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Disease Ontology feature requests


The Disease Ontology (DO) [1, 2] is an open source ontology of human diseases. We are using a subset of the DO, which we refer to as DO slim, as our primary disease vocabulary.

We plan on using this discussion to document DO feature requests related to our project. Individuals who contribute to the DO to assist our project should post here so their efforts can be rewarded.

MeSH cross-reference additions

Of our 137 DO slim terms, 19 did not contain a MeSH (MSH) xref. We manually mapped 16 of these terms (tsv download):

doid_codedoid_namemesh_idmesh_name
DOID:0050741alcohol dependenceD000437Alcoholism
DOID:0050742nicotine dependenceD014029Tobacco Use Disorder
DOID:0060119pharynx cancerD010610Pharyngeal Neoplasms
DOID:10021duodenum cancerD004379Duodenal Neoplasms
DOID:10153ileum cancerD007078Ileal Neoplasms
DOID:1115sarcomaD012509Sarcoma
DOID:11615penile cancerD010412Penile Neoplasms
DOID:11920tracheal cancerD014134Tracheal Neoplasms
DOID:1324lung cancerD008175Lung Neoplasms
DOID:1725peritoneum cancerD010534Peritoneal Neoplasms
DOID:1781thyroid cancerD013964Thyroid Neoplasms
DOID:4362cervical cancerD002583Uterine Cervical Neoplasms
DOID:4481allergic rhinitisD065631Rhinitis, Allergic
DOID:8398osteoarthritisD010003Osteoarthritis
DOID:8893psoriasisD011565Psoriasis
DOID:90degenerative disc diseaseD055959Intervertebral Disc Degeneration

Comprehensive MeSH cross-references will enable literature mining through MEDLINE.

Mistakes in xref resource abbreviations

MedDRA cross-references are inconsistently denoted with MedDRA and MEDDRA.

The following examples include snippets from the HumanDO.obo (revision 2810). Unless otherwise noted, the errors are on the last copied line.

IDC should be ICD for the International Classification of Diseases (last two lines):

[Term]
id: DOID:0060236
name: xanthinuria
def: "A purine-pyrimidine metabolic disorder characterized by deficiency of xanthine oxidase, resulting in excretion of large amounts of xanthine in the urine and the formation of xanthine stones." [url:http\://en.wikipedia.org/wiki/Xanthinuria, url:http\://www.ncbi.nlm.nih.gov/pubmed/4369449]
comment: NT MGI.
subset: DO_MGI_slim
synonym: "xanthine dehydrogenase deficiency" EXACT []
synonym: "xanthine oxidase deficiency" EXACT []
xref: HP:0010934
xref: IDC10CM:E79.8
xref: IDC9CM:277.2

IDC should be ICD:

[Term]
id: DOID:0060332
name: mitochondrial complex V (ATP synthase) deficiency nuclear type 3
def: "A mitochondrial metabolism disease that has material basis in mutation in the ATP5E gene on chromosome 20q13." [url:http\://omim.org/entry/614053]
subset: DO_MGI_slim
synonym: "MC5DN3" EXACT []
xref: IDC10CM:E88.8

IDC should be ICD:

[Term]
id: DOID:5212
name: congenital disorder of glycosylation
def: "A carbohydrate metabolic disorder that involves deficient or defective glycosylation of a variety of tissue proteins and/or lipids." [url:http\://en.wikipedia.org/wiki/Congenital_disorder_of_glycosylation]
comment: Xref MGI.
subset: DO_MGI_slim
synonym: "carbohydrate-deficient glycoprotein syndrome" EXACT []
xref: ICD10CM:77.8
xref: IDC9CM:271.8

UML_CUI should be UMLS_CUI for the Unified Medical Language System:

[Term]
id: DOID:0060313
name: tracheomalacia
def: "A tracheal disease characterized by flaccidity of the tracheal support cartilage." [url:http\://en.wikipedia.org/wiki/Tracheomalacia]
comment: PRISM.
synonym: "congenital tracheomalacia" EXACT []
xref: HP:0002779
xref: ICD10CM:Q32.0
xref: MSH:C557675
xref: NCI:C98634
xref: ORDO:95430
xref: UML_CUI:C0392109

UMLS should be UMLS_CUI for consistency:

[Term]
id: DOID:0060217
name: Cogan-Reese syndrome
def: "A rare eye disease characterized by variable iris atrophy, pigmented and pedunculated nodules located_in iris and attachment of the iris to the cornea (peripheral anterior synechiae) and characterized_by glaucoma." [url:http\://en.wikipedia.org/wiki/Iridocorneal_endothelial_syndrome, url:http\://rarediseases.info.nih.gov/gard/6125/cogan-reese-syndrome/resources/1]
xref: ICD10CM:H21.1
xref: MEDDRA:10059200
xref: ORDO:98980
xref: UMLS:C1168173

UMLS cross-reference additions

Of our 137 DO slim terms, 6 did not contain a UMLS (UMLS_CUI) xref. We manually mapped 5 of these terms (tsv download):

doid_codedoid_nameumls_cuiumls_name
DOID:0050156idiopathic pulmonary fibrosisC1800706Idiopathic Pulmonary Fibrosis
DOID:0050425restless legs syndromeC0035258Restless Legs Syndrome
DOID:0050741alcohol dependenceC0001973Alcoholic Intoxication, Chronic
DOID:0050742nicotine dependenceC0028043Nicotine Dependence
DOID:0060119pharynx cancerC0031347Pharyngeal Neoplasms

There are some additional Disease Ontology feature requests I created on GitHub Issues but didn't get around to posting here until now:

Resolved:

Ongoing:

 
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Daniel Himmelstein (2015) Disease Ontology feature requests. Thinklab. doi:10.15363/thinklab.d68
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