search

DiseaseOntology / HumanDiseaseOntology

Repository for the Human Disease Ontology.
Creative Commons Zero v1.0 Universal
329 stars 108 forks source link

Disease Ontology should provide base file #951

Closed matentzn closed 3 years ago

matentzn commented 3 years ago

To enable seemless integration of multiple ontologies together, we have been pushing so called "base" files forward, that is, versions of the ontology that only contain axioms defined in that ontology (no imports).

A specification of "base" in form of a ROBOT query can be found here: https://github.com/INCATools/ontology-development-kit/blob/master/docs/ReleaseArtefacts.md#release-artefact-1-base-required

This is also necessary to do the ROBOT checks correctly, as that is the only way to ensure that we are really checking the contents of your ontology, not of your imports. I think if you provide a base, this problem will go away.

lschriml commented 3 years ago

Thank you @matentzn !!

@beckyjackson -- can you add the creation of this 'base' file to our release process ?

Cheers, Lynn

beckyjackson commented 3 years ago

Disregard my last comment, I'll create a base file! It's early and I realized those files aren't quite right :)

lschriml commented 3 years ago

Thank you Becky !! Much appreciated, those old names are previously published names, and still used by some DO users.

Cheers, Lynn

lschriml commented 3 years ago

Hello @beckyjackson -- please let me know the timeframe for addressing this ticket.

Cheers, Lynn

beckyjackson commented 3 years ago

@lschriml @matentzn I've just added the base file, src/ontology/doid-base.owl or via http://purl.obolibrary.org/obo/doid/doid-base.owl

Sorry for the delay!

lschriml commented 3 years ago

@becky - Please rename (in the Make file) doid-non-classified to be the base file.

Cheers, Lynn

On Fri, Jul 2, 2021 at 11:08 AM Becky Jackson @.***> wrote:

Closed #951 https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/951.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/951#event-4971989011, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBB4DOPO6ADH3TGFNRM6BTTVXI57ANCNFSM46LM6PRA .

-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

beckyjackson commented 3 years ago

Sorry for the earlier confusion, the non classified file is different than the base file. I’ve added a base file now.

On Fri, Jul 2, 2021 at 9:27 AM lschriml @.***> wrote:

@becky - Please rename (in the Make file) doid-non-classified to be the base file.

Cheers, Lynn

On Fri, Jul 2, 2021 at 11:08 AM Becky Jackson @.***> wrote:

Closed #951 https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/951.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/951#event-4971989011 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABBB4DOPO6ADH3TGFNRM6BTTVXI57ANCNFSM46LM6PRA

.

-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St https://www.google.com/maps/search/670+W.+Baltimore+St?entry=gmail&source=g., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/951#issuecomment-873118113, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD7ZMRUOFSL2AZEE5M7DL2LTVXSITANCNFSM46LM6PRA .

lschriml commented 3 years ago

Thank you Becky !!

Sent from my iPhone

On Jul 2, 2021, at 12:40 PM, Becky Jackson @.***> wrote:

 Sorry for the earlier confusion, the non classified file is different than the base file. I’ve added a base file now.

On Fri, Jul 2, 2021 at 9:27 AM lschriml @.***> wrote:

@becky - Please rename (in the Make file) doid-non-classified to be the base file.

Cheers, Lynn

On Fri, Jul 2, 2021 at 11:08 AM Becky Jackson @.***> wrote:

Closed #951 https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/951.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/951#event-4971989011 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABBB4DOPO6ADH3TGFNRM6BTTVXI57ANCNFSM46LM6PRA

.

-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St https://www.google.com/maps/search/670+W.+Baltimore+St?entry=gmail&source=g., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/951#issuecomment-873118113, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD7ZMRUOFSL2AZEE5M7DL2LTVXSITANCNFSM46LM6PRA .

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.