| name | hgnc-api |
| description | Access the HGNC (HUGO Gene Nomenclature Committee) database to search for and retrieve gene information including symbols, names, IDs, and other metadata. |
| license | MIT |
| author | 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:
- Confirm the user input, output path, and any required config values.
- Edit the in-file
CONFIG block or documented parameters if the script uses fixed settings.
- Run
python scripts/hgnc.py with the validated inputs.
- 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
