The document discusses how the Disease Ontology (DO) team integrates information from the Online Mendelian Inheritance in Man (OMIM) resource into the DO. It describes approaches used to prioritize OMIM entries for inclusion, develop guidelines for consistent integration of different types of OMIM entries, and resolve disagreements across resources. Key questions addressed include determining if an OMIM record represents a disease, phenotype or locus, whether the disease definition has changed, and if there is agreement about disease organization between resources. Sources of input for updating OMIM cross-references include quality control reports and requests from various groups.

1. Integrating and Maintaining OMIM Cross-references in the Disease Ontology
Susan M Belloa, Cynthia L Smitha, Lynn M Schrimlb
a Mouse Genome Informatics, the Jackson Laboratory, Bar Harbor, ME, USA,
a University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
Abstract
Integrating information from multiple disease resources into the Disease Ontology (DO,
www.disease-ontology.org) requires understanding how different resources represent
disease related information. Here we present how the DO team integrates OMIM into the
DO including approaches prioritizing entries and developing guidelines for consistent
integration of different types of disease related entries in OMIM.
Funding: National Institutes of Health–National Human Genome Research Institute
(NHGRI) [U41 HG008735-01A1]
QC1: OMIM term changes
A. Has the title associated with an
OMIM ID changed?
B. Does this change represent a change
in the disease entity?
Key Comparison Questions
1. Do the changes in OMIM correspond
to changes in other resources?
2. Are new OMIM terms also present in
other resources?
3. Does the grouping/splitting of terms
agree across resources?
4. How do we resolve disagreements
across resources and document the
resolutions?
Key Questions
1. Does the OMIM record represent a disease, phenotype or locus?
A. example: erythrocyte elevated adenosine triphosphate (ticket #709)
2. Has the entity represented by the OMIM record changed?
A. example: Redefining of OMIM brain small vessel disease terms (ticket #688)
3. Is there agreement about the disease across resources?
A. example: familial adenomatous polyposis (ticket #292)
4. Is there agreement about the organization of the group of diseases across
resources?
A.example: Parkinson’s disease subtypes (ticket #702)
Sources of OMIM Input
1. Quality Control (QC) reports
2. GitHub tracker tickets and lists from various groups
(MGI, RGD, FlyBase, UniProt, ZFIN, SIB, PomBase,
Wikidata)
QC2: New OMIM term
A. Is this a disease?
B. Does the disease appear in other
resources?
C. Is this part of a phenotypic series?
QC3: Obsolete OMIM terms
A. Has the OMIM ID been merged to
another disease?
B. Have other resources made similar
changes?
Prioritizing requests
A. Has the OMIM term been
requested by multiple groups?
B. Is there strong evidence for the
disease in multiple resources?
Create New DO term in ROBOT
A. Is there a consistent definition
across references for the disease
B. Is there strong evidence for the
disease in multiple resources?
Current
DO
Updated
DO
Frequently Used Resources