Releases: DiseaseOntology/HumanDiseaseOntology
DO January 2025 release
This release of the Human Disease Ontology includes 11,765 disease classes, 9,446 with textual definitions (80.3%). It also includes text describing diseases of the physical disorders branch (labels, definitions, and synonyms) in Spanish!
Spanish translations can be found along with the corresponding English text in the DO's new doid-international.owl file, or on their own in the Spanish version of the DO, doid-es.owl.
The persistent URLs (PURLs) for the new files containing translated text are:
- doid-international.owl -
http://purl.obolibrary.org/obo/doid/translations/doid-international.owl - doid-es.owl -
http://purl.obolibrary.org/obo/doid/translations/doid-es.owl
A number of data updates are also included in this release, including revision and expansion of OMIM genetic susceptibilities (which the DO team maintains as an import) and the updates to diseases listed below.
Diseases revised & expanded
- Duane retraction syndrome (subtypes)
- adult onset demyelinating leukodystrophies
- familial restrictive cardiomyopathy (subtypes)
- visceral heterotaxy (subtypes)
Diseases revised
- acromesomelic dysplasia subtypes
- adiposis dolorosa
- autosomal dominant distal hereditary motor neuronopathy 2
- hemophilias
- autosomal recessive nonsyndromic deafness 26
- cerebrotendinous xanthomatosis
- congenital nongoitrous hypothyroidism 3
- proteasome-associated autoinflammatory syndrome 1
- retinitis pigmentosa 32
- septooptic dysplasia
- spermatogenic failure subtypes
- spondylometaphyseal dysplasia Algerian type
New diseases
- autosomal dominant primary microcephaly subtypes
- autosomal recessive axonal Charcot-Marie-Tooth disease with vocal cord paresis
- hereditary pyropoikilocytosis
- mitochondrial DNA depletion syndrome-21"
DO December 2024 release
This release of the Human Disease Ontology includes 11,731 disease classes, 9,410 with textual definitions (80.2%).
Classification of CAMRQ3/SCAR34, appendicitis, and childhood leukemias have been revised. Bryant-Li-Bhoj neurodevelopmental syndromes and nonphotosensitive trichothiodystrophies have been added, as have definitions for hydronephrosis and ureteral obstruction. Subtypes have been added, along with revision to existing diseases, for congenital hemolytic anemias, pseudohypoparathyroidisms, combined pituitary hormone deficiencies, and Wieacker-Wolff syndromes (female-restricted added).
Full Changelog: v2024-11-27...v2024-12-18
DO November 2024 release
This release of the Human Disease Ontology includes 11,708 disease classes, 9,383 with textual definitions (80.1%).
New diseases include autoinflammatory syndrome, ring chromosome syndromes, and new subtypes for AML, B-ALL, congenital amegakaryocytic thrombocytopenia, advanced sleep phase syndrome, sideroblastic anemia, craniosynostosis, and ovarian dysgenesis.
Disease classifications have been revised to fix malignant mesotheliomas and to reclassify autoinflammatory syndromes under this new term including: proteosome-associated autoinflammatory syndrome, congenital amegakaryocytic thrombocytopenia, familial Behcet-like autoinflammatory syndrome, familial cold autoinflammatory syndrome, familial Mediterranean fever, and TNF receptor-associated periodic syndrome.
Additional revisions include the definitions of MASLD, MetALD, and congenital disorder of deglycosylation; added cross-references for B-ALL subtypes; and updated definition sources to replace inaccessible sources.
Obsoleted disease(s)
| ID | label | term replaced by |
|---|---|---|
| DOID:0080546 | non-alcoholic fatty liver | metabolic dysfunction-associated steatotic liver disease (DOID:0080208) |
Full Changelog: v2024-11-01...v2024-11-27
DO October 2024 release
This release of the Human Disease Ontology includes 11,684 disease classes, 9,358 with textual definitions (80.0%).
Diseases that have been revised and/or updated with additional subtypes include glycine encephalopathies, FACS, mitochondrial trifunctional protein deficiencies, autosomal dominant isolated macrothrombocytopenias, poor metabolism of thiopurines, retinitis pigmentosa 17, and Axenfeld-Rieger syndrome.
New diseases include APLAID, striatal degeneration 2, congenital amegakaryocytic thrombocytopenia 2, and rhabdoid tumor predisposition syndrome with subtypes.
This release also includes a new subset focused on childhood cancers DO_childhood_cancer_slim and a minor change to the DO_MGI_slim, as well as, expanded chest-related anatomical and onset logical axioms.
Full Changelog: v2024-09-27...v2024-11-01
DO September 2024 release
This release of the Human Disease Ontology includes 11,670 disease classes, 9,341 with textual definitions (80.0%).
Diseases that have been revised and/or updated include renal glycosuria, autosomal dominant nonsyndromic deafness (DFNA) subtypes, peeling skin syndrome 3, congenital disorders of deglycosylation, 'short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies', pancreatic ageneses, preaxial polydactylies, thoracic and breast disease classifications, diseases related to neoprene allergy, and hypogonadism.
New diseases include chromosome 11 partial duplication syndrome, encephalopathy due to defective mitochondrial and peroxisomal fission 2, intellectual disability and myopathy syndrome, bent bone dysplasia syndromes, and digenic dyskeratosis congenita.
Full Changelog: v2024-08-29...v2024-09-27
DO August 2024 release
This release of the Human Disease Ontology includes 11,644 disease classes, 9,315 with textual definitions (80.0%). Diseases that have been revised and/or added include spermatogenic failure subtypes, polycystic liver diseases, dialysis disequilibrium syndrome, and anterior horn cell disease. 'disease has location' (anatomy) axioms have been added to various diseases.
Additionally, 4 diseases have been obsoleted. Annotations should be replaced by existing terms as follows:
| obsoleted | replaced by |
|---|---|
| 'dilated cardiomyopathy 3B' (DOID:0081164) | 'X-linked dilated cardiomyopathy' (DOID:0110461) |
| 'interleukin-7 receptor alpha deficiency' (DOID:0060015) | 'severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, Nk cell-positive' (DOID:0090014) |
| 'dystonia, DOPA-responsive' (DOID:0060963) | 'dopa-responsive dystonia' (DOID:0090043; previously 'dystonia 5') |
| 'autosomal dominant nonsyndromic deafness 52' (DOID:0110578) | 'autosomal dominant nonsyndromic deafness 15' (DOID:0110546) |
Full Changelog: v2024-07-31...v2024-08-29
DO July 2024 release
This release of the Human Disease Ontology includes 11,612 disease classes, 9,280 with textual definitions (79.9%). Diseases that have been revised and/or expanded include CAMRQ syndrome, mosaic variegated aneuploidy syndromes, Fanconi anemia complementation groups, mal de Meleda, common cold, scarlet fever, Machado-Joseph disease, hematopoietic system disease, palmoplantar keratosis, glucose metabolism diseases, and polycystic liver diseases.
Additionally, synonyms that are considered acronyms, including initialisms & alphebetisms as defined in the new OBO Metadata Ontology acronym (OMO:0003012) annotation property, have been annotated as such. All acronyms remain synonyms with no change to their synonym type relationships (exact, broad, narrow, related). Instead, an additional annotation has been applied to the disease-synonym type-synonym triples as an owl:Axiom.
Examples of acronym annotations & how to access them
OBO format (e.g. doid.obo)
'Lambert-Eaton myasthenic syndrome' (DOID:0050214) 'LEMS' acronym
[Term]
...
synonym: "Lambert-Eaton syndrome" EXACT []
synonym: "LEMS" EXACT OMO:0003012 []
...
RDF/XML (e.g. doid.owl)
'drug-induced lupus erythematosus' (DOID:0040093) 'DILE' acronym
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/DOID_0040093"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
<owl:annotatedTarget xml:lang="en">DILE</owl:annotatedTarget>
<oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/OMO_0003012"/>
</owl:Axiom>
OWL Functional Syntax (e.g. doid-edit.owl)
'Polyomavirus-associated nephropathy' (DOID:0040086) 'PVAN' acronym
AnnotationAssertion(Annotation(oboInOwl:hasSynonymType obo:OMO_0003012) oboInOwl:hasExactSynonym obo:DOID_0040086 "PVAN"@en)
Extracting acronyms with SPARQL
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
SELECT ?class ?label ?synonym_type ?acronym
WHERE {
VALUES ?synonym_type {
oboInOwl:hasExactSynonym oboInOwl:hasBroadSynonym
oboInOwl:hasNarrowSynonym oboInOwl:hasRelatedSynonym
}
?class a owl:Class ;
rdfs:label ?label ;
?synonym_type ?acronym .
[] a owl:Axiom ;
owl:annotatedSource ?class ;
owl:annotatedProperty ?synonym_type ;
owl:annotatedTarget ?acronym ;
oboInOwl:hasSynonymType obo:OMO_0003012 .
}Additional SPARQL queries for extracting acronyms can be found at https://github.com/DiseaseOntology/SPARQLqueries/tree/main/Datasets/Synonyms.
Full Changelog: v2024-06-28...v2024-07-31
Discussion regarding how acronyms are to be annotated across OBO ontologies can be found at information-artifact-ontology/ontology-metadata#135.
DO June 2024 release
This release of the Human Disease Ontology includes 11,598 disease classes, 9,265 with textual definitions (79.9%). Diseases that have been revised and/or expanded include thyroid carcinomas, polycystic liver diseases, primary pigmented nodular adrenocortical diseases, Robinow syndromes, WHIM syndromes, palmoplantar keratodermas, and renal hypomagnesemias. The acquired metabolic diseases auto-brewery syndrome and bladder fermentation syndrome have been added and a number of UMLS and related mappings have been revised and updated. An issue with idiopathic pulmonary fibrosis that arose in the previous release has also been fixed (issue #1341).
Full Changelog: v2024-05-29...v2024-06-28
DO May 2024 release
In this release of the Human Disease Ontology, all cross-references to OMIM in all files have had their prefixes changed from 'OMIM' to 'MIM' to align with OMIM. Prefixes will stably remain 'MIM' going forward. We apologize for any inconvenience this may cause.
There are now 11,575 disease classes, 9,237 with textual definitions (79.8%) in the ontology with revisions and additions to amino acid metabolic disorders, polycystic kidney diseases, galactosemias, hypotrichosis, episodic ataxias, Loeys-Dietz syndromes, orofaciodigital syndrome, and holoprosencephalies.
What's Changed
- Implement OMIM-to-MIM prefix change requested by OMIM by @allenbaron in #1334
Full Changelog: v2024-04-30...v2024-05-29
Contributors
Assets 2
DO April Release
The DO's April 2024 release includes: 11,550 human disease terms. This release includes classification revisions for anemia, and B-cell lymphoma; the addition of genes to additional DOID definitions; the addition of disease subtypes for: cone-rod dystrophy; amelogenesis imperfecta, anemia, Ullrich congenital muscular dystrophy and autosomal recessive intellectual developmental disorder 82; the addition of new DOIDs: interstitial lung disease, large B-cell lymphoma, hyperimmunoglobulinemia D periodic fever syndrome, and PFAPA syndrome.