![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](https://image.slidesharecdn.com/icbo2019diseaseontologymgi-190711195601/75/omim-integration-in-human-disease-ontology-1-2048.jpg?cb=1669144561)
OMIM Integration in Human Disease Ontology
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Genetic diseases in the Human Disease Ontology are cross mapped to OMIM (www.omim.org). Here we present the process on data integration and management for coordinating data updates across resources.
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OMIM Integration in Human Disease Ontology
- 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