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ncbi-gene-search

스타36

포크5

업데이트2026년 4월 5일 05:10

Use this skill to search NCBI Gene by symbol and organism, then fetch compact official Entrez Gene summaries. Do not use it for variant interpretation, transcript-level modeling, or bulk offline annotation.

설치

Codex 또는 Claude로 설치 이 Prompt를 복사해 Codex, Claude 또는 다른 어시스턴트에 붙여 넣으면 Skill 페이지를 검토하고 설치를 진행할 수 있습니다.

Manus에서 실행

출처

ma-compbio-lab

ma-compbio-lab/SkillFoundry

GitHub 저장소 열기 Creator 저장소 보기

다운로드

Manus에서 실행

Purpose

Resolve a gene symbol through NCBI E-utilities and return concise Gene database summaries.

When to use

You need an official Entrez Gene identifier for a symbol and species.
You want a quick NCBI summary before a larger genomics workflow.

When not to use

You need transcript-level coordinates or large-batch annotation.
You need clinical interpretation or variant effect prediction.
You need offline execution.

Inputs

Gene symbol
Optional species, maximum result count, email, and output path

Outputs

JSON payload containing the query, matched Gene IDs, and compact gene summaries

Requirements

Python 3.10+
Network access to eutils.ncbi.nlm.nih.gov

Procedure

Run python3 skills/genomics/ncbi-gene-search/scripts/search_ncbi_gene.py --symbol BRCA1 --species "homo sapiens" --retmax 1 --out skills/genomics/ncbi-gene-search/assets/brca1_gene_summary.json.
Inspect the genes list for gene_id, symbol, description, organism, and map_location.
Use the NCBI gene ID in downstream lookup or literature workflows when needed.

Validation

Command exits successfully.
search.ids contains at least one Gene ID for a known symbol.
The first result has a non-empty symbol and organism.

Failure modes and fixes

No hits: confirm the symbol and organism spelling.
Unexpected species: make the organism explicit with --species.
Too many matches: lower --retmax and review the returned summaries.

Safety and limits

Metadata lookup only.
This skill does not perform variant interpretation or clinical classification.

Example

python3 skills/genomics/ncbi-gene-search/scripts/search_ncbi_gene.py --symbol TP53 --species "homo sapiens" --retmax 1

Provenance

NCBI E-utilities: https://www.ncbi.nlm.nih.gov/books/NBK25501/
NCBI Developer APIs: https://www.ncbi.nlm.nih.gov/home/develop/api/

Related skills

ensembl-gene-lookup
ncbi-pubmed-search

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name	ncbi-gene-search
description	Use this skill to search NCBI Gene by symbol and organism, then fetch compact official Entrez Gene summaries. Do not use it for variant interpretation, transcript-level modeling, or bulk offline annotation.

Purpose

Resolve a gene symbol through NCBI E-utilities and return concise Gene database summaries.

When to use

You need an official Entrez Gene identifier for a symbol and species.
You want a quick NCBI summary before a larger genomics workflow.

When not to use

You need transcript-level coordinates or large-batch annotation.
You need clinical interpretation or variant effect prediction.
You need offline execution.

Inputs

Gene symbol
Optional species, maximum result count, email, and output path

Outputs

JSON payload containing the query, matched Gene IDs, and compact gene summaries

Requirements

Python 3.10+
Network access to eutils.ncbi.nlm.nih.gov

Procedure

Run python3 skills/genomics/ncbi-gene-search/scripts/search_ncbi_gene.py --symbol BRCA1 --species "homo sapiens" --retmax 1 --out skills/genomics/ncbi-gene-search/assets/brca1_gene_summary.json.
Inspect the genes list for gene_id, symbol, description, organism, and map_location.
Use the NCBI gene ID in downstream lookup or literature workflows when needed.

Validation

Command exits successfully.
search.ids contains at least one Gene ID for a known symbol.
The first result has a non-empty symbol and organism.

Failure modes and fixes

No hits: confirm the symbol and organism spelling.
Unexpected species: make the organism explicit with --species.
Too many matches: lower --retmax and review the returned summaries.

Safety and limits

Metadata lookup only.
This skill does not perform variant interpretation or clinical classification.

Example

python3 skills/genomics/ncbi-gene-search/scripts/search_ncbi_gene.py --symbol TP53 --species "homo sapiens" --retmax 1

Provenance

NCBI E-utilities: https://www.ncbi.nlm.nih.gov/books/NBK25501/
NCBI Developer APIs: https://www.ncbi.nlm.nih.gov/home/develop/api/

Related skills

ensembl-gene-lookup
ncbi-pubmed-search