Universal Skills

Constructs deep-links and URLs for the AlphaGenome Atlas website. Supports generating single-variant exploration links (1-based chr:pos:ref>alt), genomic locus views (1-based closed chr:start-end), candidate summary tables, and AlphaGenome reference vs. alternate predictions

google-deepmind / alphagenome-single-variant-analysis

Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API

skillapi

google-deepmind / chembl-database

Query the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures

google-deepmind / gtex-database

Use when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.

google-deepmind / human-protein-atlas-database

Use when you want to retrieve semi-quantitative protein expression and spatial localisation data from the Human Protein Atlas (HPA).

google-deepmind / literature-search-europepmc

Search Europe PMC for scientific literature and download open-access full texts and PDFs. Retrieve full-text XML/plain text by PMCID, get citation lists and bibliography.

skillpdfdatabase

google-deepmind / ncbi-sequence-fetch

Retrieve protein and nucleotide sequences from NCBI databases using E-utilities. Supports direct accession lookup, CDS translation, gene+organism search, locus lookup, PubMed-linked sequences, patent protein extraction, and organism+length fallback search

google-deepmind / openfda-database

Query, search, and download data from the openFDA API for drugs, devices, foods, tobacco, cosmetics, animal and veterinary products, substances, and transparency data.

google-deepmind / pdb-database

Use when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands). Supports searching by sequence similarity, structure similarity, chemical and other attributes.

google-deepmind / pubmed-database

Search PubMed for scientific literature, including published clinical trials. Fetch abstracts and full text. Link published research to biological databases (gene, protein, nucleotide, PubChem) to discover associations between papers and specific compounds or genes.

google-deepmind / ucsc-conservation-and-tfbs

Fetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor Binding Sites (TFBS) from the UCSC Genome Browser

google-deepmind / encode-ccres-database

Query the ENCODE Registry of cis-Regulatory Elements (cCREs) via the SCREEN GraphQL API, or make custom queries to the ENCODE Portal REST API for experiments and files (ChIP-seq peaks, etc.)

skillapigraphql+2

google-deepmind / literature-search-biorxiv

Browse, filter, and download life sciences, biology, and medical preprints from bioRxiv and medRxiv. Supports fetching paper metadata by DOI, and browsing by date range with category and keyword filters.

google-deepmind / literature-search-openalex

Query the OpenAlex scholarly database for research papers, authors, institutions, topics, sources, publishers, funders, geo-locations, and keywords

skillpdfdatabase

google-deepmind / opentargets-database

Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.

skillapigraphql+1

google-deepmind / embl-ebi-ols

Query and search the EMBL-EBI Ontology Lookup Service (OLS) for biomedical ontology terms, definitions, and hierarchies across 250+ ontologies (e.g., GO, DOID, HP)

google-deepmind / ensembl-database

Query the Ensembl database to resolve gene, transcript, and protein IDs, fetch genomic or protein sequences, retrieve gene structures (exons), and get variant consequence and effect predictions (VEP).

google-deepmind / pubchem-database

Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics

google-deepmind / quickgo-database

Query the QuickGO and Evidence & Conclusion Ontology (ECO) REST API. Use this when you need to map genes to biological processes, molecular functions, or cellular components, find genes associated with a specific pathway/GO term, or explore the Gene Ontology hierarchy.

skillapirest+1

google-deepmind / workflow-skill-creator

Distills a completed user workflow or interaction into a reusable agent skill

google-deepmind / clinical-trials-database

Query ClinicalTrials.gov via APIv2

google-deepmind / credentials

Instructions for handling API keys and credentials safely, verifying their presence, and prompting the user to add them if missing using a safe protocol.

skillapi

google-deepmind / jaspar-database

Query the JASPAR database for Transcription Factor (TF) binding profiles

google-deepmind / literature-search-arxiv

Search for scientific papers, preprints, and publications on arXiv. Extract metadata, abstracts, and download full-text PDFs or HTML versions of papers

skillpdf

google-deepmind / pymol

Visualize, analyze, and render protein and molecular structures using PyMOL

skillimage

google-deepmind / reactome-database

Query the Reactome database (Analysis and Content Services)

skillreactdatabase

google-deepmind / unibind-database

Queries the UniBind database for experimentally validated transcription factor (TF) binding sites

google-deepmind / protein-sequence-similarity-search

Searches for homologous protein sequences using MMseqs2 (fast, default) or BLAST (comprehensive, fallback). Trigger this whenever the user provides a protein sequence or FASTA file and asks to find homologues, sequence matches, or wants to infer protein function based on sequence similarity, but not…

google-deepmind / alphafold-database-fetch-and-analyze

Retrieve and analyze AlphaFold predicted structures for a protein

google-deepmind / gnomad-database

Query the Genome Aggregation Database (gnomAD)