BRCA1 doesn't get mapped from OMIM to DO anymore

[aaronkw]

BRCA1 is associated with OMIM:604370 (BREAST-OVARIAN CANCER). However, that OMIM term is not longer mapped to any Disease Ontology term - it was previously mapped to 'hereditary breast ovarian cancer' (DOID:5683) but that term no longer exists.

[sbello]

The OMIM record 604370 is one of the OMIM susceptibility records that we mapped using the 'contributes to condition' relationship. If you use the DOID-merged.obo file you will find these relationships.

On Mon, Oct 23, 2017 at 11:03 AM, Aaron Wong notifications@github.com wrote:

BRCA1 is associated with OMIM:604370 (BREAST-OVARIAN CANCER). However, that OMIM term is not longer mapped to any Disease Ontology term - it was previously mapped to 'hereditary breast ovarian cancer' (DOID:5683) but that term no longer exists.

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[aaronkw]

Thanks for the quick response! In the non-merged versions (at least) shouldn't OMIM:604370 be included as an xref to DOID:5683, even if it's a susceptibility? BRCA1 is the canonical example and right now, DOID:5683 has no OMIM xrefs, which doesn't seem quite right.

[lschriml]

Hello Aaron, Thank you for your interest in the Disease Ontology !! We greatly appreciate your input and point of view.

For the Disease Ontology (DO), our OMIM links (xrefs), connect the DO's ontology terms with OMIM's phenotype records (- in terms of linkage - are necessary for the disease) . In this case, OMIM:604370 represents a susceptibility to breast cancer (in terms of linkage - increases risk but is neither necessary nor sufficient for disease expression.

Apologies for any confusion. We are working to clarify the disease to phenotype associated between DO and OMIM, while still capturing the susceptibility OMIM connections.

Cheers, Lynn

Lynn Schriml Principal Investigator Disease Ontology project

On Mon, Oct 23, 2017 at 11:03 AM, Aaron Wong notifications@github.com wrote:

BRCA1 is associated with OMIM:604370 (BREAST-OVARIAN CANCER). However, that OMIM term is not longer mapped to any Disease Ontology term - it was previously mapped to 'hereditary breast ovarian cancer' (DOID:5683) but that term no longer exists.

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-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 801 W. Baltimore St., Room 659 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 lschriml@som.umaryland.edu

[aaronkw]

Hi Lynn,

Thanks again for your response. Our lab uses DO extensively so we greatly appreciate the efforts behind this resource. We also use the xrefs as part of many projects and we noticed this change. I'm curious about this case though, where the phenotype definition implies susceptibility ('An autosomal dominant disease characterized by the higher than normal tendency to develop breast and ovarian cancers in genetically related families.').

Best, Aaron

[lschriml]

Hello Aaron, It is always great to hear how the DO is being utilized. I would like to hear more about your project and to include your lab on on our DO users page.

As you mention, in our definition of this disease we do indicate the susceptibility. I agree with you, that we should clarify this connection. I will add text to the definition of the term, to explain the susceptibility connection in more detail.

The OMIM xrefs in the DO link to phenotypes where the connection is definitive. We created logical definitions to move the OMIM IDs that represent 'susceptibility'. In order to capture these data connections within the DO, we created additional file types of the DO. I suggest utilizing the DO's owl file to see these data connections: http://purl.obolibrary.org/obo/doid.owl

This file can be visualized at the EBI Ontology Lookup Service. https://www.ebi.ac.uk/ols/ontologies/doid

Cheers, Lynn

​

[lschriml]

I have updated the DO file, to help clarify this disease term and it's associated OMIM IDs. Cheers, Lynn