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[bioontology-support] Which ontology should have the class of "thioredoxin system"?

John Graybeal jgraybeal at stanford.edu
Sun Apr 7 21:07:32 PDT 2019


Hello Michael,

We are not experts on the ontologies in BioPortal, but here's what I did to learn a bit more about this question. I encourage others on this list to provide more domain-specific feedback.

I went to the BioPortal home page (bioportal.bioontology.org<http://bioportal.bioontology.org>) and entered 'thioredoxin' in the class search field. BioPortal found matches in 20 ontologies.

Interestingly, of the 3 ontologies with definitions (NCIT, CRISP, and PR [Protein Ontology], the 3 definitions are appear to be distinct:
- NCIT: Thioredoxin (105 aa, ~12 kDa) is encoded by the human TXN gene. This protein plays a role in redox reactions, signaling and immunity
- CRISP: family of small (13 kD) electron carrier proteins which mediate a number of reactions, including the conversion of ribonucleotides (RNA precursors) to deoxyribonucleotides (DNA precursors) by ribonucleotide reductase.
- PR: A protein that is a translation product of the human TXN gene or a 1:1 ortholog thereof. Category=gene.

The first and third consider this term a protein, but the second considers it a family of proteins—which to me (naively) sounds like a system.

A more thorough investigation could look at the 20 uses, to see if any of them model this term as a system. Perhaps emails to each of the ontology owners would obtain even more insight.

In addition to other comments that hopefully will be made on this list, there are two other paths that may yield additional insight:
- You could contact the OBO support list (obo-discuss at googlegroups.com<mailto:obo-discuss at googlegroups.com>) to see what the ontologists of that 'system of ontologies' thinks
- I've contacted colleagues at University of Miami and Collaborative Drug Discovery who are working with us a term request system. This is an interesting use case that our team has not discussed (so thanks for that!), but maybe they will actually have a particular recommendation for it.

John




On Apr 7, 2019, at 7:13 PM, Michael Liu <megapode32559 at gmail.com<mailto:megapode32559 at gmail.com>> wrote:

Hi,

"thioredoxin system" is a commonly mentioned phrase in recent
literature. But I don't find the exact term in any ontologies.

https://www.ncbi.nlm.nih.gov/pubmed/?term=%22thioredoxin+system%22%5Btiab%5D

Gene Ontology has a class named "thioredoxin reduction". But it is not
exactly the same as "thioredoxin system".

Do you know which ontology would be appropriate to include "thioredoxin system"?

Thanks.

--
Best wishes,
Michael
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