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uniprot-skill

Submit compact UniProt REST API requests for UniProtKB, UniRef, UniParc, and FASTA stream endpoints. Use when a user wants concise UniProt summaries; save raw JSON or FASTA only on request.

Stars
1,305
Source
openai/plugins
Updated
2026-05-30
Slug
openai--plugins--uniprot-skill
View on GitHubRaw SKILL.md

// install — copy + paste into any project

mkdir -p .claude/skills && curl -fsSL https://raw.githubusercontent.com/openai/plugins/HEAD/plugins/life-science-research/skills/uniprot-skill/SKILL.md -o .claude/skills/uniprot-skill.md

Drops the SKILL.md into .claude/skills/uniprot-skill.md. Works with Claude Code, Cursor, and any agent that loads SKILL.md files from .claude/skills/.

Operating rules

  • Use scripts/rest_request.py for all UniProt API calls.
  • Use base_url=https://rest.uniprot.org.
  • The script accepts max_items; for search endpoints, start with API size=10 and max_items=10.
  • Single accession or cluster lookups usually do not need max_items.
  • Re-run requests in long conversations instead of relying on older tool output.
  • Treat displayed ... in tool previews as UI truncation, not part of the real request.
  • If the user asks for full JSON or FASTA, set save_raw=true and report the saved file path instead of pasting the payload into chat.

Execution behavior

  • Return concise markdown summaries from the script JSON by default.
  • Return the script JSON verbatim only if the user explicitly asks for machine-readable output.
  • Prefer these paths: uniprotkb/search, uniprotkb/<accession>, uniref/<cluster>, uniparc/search, and uniprotkb/stream.
  • For stream, use response_format=text so the script returns only a short text_head unless raw output is requested.

Input

  • Read one JSON object from stdin.
  • Required fields: base_url, path
  • Optional fields: method, params, headers, json_body, form_body, record_path, response_format, max_items, max_depth, timeout_sec, save_raw, raw_output_path
  • Common UniProt patterns:
    • {"base_url":"https://rest.uniprot.org","path":"uniprotkb/search","params":{"query":"gene:TP53 AND organism_id:9606","fields":"accession,gene_names","size":10,"format":"json"},"record_path":"results","max_items":10}
    • {"base_url":"https://rest.uniprot.org","path":"uniprotkb/P04637","params":{"format":"json"}}
    • {"base_url":"https://rest.uniprot.org","path":"uniprotkb/stream","params":{"query":"organism_id:562","format":"fasta","size":2},"response_format":"text"}

Output

  • Success returns ok, source, path, method, status_code, warnings, and either compact records, a compact summary, or text_head.
  • Use raw_output_path when save_raw=true.
  • Failure returns ok=false with error.code and error.message.

Execution

echo '{"base_url":"https://rest.uniprot.org","path":"uniprotkb/search","params":{"query":"gene:TP53 AND organism_id:9606","fields":"accession,gene_names","size":10,"format":"json"},"record_path":"results","max_items":10}' | python scripts/rest_request.py

References

  • No additional runtime references are required; keep the import package limited to this file and scripts/rest_request.py.