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) (required) Orphanet ORPHA code

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

Example Usage:

query = {
    "name": "Orphanet_get_classification",
    "arguments": {
        "orpha_code": "example_value"
    }
}
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) (required) Orphanet ORPHA code (e.g., 558, 166024). Can include ORPHA: prefix.

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

Example Usage:

query = {
    "name": "Orphanet_get_disease",
    "arguments": {
        "orpha_code": "example_value"
    }
}
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) (required) Orphanet ORPHA code (e.g., 558 for Marfan, 586 for Cystic Fibrosis)

Example Usage:

query = {
    "name": "Orphanet_get_epidemiology",
    "arguments": {
        "orpha_code": "example_value"
    }
}
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) (required) Gene symbol (e.g., ‘FBN1’, ‘BRCA1’, ‘HTT’) or gene name keyword (e.g., ‘fibrillin’, ‘huntingtin’). Symbols are auto-resolved.

Example Usage:

query = {
    "name": "Orphanet_get_gene_diseases",
    "arguments": {
        "gene_name": "example_value"
    }
}
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) (required) Orphanet ORPHA code for the disease

Example Usage:

query = {
    "name": "Orphanet_get_genes",
    "arguments": {
        "orpha_code": "example_value"
    }
}
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) (required) 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)

Example Usage:

query = {
    "name": "Orphanet_get_icd_mapping",
    "arguments": {
        "orpha_code": "example_value"
    }
}
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) (required) Orphanet ORPHA code (e.g., 558 for Marfan, 399 for Huntington)

Example Usage:

query = {
    "name": "Orphanet_get_natural_history",
    "arguments": {
        "orpha_code": "example_value"
    }
}
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) (required) Orphanet ORPHA code (e.g., 558 for Marfan, 586 for Cystic Fibrosis)

Example Usage:

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

Orphanet_search_by_name (Type: OrphanetTool)

Search for rare diseases by exact or partial name match in Orphanet. More precise than keyword se…

Orphanet_search_by_name tool specification

Tool Information:

  • Name: Orphanet_search_by_name

  • Type: OrphanetTool

  • Description: Search for rare diseases by exact or partial name match in Orphanet. More precise than keyword search. Returns ORPHA codes and disease names. Supports exact matching mode for disambiguation.

Parameters:

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

  • name (string) (required) 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)

Example Usage:

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

Orphanet_search_diseases (Type: OrphanetTool)

Search Orphanet for rare diseases by keyword. Orphanet is the reference portal for rare diseases …

Orphanet_search_diseases tool specification

Tool Information:

  • Name: Orphanet_search_diseases

  • Type: OrphanetTool

  • Description: Search Orphanet for rare diseases by keyword. Orphanet is the reference portal for rare diseases and orphan drugs. Returns disease names, ORPHA codes, and synonyms. No authentication required. Supports multiple languages (en, fr, de, es, it, pt, pl, nl).

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.

  • 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)