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monarch-initiative / vertebrate-breed-ontology

https://monarch-initiative.github.io/vertebrate-breed-ontology/
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Consider starting a collaboration with Jax on a controlled vocab on strains #39

Open matentzn opened 2 years ago

matentzn commented 2 years ago

Jackson Labs have a pretty awesome nomenclature of mouse strains: http://www.informatics.jax.org/mgihome/nomen/strains.shtml

Maybe its worth collaborating with them once the strain vs breed debate is settled

matentzn commented 2 years ago

Maybe this will be much harder than my naive mind thought. From a convo with @sbello on slack:

There have been

many discussions about ontologies for strains. The issue is these are really a genealogy rather than an ontology with complicated relations between strains. Reasoning across such a thing would almost invariably end in errors and incorrect conclusions. RGD has a very simple ontology which is very flat and really just organizes the strains by type but doesn't capture the relations between strains. MGI has a genealogy chart (http://www.informatics.jax.org/mgihome/genealogy/ ) but it hasn't been updated in 20+ years.

sabrinatoro commented 2 years ago

this issue is part of #36

sbello commented 2 years ago

You could also take a look at the rat strain ontology from RGD http://purl.obolibrary.org/obo/RS_0000457 Something like that would be fairly easy (I think) to generate for mouse from the strain name type and strain attribute tags in MGI It depends on if all you want is broad classification of strain types rather than relations between strains.