google-deepmind/science-skills
Skill Claude CodeCodex
Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid sequence — ask for a…
google-deepmind/science-skills
Skill Claude CodeCodex
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about non-coding variant effects, pathogenicity, clinical significance, disease associations, functional effects, gene…
google-deepmind/science-skills
Skill Claude CodeCodex
Query the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures. Use when the user asks about compounds, targets, IC50/Ki values, drug mechanisms, or structure searches.
google-deepmind/science-skills
Skill Claude CodeCodex
Query ClinicalTrials.gov via APIv2. Use when you want to search for trials by condition, drug, location, status, or phase; retrieve trial details by NCT ID; check eligibility/inclusion criteria; count trials across conditions or time periods; identify a sponsor's trial portfolio; find recruiting trials for patient…
google-deepmind/science-skills
Skill Claude CodeCodex
Use 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/science-skills
Skill Claude CodeCodex
Instructions 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/science-skills
Skill Claude CodeCodex
Use 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. For an rsID, returns variant type, gene associations, clinical significance, allele frequencies, and genomic coordinates…
google-deepmind/science-skills
Skill Claude CodeCodex
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). Use when the user asks to search for terms, retrieve details, navigate hierarchies (parents, children, ancestors), look up properties and individuals, get…
google-deepmind/science-skills
Skill Claude CodeCodex
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.). Use when you want to query regulatory annotations or raw experimental data across human cell types.
google-deepmind/science-skills
Skill Claude CodeCodex
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). Use this skill as a primary ID translator, genomic sequence database and variant effect prediction tool.
google-deepmind/science-skills
Skill Claude CodeCodex
Performs 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. Do NOT use if the user only provides a protein…
google-deepmind/science-skills
Skill Claude CodeCodex
Query the Genome Aggregation Database (gnomAD). Use when determining the rarity or allele frequency of specific genetic variants, retrieving gene constraint metrics (pLI, LOEUF) to assess loss-of-function intolerance, finding variants in a genomic region or gene, or querying structural variants. Don't use for…
google-deepmind/science-skills
Skill Claude CodeCodex
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/science-skills
Skill Claude CodeCodex
Use when you want to retrieve semi-quantitative protein expression and spatial localisation data from the Human Protein Atlas (HPA).
google-deepmind/science-skills
Skill Claude CodeCodex
Identify 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. InterPro-N significantly expands…
google-deepmind/science-skills
Skill Claude CodeCodex
Query the JASPAR database for Transcription Factor (TF) binding profiles. Use when retrieving Position Frequency Matrices (PFMs) or Position Weight Matrices (PWMs) for specific TFs, resolving gene symbols to JASPAR Matrix IDs, or getting TF metadata. Supports multiple output formats (MEME, TRANSFAC, PFM, JASPAR, YAML).
google-deepmind/science-skills
Skill Claude CodeCodex
Search for scientific papers, preprints, and publications on arXiv. Extract metadata, abstracts, and download full-text PDFs or HTML versions of papers. Use when the user asks to find research papers, literature, or specific arXiv IDs.
google-deepmind/science-skills
Skill Claude CodeCodex
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. Keyword filtering is local, so date ranges MUST be narrow (1-4 weeks) with a category to prevent timeouts.
google-deepmind/science-skills
Skill Claude CodeCodex
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.
google-deepmind/science-skills
Skill Claude CodeCodex
Query the OpenAlex scholarly database for research papers, authors, institutions, topics, sources, publishers, funders, geo-locations, and keywords. Use when searching academic papers, resolving DOIs, downloading open-access PDFs, finding an author's publications, aggregating bibliometric data (citation counts…
google-deepmind/science-skills
Skill Claude CodeCodex
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. Use when you need to fetch biological sequences by accession…
google-deepmind/science-skills
Skill Claude CodeCodex
Query, search, and download data from the openFDA API for drugs, devices, foods, tobacco, cosmetics, animal and veterinary products, substances, and transparency data. Use for FDA adverse events, recalls, labeling, approvals, shortages, 510(k) clearances, NDC lookups, and any FDA safety or regulatory data query across…
google-deepmind/science-skills
Skill Claude CodeCodex
Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
google-deepmind/science-skills
Skill Claude CodeCodex
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. Also use to get metadata about biomolecular structure experiments.