Install
openclaw skills install life-science-database-queryLife Science Database Query
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.