bio-db-tools

Files (2)

• SKILL.md
• bio_db_lookup.py · templates/

SKILL.md (first lines)

# Bio DB Tools

Use this skill when the user asks to search or fetch data from public biology knowledge bases rather than analyze local files.

Typical triggers:
- protein function, accession, annotation, sequence metadata, domain architecture
- experimental PDB structures or AlphaFold models
- ClinVar pathogenicity or variant significance
- dbSNP rsIDs or gnomAD population-frequency / constraint lookups
- Ensembl gene coordinates, transcripts, or rsIDs
- GEO datasets, pathway databases, or interaction networks
- drug target and disease association evidence

## Environment Check

The bundled template uses Python plus HTTP APIs. Check first.

```bash
which python3 || true
python3 - <<'PY'
mods = ["requests"]
for name in mods:
    try:
        __import__(name)
        print(f"{name}: ok")
    except Exception as exc:
        print(f"{name}: missing ({exc})")
PY
```

If outbound network access is blocked, say so explicitly before claiming the lookup ran.

## Bundled Asset

Use the reusable template instead of rewriting API snippets every time:

- `templates/bio_db_lookup.py`

Supported sources:
- `uniprot`
- `pdb`
- `alphafold`
- `clinvar`
- `dbsnp`
- `gnomad`
- `ensembl`
- `geo`
- `interpro`
- `kegg`
- `opentargets`
- `reactome`
- `stringdb`

## Quick Start

```bash
python3 templates/bio_db_lookup.py uniprot \
  --query TP53 \
  --organism-id 9606 \
  --output bio/uniprot_tp53.csv \
  --summary bio/uniprot_tp53.json
```

```bash
python3 templates/bio_db_lookup.py pdb \
  --query "EGFR kinase inhibitor" \
  --limit 5 \
  --output bio/pdb_egfr.csv \
  --summary bio/pdb_egfr.json
```

```bash
python3 templates/bio_db_lookup.py clinvar \
  --query 'BRCA1[gene] AND clinsig_pathogenic[prop]' \
  --output bio/clinvar_brca1.csv \
  --summary bio/clinvar_brca1.json
```

```bash
python3 templates/bio_db_lookup.py gnomad \
  --mode gene-constraint \
  --gene-symbol BRCA1 \
  --output bio/gnomad_brca1.csv \
  --summary bio/gnomad_brca1.json
```

```bash
python3 templates/bio_db_lookup.py reactome \
  --mode enrichment \
  --gene BRCA1 --gene BRCA2 --gene TP53 --gene ATM \
  --output bio/reactome_dna_repair.csv \
  --summary bio/reactome_dna_repair.json
```

## Working Rules

1. Save both a machine-readable result file and a short summary JSON.
2. Report the exact database, query string, species, and any filters used.
3. Prefer exact identifiers when available: UniProt accession, PDB ID, Ensembl ID, rsID, ClinVar query, Reactome stable ID.
4. Return direct links for the user whenever the database exposes stable pages.
5. Distinguish clearly between:
   - search hits
   - record detail
   - enrichment or network evidence
6. If the remote API returns nothing, say that explicitly instead of inferring a biological conclusion.
7. Treat these sources as lookup surfaces, not experimental validation.

## Common Patterns

### Protein annotation

```bash
python3 templates/bio_db_lookup.py uniprot \
  --accession P04637 \
  --output bio/uniprot_p04637.csv \
  --summary bio/uniprot_p04637.json
```

### Experimental structure lookup

From DrugClaw/DrugClaw, Apache-2.0.

More from DrugClaw/DrugClaw