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Agent skill

Gene Database

by aipoch in aipoch/medical-research-skills

Query the NCBI Gene database via E-utilities and the NCBI Datasets API; use it when you need to search genes by symbol/ID and retrieve annotations (RefSeq, GO, location, phenotype) for single or…

MITAuto-check passedResearch & Science

Install Gene Database

skills CLI
$ npx skills add aipoch/medical-research-skills --skill gene-database -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install aipoch/medical-research-skills gene-database --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Evidence Insight/gene-database' .claude/skills/gene-database && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
gene-database
GitHub stars
2k
Token cost
~1.3k tokens
SKILL.md length
476 words
Files
7 (incl. scripts, references)
Skills in repo
567
Repo updated
First seen
Licence
MIT

At a glance

Query the NCBI Gene database via E-utilities and the NCBI Datasets API; use it when you need to search genes by symbol/ID and retrieve annotations (RefSeq, GO, location, phenotype) for single or…

  • Works in 3 steps: Search by symbol/name (E-utilities /… → Retrieve gene information by Gene ID → Batch lookup for gene list annotation
  • You need to search genes by symbol/ID and retrieve annotations (RefSeq
  • SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 1 more section
  • Runs Python scripts from its folder; calls python

What it does

Gene Database is an agent skill from aipoch/medical-research-skills. Query the NCBI Gene database via E-utilities and the NCBI Datasets API; use it when you need to search genes by symbol/ID and retrieve annotations (RefSeq, GO, location, phenotype) for single or batch gene lists.

Its SKILL.md is about 1.3k tokens, which your agent loads only when the skill is triggered. The skill folder holds 8 other files, including scripts and reference files (for example `gene-database_audit_result_v1.json`, `references/api_reference.md` and `references/common_workflows.md`).

It sits in Research & Science. It works with NCBI. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

  • You need to search genes by symbol/ID and retrieve annotations (RefSeq
  • Phenotype) for single
  • Batch gene lists

Example prompts

  • “/gene-database”

Requirements

  • Python 3

Workflow steps

3 steps, taken from the step headings in SKILL.md.

  1. Search by symbol/name (E-utilities / ESearch)
  2. Retrieve gene information by Gene ID
  3. Batch lookup for gene list annotation

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 3 files in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • ncbi.nlm.nih.gov

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Gene Database loads about 1.3k tokens when it runs, and up to ~6.5k if it reads all its reference files. Until then it costs about 57 tokens; SKILL.md has 476 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~57
When it runs · the whole SKILL.md, loaded when a task matches
~1.3k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~6.5k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 476 words, ~1,308 tokens.

Download SKILL.mdSave it as .claude/skills/gene-database/SKILL.md (or your agent's skills folder). This skill also uses 6 other files; get the full folder from GitHub.
name
gene-database
description
Query the NCBI Gene database via E-utilities and the NCBI Datasets API; use it when you need to search genes by symbol/ID and retrieve annotations (RefSeq, GO, location, phenotype) for single or batch gene lists.
license
MIT
author
AIPOCH

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

When to Use

  • You have a gene symbol (e.g., BRCA1) and need the correct NCBI Gene ID for a specific organism.
  • You have an NCBI Gene ID and need consolidated metadata (aliases, RefSeq accessions, genomic location, GO, literature links).
  • You need to annotate a gene panel (dozens to thousands of genes) with consistent identifiers and core annotations.
  • You want to search genes by biological context (GO terms, phenotype/disease keywords, pathway terms) and then retrieve details for the hits.
  • You are building a pipeline that must respect NCBI rate limits and handle retries for transient API failures.

Key Features

  • Symbol/name search with organism scoping using E-utilities (ESearch).
  • Gene record retrieval by ID using E-utilities (EFetch/ESummary) in JSON/XML/text-oriented outputs.
  • Streamlined, gene-focused retrieval using the NCBI Datasets API (metadata + sequences/links in a single workflow).
  • Batch lookup utilities with basic rate-limit awareness and output aggregation.
  • Supports common annotation fields: nomenclature/aliases, RefSeq transcripts/proteins, genomic location, GO annotations, phenotype/disease keywords, and related literature references.

Dependencies

  • Python 3.9+
  • requests >= 2.28
  • NCBI E-utilities (Entrez) HTTP API (public service)
  • NCBI Datasets HTTP API (public service)
  • Optional: NCBI API key (recommended for higher throughput)

Example Usage

The following examples assume the repository provides these scripts:

  • scripts/query_gene.py
  • scripts/fetch_gene_data.py
  • scripts/batch_gene_lookup.py
1) Search by symbol/name (E-utilities / ESearch)
bash
python scripts/query_gene.py --search "BRCA1" --organism "human"

Example advanced query strings:

bash
python scripts/query_gene.py --search "insulin[gene name] AND human[organism]"
python scripts/query_gene.py --search "dystrophin[gene name] AND muscular dystrophy[disease]"
python scripts/query_gene.py --search "human[organism] AND 17q21[chromosome]"
2) Retrieve gene information by Gene ID

Using E-utilities (format-oriented retrieval):

bash
python scripts/query_gene.py --id 672 --format json

Using NCBI Datasets API (consolidated gene payload):

bash
python scripts/fetch_gene_data.py --gene-id 672

Or by symbol + taxon:

bash
python scripts/fetch_gene_data.py --symbol BRCA1 --taxon human
python scripts/fetch_gene_data.py --symbol TP53 --taxon "Homo sapiens" --output json
3) Batch lookup for gene list annotation

From a file of symbols (organism required for symbol disambiguation):

bash
python scripts/batch_gene_lookup.py --file gene_list.txt --organism human

From a comma-separated list of Gene IDs:

bash
python scripts/batch_gene_lookup.py --ids 672,7157,5594 --output results.json

Implementation Details

API selection guidance
  • Use E-utilities when you need:
    • complex Entrez query syntax (fielded queries, boolean logic),
    • cross-database patterns,
    • fine control over search and retrieval steps (ESearch → ESummary/EFetch).
  • Use NCBI Datasets API when you need:
    • a streamlined gene-centric retrieval path,
    • consolidated metadata (and often sequence-related links) with fewer round trips.
Show full SKILL.md (169 more words)Show less
Query patterns (E-utilities)

Typical fielded query components include:

  • "<SYMBOL>" plus organism scoping: BRCA1[gene name] AND human[organism]
  • GO term searches (example): GO:0006915[biological process]
  • Phenotype/disease keywords (example): diabetes[phenotype] AND mouse[organism]
  • Pathway keywords (example): insulin signaling pathway[pathway]
Rate limits and API keys
  • Without an API key (typical defaults):
    • E-utilities: ~3 requests/sec
    • Datasets API: ~5 requests/sec
  • With an NCBI API key:
    • both can be used up to ~10 requests/sec (service-dependent)

Obtain an API key from: https://www.ncbi.nlm.nih.gov/account/

Error handling recommendations
  • Handle standard HTTP errors:
    • 400: invalid/malformed query or parameters
    • 404: Gene ID not found
    • 429: rate limit exceeded
  • Use exponential backoff with jitter for retries on 429/5xx.
  • Cache results for repeated lookups (especially in batch annotation workflows).
Output/data formats

Depending on endpoint/script options, gene data may be returned as:

  • JSON (recommended for pipelines)
  • XML (legacy/verbose metadata)
  • Text summaries
  • Sequence-oriented formats such as FASTA or GenBank (when supported by the chosen endpoint/workflow)
Additional references

If present in the repository, consult:

  • references/api_reference.md for endpoint/parameter details and response structures
  • references/common_workflows.md for additional query patterns and end-to-end examples

© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 6 other files (scripts, references) in scientific-skills/Evidence Insight/gene-database of aipoch/medical-research-skills.

  • SKILL.md
  • gene-database_audit_result_v1.json
  • references/api_reference.md
  • references/common_workflows.md
  • scripts/batch_gene_lookup.py
  • scripts/fetch_gene_data.py
  • scripts/query_gene.py

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Gene Database next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

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Works with

Categories

Questions about Gene Database

What does Gene Database do?

Query the NCBI Gene database via E-utilities and the NCBI Datasets API; use it when you need to search genes by symbol/ID and retrieve annotations (RefSeq, GO, location, phenotype) for single or…. Gene Database is an agent skill from aipoch/medical-research-skills. Query the NCBI Gene database via E-utilities and the NCBI Datasets API; use it when you need to search genes by symbol/ID and retrieve annotations (RefSeq, GO, location, phenotype) for single or batch gene lists.

When should I use Gene Database?

Gene Database fits situations like: you need to search genes by symbol/ID and retrieve annotations (RefSeq; phenotype) for single; batch gene lists.

How do I install Gene Database in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill gene-database -a claude-code`. Or copy the skill folder (scientific-skills/Evidence Insight/gene-database in aipoch/medical-research-skills) into .claude/skills/gene-database in your project. Claude Code loads it when a task matches its description.

How do I install Gene Database in Codex?

Run `npx skills add aipoch/medical-research-skills --skill gene-database -a codex`. Or copy the skill folder (scientific-skills/Evidence Insight/gene-database in aipoch/medical-research-skills) into .agents/skills/gene-database in your project. Codex loads it when a task matches its description.

Can I use Gene Database in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aipoch/medical-research-skills --skill gene-database -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/gene-database, .gemini/skills/gene-database, .github/skills/gene-database and .opencode/skills/gene-database in your project.

What does Gene Database need to run?

Going by SKILL.md and its folder, Gene Database needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Gene Database access the network?

SKILL.md names 1 domain. As links in the text: ncbi.nlm.nih.gov. This is read from the text; nothing was executed.

Is Gene Database safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Gene Database use?

Gene Database is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Gene Database use?

About 1.3k tokens (SKILL.md is roughly 5.2k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 5.2k tokens, read only when the agent opens those files.

What are the alternatives to Gene Database?

Skills that share tags, products or a category with Gene Database: Bio Ensembl REST (GPTomics/bioSkills, 1.2k stars), Kegg Database (jaechang-hits/SciAgent-Skills, 370 stars), Dbsnp Database (jaechang-hits/SciAgent-Skills, 370 stars) and Dbsnp Database (google-deepmind/science-skills, 3.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Gene Database?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,973 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.