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):

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):

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

Resolved:

• Rename/synonym request: "chronic kidney failure" to "chronic kidney disease"
• Inaccurate cross-references for coronary artery disease

Ongoing:

• Improving the the depression hierarchy