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Disease, phenotype and ontology queries: parameters and notes

See the tutorial for usage and examples.

Each function includes its purpose, API, inputs, outputs, example code and result description. Prepare any required credentials, local files and optional dependencies; remote results vary with database releases and query time.

Retrieve disease-associated genes and association scores

dnakit.databases.dis_ge_net_get_disease_genes(*, operation=None, disease, min_score=None, limit=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: get_disease_genes)
disease string Required Disease ID (UMLS CUI) or disease name
min_score number None Minimum association score (0-1). Default: no filter
limit integer None Maximum genes to return (default: 50)
verbose bool True Progress flag.

Configure before running: DISGENET_API_KEY.

Filter gene–disease associations by source and score

dnakit.databases.dis_ge_net_get_gda(*, operation=None, gene=None, disease=None, source=None, min_score=None, limit=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: get_gda)
gene string None Gene symbol (optional if disease provided)
disease string None Disease ID/UMLS CUI (optional if gene provided)
source string None Data source filter: CURATED, ANIMAL_MODELS, LITERATURE, etc.
min_score number None Minimum GDA score (0-1). Higher = stronger evidence.
limit integer None Maximum results (default: 25)
verbose bool True Progress flag.

Configure before running: DISGENET_API_KEY.

Retrieve variant–disease association evidence

dnakit.databases.dis_ge_net_get_vda(*, operation=None, variant=None, gene=None, limit=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: get_vda)
variant string None Variant rsID (e.g., rs1234) - optional if gene provided
gene string None Gene symbol to get all variants - optional if variant provided
limit integer None Maximum results (default: 25)
verbose bool True Progress flag.

Configure before running: DISGENET_API_KEY.

Find disease-associated genes by UMLS concept ID

dnakit.databases.dis_ge_net_search_disease(*, operation=None, disease, limit=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: search_disease)
disease string Required UMLS CUI for the disease, e.g. 'C0006142' (breast cancer). Free-text disease names are NOT accepted -- resolve one via umls_search_concepts first.
limit integer None Maximum associations to return (default: 10)
verbose bool True Progress flag.

Configure before running: DISGENET_API_KEY.

Find diseases associated with a gene symbol

dnakit.databases.dis_ge_net_search_gene(*, operation=None, gene, limit=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: search_gene)
gene string Required Gene symbol (e.g., BRCA1, TP53, EGFR)
limit integer None Maximum associations to return (default: 10)
verbose bool True Progress flag.

Configure before running: DISGENET_API_KEY.

Summarize GenCC gene–disease validity classifications

dnakit.databases.gen_cc_get_classifications(*, operation=None, gene_symbol=None, disease=None, submitter=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: get_classifications)
gene_symbol string None Optional HGNC gene symbol to filter classification stats (e.g., 'GBA', 'BRCA2')
disease string None Optional disease name substring to filter classification stats (e.g., 'Gaucher', 'breast cancer')
submitter string None Optional filter by submitting organization name (e.g., 'ClinGen', 'Ambry', 'Genomics England')
verbose bool True Progress flag.

Search GenCC gene evidence for a disease

dnakit.databases.gen_cc_search_disease(*, operation=None, disease=None, disease_name=None, classification=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: search_disease)
disease string None Disease name or ID to search (e.g., 'Marfan syndrome', 'MONDO:0007947', 'breast cancer')
disease_name string None Alias for disease. Disease name or ID to search.
classification string None Optional filter by classification level (e.g., Definitive, Strong)
verbose bool True Progress flag.

Retrieve GenCC gene–disease classifications

dnakit.databases.gen_cc_search_gene(*, operation=None, gene_symbol, classification=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: search_gene)
gene_symbol string Required HGNC gene symbol (e.g., BRCA2, TP53, FBN1, CFTR)
classification string None Optional filter by classification level (e.g., Definitive, Strong, Moderate, Limited)
verbose bool True Progress flag.

Retrieve diseases associated with multiple HPO phenotypes

dnakit.databases.get_joint_associated_diseases_by_hpo_id_list(*, HPO_ID_list, limit=None, offset=None, verbose=True)

Parameter Type Required / default Description and constraints
HPO_ID_list array Required List of phenotypes or symptoms {"items": {"type": "string", "description": "The HPO ID of the phenotype or symptom."}}
limit integer None Number of entries to fetch.
offset integer None Number of initial entries to skip.
verbose bool True Progress flag.

Retrieve diseases associated with an HPO phenotype

dnakit.databases.hpo_get_diseases_by_phenotype(*, term_id=None, limit=None, offset=None, hp_id=None, verbose=True)

Parameter Type Required / default Description and constraints
term_id string None HPO term identifier (e.g., 'HP:0001250'). Must start with 'HP:' followed by 7 digits.
limit integer | null None Maximum number of results to return (1-500, default 50). Phenotype terms can be linked to thousands of diseases.
offset integer | null None Number of results to skip before returning 'limit' results (default 0). Use with the response's metadata.has_more/metadata.total to page through phenotypes with more diseases than fit in one call.
hp_id string None DNAKit optional alias for term_id
verbose bool True Progress flag.

Retrieve genes associated with an HPO phenotype

dnakit.databases.hpo_get_genes_by_phenotype(*, term_id, limit=None, offset=None, verbose=True)

Parameter Type Required / default Description and constraints
term_id string Required HPO term identifier (e.g., 'HP:0001250'). Must start with 'HP:' followed by 7 digits.
limit integer | null None Maximum number of results to return (1-500, default 50). Phenotype terms can be linked to thousands of genes.
offset integer | null None Number of results to skip before returning 'limit' results (default 0). Use with the response's metadata.has_more/metadata.total to page through phenotypes with more genes than fit in one call.
verbose bool True Progress flag.

Retrieve HPO term definitions and synonyms

dnakit.databases.hpo_get_term(*, term_id, verbose=True)

Parameter Type Required / default Description and constraints
term_id string Required HPO term identifier. Must start with 'HP:' followed by 7 digits. Examples: 'HP:0001250' (Seizure), 'HP:0001263' (Global developmental delay), 'HP:0000252' (Microcephaly), 'HP:0001249' (Intellectual disability).
verbose bool True Progress flag.

Search HPO phenotype terms by keyword

dnakit.databases.hpo_search_terms(*, query, max_results=None, verbose=True)

Parameter Type Required / default Description and constraints
query string Required Search keyword for phenotype terms. Examples: 'seizure', 'intellectual disability', 'cardiomyopathy', 'scoliosis', 'microcephaly'.
max_results integer | null None Maximum number of results to return (default 10, max 50).
verbose bool True Progress flag.

Aggregate human gene identifiers and annotations

dnakit.databases.marrvel_get_gene(*, symbol=None, gene_symbol=None, gene=None, verbose=True)

Parameter Type Required / default Description and constraints
symbol string | null None HGNC gene symbol, e.g. 'CFTR', 'BRCA1'.
gene_symbol string | null None Alias for symbol.
gene string | null None Alias for symbol.
verbose bool True Progress flag.

Provide at least one of these parameter groups: symbol; gene_symbol; gene.

Retrieve OMIM phenotypes and inheritance for a gene

dnakit.databases.marrvel_get_omim_phenotypes(*, symbol=None, gene_symbol=None, gene=None, verbose=True)

Parameter Type Required / default Description and constraints
symbol string | null None HGNC gene symbol, e.g. 'CFTR', 'BRCA1'.
gene_symbol string | null None Alias for symbol.
gene string | null None Alias for symbol.
verbose bool True Progress flag.

Provide at least one of these parameter groups: symbol; gene_symbol; gene.

Retrieve Monarch gene–disease associations

dnakit.databases.monarch_get_gene_diseases(*, subject, limit=None, offset=None, verbose=True)

Parameter Type Required / default Description and constraints
subject string Required Gene CURIE identifier (e.g., 'HGNC:11998' for TP53). Use Monarch_search_gene to find this.
limit integer None Maximum disease associations to return (default: 100)
offset integer None Number of initial entries to skip.
verbose bool True Progress flag.

Retrieve cross-species gene–phenotype associations

dnakit.databases.monarch_get_gene_phenotypes(*, subject, limit=None, offset=None, verbose=True)

Parameter Type Required / default Description and constraints
subject string Required Gene CURIE identifier (e.g., 'HGNC:11998' for TP53, 'HGNC:1100' for BRCA1). Use Monarch_search_gene to find this.
limit integer None Maximum phenotype associations to return (default: 100)
offset integer None Number of initial entries to skip.
verbose bool True Progress flag.

Search Monarch biomedical entities by name

dnakit.databases.monarch_search(*, query, category=None, limit=None, verbose=True)

Parameter Type Required / default Description and constraints
query string Required Search query: gene names, disease names, phenotype terms. Examples: 'BRCA1', 'Alzheimer', 'seizure', 'insulin resistance'.
category string None Filter by entity category. Options: 'biolink:Gene', 'biolink:Disease', 'biolink:PhenotypicFeature'. Default: all categories.
limit integer None Maximum results (default: 10, max: 50).
verbose bool True Progress flag.

Search Monarch genes and cross-species identifiers

dnakit.databases.monarch_search_gene(*, query, limit=None, offset=None, verbose=True)

Parameter Type Required / default Description and constraints
query string Required Gene symbol or name (e.g., 'TP53', 'BRCA1', 'WDR7')
limit integer None Number of results to return (default: 10)
offset integer None Number of initial entries to skip.
verbose bool True Progress flag.

Query cross-species biomedical associations

dnakit.databases.monarch_v3_get_associations(*, subject=None, object=None, category, limit=None, verbose=True)

Parameter Type Required / default Description and constraints
subject string None Subject-side entity CURIE, i.e. the entity on the LEFT of the association (the arrow's source). For gene->disease categories (CausalGeneToDiseaseAssociation, CorrelatedGeneToDiseaseAssociation) the subject is the GENE; for gene->phenotype and gene->pathway the subject is the gene; for DiseaseToPhenotypicFeatureAssociation the subject is the disease. Examples: 'HGNC:11998' (TP53), 'MONDO:0005148' (type 2 diabetes), 'HP:0001250' (seizure). Optional, but at least one of 'subject' / 'object' must be supplied.
object string None Object-side entity CURIE, i.e. the entity on the RIGHT of the association (the arrow's target). Use this to query the association backwards. For gene->disease categories the object is the DISEASE, so 'which genes cause this disease?' is object='MONDO:0006559' with category='biolink:CausalGeneToDiseaseAssociation'; for gene/disease->phenotype categories the object is the HP phenotype term. Optional, but at least one of 'subject' / 'object' must be supplied. Supplying both narrows to associations linking exactly that pair.
category string Required Biolink association category, written as subject->object. Options: 'biolink:GeneToPhenotypicFeatureAssociation' (gene->phenotypes), 'biolink:DiseaseToPhenotypicFeatureAssociation' (disease->phenotypes), 'biolink:CorrelatedGeneToDiseaseAssociation' (gene->diseases, correlated), 'biolink:CausalGeneToDiseaseAssociation' (gene->diseases, causal), 'biolink:GeneToPathwayAssociation' (gene->pathways), 'biolink:VariantToDiseaseAssociation' (variant->diseases), 'biolink:GeneToExpressionSiteAssociation' (gene->expression sites/tissues). The left-hand side goes in 'subject' and the right-hand side goes in 'object'.
limit integer None Maximum number of associations to return (default: 20, max: 200).
verbose bool True Progress flag.

Retrieve biomedical entity details by CURIE

dnakit.databases.monarch_v3_get_entity(*, entity_id, verbose=True)

Parameter Type Required / default Description and constraints
entity_id string Required Entity CURIE identifier. Examples: 'HGNC:11998' (TP53), 'HGNC:1100' (BRCA1), 'MONDO:0005148' (type 2 diabetes), 'HP:0001250' (seizure), 'OMIM:191170' (Li-Fraumeni syndrome).
verbose bool True Progress flag.

Summarize disease phenotypes by body system

dnakit.databases.monarch_v3_get_histopheno(*, entity_id, verbose=True)

Parameter Type Required / default Description and constraints
entity_id string Required Disease CURIE identifier. Examples: 'MONDO:0007947' (Marfan syndrome), 'MONDO:0005148' (type 2 diabetes), 'MONDO:0004975' (Alzheimer disease), 'MONDO:0005015' (diabetes mellitus).
verbose bool True Progress flag.

Retrieve cross-ontology identifier mappings

dnakit.databases.monarch_v3_get_mappings(*, entity_id, limit=None, verbose=True)

Parameter Type Required / default Description and constraints
entity_id string Required Entity CURIE identifier to find mappings for. Examples: 'MONDO:0005148' (type 2 diabetes), 'MONDO:0007947' (Marfan syndrome), 'HP:0001250' (seizure).
limit integer None Maximum number of mappings to return (default: 20, max: 100).
verbose bool True Progress flag.

Find diseases by phenotype semantic similarity

dnakit.databases.monarch_v3_phenotype_similarity_search(*, phenotypes, group=None, limit=None, verbose=True)

Parameter Type Required / default Description and constraints
phenotypes array Required List of HPO term CURIEs representing observed phenotypes. Examples: ['HP:0001250', 'HP:0001249', 'HP:0002353'] for seizure + intellectual disability + EEG abnormality. {"items": {"type": "string"}}
group string None Entity group to search against. Default: 'Human Diseases'. Options: 'Human Diseases', 'Mouse', 'Rat', 'Zebrafish', 'C. elegans', 'Drosophila'.
limit integer None Maximum number of matching diseases to return (default: 10, max: 50).
verbose bool True Progress flag.

Search Monarch knowledge graph entities and categories

dnakit.databases.monarch_v3_search(*, query=None, limit=None, category=None, q=None, verbose=True)

Parameter Type Required / default Description and constraints
query string None Search query. Can be gene names, disease names, phenotype terms, etc. Examples: 'BRCA1', 'breast cancer', 'seizure', 'insulin resistance'.
limit integer None Maximum results to return (default: 10, max: 50).
category string None Filter by entity category. Options: 'biolink:Gene', 'biolink:Disease', 'biolink:PhenotypicFeature', 'biolink:NamedThing'. Default: all categories.
q string None Alias for query parameter.
verbose bool True Progress flag.

Retrieve ontology term ancestors

dnakit.databases.ols_get_term_ancestors(*, operation=None, term_iri=None, term_id=None, ontology=None, include_obsolete=None, size=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None The operation to perform (get_term_ancestors)
term_iri string None The full IRI of the term (e.g., http://www.ebi.ac.uk/efo/EFO_0000408)
term_id string None Short-form CURIE (e.g., 'HP:0001928', 'GO:0008150'). Ontology is auto-inferred from prefix.
ontology string None Ontology ID (e.g., 'hp', 'go', 'efo'). Auto-inferred from term_id prefix when not supplied.
include_obsolete boolean None Include obsolete terms (default: false)
size integer None Number of results to return (default: 20)
verbose bool True Progress flag.

Retrieve ontology term children

dnakit.databases.ols_get_term_children(*, operation=None, term_iri=None, term_id=None, ontology=None, include_obsolete=None, size=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None The operation to perform (get_term_children)
term_iri string None The full IRI of the term (e.g., http://www.ebi.ac.uk/efo/EFO_0000408)
term_id string None Short-form CURIE (e.g., 'HP:0001928', 'GO:0008150'). Ontology is auto-inferred from prefix.
ontology string None Ontology ID (e.g., 'hp', 'go', 'efo'). Auto-inferred from term_id prefix when not supplied.
include_obsolete boolean None Include obsolete terms (default: false)
size integer None Number of results to return (default: 20)
verbose bool True Progress flag.

Retrieve ontology term details

dnakit.databases.ols_get_term_info(*, operation=None, id=None, term_id=None, term_iri=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None The operation to perform (get_term_info)
id string None Ontology term ID or IRI (e.g. HP:0001903, http://purl.obolibrary.org/obo/HP_0001903)
term_id string None Alias for id — ontology term ID (e.g. HP:0001903)
term_iri string None Alias for id. Full IRI or short-form ID (e.g., GO:0008150, EFO:0003971). Same as id.
verbose bool True Progress flag.

Search ontology terms by keyword

dnakit.databases.ols_search_terms(*, operation=None, query, rows=None, size=None, ontology=None, exact_match=None, include_obsolete=None, limit=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None The operation to perform (search_terms)
query string Required The search query for terms
rows integer None Number of results to return (default: 10). Alias: size.
size integer None Alias for rows. Number of results to return (default: 10).
ontology string None Filter by specific ontology (optional)
exact_match boolean None Restrict results to exact matches (default: false). The query must equal a term's label or one of its exact synonyms in full - substring and word-overlap hits are excluded, so 'fibroblast' returns CL:0000057 but not 'skin fibroblast'. If the query is instead an identifier (a CURIE such as 'CL:0000084', the OBO underscore form 'CL_0000084', or a full IRI), the exact match is applied to the obo_id/short_form/iri fields, which returns that identifier in every ontology that declares it - pass ontology to narrow it to one.
include_obsolete boolean None Include obsolete terms (default: false)
limit integer | null None Alias for rows. Maximum number of results to return (default: 10, max: 100).
verbose bool True Progress flag.

Retrieve an OMIM clinical phenotype synopsis

dnakit.databases.omim_get_clinical_synopsis(*, operation=None, mim_number, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: get_clinical_synopsis)
mim_number string Required OMIM MIM number for phenotype (e.g., 219700 for cystic fibrosis)
verbose bool True Progress flag.

Configure before running: OMIM_API_KEY.

Retrieve an OMIM entry by MIM number

dnakit.databases.omim_get_entry(*, operation=None, mim_number, include=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: get_entry)
mim_number string Required OMIM MIM number (e.g., 164730, 219700). Can include OMIM: prefix.
include string None Data sections to include (default: text,clinicalSynopsis,geneMap)
verbose bool True Progress flag.

Configure before running: OMIM_API_KEY.

Retrieve OMIM gene–disease and chromosome mappings

dnakit.databases.omim_get_gene_map(*, operation=None, mim_number=None, chromosome=None, limit=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: get_gene_map)
mim_number string None OMIM MIM number for specific gene (optional if chromosome provided)
chromosome string None Chromosome number (1-22, X, Y) to get all genes (optional if mim_number provided)
limit integer None Maximum results for chromosome query (default: 50, max: 100)
verbose bool True Progress flag.

Configure before running: OMIM_API_KEY.

Search Mendelian disorders and associated genes

dnakit.databases.omim_search(*, operation=None, query, limit=None, start=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: search)
query string Required Search query - gene name (BRCA1), disease (cystic fibrosis), or phenotype (intellectual disability)
limit integer None Maximum results (default: 10, max: 20)
start integer None Offset for pagination (default: 0)
verbose bool True Progress flag.

Configure before running: OMIM_API_KEY.

Retrieve a rare disease classification hierarchy

dnakit.databases.orphanet_get_classification(*, operation=None, orpha_code=None, lang=None, orphacode=None, orpha_id=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: get_classification)
orpha_code string | integer None Orphanet ORPHA code
lang string None Language code (default: en)
orphacode integer | string None Alias for orpha_code (the Orphanet disease code).
orpha_id integer | string None Alias for orpha_code (the Orphanet disease code).
verbose bool True Progress flag.

Retrieve rare disease details by ORPHA code

dnakit.databases.orphanet_get_disease(*, operation=None, orpha_code=None, lang=None, orphacode=None, orpha_id=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: get_disease)
orpha_code string | integer None Orphanet ORPHA code (e.g., 558, 166024). Can include ORPHA: prefix.
lang string None Language code (default: en)
orphacode integer | string None Alias for orpha_code (the Orphanet disease code).
orpha_id integer | string None Alias for orpha_code (the Orphanet disease code).
verbose bool True Progress flag.

Retrieve reported gene associations for an ORPHA disorder

dnakit.databases.orphanet_get_disease_genes(*, orpha_code, verbose=True)

Parameter Type Required / default Description and constraints
orpha_code string Required Orphanet ORPHA disorder identifier.
verbose bool True Progress flag.

Retrieve rare disease prevalence and incidence

dnakit.databases.orphanet_get_epidemiology(*, operation=None, orpha_code=None, orphacode=None, orpha_id=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: get_epidemiology)
orpha_code string | integer None Orphanet ORPHA code (e.g., 558 for Marfan, 586 for Cystic Fibrosis)
orphacode integer | string None Alias for orpha_code (the Orphanet disease code).
orpha_id integer | string None Alias for orpha_code (the Orphanet disease code).
verbose bool True Progress flag.

Find rare diseases associated with a gene

dnakit.databases.orphanet_get_gene_diseases(*, operation=None, gene_name=None, gene_symbol=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: get_gene_diseases)
gene_name string None 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 None Alternative to gene_name: standard HGNC gene symbol (e.g., 'GBA1', 'FBN1'). Note: Orphanet uses current HGNC symbols (e.g., 'GBA1' not 'GBA').
verbose bool True Progress flag.

Retrieve rare disease genes and association types

dnakit.databases.orphanet_get_genes(*, operation=None, orpha_code=None, orphacode=None, orpha_id=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: get_genes)
orpha_code string | integer None Orphanet ORPHA code for the disease
orphacode integer | string None Alias for orpha_code (the Orphanet disease code).
orpha_id integer | string None Alias for orpha_code (the Orphanet disease code).
verbose bool True Progress flag.

Map rare disease codes to other medical coding systems

dnakit.databases.orphanet_get_icd_mapping(*, operation=None, orpha_code=None, coding_system=None, lang=None, orphacode=None, orpha_id=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: get_icd_mapping)
orpha_code string | integer None Orphanet ORPHA code (e.g., 558 for Marfan, 586 for Cystic Fibrosis)
coding_system string None Which coding system to retrieve: all, icd10, icd11, omim, snomed. Default: all
lang string None Language code (default: en)
orphacode integer | string None Alias for orpha_code (the Orphanet disease code).
orpha_id integer | string None Alias for orpha_code (the Orphanet disease code).
verbose bool True Progress flag.

Retrieve rare disease onset and inheritance information

dnakit.databases.orphanet_get_natural_history(*, operation=None, orpha_code=None, orphacode=None, orpha_id=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: get_natural_history)
orpha_code string | integer None Orphanet ORPHA code (e.g., 558 for Marfan, 399 for Huntington)
orphacode integer | string None Alias for orpha_code (the Orphanet disease code).
orpha_id integer | string None Alias for orpha_code (the Orphanet disease code).
verbose bool True Progress flag.

Retrieve rare disease phenotypes and frequencies

dnakit.databases.orphanet_get_phenotypes(*, operation=None, orpha_code=None, orpha_id=None, orphacode=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: get_phenotypes)
orpha_code string | integer None Orphanet ORPHA code (e.g., 558 for Marfan, 586 for Cystic Fibrosis)
orpha_id string | integer None Alias for orpha_code. Orphanet ORPHA code (e.g., 558 for Marfan)
orphacode integer | string None Alias for orpha_code (the Orphanet disease code).
verbose bool True Progress flag.

Search rare diseases by complete or partial name

dnakit.databases.orphanet_search_by_name(*, operation=None, name=None, exact=None, lang=None, limit=None, query=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: search_by_name)
name string None Disease name to search (e.g., 'Marfan syndrome')
exact boolean None If true, match exact name only. Default: false
lang string None Language code (default: en)
limit integer None Maximum number of results to return (default: 20, max: 200)
query string None Alias for name. Disease name to search for in Orphanet.
verbose bool True Progress flag.

Search rare diseases by keyword

dnakit.databases.orphanet_search_diseases(*, operation=None, query, limit=None, lang=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: search_diseases)
query string Required Search query - disease name or keyword (e.g., 'Marfan', 'muscular dystrophy')
limit integer None 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 None Language code (en, fr, de, es, it, pt, pl, nl). Default: en
verbose bool True Progress flag.

Resolve a disease name to an EFO term

dnakit.databases.osl_get_efo_id_by_disease_name(*, disease, verbose=True)

Parameter Type Required / default Description and constraints
disease string Required Disease name or free-text query (e.g., 'diabetes mellitus').
verbose bool True Progress flag.