Gene2Phenotype Tools

Configuration File: gene2phenotype_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the gene2phenotype_tools.json configuration file.

Available Tools

G2P_get_gene (Type: BaseRESTTool)

Get Gene2Phenotype information for a specific gene by symbol. Returns gene location, cross-refere…

G2P_get_gene tool specification

Tool Information:

  • Name: G2P_get_gene

  • Type: BaseRESTTool

  • Description: Get Gene2Phenotype information for a specific gene by symbol. Returns gene location, cross-references to HGNC/Ensembl/OMIM, gene synonyms, and genomic coordinates. This provides the gene-level data without disease associations. For disease associations, use G2P_search with the gene name instead.

Parameters:

  • gene_symbol (string) (required) Gene symbol (e.g., ‘BRCA1’, ‘TP53’, ‘EGFR’, ‘SCN1A’)

Example Usage:

query = {
    "name": "G2P_get_gene",
    "arguments": {
        "gene_symbol": "example_value"
    }
}
result = tu.run(query)

G2P_get_panel (Type: BaseRESTTool)

Get summary statistics for a Gene2Phenotype clinical panel. G2P organizes gene-disease associatio…

G2P_get_panel tool specification

Tool Information:

  • Name: G2P_get_panel

  • Type: BaseRESTTool

  • Description: Get summary statistics for a Gene2Phenotype clinical panel. G2P organizes gene-disease associations into expert-curated panels: DD (developmental disorders), Cancer, Skeletal, Eye, Cardiac, Ear, Skin, and Prenatal. Returns panel name, description, last update date, total records count, total genes, and breakdown by confidence level (definitive, strong, moderate, limited).

Parameters:

  • panel (string) (required) Panel name: ‘cancer’, ‘dd’ (developmental disorders), ‘skeletal’, ‘eye’, ‘cardiac’, ‘ear’, ‘skin’, ‘prenatal’

Example Usage:

query = {
    "name": "G2P_get_panel",
    "arguments": {
        "panel": "example_value"
    }
}
result = tu.run(query)

G2P_get_record (Type: BaseRESTTool)

Get detailed Gene2Phenotype (G2P) record for a specific gene-disease association by its stable ID…

G2P_get_record tool specification

Tool Information:

  • Name: G2P_get_record

  • Type: BaseRESTTool

  • Description: Get detailed Gene2Phenotype (G2P) record for a specific gene-disease association by its stable ID. Returns comprehensive clinical genetics information including locus details (gene symbol, genomic coordinates, cross-references), genotype/inheritance pattern, variant consequences (with Sequence Ontology terms), molecular mechanism with evidence, disease details with ontology terms, confidence level, and supporting publications. Use G2P_search first to find stable IDs.

Parameters:

  • stable_id (string) (required) G2P stable identifier (e.g., ‘G2P01796’, ‘G2P00119’, ‘G2P00979’). Get IDs from G2P_search results.

Example Usage:

query = {
    "name": "G2P_get_record",
    "arguments": {
        "stable_id": "example_value"
    }
}
result = tu.run(query)

G2P_search (Type: BaseRESTTool)

Search the Gene2Phenotype (G2P) database for gene-disease associations curated by clinical geneti…

G2P_search tool specification

Tool Information:

  • Name: G2P_search

  • Type: BaseRESTTool

  • Description: Search the Gene2Phenotype (G2P) database for gene-disease associations curated by clinical geneticists. G2P is maintained by EBI and provides expert-curated evidence for gene-disease relationships used in clinical diagnosis. Returns gene-disease pairs with genotype (monoallelic/biallelic), molecular mechanism (loss/gain of function), clinical panel assignment (DD, Cancer, Skeletal, etc.), and confidence level (definitive, strong, moderate, limited). Useful for clinical variant interpretation and genetic diagnosis.

Parameters:

  • query (string) (required) Search query - gene symbol (e.g., ‘BRCA1’, ‘TP53’) or disease name (e.g., ‘epilepsy’, ‘cardiomyopathy’, ‘cancer’)

  • page ([‘integer’, ‘null’]) (optional) Page number for pagination (default 1)

Example Usage:

query = {
    "name": "G2P_search",
    "arguments": {
        "query": "example_value"
    }
}
result = tu.run(query)