Closed sierra-moxon closed 1 year ago
@sierra-moxon can you comment on the advantage of us creating a specific translator subset vs us giving you two lines of code that achieve the same thing as a preprocessing step for Translator?
@sierra-moxon do you think we should actually obsolete these terms that you'd like to exclude in your subset? @sabrinatoro noted we probably need to review the psychiatric disorder branch in Mondo. (There is a related discussion for this: https://github.com/monarch-initiative/mondo/discussions/2678)
Hi @nicolevasilevsky - @matentzn and I met this morning and he showed me the code to create this -- it works great! :) Thank you both for the help here. I think we can make this standalone code work for Translator, the benefits here are that Translator folks can work on their own timeline to add/remove terms from the subset. The drawbacks are that Translator is using a non-official subset from Mondo (but its probably ok). I'll let you know if there are any concerns with this.
that's so cool! Will you be able to update the subset based on the Mondo releases?
Should we close this ticket?
Per the obsoletion questions, I think https://github.com/monarch-initiative/mondo/issues/6366, https://github.com/monarch-initiative/mondo/issues/6364 cover a couple of instances that I found that I think should be obsoleted (and these are included in this exclusion list). I would agree that the branch itself should be refactored a bit; there are terms not in Mondo that are in the DSM-5 PDF and others that have been changed.
I'm going to close this one as completed! thanks so much again @matentzn and @nicolevasilevsky !
I'll add to this ticket as folks at Translator explore the ontology, if that is ok? Translator would like to have a subset of MONDO that excludes terms that don't match their use cases.
Exclusion rules: any disease or disorder that is this term or a subclass_of or part_of this term: https://www.ebi.ac.uk/ols4/ontologies/mondo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0000947?lang=en
any disease or disorder that is this term or a subclass_of or part_of this term: https://www.ebi.ac.uk/ols4/ontologies/mondo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0000595?lang=en
any disease or disorder that is this term or a subclass_of or part_of this term: https://www.ebi.ac.uk/ols4/ontologies/mondo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0001500?lang=en
any disease or disorder that is this term or a subclass_of this term: https://www.ebi.ac.uk/ols/ontologies/mondo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMONDO_0005583