Closed mah11 closed 2 years ago
Hey @mah11
Unfortunately, this may be a pretty tough sell here: most of the terms in FYECO should be in other OBO ontologies. Is your situation that:
Does this summarise the situation correctly?
Hi Nico, This does summarize the situation. Ideally we would migrate the 381 terms to another ontology, but we I don't have time to do the requests right now, and we need all of the terms in one place before we can migrate. So if anyone is happy to ingest FYECO for us, we can easily make the switch.
External users should at least be able to trace the conditions if they really want to, although for non-PomBase users the conditions like (agar plates, liquid culture, standard temperature, media etc) are not really critical for the interpretation of the phenotype ( some databases do not even capture this detail), hence the low priority nature of this for me right now. I see it as a temporary solution.
Alright, in this case, rather than adding FYECO to OBO foundry, I would suggest the following:
Would this work for you? it will give you time to migrate without putting the burden on you that you have to (this could be done as part of another grant), and you don't need to worry anyone ever taking up this space.
That sounds like a good solution!
Here it is:
https://github.com/biopragmatics/bioregistry/issues/268
If you are happy with this,let me us know :)
Discussed on 12-14-2021 call. Thank you for applying for OBO registration. But we think to register to bioregistry is the best solution. If you want, we'd like to help you to submit the terms you need to existing OBO Foundry ontologies.
Use this form to register a new ontology with the OBO Foundry. Please read the instructions provided here: http://obofoundry.org/docs/NewOntologyRegistrationInstructions.html
Ontology title
Fission Yeast Experimental Conditions Ontology
Requested ID space
FYECO
Ontology location
https://github.com/pombase/fypo/
Contact person
Name: Val Wood Email address: vw253 at cam.ac.uk GitHub username: ValWood
Issue tracker
https://github.com/pombase/fypo/issues Use FYECO label
Ontology license
Available ontology formats
OBO
What domain is the ontology intended to cover?
Brief descriptions of experimental conditions relevant to fission yeast biology (and therefore also to many other microbial species)
Related OBO Foundry ontologies
OBI
Intended use/related projects
Used for phenotype annotations in PomBase and JaponicusDB; FYECO could be regarded as a small subset of OBI, where using OBI directly would be overkill
Data source
https://raw.githubusercontent.com/pombase/fypo/master/fyeco.obo
Additional comments or remarks
This ontology has been developed mainly for in-house usage by the two fission yeast MODs named above. We're registering it here primarily to avoid namespace clashes. Meeting the remaining checklist criteria would require resources we don't have at present.
@ValWood @kimrutherford @cmungall
OBO Foundry pre-registration checklist
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by- [X]
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