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infectious-disease-ontology-extensions / Fork-From-IDOCore

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Adding terms for antibodies and antigens to IDO Core #9

Open PhiBabs935 opened 4 years ago

PhiBabs935 commented 4 years ago

In line with expanding coverage of assays/testing, we need to import terms for antibodies and antigens into IDO Core.

I found that many ontologies have different terms for these. Unfortunately, most are not OBO ontologies.

The Gene Ontology has the term "immunoglobulin complex, circulating" which is annotated as having 'antibody' as an exact synonym. http://purl.obolibrary.org/obo/GO_0042571 -IDO Core currently imports this term's direct parent, GO:immunoglobulin complex, so we should just add that I believe. I emailed Lindsay to confirm this. UPDATE: Lindsay said that we should indeed add "immunoglobulin complex, circulating" for antibody.

UPDATE: we can import the term 'antigen' from OBI: http://purl.obolibrary.org/obo/OBI_1110034 UPDATE: actually, maybe the CHebi version of this term would be better We could also import from OBI: Antigen specific antibodies assay = def An analyte assay that measures the presence or amount of antibodies to a specified antigen.

linikujp commented 4 years ago

Alex Diehl has developed an antibody ontology, unpublished. It will be good to ask him about the choice of the terms. In one of recent email discussion with Alex about using his antibody ontology, he suggested to use ‘recognizes’ relation for corresponding antigen and antibody :

For human antibodies against COVID-19, you could use the ‘recognizes’ relation (http://purl.obolibrary.org/obo/REO_0000511) we took from the Reagent Ontology, along with a Protein Ontology identifier for the SARS-CoV2 target protein, as listed in the following two files:

Note that the ‘recognizes’ relation is not part of RO, and the purl does not resolve properly, but it is defined in REO as

a type of targeting relation reserved to describe the relation between an adaptive immune receptor complex and its antigenic target, as antibodies are generated with the function of targeting a specific antigen. For example, antibody x 'recognizes' antigen y if x interacts with an epitope part of y (above some threshhold affinity), and thereby realizes the binding function of the antibody.

PhiBabs935 commented 4 years ago

Thanks! Alex plans on starting to work with us on this stuff soon. I will reach out to him about this particular issue soon.

johnbeve commented 4 years ago

@Regina-Hurley might be able to use Alex's definitions of antigens here