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hgnc-api

Access the HGNC (HUGO Gene Nomenclature Committee) database to search for and retrieve gene information including symbols, names, IDs, and other metadata.

Published by aipoch ↗aipoch/medical-research-skills

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hgnc-api

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Use hgnc-api with Python 3.10+ to retrieve standardized HGNC symbols, names, IDs, and available metadata for [gene terms], returning a reproducible results file at [output path].

Required inputs

  • [gene terms]
  • [output path]

User-approved starter prompt based on a pinned source version; check current skill requirements before running. Task evidence ↗

SKILL.md

name: hgnc-apidescription: Access the HGNC (HUGO Gene Nomenclature Committee) database to search for and retrieve gene information including symbols, names, IDs, and other metadata.license: MITauthor: AIPOCH

Source: https://github.com/aipoch/medical-research-skills

HGNC API Skill

Access the HGNC database to retrieve standardized gene nomenclature and associated resources.

When to Use

  • Use this skill when you need access the hgnc (hugo gene nomenclature committee) database to search for and retrieve gene information including symbols, names, ids, and other metadata in a reproducible workflow.
  • Use this skill when a evidence insight task needs a packaged method instead of ad-hoc freeform output.
  • Use this skill when the user expects a concrete deliverable, validation step, or file-based result.
  • Use this skill when scripts/hgnc.py is the most direct path to complete the request.
  • Use this skill when you need the hgnc-api package behavior rather than a generic answer.

Key Features

  • Scope-focused workflow aligned to: Access the HGNC (HUGO Gene Nomenclature Committee) database to search for and retrieve gene information including symbols, names, IDs, and other metadata.
  • Packaged executable path(s): scripts/hgnc.py.
  • Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

  • Python: 3.10+. Repository baseline for current packaged skills.
  • Third-party packages: not explicitly version-pinned in this skill package. Add pinned versions if this skill needs stricter environment control.

Example Usage

cd "20260316/scientific-skills/Evidence Insight/hgnc-api"
python -m py_compile scripts/hgnc.py
python scripts/hgnc.py --help

Example run plan:

  1. Confirm the user input, output path, and any required config values.
  2. Edit the in-file CONFIG block or documented parameters if the script uses fixed settings.
  3. Run python scripts/hgnc.py with the validated inputs.
  4. Review the generated output and return the final artifact with any assumptions called out.

Implementation Details

  • Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
  • Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
  • Primary implementation surface: scripts/hgnc.py.
  • Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
  • Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.

Tools

fetch

Retrieve detailed gene records from HGNC.

  • term (string): The identifier to look up (e.g., "BRAF", "HGNC:1097").
  • field (string, optional): The field to query against. Defaults to "symbol".

Command:

python scripts/hgnc.py fetch "{term}" --field "{field}"

search

Search for genes using keywords or identifiers. Returns hgnc_id, symbol, and score.

  • term (string): The search query.
  • field (string, optional): Specific field to search in.

Command:

python scripts/hgnc.py search "{term}" --field "{field}"

get_info

Get service status and metadata.

Command:

python scripts/hgnc.py info