bio-database-evidence

1# Bio Database Evidence
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3## Use This Skill For
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5Use this skill when the main task is biological database lookup, annotation, or evidence gathering across one or more biological sources:
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7- Gene annotation, identifiers, RefSeq, Ensembl IDs, orthologs, VEP, GO, and genomic coordinates.
8- Variant clinical significance, VUS interpretation support, ClinVar review status, cancer mutations, and COSMIC evidence.
9- GWAS Catalog trait associations, rs IDs, p-values, summary statistics, and genetic epidemiology evidence.
10- Pathway mapping, ID conversion, KEGG pathways, Reactome enrichment, disease pathways, and pathway evidence.
11- Target-disease association evidence, tractability, safety, known drugs, and Open Targets evidence.
12- Protein structure evidence from AlphaFold DB or RCSB PDB, including UniProt IDs, mmCIF/PDB downloads, pLDDT, PAE, and structure metadata.
13- Protein-protein interaction evidence, STRING networks, hub proteins, and enrichment evidence.
14- Reference single-cell data lookup from CELLxGENE Census when the user asks for census metadata or expression data, not full downstream analysis.
15- Cross-database biological ID mapping and evidence tables across multiple resources.
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17## Do Not Use This Skill For
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19- Single-cell RNA-seq analysis, clustering, UMAP, marker genes, cell annotation, AnnData/h5ad container editing, or scVI/scANVI batch-correction planning. Use `scanpy`.
20- Bulk RNA-seq differential expression. Use `pydeseq2`.
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