Import PATO:'chronological age'

[timalamenciak]

Per import process here: https://github.com/EnvironmentOntology/envo/wiki/Import-terms-from-other-ontologies - closes #1587

[pbuttigieg]

Hi @timalamenciak this sets up the import target, but you'll have to trigger the import process in the Makefile, in the docker container.

you'll see that the pato import owl file will change too

[pbuttigieg]

Thanks @timalamenciak

@matentzn @cmungall

I'm not sure why the make process for PATO generates an OWL file with so much CHEBI in it.

The PATO terms we need are in there.

Is this why there's a merge process downstream ?

[cmungall]

I'm not sure why the make process for PATO generates an OWL file with so much CHEBI in it.

See: https://oboacademy.github.io/obook/tutorial/project-ontology-development/?h=slme#extracting-modules
For the most accessible description.

I updated this to document the new subset method, which is what ENVO should use: https://robot.obolibrary.org/extract#subset

[pbuttigieg]

I'm not sure why the make process for PATO generates an OWL file with so much CHEBI in it.

See: https://oboacademy.github.io/obook/tutorial/project-ontology-development/?h=slme#extracting-modules
For the most accessible description.

It's still unclear why so many CHEBI terms are in the PATO import. But if this is expected behaviour, then @timalamenciak we can disregard

I updated this to document the new subset method, which is what ENVO should use: https://robot.obolibrary.org/extract#subset

We won't use OBO format anymore - it's a lock in and anti-FAIR. I assume robot can process other formats for the subset definition ?