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obophenotype / upheno

The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
https://obophenotype.github.io/upheno/
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Re-generation of imports leads to build errors #229

Closed drseb closed 7 years ago

drseb commented 7 years ago

Hi,

with the re-run of make imports/xxx.owl, we are now having issues with logic inconsistencies. See e.g. https://travis-ci.org/obophenotype/human-phenotype-ontology/jobs/232460614 or http://build.berkeleybop.org/job/build-hp-edit/1946/console

This comes from one of the re-mireoted ontologies, i.e. chebi or uberon or GO.

Any ideas how to quickly fix this @cmungall ?

cmungall commented 7 years ago

The most common cause of this is two separate uberon imports in the chain, each coming from different versions. Need a quicker way to analyze these than looking in Protege..

@nicolevasilevsky can you take a look and generate an explanation, and see if the axioms are coming from 2 places?

drseb commented 7 years ago

screen shot 2017-05-15 at 19 18 08

@cmungall Why are there disjointness axioms in uberon? I thought we remove them for the import purpose?

cmungall commented 7 years ago

They're there for detecting errors. I don't recall removing them in imports. On Mon, May 15, 2017 at 10:19 Sebastian Köhler notifications@github.com wrote:

[image: screen shot 2017-05-15 at 19 18 08] https://cloud.githubusercontent.com/assets/5172897/26070022/521bc1a6-39a3-11e7-8ebd-50ba8abf3d18.png

@cmungall https://github.com/cmungall Why are there disjointness axioms in uberon? I thought we remove them for the import purpose?

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cmungall commented 7 years ago

Related ticket: https://github.com/obophenotype/uberon/issues/1189

It looks like there is a very stale set of uberon axioms kicking around in the import chain, conj-sac hasn't been part of the eyeball since 2015: https://github.com/obophenotype/uberon/commit/914304d75a48ed17a9edb175be36bbc60f9666f2

drseb commented 7 years ago

fixed