Rgd Tools

Configuration File: rgd_tools.json Tool Type: Local Tools Count: 6

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

Available Tools

RGD_get_annotations (Type: RGDTool)

Get disease, phenotype, pathway, and GO annotations for a rat gene from RGD. Returns curated anno…

RGD_get_annotations tool specification

Tool Information:

  • Name: RGD_get_annotations

  • Type: RGDTool

  • Description: Get disease, phenotype, pathway, and GO annotations for a rat gene from RGD. Returns curated annotations with ontology terms, evidence codes, and qualifiers. Filter by aspect: D=Disease, P=Pathway, W=Phenotype, F=Molecular Function, C=Cellular Component, E=Expression. Essential for rat disease model research and toxicogenomics.

Parameters:

  • rgd_id (string) (required) RGD gene ID (e.g., ‘2218’ for Brca1)

  • aspect (string) (optional) Filter by annotation type: ‘D’ (Disease), ‘P’ (Pathway), ‘W’ (Phenotype), ‘F’ (Function), ‘C’ (Component), ‘E’ (Expression). Leave empty for all.

Example Usage:

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

RGD_get_gene (Type: RGDTool)

Get detailed rat gene information from the Rat Genome Database by RGD ID. Returns gene symbol, na…

RGD_get_gene tool specification

Tool Information:

  • Name: RGD_get_gene

  • Type: RGDTool

  • Description: Get detailed rat gene information from the Rat Genome Database by RGD ID. Returns gene symbol, name, description (including AGR-aggregated functional summary with disease associations, pathways, and interactions), gene type, and Ensembl cross-reference. Use when looking up specific rat genes for toxicology, pharmacology, or disease model research.

Parameters:

  • rgd_id (string) (required) RGD gene ID (numeric, e.g., ‘2218’ for Brca1). Can include ‘RGD:’ prefix.

Example Usage:

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

RGD_get_orthologs (Type: RGDTool)

Get orthologs of a rat gene across species (human, mouse, chinchilla, dog, pig, etc.) from RGD. R…

RGD_get_orthologs tool specification

Tool Information:

  • Name: RGD_get_orthologs

  • Type: RGDTool

  • Description: Get orthologs of a rat gene across species (human, mouse, chinchilla, dog, pig, etc.) from RGD. Returns ortholog gene symbols, RGD IDs, names, and species. Use for cross-species comparison in model organism genetics, finding human disease gene orthologs in rat.

Parameters:

  • rgd_id (string) (required) RGD gene ID (e.g., ‘2218’ for Brca1)

Example Usage:

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

RGD_get_qtls_in_region (Type: RGDTool)

Get QTLs (Quantitative Trait Loci) overlapping a genomic region from the Rat Genome Database (RGD…

RGD_get_qtls_in_region tool specification

Tool Information:

  • Name: RGD_get_qtls_in_region

  • Type: RGDTool

  • Description: Get QTLs (Quantitative Trait Loci) overlapping a genomic region from the Rat Genome Database (RGD’s flagship data type). Returns QTL symbol, name, RGD ID, LOD score, p-value, and inheritance type. Requires a chromosome, start/stop coordinates, and a map_key identifying the assembly (e.g., 360 for rat rn7/GRCr8, 38 for human GRCh38, 35 for mouse GRCm39). Example: chromosome=’10’, start=1, stop=50000000, map_key=360 returns QTL Uae41 ‘Urinary albumin excretion QTL 41’ lod=5.26 rgdId=7387235.

Parameters:

  • chromosome (string) (required) Chromosome name, e.g. ‘10’ or ‘chr10’.

  • start (integer) (required) Region start coordinate (1-based).

  • stop (integer) (required) Region stop coordinate.

  • map_key (integer) (required) Assembly map key. 360=rat rn7/GRCr8, 372=rat mRatBN7.2, 38=human GRCh38, 17=human GRCh37, 35=mouse GRCm39, 18=mouse GRCm38.

Example Usage:

query = {
    "name": "RGD_get_qtls_in_region",
    "arguments": {
        "chromosome": "example_value",
        "start": 10,
        "stop": 10,
        "map_key": 10
    }
}
result = tu.run(query)

RGD_resolve_symbol_or_region (Type: RGDTool)

Resolve a rat gene symbol to its native RGD record/ID, or list genes overlapping a genomic region…

RGD_resolve_symbol_or_region tool specification

Tool Information:

  • Name: RGD_resolve_symbol_or_region

  • Type: RGDTool

  • Description: Resolve a rat gene symbol to its native RGD record/ID, or list genes overlapping a genomic region. Symbol mode: provide ‘symbol’ (and optional species_type_key, default 3=rat) -> returns RGD key, rgd_id, name, type. Region mode: provide chromosome + start + stop + map_key -> returns genes in that interval. Example: symbol=’Tp53’ returns key=1887 rgd_id=3889 name=’tumor protein p53’; region chromosome=’10’, start=1, stop=5000000, map_key=360 returns Mir484 rgdId=2325341.

Parameters:

  • symbol ([‘string’, ‘null’]) (optional) Rat gene symbol, e.g. ‘Tp53’. Use this for symbol mode.

  • species_type_key ([‘integer’, ‘null’]) (optional) Species type key for symbol mode (default 3=rat, 1=human, 2=mouse).

  • chromosome ([‘string’, ‘null’]) (optional) Chromosome for region mode, e.g. ‘10’.

  • start ([‘integer’, ‘null’]) (optional) Region start (region mode).

  • stop ([‘integer’, ‘null’]) (optional) Region stop (region mode).

  • map_key ([‘integer’, ‘null’]) (optional) Assembly map key for region mode (e.g. 360 for rat rn7).

Example Usage:

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

RGD_search_genes (Type: RGDTool)

Search for rat genes by symbol or keyword in the Rat Genome Database. Returns matching genes with…

RGD_search_genes tool specification

Tool Information:

  • Name: RGD_search_genes

  • Type: RGDTool

  • Description: Search for rat genes by symbol or keyword in the Rat Genome Database. Returns matching genes with RGD IDs, symbols, names, types, and descriptions. Supports rat, human, and mouse species. Use for finding rat orthologs, toxicology studies, or rat disease model genes.

Parameters:

  • query (string) (required) Gene symbol or keyword (e.g., ‘Brca1’, ‘Tp53’, ‘insulin’)

  • species (string) (optional) Species to search: ‘rat’ (default), ‘human’, ‘mouse’

Example Usage:

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