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, GO, and expression annotations for an RGD gene with limit/offset…

RGD_get_annotations tool specification

Tool Information:

  • Name: RGD_get_annotations

  • Type: RGDTool

  • Description: Get disease, phenotype, pathway, GO, and expression annotations for an RGD gene with limit/offset pagination and explicit total/has_more metadata. Returns ontology terms, evidence codes, qualifiers, data sources, and complete annotation notes; notes are not shortened. Filter by aspect: D=Disease, P=Pathway, W=Phenotype, F=Molecular Function, C=Cellular Component, E=Expression.

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.

  • limit (integer) (optional) Maximum number of filtered annotations to return in this page.

  • offset (integer) (optional) Zero-based offset after aspect filtering. Use metadata.next_offset for the next page.

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 RGD with limit/offset pagina…

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 RGD with limit/offset pagination and explicit total/has_more metadata. Returns QTL symbol, name, RGD ID, LOD score, p-value, variance, and inheritance type. Requires chromosome, coordinates, and an assembly map_key such as 360 for rat rn7/GRCr8.

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.

  • limit (integer) (optional) Maximum number of overlapping QTLs to return in this page.

  • offset (integer) (optional) Zero-based QTL offset. Use metadata.next_offset for the next page.

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 gene symbol to its native RGD record, or list genes overlapping a genomic region. Symbo…

RGD_resolve_symbol_or_region tool specification

Tool Information:

  • Name: RGD_resolve_symbol_or_region

  • Type: RGDTool

  • Description: Resolve a gene symbol to its native RGD record, or list genes overlapping a genomic region. Symbol mode returns one record. Region mode supports limit/offset pagination and reports total_genes, has_more, and next_offset so large chromosome intervals are fully reachable.

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).

  • limit (integer) (optional) Region mode only: maximum number of overlapping genes to return in this page.

  • offset (integer) (optional) Region mode only: zero-based gene offset. Use metadata.next_offset for the next page.

Example Usage:

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

RGD_search_genes (Type: RGDTool)#

Search rat, human, or mouse genes through RGD/Alliance by symbol or keyword. Returns IDs, symbols…

RGD_search_genes tool specification

Tool Information:

  • Name: RGD_search_genes

  • Type: RGDTool

  • Description: Search rat, human, or mouse genes through RGD/Alliance by symbol or keyword. Returns IDs, symbols, names, species, and every synonym with synonym_count; aliases are not limited to the former first five. Use for gene resolution, ortholog work, toxicology, and disease models.

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)