add qc workflow #1240

wdduncan · 2021-11-16T01:37:21Z

No description provided.

wdduncan · 2021-11-16T01:50:22Z

@cmungall I ran make test locally (which is called in the qc.yml workflow. It found a number of equivalence errors (see below). Do you want to merge this now, or fix these errors first?

2021-11-15 20:46:45,984 ERROR org.obolibrary.robot.ReasonOperation - No equivalent class axioms are allowed
2021-11-15 20:46:45,985 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: <http://purl.obolibrary.org/obo/FOODON_00001142> == <http://purl.obolibrary.org/obo/FOODON_00001765>
2021-11-15 20:46:45,985 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: <http://purl.obolibrary.org/obo/FOODON_03301103> == <http://purl.obolibrary.org/obo/FOODON_00001100>
2021-11-15 20:46:45,985 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: <http://purl.obolibrary.org/obo/FOODON_00001142> == <http://purl.obolibrary.org/obo/FOODON_03310791>
2021-11-15 20:46:45,985 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: <http://purl.obolibrary.org/obo/FOODON_03460231> == <http://purl.obolibrary.org/obo/FOODON_03460229>
2021-11-15 20:46:45,985 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: <http://purl.obolibrary.org/obo/ENVO_01001479> == <http://purl.obolibrary.org/obo/ENVO_01001784>
2021-11-15 20:46:45,985 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: <http://purl.obolibrary.org/obo/FOODON_00001765> == <http://purl.obolibrary.org/obo/FOODON_03310226>
2021-11-15 20:46:45,985 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: <http://purl.obolibrary.org/obo/FOODON_00001765> == <http://purl.obolibrary.org/obo/FOODON_03310791>
2021-11-15 20:46:45,985 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: <http://purl.obolibrary.org/obo/FOODON_00001142> == <http://purl.obolibrary.org/obo/FOODON_03310226>
2021-11-15 20:46:45,985 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: <http://purl.obolibrary.org/obo/FOODON_03310226> == <http://purl.obolibrary.org/obo/FOODON_03310791>
make: *** [envo-full.owl] Error 1
rm imports/fao_combined_seed.tsv imports/chebi_combined_seed.tsv imports/pato_combined_seed.tsv imports/go_combined_seed.tsv imports/pco_combined_seed.tsv imports/po_combined_seed.tsv imports/ro_combined_seed.tsv imports/ncbitaxon_combined_seed.tsv imports/uberon_combined_seed.tsv imports/iao_combined_seed.tsv imports/obi_combined_seed.tsv

cmungall · 2021-11-16T06:36:30Z

Sigh, I guess these crept in while we wre in the phase where we had no checking of PRs and things were merged in?

You you show explanations for each (robot explain)

The foodon ones are unusual - envo should not cause foodon to be unsatisfiable, could it be

superimposition of different releases
foodon latest release is incoherent

wdduncan · 2021-11-16T16:44:50Z

@cmungall I don't know the provenance of how the offenders made it into EnvO. I can create a ticket to focus on fixing these issues.

It is also worth noting that make test calls owltools. So that will have to be installed into the PR image.

cmungall · 2021-11-16T18:56:06Z

owltools is in ODK

cmungall · 2021-11-16T19:05:40Z

@ddooley ^^^

cmungall · 2021-11-16T19:06:50Z

do we have a ticket about removing the foodon import

currently it's only used in 3 places:

✗ grep FOODON envo-edit.owl | grep -v ^Ann
EquivalentClasses(<http://purl.obolibrary.org/obo/ENVO_01000929> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/ENVO_2100000> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002507> <http://purl.obolibrary.org/obo/FOODON_00001287>)))
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000047> <http://purl.obolibrary.org/obo/FOODON_00002403>)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000055> <http://purl.obolibrary.org/obo/FOODON_00002403>)

cmungall · 2021-11-16T20:01:06Z

@wdduncan I suggest for now we switch off equivalence checking, get this merged, and then make a PR to re-introduce it, which we do as soon as foodon is fixed

ddooley · 2021-11-17T18:19:38Z

Hmm. the hominy equivalence is wrong - probably intended to be a conjunction, not a disjunction but even so, still not sufficient differentia. I've dropped it and will do new release shortly.

ddooley · 2021-11-17T20:22:39Z

I have dropped the hominy equivalence; It may be that all the above "no equivalent axioms are allowed" items are eliminated as a result.

cmungall · 2022-01-18T18:23:17Z

This has become urgent - where do we stand with this?

ddooley · 2022-01-18T19:15:28Z

From FoodOn's side a refresh of that import should resolve equivalency issue.
But the larger decision of whether to import FoodOn remains. I know the import originally stemmed from wanting to maintain the presence of the 600+ food terms that ENVO originally had and then gave to FoodOn (with FoodOn ids). But I don't see why people shouldn't just utilize FoodOn directly for food items, just as they go to NCBITaxon for organisms.

wdduncan · 2022-01-21T20:20:33Z

@cmungall I updated the FOODON imports on my machine by running make imports/foodon_import.obo. This modified a number of files:

        modified:   imports/chebi_import.obo
	modified:   imports/chebi_import.owl
	modified:   imports/foodon_import.obo
	modified:   imports/foodon_import.owl
	modified:   imports/iao_import.obo
	modified:   imports/obi_import.obo
	modified:   imports/obi_import.owl
	modified:   imports/pato_import.obo
	modified:   imports/pato_import.owl
	modified:   imports/po_import.obo
	modified:   imports/po_import.owl

The number of files changed makes @ddooley and myself hesitant to push these changes to the repo. Also, we noticed that a number of FOODON classes were not properly placed in the ENVO hierarchy (see screenshot).

In any case, I ran make test using the new imports and the following errors were reported (comments added):

# fluid astronomical body part == compound astronomical body part
ERROR Equivalence: <http://purl.obolibrary.org/obo/ENVO_01001479> == <http://purl.obolibrary.org/obo/ENVO_01001784> 

# chebi:role == bfo:role
ERROR Equivalence: <http://purl.obolibrary.org/obo/CHEBI_50906> == <http://purl.obolibrary.org/obo/BFO_0000023>

Not sure what the best path forward is. One option is to relax the equivalent action check:

reason --reasoner ELK --equivalent-classes-allowed none --exclude-tautologies structural

merge the PR, and deal with the updates to FOODON in a separate PR.

cmungall · 2022-01-21T20:29:55Z

we noticed that a number of FOODON classes were not properly placed in the ENVO hierarchy (see screenshot).

This is already a problem: https://www.ebi.ac.uk/ols/ontologies/envo

let's not try and solve all problems with this PR. Adding github actions and fixing inconsistencies will be a major step forward. Let's get this merged ASAP then improve imports

cmungall · 2022-01-21T20:30:58Z

ERROR Equivalence: http://purl.obolibrary.org/obo/ENVO_01001479 == http://purl.obolibrary.org/obo/ENVO_01001784

didn't we solve this? Maybe a rebase would fix?

In any case, I agree with your strategy. Relax the constraints for now (we effectively have none now), then iterate

wdduncan · 2022-01-21T20:47:04Z

@cmungall Re After relaxing the equivalent classes check and running make test , the following errors were reported:

ERROR	duplicate_label_synonym	garden	has_exact_synonym	garden
ERROR	duplicate_label_synonym	ocean	has_exact_synonym	ocean
ERROR	duplicate_label_synonym	sea	has_exact_synonym	sea
ERROR	duplicate_label_synonym	stream	has_exact_synonym	stream
ERROR	duplicate_label_synonym	reservoir	has_exact_synonym	reservoir

These duplicate labels are related to synonyms that have a database cross reference to the Geonames:feature. E.g.:

Do you want me to fix these or relax this check too?

cmungall · 2022-01-21T20:56:06Z

I think we should fix synonyms as a separate Pr. there is an old ticket about this

…

On Fri, Jan 21, 2022 at 12:47 PM Bill Duncan ***@***.***> wrote: @cmungall <https://github.com/cmungall> Re After relaxing the equivalent classes check and running make test , the following errors were reported: ERROR duplicate_label_synonym garden has_exact_synonym garden ERROR duplicate_label_synonym ocean has_exact_synonym ocean ERROR duplicate_label_synonym sea has_exact_synonym sea ERROR duplicate_label_synonym stream has_exact_synonym stream ERROR duplicate_label_synonym reservoir has_exact_synonym reservoir These duplicate labels are related to synonyms that have a database cross reference to the Geonames:feature. E.g.: [image: image] <https://user-images.githubusercontent.com/3186638/150597956-7143e741-72a2-49e0-9070-728265626c02.png> Do you want me to fix these or relax this check too? — Reply to this email directly, view it on GitHub <#1240 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMOKWZUG6IFCZVMZGNDDUXHA5JANCNFSM5IDCH3QQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

add qc workflow

3f44d9f

wdduncan requested a review from cmungall November 16, 2021 01:38

update path to makefile

98003bf

wdduncan marked this pull request as draft November 16, 2021 17:01

cmungall mentioned this pull request Nov 16, 2021

compound and fluid astronomical body parts have the same logical def leading to equivalence #1241

Open

This was referenced Nov 16, 2021

remove foodon import #945

Open

incorrect equivalence axiom for hominy FoodOntology/foodon#163

Closed

Merge branch 'master' into add-qc-workflow

510585c

set --equivalent-classes-allowed all

2051516

wdduncan marked this pull request as ready for review January 21, 2022 21:17

cmungall approved these changes Jan 21, 2022

View reviewed changes

wdduncan merged commit f48f8ec into master Jan 21, 2022

wdduncan deleted the add-qc-workflow branch January 21, 2022 23:21

wdduncan mentioned this pull request Jan 28, 2022

update FOODON import #1285

Closed

This was referenced Jan 28, 2022

remove duplicate synonyms #1286

Closed

Issue 1286: remove exact synonyms that match label #1289

Merged

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

add qc workflow #1240

add qc workflow #1240

wdduncan commented Nov 16, 2021

wdduncan commented Nov 16, 2021

cmungall commented Nov 16, 2021

wdduncan commented Nov 16, 2021

cmungall commented Nov 16, 2021

cmungall commented Nov 16, 2021 •

edited

cmungall commented Nov 16, 2021

cmungall commented Nov 16, 2021

ddooley commented Nov 17, 2021

ddooley commented Nov 17, 2021

cmungall commented Jan 18, 2022

ddooley commented Jan 18, 2022

wdduncan commented Jan 21, 2022

cmungall commented Jan 21, 2022

cmungall commented Jan 21, 2022

wdduncan commented Jan 21, 2022

cmungall commented Jan 21, 2022 via email

add qc workflow #1240

add qc workflow #1240

Conversation

wdduncan commented Nov 16, 2021

wdduncan commented Nov 16, 2021

cmungall commented Nov 16, 2021

wdduncan commented Nov 16, 2021

cmungall commented Nov 16, 2021

cmungall commented Nov 16, 2021 • edited

cmungall commented Nov 16, 2021

cmungall commented Nov 16, 2021

ddooley commented Nov 17, 2021

ddooley commented Nov 17, 2021

cmungall commented Jan 18, 2022

ddooley commented Jan 18, 2022

wdduncan commented Jan 21, 2022

cmungall commented Jan 21, 2022

cmungall commented Jan 21, 2022

wdduncan commented Jan 21, 2022

cmungall commented Jan 21, 2022 via email

cmungall commented Nov 16, 2021 •

edited