Geo Search API

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

GEO Search API

This skill allows searching the NCBI Gene Expression Omnibus (GEO) database.

When to Use

• Use this skill when the request matches its documented task boundary.
• Use it when the user can provide the required inputs and expects a structured deliverable.
• Prefer this skill for repeatable, checklist-driven execution rather than open-ended brainstorming.

Key Features

• Scope-focused workflow aligned to: Search for gene expression DataSets and Profiles in the NCBI GEO database. Use this skill when the user wants to find microarray, RNA-seq, or other genomic data by keywords, organism, author, or specific fields.
• Packaged executable path(s): scripts/search_geo.py.
• Reference material available in references/ for task-specific guidance.
• 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

See ## Usage above for related details.

cd "20260316/scientific-skills/Evidence Insight/geo-search-api"
python -m py_compile scripts/search_geo.py
python scripts/search_geo.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/search_geo.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/search_geo.py.
• Reference guidance: references/ contains supporting rules, prompts, or checklists.
• 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.

Usage

The skill provides a Python script to execute searches against the NCBI Entrez API.

Script: scripts/search_geo.py

Use this script to perform searches.

Arguments:

• query: (Required) The main search terms (e.g., "breast cancer", "GSE12345").
• --filters: (Optional) JSON string of field-specific filters.
  • Example: '{"Organism": "Homo sapiens", "Author": "Smith"}'
  • See references/query_fields.json for supported fields.
• --db: (Optional) Target database. gds (DataSets/Series) or geoprofiles. Default: gds.
• --limit: (Optional) Maximum number of results. Default: 10.
• --email: (Optional) User email (recommended for NCBI E-utilities).
• --api_key: (Optional) NCBI API Key (recommended for higher rate limits).

Example:

python scripts/search_geo.py "diabetes" --filters '{"Organism": "Mus musculus", "DataSet Type": "expression profiling by array"}' --limit 5

Query Construction

Queries are constructed by combining the main query term with any provided filters using the AND operator. Field aliases (e.g., ORGN for Organism) are handled automatically by the NCBI API, but using full names from references/query_fields.json is recommended for clarity.

References

• query_fields.json: List of valid search fields and their aliases.

When Not to Use

• Do not use this skill when the required source data, identifiers, files, or credentials are missing.
• Do not use this skill when the user asks for fabricated results, unsupported claims, or out-of-scope conclusions.
• Do not use this skill when a simpler direct answer is more appropriate than the documented workflow.