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

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.

DO March 2024 Release

This release includes 11,537 disease terms; 8,419 SubClassOf axioms. The addition of 26 new disease terms. This month the DO was updated, we added Peroxisome biogenesis disorder and dystonia subtypes, reclassified Zellweger syndrome subtypes, updated frontotemporal dementia and/or amyotrophic lateral sclerosis and Ohdo syndrome subtype nomenclature, added neurodevelopmental disorder with poor growth and behavioral abnormalities, Stolerman neurodevelopmental syndrome, Nicolaides-Baraitser syndrome, blepharophimosis-impaired intellectual development syndrome, and microcephaly-micromelia syndrome and microcephaly, short stature, Halperin-Birk syndrome and limb abnormalities; revised Lisch epithelial corneal dystrophy.

DO February 2024 release

This release of the Human Disease Ontology includes 11,511 disease classes, 9,160 with textual definitions (79.6%). Diseases that have been revised and/or expanded include CACNA1C-related diseases, long QT syndromes, LAL-D, ARVC, autosomal recessive distal hereditary motor neuronopathy 8, Pick's disease, hyper IgM syndromes, hypoparathyroidism, parasitic protozoa infectious diseases, and Canavan disease. New diseases include 'syndromic X-linked intellectual developmental disorder bain type', SPATCCM, ACM subtypes, 'neurodevelopmental disorder with microcephaly, epilepsy, and brain atrophy', 'developmental delay, dysmorphic facies, and brain anomalies', and 'infantile hypotonia with psychomotor retardation and characteristic facies-3'.

Full Changelog: v2024-01-31...v2024-02-28

DO January 2024 release

This release of the Human Disease Ontology includes 11,501 disease classes, 9,146 with textual definitions (79.5%). Diseases that have been revised and expanded include aniridia, osteosarcomas, distal spinal muscular atrophies, distal hereditary motor neuropathies, peeling skin syndromes, pyridoxine-dependent epilepsies, and Graves disease. New diseases include foveal hypoplasias, developmental dysplasias of the hip, familial focal epilepsies with variable foci, dystonia subtypes, Sifrim-Hitz-Weiss syndrome, cepacia syndrome, round cell sarcoma subtypes, Borrelia miyamotoi disease, PLACK syndrome, familial multiple lipomatosis, and retinal macular dystrophy 2. A number of definitions have additionally been updated with NHGRI sources and xrefs to obsolete EFO terms have been removed.

Full Changelog: v2023-12-20...v2024-01-31