Orphanet Tools#

Configuration File: orphanet_tools.json Tool Type: Local Tools Count: 10

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

Available Tools#

Orphanet_get_classification (Type: OrphanetTool)#

Get disease classification hierarchy from Orphanet. Returns parent and child disease categories s…

Orphanet_get_classification tool specification

Tool Information:

  • Name: Orphanet_get_classification

  • Type: OrphanetTool

  • Description: Get disease classification hierarchy from Orphanet. Returns parent and child disease categories showing where a disease fits in the rare disease taxonomy. Useful for understanding disease relationships.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_classification)

  • orpha_code ([‘string’, ‘integer’]) (optional) Orphanet ORPHA code

  • lang (string) (optional) Language code (default: en)

  • orphacode ([‘integer’, ‘string’]) (optional) Alias for orpha_code (the Orphanet disease code).

  • orpha_id ([‘integer’, ‘string’]) (optional) Alias for orpha_code (the Orphanet disease code).

Example Usage:

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

Orphanet_get_disease (Type: OrphanetTool)#

Get detailed information about a rare disease by ORPHA code. Returns disease name, definition, sy…

Orphanet_get_disease tool specification

Tool Information:

  • Name: Orphanet_get_disease

  • Type: OrphanetTool

  • Description: Get detailed information about a rare disease by ORPHA code. Returns disease name, definition, synonyms, and classification. ORPHA codes are unique Orphanet identifiers (e.g., 558 for Marfan syndrome). No authentication required.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_disease)

  • orpha_code ([‘string’, ‘integer’]) (optional) Orphanet ORPHA code (e.g., 558, 166024). Can include ORPHA: prefix.

  • lang (string) (optional) Language code (default: en)

  • orphacode ([‘integer’, ‘string’]) (optional) Alias for orpha_code (the Orphanet disease code).

  • orpha_id ([‘integer’, ‘string’]) (optional) Alias for orpha_code (the Orphanet disease code).

Example Usage:

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

Orphanet_get_epidemiology (Type: OrphanetTool)#

Get epidemiology data (prevalence, incidence) for a rare disease from Orphanet. Returns prevalenc…

Orphanet_get_epidemiology tool specification

Tool Information:

  • Name: Orphanet_get_epidemiology

  • Type: OrphanetTool

  • Description: Get epidemiology data (prevalence, incidence) for a rare disease from Orphanet. Returns prevalence estimates by geographic region and type (point prevalence, birth prevalence, annual incidence). Data includes validation status and literature sources.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_epidemiology)

  • orpha_code ([‘string’, ‘integer’]) (optional) Orphanet ORPHA code (e.g., 558 for Marfan, 586 for Cystic Fibrosis)

  • orphacode ([‘integer’, ‘string’]) (optional) Alias for orpha_code (the Orphanet disease code).

  • orpha_id ([‘integer’, ‘string’]) (optional) Alias for orpha_code (the Orphanet disease code).

Example Usage:

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

Orphanet_get_gene_diseases (Type: OrphanetTool)#

Get rare diseases associated with a gene from Orphanet. Accepts gene symbols (e.g., ‘FBN1’, ‘BRCA…

Orphanet_get_gene_diseases tool specification

Tool Information:

  • Name: Orphanet_get_gene_diseases

  • Type: OrphanetTool

  • Description: Get rare diseases associated with a gene from Orphanet. Accepts gene symbols (e.g., ‘FBN1’, ‘BRCA1’, ‘HTT’) or gene name keywords (e.g., ‘fibrillin’, ‘huntingtin’, ‘dystrophin’). Gene symbols are auto-resolved to full names. Returns disease ORPHA codes, gene symbols, association types, and genomic locus information.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_gene_diseases)

  • gene_name (string) (optional) Gene symbol or name keyword (e.g., ‘FBN1’, ‘BRCA1’, ‘huntingtin’). Use gene_symbol for standard HGNC symbols. Note: Orphanet uses current HGNC symbols (e.g., ‘GBA1’ not ‘GBA’).

  • gene_symbol ([‘string’, ‘null’]) (optional) Alternative to gene_name: standard HGNC gene symbol (e.g., ‘GBA1’, ‘FBN1’). Note: Orphanet uses current HGNC symbols (e.g., ‘GBA1’ not ‘GBA’).

Example Usage:

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

Orphanet_get_genes (Type: OrphanetTool)#

Get genes associated with a rare disease from Orphanet. Returns gene symbols, names, and associat…

Orphanet_get_genes tool specification

Tool Information:

  • Name: Orphanet_get_genes

  • Type: OrphanetTool

  • Description: Get genes associated with a rare disease from Orphanet. Returns gene symbols, names, and association types (causative, modifier, susceptibility). Essential for rare disease genetic diagnosis.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_genes)

  • orpha_code ([‘string’, ‘integer’]) (optional) Orphanet ORPHA code for the disease

  • orphacode ([‘integer’, ‘string’]) (optional) Alias for orpha_code (the Orphanet disease code).

  • orpha_id ([‘integer’, ‘string’]) (optional) Alias for orpha_code (the Orphanet disease code).

Example Usage:

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

Orphanet_get_icd_mapping (Type: OrphanetTool)#

Get cross-references between Orphanet ORPHA codes and other medical coding systems (ICD-10, ICD-1…

Orphanet_get_icd_mapping tool specification

Tool Information:

  • Name: Orphanet_get_icd_mapping

  • Type: OrphanetTool

  • Description: Get cross-references between Orphanet ORPHA codes and other medical coding systems (ICD-10, ICD-11, OMIM, SNOMED-CT). Essential for mapping rare disease codes across clinical and research nomenclatures. Returns mapping relationships and validation status.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_icd_mapping)

  • orpha_code ([‘string’, ‘integer’]) (optional) Orphanet ORPHA code (e.g., 558 for Marfan, 586 for Cystic Fibrosis)

  • coding_system (string) (optional) Which coding system to retrieve: all, icd10, icd11, omim, snomed. Default: all

  • lang (string) (optional) Language code (default: en)

  • orphacode ([‘integer’, ‘string’]) (optional) Alias for orpha_code (the Orphanet disease code).

  • orpha_id ([‘integer’, ‘string’]) (optional) Alias for orpha_code (the Orphanet disease code).

Example Usage:

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

Orphanet_get_natural_history (Type: OrphanetTool)#

Get natural history data for a rare disease from Orphanet. Returns average age of onset and type …

Orphanet_get_natural_history tool specification

Tool Information:

  • Name: Orphanet_get_natural_history

  • Type: OrphanetTool

  • Description: Get natural history data for a rare disease from Orphanet. Returns average age of onset and type of inheritance. Useful for understanding disease progression patterns and genetic counseling.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_natural_history)

  • orpha_code ([‘string’, ‘integer’]) (optional) Orphanet ORPHA code (e.g., 558 for Marfan, 399 for Huntington)

  • orphacode ([‘integer’, ‘string’]) (optional) Alias for orpha_code (the Orphanet disease code).

  • orpha_id ([‘integer’, ‘string’]) (optional) Alias for orpha_code (the Orphanet disease code).

Example Usage:

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

Orphanet_get_phenotypes (Type: OrphanetTool)#

Get HPO (Human Phenotype Ontology) phenotypes associated with a rare disease from Orphanet. Retur…

Orphanet_get_phenotypes tool specification

Tool Information:

  • Name: Orphanet_get_phenotypes

  • Type: OrphanetTool

  • Description: Get HPO (Human Phenotype Ontology) phenotypes associated with a rare disease from Orphanet. Returns HPO terms with their frequency (Very frequent, Frequent, Occasional, Very rare, Excluded) and whether they are diagnostic criteria. Essential for phenotype-driven rare disease diagnosis.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_phenotypes)

  • orpha_code ([‘string’, ‘integer’]) (optional) Orphanet ORPHA code (e.g., 558 for Marfan, 586 for Cystic Fibrosis)

  • orpha_id ([‘string’, ‘integer’]) (optional) Alias for orpha_code. Orphanet ORPHA code (e.g., 558 for Marfan)

  • orphacode ([‘integer’, ‘string’]) (optional) Alias for orpha_code (the Orphanet disease code).

Example Usage:

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

Orphanet_search_by_name (Type: OrphanetTool)#

Search rare diseases by exact or partial name match in Orphanet. Partial matches are recoverably …

Orphanet_search_by_name tool specification

Tool Information:

  • Name: Orphanet_search_by_name

  • Type: OrphanetTool

  • Description: Search rare diseases by exact or partial name match in Orphanet. Partial matches are recoverably paginated: start with offset=0 and continue with data.next_offset while data.has_more is true.

Parameters:

  • operation (string) (optional) Operation type (fixed: search_by_name)

  • name (string) (optional) Disease name to search (e.g., ‘Marfan syndrome’)

  • exact (boolean) (optional) If true, match exact name only. Default: false

  • lang (string) (optional) Language code (default: en)

  • limit (integer) (optional) Maximum number of results to return (default: 20, max: 200)

  • offset (integer) (optional) Zero-based name-match offset. Continue with data.next_offset.

  • query (string) (optional) Alias for name. Disease name to search for in Orphanet.

Example Usage:

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

Orphanet_search_diseases (Type: OrphanetTool)#

Search Orphanet rare diseases by keyword. Fuzzy searches can return thousands of matches, so resu…

Orphanet_search_diseases tool specification

Tool Information:

  • Name: Orphanet_search_diseases

  • Type: OrphanetTool

  • Description: Search Orphanet rare diseases by keyword. Fuzzy searches can return thousands of matches, so results are recoverably paginated: start with offset=0 and continue with data.next_offset while data.has_more is true. data.total_count is the complete match count.

Parameters:

  • operation (string) (optional) Operation type (fixed: search_diseases)

  • query (string) (required) Search query - disease name or keyword (e.g., ‘Marfan’, ‘muscular dystrophy’)

  • limit (integer) (optional) Maximum number of results to return (default: 20, max: 200). The API may return thousands of fuzzy matches; use this to control output size.

  • offset (integer) (optional) Zero-based fuzzy-match offset. Continue with data.next_offset.

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

Example Usage:

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