life-science-database-query

name

life-science-database-query

description

General life-sciences research copilot bundling 50 modular sub-skills across human genetics, variant interpretation, functional genomics, expression, pathway biology, protein structure, chemistry, clinical evidence, literature, and public study discovery. Use when a user asks any life-sciences question that may require one or more public databases. The research-router-skill is the default entry point for broad or ambiguous requests; individual sub-skills can be invoked directly for narrow, single-source lookups.

Life-Science Database Query Skill

This skill packages a broad set of modular sub-skills that can be composed to answer questions across every major area of life-sciences research. Each sub-skill maps to one or more public databases and carries its own operating rules and execution scripts.

When To Use This Skill

• The user asks a broad life-sciences question ("what is known about …", "tell me about this gene/variant/compound …")
• The user wants a specific public-database lookup (gnomAD, UniProt, ChEMBL, ClinicalTrials.gov, etc.)
• The user needs multi-source evidence synthesis (genetics + expression, structure + chemistry, clinical + literature)
• The user wants locus-to-gene prioritization, PheWAS follow-up, or multi-cohort replication
• The user wants to discover public datasets or preprints for a research topic

Entry Point

For broad or ambiguous requests, invoke research-router-skill first. It classifies the request, normalizes entities, selects the minimum useful set of downstream sub-skills, optionally parallelizes independent evidence lanes using subagents, and synthesizes the final answer.

Use a specific sub-skill directly only when the request is clearly scoped to a single source.

Sub-Skill Directory

Sub-skill files live at skills/<sub-skill-name>/SKILL.md. Read the relevant SKILL.md before invoking any sub-skill.

Orchestration

Sub-skill	Description
research-router-skill	Route broad or ambiguous life-sciences requests to the right sub-skills, normalize entities, optionally parallelize independent evidence lanes with subagents, and synthesize a concise evidence-backed answer.

Human Genetics And Variant Evidence

Sub-skill	Description
opentargets-skill	Open Targets Platform GraphQL: target, disease, drug, variant, study, and associated-disease datasource heatmap data.
gwas-catalog-skill	GWAS Catalog REST API v2: studies, associations, SNPs, EFO traits, genes, publications, and loci.
clinvar-variation-skill	ClinVar Clinical Tables and NCBI Variation: search, VCV, RCV, SCV, and RefSNP lookups.
gnomad-graphql-skill	gnomAD GraphQL: allele frequency, gene constraint, and variant-context queries.
ensembl-skill	Ensembl REST API: lookup, overlap, cross-reference, and variation endpoints.
eva-skill	European Variation Archive REST: species metadata and archived variant lookups.
epigraphdb-skill	EpiGraphDB API: ontology, literature, Mendelian randomisation, gene-drug, and support-path evidence.
genebass-gene-burden-skill	Genebass gene-burden PheWAS for one Ensembl gene ID and one burden set.
gtex-eqtl-skill	GTEx v2 API: single-tissue eQTL associations from rsID, GRCh37, or GRCh38 input.
eqtl-catalogue-skill	eQTL Catalogue API: association retrieval and documented metadata endpoints.
locus-to-gene-mapper-skill	Multi-skill locus-to-gene prioritization chain (EFO → GWAS → coordinates → Open Targets L2G/coloc → eQTL → burden/coding context).
finngen-phewas-skill	FinnGen PheWAS: single-variant association summaries (GRCh38 query).
ukb-topmed-phewas-skill	UKB-TOPMed PheWAS: single-variant association summaries (GRCh38 query).
biobankjapan-phewas-skill	BioBank Japan PheWAS: single-variant association summaries (GRCh37 query).
tpmi-phewas-skill	TPMI PheWAS: single-variant association summaries (GRCh38 query).

Expression, Cell Context, And Functional Genomics

Sub-skill	Description
bgee-skill	Bgee SPARQL: healthy wild-type expression metadata with ontology-aware lookup patterns.
human-protein-atlas-skill	Human Protein Atlas: gene JSON, search downloads, and tissue or cell-line lookups.
cellxgene-skill	CELLxGENE Discover API: public single-cell collection and dataset metadata.
encode-skill	ENCODE REST API: object lookups, portal-style search, and metadata retrieval.
rnacentral-skill	RNAcentral API: RNA entry browsing, single-entry lookup, and cross-reference retrieval.

Protein, Structure, Pathway, And Functional Biology

Sub-skill	Description
alphafold-skill	AlphaFold Protein Structure Database API: prediction, UniProt summary, sequence summary, and annotation lookups.
rcsb-pdb-skill	RCSB PDB: core metadata, Search API queries, and FASTA downloads.
uniprot-skill	UniProt REST API: UniProtKB, UniRef, UniParc, and FASTA stream endpoints.
string-skill	STRING API: network, interaction-partner, and enrichment endpoints.
quickgo-skill	QuickGO: GO terms, annotations, and ontology traversal.
reactome-skill	Reactome ContentService: pathway, event, participant, search, and diagram data.
rhea-skill	Rhea: biochemical reaction search for reactions and reaction IDs.

Chemistry, Metabolites, And Pharmacology

Sub-skill	Description
bindingdb-skill	BindingDB REST API: ligand-target binding lookups by PDB, UniProt, or similarity search.
chembl-skill	ChEMBL API: activity, molecule, target, mechanism, and text-search endpoints.
pubchem-pug-skill	PubChem PUG REST: compound properties, descriptions, assay summaries, and substance metadata.
chebi-skill	ChEBI 2.0 API: chemical search, compound lookup, ontology traversal, and structure metadata.
pharmgkb-skill	PharmGKB API: genes, variants, clinical annotations, dosing guidelines, and search.
hmdb-skill	HMDB: metabolite, protein, disease, and pathway search.

Clinical, Translational, And Disease Evidence

Sub-skill	Description
clinicaltrials-skill	ClinicalTrials.gov API v2: study search, metadata, enums, search areas, and field statistics.
cbioportal-skill	cBioPortal API: studies, molecular profiles, mutations, clinical data, and samples.
civic-skill	CIViC GraphQL: cancer variant interpretation schema inspection and targeted evidence retrieval.
ipd-skill	IPD REST: HLA allele and cell-level metadata using the public IPD query API.

Literature, Search, And Public Study Discovery

Sub-skill	Description
ncbi-entrez-skill	NCBI Entrez E-Utilities: PubMed, Gene, Protein, Nucleotide, PMC metadata, and GEO metadata workflows.
ncbi-pmc-skill	NCBI PMC Open Access: article and file availability metadata.
biorxiv-skill	bioRxiv and medRxiv API: preprint details, publication linkage, and DOI lookups.
biostudies-arrayexpress-skill	BioStudies and ArrayExpress API: free-text search and accession-based study retrieval.
ncbi-datasets-skill	NCBI Datasets v2: assembly, genome, taxonomy, and related metadata endpoints.
ncbi-blast-skill	NCBI BLAST Common URL API: submit, poll, and summarize nucleotide or protein BLAST jobs.
ncbi-clinicaltables-skill	Clinical Tables NCBI Gene: human gene lookup, pagination, and field selection.

Multi-Omics, Proteomics, And Specialized Data Sources

Sub-skill	Description
pride-skill	PRIDE Archive API: proteomics project discovery and project-level metadata.
proteomexchange-skill	ProteomeXchange PROXI: datasets, libraries, peptidoforms, proteins, PSMs, spectra, and USI examples.
metabolights-skill	MetaboLights: study discovery and study-level metabolomics metadata.
mgnify-skill	MGnify API: microbiome studies, samples, and biome metadata.
efo-ontology-skill	EFO OLS4: search, term lookup, children, and descendants for ontology resolution.

Routing Heuristics

Choose the minimum sub-skills needed to answer the question.

Research objective	Recommended sub-skills
Target or disease background	opentargets-skill, gwas-catalog-skill, gtex-eqtl-skill, human-protein-atlas-skill
Variant interpretation	clinvar-variation-skill, gnomad-graphql-skill, ensembl-skill, one or more PheWAS skills
Locus-to-gene prioritization	locus-to-gene-mapper-skill (or its component sub-skills for custom workflows)
Multi-cohort PheWAS replication	finngen-phewas-skill, ukb-topmed-phewas-skill, biobankjapan-phewas-skill, tpmi-phewas-skill
Expression and tissue context	bgee-skill, human-protein-atlas-skill, cellxgene-skill, gtex-eqtl-skill
Protein structure and function	alphafold-skill, rcsb-pdb-skill, uniprot-skill, reactome-skill
Chemistry and pharmacology	chembl-skill, bindingdb-skill, pubchem-pug-skill, pharmgkb-skill
Entity normalization	efo-ontology-skill, ncbi-clinicaltables-skill, ensembl-skill, uniprot-skill
Clinical and cancer evidence	clinicaltrials-skill, cbioportal-skill, civic-skill, opentargets-skill
Literature and preprints	ncbi-entrez-skill, ncbi-pmc-skill, biorxiv-skill
Public dataset discovery	biostudies-arrayexpress-skill, ncbi-datasets-skill, pride-skill, metabolights-skill, mgnify-skill
Sequence similarity search	ncbi-blast-skill
Pathway and reaction context	reactome-skill, rhea-skill, quickgo-skill, string-skill
Microbiome context	mgnify-skill
Metabolomics context	metabolights-skill, hmdb-skill
Proteomics context	pride-skill, proteomexchange-skill

Subagent Guidance

When subagents are available, use them as bounded retrieval and analysis accelerators for independent evidence lanes.

Good candidates for parallelization:

• genetics versus expression evidence for the same gene or variant
• structure versus chemistry for the same target
• literature versus clinical evidence for the same disease
• multiple PheWAS cohorts for the same variant

Keep the coordinating agent responsible for:

• interpreting the user request and defining scope
• resolving identifiers and canonical entities
• reconciling conflicting evidence across sources
• writing the final synthesis

Each subagent should receive a bounded objective and return concise findings, caveats, sources used, and any artifact paths.

Evidence Quality Notes

• Cross-check orthogonal evidence types rather than over-indexing on one source.
• Call out ancestry limitations, tissue specificity, study design caveats, and evidence gaps explicitly.
• Treat heatmap breadth (Open Targets datasource scores) as evidence-source context, not proof of causality or direction of effect.
• For variant lookups, verify coordinate build (GRCh37 vs GRCh38) before querying cohort-specific PheWAS skills.