Annotate SYMP_0000462 as ontology root with IAO_0000700

DiseaseOntology / SymptomOntology

The symptom ontology was designed around the guiding concept of a symptom being: “A perceived change in function, sensation or appearance reported by a patient indicative of a disease”. Understanding the close relationship of Signs and Symptoms, where Signs are the objective observation of an illness, the Symptom Ontology will work to broaden it’s scope to capture and document in a more robust manor these two sets of terms. Understanding that at times, the same term may be both a Sign and a Symptom. The Symptom Ontology is available under CC0 license (https://creativecommons.org/publicdomain/zero/1.0/).

Creative Commons Zero v1.0 Universal

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Annotate SYMP_0000462 as ontology root with IAO_0000700 #12

Closed cthoyt closed 2 years ago

cthoyt commented 2 years ago

What this Does

Add a new annotation property has ontology root term (IAO:0000700) to the ontology
Apply this property at the ontology level to annotate symptom (SYMP:0000462) as the root.

It's true that this is already logically the root element, but this makes it explicit.

Why this is helpful

the Ontology Lookup Service uses this to help better display ontologies
if SYMP_0000462 ever is aligned with an upper ontology like BFO, it still will be the thing shown on OLS as the "root"
this will be generally useful for things like alignment with COB since it makes it easier to figure out where the work will be

cc @matentzn

lschriml commented 2 years ago

Thank you for the suggestion, please submit these kinds of requests as tickets rather than pull requests.

Cheers, Lynn

matentzn commented 2 years ago

We are trying to coordinate this across all obo ontologies - and will open a hundred pull requests. Just so we understand the resistance against this: what are your concerns (see cob channel in obo slack)

lschriml commented 2 years ago

Hello @matentzn -- Happy to coordinate with this effort. Our workflow for direct edits to our suite of ontologies is to have requests submitted via Issue requests, rather than Pull requests. This is done to maintain file integrity. We greatly appreciate everyone's efforts to unify usage across ontologies, however, when we outlined tasks that would be done centrally by the obo foundry group, it did not include editing individual ontologies. It included editing the metadata on the obo foundry site only. I hope you can understand that we choose to maintain our ontologies in this way. Cheers, Lynn

matentzn commented 2 years ago

Can you elaborate what you mean by "file integrity"? Are you saying you do not accept any pull requests from your community at all?

lschriml commented 2 years ago

@matentzn -- yes, I am saying for the DO suite of ontologies, we only rarely accept pull requests. Our preferred method is for suggestions to be made via tickets.

matentzn commented 2 years ago

Alright then we will respect your process for now and add issues on the remaining DO-suite ontologies. Can we either accept this one here as an exception, or pretend it is an issue?

allenbaron commented 2 years ago

We're going to merge this PR while we work on adding OMO as an import across all of our ontologies. Thanks for your patience and help.