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name: web-databases-and-biosql description: "Use Biopython web/database retrieval, offline public-database parsers, and optional BioSQL safely." disable-model-invocation: true metadata: disco-role: operating license: NOASSERTION

Biopython web databases and BioSQL

Use this sub-skill when a task involves Biopython's public biological database clients, database-specific parsers, or BioSQL integration:

• NCBI Entrez E-utilities through Bio.Entrez.
• PubMed/MEDLINE, GenBank flat files, Swiss-Prot/UniProt, ExPASy, and KEGG records.
• Online BLAST submission only for Bio.Blast.qblast etiquette and network cautions.
• Optional BioSQL relational storage through the BioSQL package.

First routing decision

1. Online retrieval requested: confirm network permission, user identity metadata, expected request count, retry/rate policy, and whether data may be sent to the remote service. Do not run online retrieval as a default smoke check.
2. Already-downloaded records: prefer offline parsing with Bio.Entrez.read/parse, Bio.Medline, Bio.SwissProt, Bio.ExPASy.*, Bio.KEGG.*, or Bio.GenBank as appropriate.
3. General sequence file I/O: route to the file I/O sub-skill for ordinary SeqIO/AlignIO parsing, indexing, and conversion.
4. BLAST result object analysis: route to the alignment/search sub-skill. This sub-skill only covers online qblast safety and saving returned handles.
5. BioSQL: treat database servers, schema loading, and third-party DB drivers as optional. Do not require full server setup unless the user explicitly asks for BioSQL persistence.

References

• references/web-database-workflows.md for Entrez, Medline, GenBank, SwissProt, UniProt, ExPASy, KEGG, and qblast workflows.
• references/biosql-reference.md for BioSQL driver choices, connection patterns, and optional setup boundaries.
• references/troubleshooting.md for rate limits, parser modes, validation errors, network failures, and database-driver problems.

Offline check

Run python scripts/offline_database_parsers_smoke.py from this sub-skill directory, or run it by path from any working directory. It performs only in-memory parser/import checks and prints PASS on success.