Orphadata Tools#

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

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

Available Tools#

Orphadata_get_disorder (Type: OrphadataTool)#

Retrieve a rare disease from Orphanet by ORPHAcode, with synonyms, disorder type, and cross-refer…

Orphadata_get_disorder tool specification

Tool Information:

  • Name: Orphadata_get_disorder

  • Type: OrphadataTool

  • Description: Retrieve a rare disease from Orphanet by ORPHAcode, with synonyms, disorder type, and cross-references to OMIM, ICD-10, ICD-11, MeSH, UMLS, and MedDRA. Orphadata is the machine-readable distribution of Orphanet and a Global Core Biodata Resource. Example: orphacode=558 (Marfan syndrome). Use Orphadata_search_by_name to find ORPHAcodes from a disease name.

Parameters:

  • orphacode ([‘integer’, ‘string’]) (required) ORPHAcode, e.g. 558.

  • lang ([‘string’, ‘null’]) (optional) Language code: en, fr, de, es, it, nl, pt, pl. Default en.

Example Usage:

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

Orphadata_get_epidemiology (Type: OrphadataTool)#

Retrieve Orphanet prevalence and epidemiology estimates for a rare disease by ORPHAcode, includin…

Orphadata_get_epidemiology tool specification

Tool Information:

  • Name: Orphadata_get_epidemiology

  • Type: OrphadataTool

  • Description: Retrieve Orphanet prevalence and epidemiology estimates for a rare disease by ORPHAcode, including prevalence class, geographic area, point/birth prevalence type, and validation status. Useful for rare-disease burden and trial feasibility questions. Example: orphacode=558.

Parameters:

  • orphacode ([‘integer’, ‘string’]) (required) ORPHAcode, e.g. 558.

  • lang ([‘string’, ‘null’]) (optional) Language code. Default en.

Example Usage:

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

Orphadata_get_phenotypes (Type: OrphadataTool)#

Retrieve HPO phenotype annotations for a rare disease by ORPHAcode, with each phenotype’s frequen…

Orphadata_get_phenotypes tool specification

Tool Information:

  • Name: Orphadata_get_phenotypes

  • Type: OrphadataTool

  • Description: Retrieve HPO phenotype annotations for a rare disease by ORPHAcode, with each phenotype’s frequency in that disease (e.g. ‘Very frequent (99-80%)’) and whether it is a diagnostic criterion. Complements the HPO_* tools, which start from a phenotype rather than a disease. Example: orphacode=558.

Parameters:

  • orphacode ([‘integer’, ‘string’]) (required) ORPHAcode, e.g. 558.

  • limit ([‘integer’, ‘null’]) (optional) Maximum phenotypes to return. Omit for all.

  • lang ([‘string’, ‘null’]) (optional) Language code. Default en.

Example Usage:

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

Orphadata_search_by_name (Type: OrphadataTool)#

Find rare diseases in Orphanet by name or synonym, returning ORPHAcodes for use with the other Or…

Orphadata_search_by_name tool specification

Tool Information:

  • Name: Orphadata_search_by_name

  • Type: OrphadataTool

  • Description: Find rare diseases in Orphanet by name or synonym, returning ORPHAcodes for use with the other Orphadata tools. Matching is on full clinical names, so prefer ‘Marfan syndrome’ over ‘Marfan’. Example: name=’Cystic fibrosis’.

Parameters:

  • name (string) (required) Disease name or synonym, e.g. ‘Marfan syndrome’.

  • lang ([‘string’, ‘null’]) (optional) Language code. Default en.

Example Usage:

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