google-deepmind
google-deepmind / alphagenome-atlas-website-links
3.1kConstructs 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
3.1kAnalyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API
google-deepmind / alphagenome-variant-impact-score
3.1kScore, annotate, and analyze the functional impact of genetic variants using AlphaGenome Variant Impact (AVI) scores. Query variants in chr:pos:ref>alt format, annotate VCF/tabular callsets, perform saturation mutagenesis window scans (1-based closed chr:start-end), and extract GENCODE v46 GTF gene/…
google-deepmind / chembl-database
3.1kQuery the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures
google-deepmind / clinvar-database
3.1kUse when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls for human genomic variants.
google-deepmind / credentials
3.1kInstructions for handling API keys and credentials safely, verifying their presence, and prompting the user to add them if missing using a safe protocol.
google-deepmind / dbsnp-database
3.1kUse when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database. Resolves between rsIDs, genomic coordinates in VCF format, and HGVS strings.
google-deepmind / embl-ebi-ols
3.1kQuery 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 / encode-ccres-database
3.1kQuery 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.)
google-deepmind / ensembl-database
3.1kQuery 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 / foldseek-structural-search
3.1kPerforms 3D structural searches of proteins against various databases (PDB, AlphaFold, CATH, MGnify, etc.) using the Foldseek API. Use ONLY when the user provides a physical 3D coordinate file (.cif, .mmcif, or .pdb) and wants to find structurally similar proteins.
google-deepmind / gtex-database
3.1kUse 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
3.1kUse when you want to retrieve semi-quantitative protein expression and spatial localisation data from the Human Protein Atlas (HPA).
google-deepmind / interpro-database
3.1kIdentify domains, families, and sites in proteins; find all proteins in a family or sharing a domain; explore species distribution for a domain; annotate genomes with protein families and GO terms. InterPro combines 14 databases (e.g., Pfam, CDD) into one searchable resource.
google-deepmind / literature-search-arxiv
3.1kSearch for scientific papers, preprints, and publications on arXiv. Extract metadata, abstracts, and download full-text PDFs or HTML versions of papers
google-deepmind / literature-search-biorxiv
3.1kBrowse, 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-europepmc
3.1kSearch 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.
google-deepmind / literature-search-openalex
3.1kQuery the OpenAlex scholarly database for research papers, authors, institutions, topics, sources, publishers, funders, geo-locations, and keywords
google-deepmind / ncbi-sequence-fetch
3.1kRetrieve 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
3.1kQuery, search, and download data from the openFDA API for drugs, devices, foods, tobacco, cosmetics, animal and veterinary products, substances, and transparency data.
google-deepmind / opentargets-database
3.1kQuery Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
google-deepmind / pdb-database
3.1kUse 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 / predictingthepast
3.1kAncient text restoration, attribution, dating, contextualization, and embedding via Aeneas (Latin) / Ithaca (Ancient Greek)
google-deepmind / protein-sequence-similarity-search
3.1kSearches 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 / pubchem-database
3.1kQuery PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics
google-deepmind / pubmed-database
3.1kSearch 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 / quickgo-database
3.1kQuery 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.
google-deepmind / ucsc-conservation-and-tfbs
3.1kFetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor Binding Sites (TFBS) from the UCSC Genome Browser
google-deepmind / alphafold-database-fetch-and-analyze
3.1kRetrieve and analyze AlphaFold predicted structures for a protein
google-deepmind / jaspar-database
3.1kQuery the JASPAR database for Transcription Factor (TF) binding profiles
google-deepmind / protein-sequence-msa
3.1kPerforms multiple sequence alignment of proteins with EBI Clustal Omega
google-deepmind / pymol
3.1kVisualize, analyze, and render protein and molecular structures using PyMOL
google-deepmind / string-database
3.1kQuery the STRING database for protein-protein interactions (PPIs), functional enrichment, and homology
google-deepmind / unibind-database
3.1kQueries the UniBind database for experimentally validated transcription factor (TF) binding sites
google-deepmind / uniprot-database
3.1kAccess protein metadata, function, taxonomy, and sequences across UniProtKB, UniParc, and UniRef
google-deepmind / uv
3.1kChecks whether the uv Python package manager is installed and installs it if missing. Ensures uv is on PATH
google-deepmind / workflow-skill-creator
3.1kDistills a completed user workflow or interaction into a reusable agent skill
google-deepmind / clinical-trials-database
3.1kQuery ClinicalTrials.gov via APIv2
google-deepmind / gnomad-database
3.1kQuery the Genome Aggregation Database (gnomAD)
google-deepmind / reactome-database
3.1kQuery the Reactome database (Analysis and Content Services)