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Additional reporting to help track incoherencies #2
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Added the required information to https://github.com/bio-ontology-research-group/oboconsistencytest/blob/master/explanations-full.txt |
When adding ENVO together with UBERON, there are quite a few more classes unsatisfiable, e.g.:
These explanations take a very long time to generate, so need to find a way to speed things up before being able to provide the full list. @pbuttigieg @cmungall |
Which seems to be mainly an issue with the use of |
For full context for this particular issue, see: obophenotype/uberon#1324 This was fixed in RO in June. However, merging the post-June RO with the pre-June module extracted from RO that is merged into envo creates the zombie unsatisfiability, when combined with any version of Uberon. This will be fixed by regenerating envo/imports/ro_import and making a new envo release. However, the general issue remains. Merging two different versions of portions of ontologies is not compatible with having any kinds of constraints. This can be partially addressed by having standard approaches that make it easier to subtract out stale modules (either not merging, EnvironmentOntology/envo#576, or tagging merged/mireoted axioms, allowing for an unmireot). But even in these cases, subtle issues can arise with inferences in ontology A deriving from stale axioms in ontology B. @balhoff suggests a solution here: obophenotype/uberon#1363 but details need to be worked out. |
Thanks for providing the explanations. I have noticed that these are slow to produce. I'm not sure of a general solution. In my experience there is typically a single root cause for a set of incoherencies in any one ontology, so a sampling approach can still be very informative. |
For each row:
In the header:
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