pubmed-gene-drug-research

Gene and Drug Research

Description

This workflow is used for gene, compound, drug, and clinical variant queries. The public MCP tools have been consolidated into a new set of NCBI extended interfaces: for genes use search_gene / get_gene_details / get_gene_literature, for compounds use search_compound / get_compound_details / get_compound_literature, and for variants use search_clinvar。

Trigger Conditions

• "What is the function of this gene?"
• "What is the structure or mechanism of this drug?"
• "What is the clinical significance of this variant?"
• Mentions BRCA1, TP53, CYP2C9, warfarin, PubChem, ClinVar

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Tool Reference

Topic	Tool
Gene Search	search_gene, get_gene_details, get_gene_literature
Compound Search	search_compound, get_compound_details, get_compound_literature
Variant / ClinVar	search_clinvar
Follow-up Literature Tracking	fetch_article_details, unified_search

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Gene Workflow

1. Search for genes

search_gene(query="BRCA1", organism="human")

2. Get gene details

get_gene_details(gene_id="672")

3. Get gene-related literature

get_gene_literature(gene_id="672", limit=20)

4. Expand PubMed details

fetch_article_details(pmids="12345678,87654321")

get_gene_literature uses NCBI curated gene-to-publication links, which is usually more accurate than a simple keyword search.

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Compound / Drug Workflow

1. Search for compounds

search_compound(query="remimazolam")

2. Get compound details

get_compound_details(cid="11526795")

3. Get compound-related literature

get_compound_literature(cid="11526795", limit=20)

4. Do broader mechanism or comparison searches

unified_search(
    query="remimazolam mechanism action",
    limit=20,
    ranking="quality"
)

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ClinVar / Variant Workflow

Search for variants

search_clinvar(query="BRCA1 pathogenic")
search_clinvar(query="NM_007294.4:c.5266dupC")
search_clinvar(query="CYP2C9 drug response")

Key Usage Points

• For gene-level clinical significance:search_clinvar(query="BRCA1 pathogenic")
• For precise variants: use HGVS, for example NM_007294.4:c.5266dupC
• For pharmacogenomics: use gene + phenotype, for example CYP2C9 drug response

Currently the public interface has no standalone ClinVar detail tool. For greater precision, make the search_clinvar query more specific.

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Common Integration Workflows

Scenario 1: Gene to Literature

search_gene(query="TP53", organism="human")
get_gene_details(gene_id="7157")
get_gene_literature(gene_id="7157", limit=20)

Scenario 2: Drug to Literature

search_compound(query="propofol")
get_compound_details(cid="4943")
get_compound_literature(cid="4943", limit=20)

Scenario 3: Variant to Mechanism and Literature

search_clinvar(query="BRCA1 pathogenic")
search_gene(query="BRCA1", organism="human")
unified_search(
    query="BRCA1 pathogenic variant DNA repair",
    limit=20,
    ranking="quality"
)

Scenario 4: Pharmacogenomics

search_compound(query="warfarin")
search_gene(query="CYP2C9 warfarin metabolism", organism="human")
search_clinvar(query="CYP2C9 drug response")
unified_search(
    query="warfarin CYP2C9 pharmacogenomics",
    limit=30,
    ranking="quality"
)

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Practical Recommendations

Gene

• Prefer official symbols, for example TP53, rather than vague aliases first
• Often supplement with organism="human", to avoid mixing in mouse or other species

Compound

• Prefer generic names, rather than brand names first
• Once you have the CID, using the CID for everything afterward is the most stable

ClinVar

• The most precise is HGVS nomenclature
• The next best is gene + pathogenic or gene + condition

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Final Principles

The new public tool names should be unified as:

• search_gene
• get_gene_details
• get_gene_literature
• search_compound
• get_compound_details
• get_compound_literature
• search_clinvar