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aapm-bdsc-ontology-tg / radont

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Homo sapiens #29

Closed jonathanbona closed 3 years ago

jonathanbona commented 3 years ago

For convenience and posterity, I'm moving discussion of separate points from Mark's March 4 email titled 'AAPM abstract' into github issues.

Mark asks:

On your graffle plot from some time ago, you use NCBIT:Homo sapiens with "patient" role. Looking at NCBIT, to use this class, there are about 20 parent classes. Do we have to include them all? They also don't seem to follow the BFO ontology.

jonathanbona commented 3 years ago

I vote that we use only NCIT: Homo sapiens and assert that it is a subclass of BFO:material entity.

Bayesianworld commented 3 years ago

It would be nice to use an ontology that has some demographic classes, e.g. birthdate, gender. Even things like patient name and MRN?

andredekker commented 3 years ago

The most often used Homo Sapiens is from NCBIT not NCIT. But NCIT also has homo sapiens defined. @jonathanbona: In the above comment, do you indeed suggest using the NCIT or is this a typo and do you vote for using the NCBIT one?

andredekker commented 3 years ago

Homo sapiens defined in NCBIT but other ontologies have put it in its right place as a material entity, e.g. OBI. Should we import from there? At the moment it is not properly imported into radont.

jonathanbona commented 3 years ago

Yes. http://purl.obolibrary.org/obo/NCBITaxon_9606

Almost nothing is at the moment property imported into radont.

andredekker commented 3 years ago

@jonathanbona: I am correcting the imports. One question that i have: I use protege's Merge Ontologies function to merge the Ontofox exported (fraction of the) ontology into radont. This looks to go ok - but perhaps you do it differently?

andredekker commented 3 years ago

I imported homo sapiens.