ncbi.nlm.nih.gov/snp/, then (2)

already exist in the workspace root directory then (1) prominently notify     the user to check the terms at https://www.ncbi.nlm.nih.gov/snp/, then (2)     create the file recording the notification text and timestamp.

the user to check the terms at https://www.ncbi.nlm.nih.gov/snp/, then (2)

[Credential-related source omitted]

requests/second. The skill works without it, but a key is recommended if the     user plans many queries or encounters a 429 error. You can register for a     key for free at https://www.ncbi.nlm.nih.gov/account/settings/. You **MUST**

user plans many queries or encounters a 429 error. You can register for a     key for free at https://www.ncbi.nlm.nih.gov/account/settings/. You **MUST**     use the safe credentials protocol in the `credentials` skill to check for

key for free at https://www.ncbi.nlm.nih.gov/account/settings/. You **MUST**

-   **Use the Wrapper**: ALWAYS execute the provided wrapper script     `scripts/dbsnp_cli.py` to query the database rather than constructing custom     HTTP or curl requests. The script automatically handles rate limiting,

`scripts/dbsnp_cli.py` to query the database rather than constructing custom     HTTP or curl requests. The script automatically handles rate limiting,     retries, and JSON parsing.

HTTP or curl requests. The script automatically handles rate limiting,

You can register for a key for free at https://www.ncbi.nlm.nih.gov/account/settings/. You **MUST** use the safe

https://www.ncbi.nlm.nih.gov/account/settings/. You **MUST** use the safe

### 1. Variation Services (`https://api.ncbi.nlm.nih.gov/variation/v0/`)

### 2. E-utilities (`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/`)

[Credential-related source omitted]

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

_VARIATION_BASE_URL = "https://api.ncbi.nlm.nih.gov"

_EUTILS_BASE_URL = "https://eutils.ncbi.nlm.nih.gov"

[Credential-related source omitted]

[Credential-related source omitted]

[Credential-related source omitted]

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[Credential-related source omitted]

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[Credential-related source omitted]

"AGENT INSTRUCTION: Pause execution and inform the user that an NCBI "           "API Key is required.  Direct them to "           "https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/"

"API Key is required.  Direct them to "           "https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/"           "new-api-keys-for-the-e-utilities/ and ask them to set the "

"https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/"

[Credential-related source omitted]

[Credential-related source omitted]

2.  **User Notification**: If .licenses/embl_ebi_ols_LICENSE.txt does not     already exist in the workspace root directory then (1) prominently notify     the user to check the terms at https://www.ebi.ac.uk/ols4/api-docs, then (2)

already exist in the workspace root directory then (1) prominently notify     the user to check the terms at https://www.ebi.ac.uk/ols4/api-docs, then (2)     create the file recording the notification text and timestamp.

the user to check the terms at https://www.ebi.ac.uk/ols4/api-docs, then (2)

Base URL: `https://www.ebi.ac.uk/ols4/api`

The corresponding IRI is typically: `http://purl.obolibrary.org/obo/PREFIX_NUMBER` (e.g.,

`http://purl.obolibrary.org/obo/PREFIX_NUMBER` (e.g.,

`http://purl.obolibrary.org/obo/GO_0005634`).

@ARTICLE{McLaughlin2025,   ABSTRACT = {The Ontology Lookup Service (OLS) is an open source search engine for ontologies which is used extensively in the bioinformatics and chemistry communities to annotate biological and biomedical data wit

ABSTRACT = {The Ontology Lookup Service (OLS) is an open source search engine for ontologies which is used extensively in the bioinformatics and chemistry communities to annotate biological and biomedical data with ontology terms. Recently,

AUTHOR = {McLaughlin, James and Lagrimas, Josh and Iqbal, Haider and Parkinson, Helen and Harmse, Henriette},   URL = {https://doi.org/10.1093/bioinformatics/btaf279},   DATE = {2025-05},

URL = {https://doi.org/10.1093/bioinformatics/btaf279},

DATE = {2025-05},   DOI = {10.1093/bioinformatics/btaf279},   EPRINT = {https://academic.oup.com/bioinformatics/article-pdf/41/5/btaf279/63054843/btaf279.pdf},

DOI = {10.1093/bioinformatics/btaf279},   EPRINT = {https://academic.oup.com/bioinformatics/article-pdf/41/5/btaf279/63054843/btaf279.pdf},   ISSN = {1367-4811},

EPRINT = {https://academic.oup.com/bioinformatics/article-pdf/41/5/btaf279/63054843/btaf279.pdf},

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

url = "https://www.ebi.ac.uk/ols4/api/v2/stats"

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

RATE_LIMIT_DELAY = 0.2 MAX_RETRIES = 10 BASE_URL = "https://www.ebi.ac.uk/ols4/api"

MAX_RETRIES = 10 BASE_URL = "https://www.ebi.ac.uk/ols4/api" CLIENT = http_client.HttpClient(BASE_URL, qps=5.0)

BASE_URL = "https://www.ebi.ac.uk/ols4/api"

return "http://purl.obolibrary.org/obo/" + obo_id.replace(":", "_")

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

not already exist in the workspace root directory then (1) prominently     notify the user to check the terms at     https://www.encodeproject.org/help/rest-api/, then (2) create the file

notify the user to check the terms at     https://www.encodeproject.org/help/rest-api/, then (2) create the file     recording the notification text and timestamp.

https://www.encodeproject.org/help/rest-api/, then (2) create the file

URL = {https://doi.org/10.1038/nature11247},

@ARTICLE{Luo2020,   ABSTRACT = {The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium 

ABSTRACT = {The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium are freely accessibl

AUTHOR = {Luo, Yunhai and Hitz, Benjamin C and Gabdank, Idan and Hilton, Jason A and Kagda, Meenakshi S and Lam, Bonita and Myers, Zachary and Sud, Paul and Jou, Jennifer and Lin, Khine and Baymuradov, Ulugbek K and Graham, Keenan and Litto

URL = {https://doi.org/10.1093/nar/gkz1062},

DATE = {2020-01},   DOI = {10.1093/nar/gkz1062},   EPRINT = {https://academic.oup.com/nar/article-pdf/48/D1/D882/32874907/gkz1062.pdf},

DOI = {10.1093/nar/gkz1062},   EPRINT = {https://academic.oup.com/nar/article-pdf/48/D1/D882/32874907/gkz1062.pdf},   ISSN = {0305-1048},

EPRINT = {https://academic.oup.com/nar/article-pdf/48/D1/D882/32874907/gkz1062.pdf},

This document outlines the queries and types available in the ENCODE SCREEN GraphQL API (`https://factorbook.api.wenglab.org/graphql`), as used in the

GraphQL API (`https://factorbook.api.wenglab.org/graphql`), as used in the

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

BASE_URL = "https://www.encodeproject.org"

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

API_URL = "https://factorbook.api.wenglab.org/graphql"

qps=10,     default_headers={         "Origin": "https://screen-v2.wenglab.org",

default_headers={         "Origin": "https://screen-v2.wenglab.org",         "Referer": "https://screen-v2.wenglab.org/",

"Origin": "https://screen-v2.wenglab.org",

"Referer": "https://screen-v2.wenglab.org/",

2.  **User Notification**: If .licenses/ensembl_database_LICENSE.txt does not     already exist in the workspace root directory then (1) prominently notify     the user to check the terms at https://useast.ensembl.org/index.html and

already exist in the workspace root directory then (1) prominently notify     the user to check the terms at https://useast.ensembl.org/index.html and     https://github.com/Ensembl/ensembl-rest/wiki, then (2) create the file

the user to check the terms at https://useast.ensembl.org/index.html and

https://github.com/Ensembl/ensembl-rest/wiki, then (2) create the file

@ARTICLE{Harrison2024,   ABSTRACT = {Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades. In 

ABSTRACT = {Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades. In recent years, there has b

AUTHOR = {Harrison, Peter W and Amode, M Ridwan and Austine-Orimoloye, Olanrewaju and Azov, Andrey G and Barba, Matthieu and Barnes, If and Becker, Arne and Bennett, Ruth and Berry, Andrew and Bhai, Jyothish and Bhurji, Simarpreet Kaur and 

URL = {https://doi.org/10.1093/nar/gkad1049},

DATE = {2024-01},   DOI = {10.1093/nar/gkad1049},   EPRINT = {https://academic.oup.com/nar/article-pdf/52/D1/D891/55040594/gkad1049.pdf},

DOI = {10.1093/nar/gkad1049},   EPRINT = {https://academic.oup.com/nar/article-pdf/52/D1/D891/55040594/gkad1049.pdf},   ISSN = {0305-1048},

EPRINT = {https://academic.oup.com/nar/article-pdf/52/D1/D891/55040594/gkad1049.pdf},

This document provides a concise reference for the Ensembl REST API (`https://rest.ensembl.org`). Use it to build custom queries when the

(`https://rest.ensembl.org`). Use it to build custom queries when the

- **Base URL:** `https://rest.ensembl.org` (GRCh38). For GRCh37:

`https://grch37.rest.ensembl.org`

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

BASE_URL = "https://rest.ensembl.org"

GRCH37_URL = "https://grch37.rest.ensembl.org"

2.  **User Notification**: If .licenses/foldseek_structural_search_LICENSE.txt     does not already exist in the workspace root directory then (1) prominently     notify the user to check the terms at https://search.foldseek.com/search and

does not already exist in the workspace root directory then (1) prominently     notify the user to check the terms at https://search.foldseek.com/search and     https://github.com/steineggerlab/foldseek, then (2) create the file

notify the user to check the terms at https://search.foldseek.com/search and

https://github.com/steineggerlab/foldseek, then (2) create the file

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

CLIENT = http_client.HttpClient("https://search.foldseek.com", qps=1)

file_path = args.input_file   output_path = args.output   ticket_url = "https://search.foldseek.com/api/ticket"

ticket_url = "https://search.foldseek.com/api/ticket"

"[*] Fetching results (this might take a moment for large databases)...\n"   )   result_url = f"https://search.foldseek.com/api/result/{ticket_id}/0"

)   result_url = f"https://search.foldseek.com/api/result/{ticket_id}/0"   res = CLIENT.fetch_json(result_url, headers=headers, timeout=120)

result_url = f"https://search.foldseek.com/api/result/{ticket_id}/0"

2.  **User Notification**: If .licenses/gnomad_database_LICENSE.txt does not     already exist in the workspace root directory then (1) prominently notify     the user to check the terms at https://gnomad.broadinstitute.org/policies

already exist in the workspace root directory then (1) prominently notify     the user to check the terms at https://gnomad.broadinstitute.org/policies     and https://gnomad.broadinstitute.org/data#api, then (2) create the file

the user to check the terms at https://gnomad.broadinstitute.org/policies

and https://gnomad.broadinstitute.org/data#api, then (2) create the file

Further documentation on the data: https://gnomad.broadinstitute.org/data#api

More general database documentation: https://gnomad.broadinstitute.org/help

AUTHOR = {Karczewski, Konrad J. and Francioli, Laurent C. and Tiao, Grace and Cummings, Beryl B. and Alföldi, Jessica and Wang, Qingbo and Collins, Ryan L. and Laricchia, Kristen M. and Ganna, Andrea and Birnbaum, Daniel P. and Gauthier, La

URL = {https://doi.org/10.1038/s41586-020-2308-7},

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

CLIENT = http_client.HttpClient("https://gnomad.broadinstitute.org", qps=0.1666)

url = "https://gnomad.broadinstitute.org/api"

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

CLIENT = http_client.HttpClient("https://gnomad.broadinstitute.org", qps=0.1666)

url = "https://gnomad.broadinstitute.org/api"

url = "https://gnomad.broadinstitute.org/api"

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0

CLIENT = http_client.HttpClient("https://gnomad.broadinstitute.org", qps=0.1666)

url = "https://gnomad.broadinstitute.org/api"

url = "https://gnomad.broadinstitute.org/api"

2.  **User Notification**: If .licenses/gtex_database_LICENSE.txt does not     already exist in the workspace root directory then (1) prominently notify     the user to check the terms at https://gtexportal.org/home/license and

already exist in the workspace root directory then (1) prominently notify     the user to check the terms at https://gtexportal.org/home/license and     https://gtexportal.org/home/documentationPage#gtexApi, then (2) create the

the user to check the terms at https://gtexportal.org/home/license and

https://gtexportal.org/home/documentationPage#gtexApi, then (2) create the

AUTHOR = {{The GTEx Consortium} and Aguet, François and Anand, Shankara and Ardlie, Kristin G. and Gabriel, Stacey and Getz, Gad A. and Graubert, Aaron and Hadley, Kane and Handsaker, Robert E. and Huang, Katherine H. and Kashin, Seva and L

URL = {https://www.science.org/doi/abs/10.1126/science.aaz1776},

DATE = {2020},   DOI = {10.1126/science.aaz1776},   EPRINT = {https://www.science.org/doi/pdf/10.1126/science.aaz1776},

DOI = {10.1126/science.aaz1776},   EPRINT = {https://www.science.org/doi/pdf/10.1126/science.aaz1776},   JOURNALTITLE = {Science},

EPRINT = {https://www.science.org/doi/pdf/10.1126/science.aaz1776},

Executable file

# You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0

# #     http://www.apache.org/licenses/LICENSE-2.0 #

#     http://www.apache.org/licenses/LICENSE-2.0