菜单
Query NCBI GEO for gene expression datasets. Use when user asks about RNA-seq datasets, microarray data, expression data, GEO accessions, or finding public datasets. Triggers on "geo", "gene expression omnibus", "expression dataset", "RNA-seq dataset", "microarray dataset", "GSE", "GDS".
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
基于 SOC 职业分类
Run BLAST sequence similarity searches. Use when the user asks to BLAST a sequence, find similar sequences, identify a gene/protein, or do homology search. Triggers on "blast", "sequence similarity", "homology", "identify sequence".
Search PubMed for scientific literature. Use when the user asks to find papers, search literature, look up research, find publications, or asks about recent studies. Triggers on "pubmed", "papers", "literature", "publications", "research on", "studies about".
Query AlphaFold protein structure predictions. Use when user asks about protein structure, 3D structure, protein folding, or structure prediction. Triggers on "alphafold", "protein structure", "3D structure", "folding", "pLDDT", "structure prediction".
Query ClinVar for clinical variant significance. Use when user asks about variant pathogenicity, genetic variants, clinical significance, or disease-causing mutations. Triggers on "clinvar", "pathogenic", "variant significance", "clinical significance", "disease variant", "mutation pathogenicity".
Query STRING for protein-protein interactions. Use when user asks about protein interactions, interaction networks, binding partners, or interactome. Triggers on "string", "protein interaction", "interaction network", "binding partners", "interactome", "PPI".
| name | query-geo |
| description | Query NCBI GEO for gene expression datasets. Use when user asks about RNA-seq datasets, microarray data, expression data, GEO accessions, or finding public datasets. Triggers on "geo", "gene expression omnibus", "expression dataset", "RNA-seq dataset", "microarray dataset", "GSE", "GDS". |
Query Gene Expression Omnibus for public expression datasets.
from Bio import Entrez
import json
Entrez.email = "bioclaw@example.com"
# 1. Search GEO datasets
def search_geo(query, max_results=10, db="gds"):
handle = Entrez.esearch(db=db, term=query, retmax=max_results, sort="relevance")
record = Entrez.read(handle)
handle.close()
return record
# 2. Get dataset summaries
def geo_summary(id_list, db="gds"):
ids = ",".join(str(i) for i in id_list)
handle = Entrez.esummary(db=db, id=ids, retmode="json")
result = json.loads(handle.read())
handle.close()
return result
# 3. Search for Series (GSE)
def search_gse(keyword, organism="Homo sapiens", max_results=10):
query = f'"{keyword}" AND "{organism}"[Organism] AND gse[ETYP]'
return search_geo(query, max_results)
# Example: Find breast cancer RNA-seq datasets
search = search_gse("breast cancer RNA-seq", max_results=5)
print(f"Found {search['Count']} datasets")
if search['IdList']:
summaries = geo_summary(search['IdList'])
for uid in search['IdList']:
info = summaries['result'].get(str(uid), {})
title = info.get('title', 'N/A')
gse = info.get('accession', 'N/A')
gpl = info.get('gpl', 'N/A')
n_samples = info.get('n_samples', 'N/A')
summary = info.get('summary', 'N/A')[:200]
print(f"\n{gse}: {title}")
print(f" Platform: {gpl}, Samples: {n_samples}")
print(f" Summary: {summary}...")
print(f" URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={gse}")
"CRISPR" AND gse[ETYP]"Homo sapiens"[Organism]"Illumina"[Platform]"2024/01:2026/12"[PDAT]"breast cancer" AND "RNA-seq" AND "Homo sapiens"[Organism] AND gse[ETYP]