Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

multiple_equivalent_classes error #2130

Closed
shawntanzk opened this issue Oct 26, 2021 · 6 comments · Fixed by #2309
Closed

multiple_equivalent_classes error #2130

shawntanzk opened this issue Oct 26, 2021 · 6 comments · Fixed by #2309
Assignees
@matentzn @shawntanzk
Labels
tech

Comments

@shawntanzk
Copy link
Collaborator

Checking the report for sh run.sh make reports/uberon-edit.obo-obo-report.tsv, the other errors are multiple_equivalent_classes
Here are a few examples of them:

<style> </style>
ERROR multiple_equivalent_classes tongue muscle owl:equivalentClass 9ab79cd9-67ba-4234-8df4-ca3f4d8334b1genid2261
ERROR multiple_equivalent_classes tongue muscle owl:equivalentClass 9ab79cd9-67ba-4234-8df4-ca3f4d8334b1genid2265
ERROR multiple_equivalent_classes epithelium owl:equivalentClass 9ab79cd9-67ba-4234-8df4-ca3f4d8334b1genid3006
ERROR multiple_equivalent_classes epithelium owl:equivalentClass 9ab79cd9-67ba-4234-8df4-ca3f4d8334b1genid3010
ERROR multiple_equivalent_classes trunk or cervical vertebra owl:equivalentClass 9ab79cd9-67ba-4234-8df4-ca3f4d8334b1genid39930
ERROR multiple_equivalent_classes trunk or cervical vertebra owl:equivalentClass 9ab79cd9-67ba-4234-8df4-ca3f4d8334b1genid39934
ERROR multiple_equivalent_classes cervical vertebra endochondral element owl:equivalentClass 9ab79cd9-67ba-4234-8df4-ca3f4d8334b1genid79937
ERROR multiple_equivalent_classes cervical vertebra endochondral element owl:equivalentClass 9ab79cd9-67ba-4234-8df4-ca3f4d8334b1genid79941
ERROR multiple_equivalent_classes thoracic vertebra endochondral element owl:equivalentClass 9ab79cd9-67ba-4234-8df4-ca3f4d8334b1genid79948
ERROR multiple_equivalent_classes thoracic vertebra endochondral element owl:equivalentClass 9ab79cd9-67ba-4234-8df4-ca3f4d8334b1genid79952
ERROR multiple_equivalent_classes lumbar vertebra endochondral element owl:equivalentClass 9ab79cd9-67ba-4234-8df4-ca3f4d8334b1genid79959
ERROR multiple_equivalent_classes lumbar vertebra endochondral element owl:equivalentClass 9ab79cd9-67ba-4234-8df4-ca3f4d8334b1genid79963
@matentzn
Copy link
Contributor

This issue should be revisited when ROBOT 1.9 is released. The multiple_equivalent_classes check is much too strict in ROBOT 1.8.1

@shawntanzk shawntanzk added the blocked blocked by another issue label Oct 26, 2021
@cmungall
Copy link
Member

cmungall commented Nov 1, 2021

yes - these are all caused by an additional unonOf eq axiom on top of the defining genus-different eq axiom

@shawntanzk
Copy link
Collaborator Author

  • when ROBOT 1.9 is released, reinstate test

@matentzn
Copy link
Contributor

@shawntanzk We are ready to try this again I think, no need to wait for the next ODK.

@shawntanzk
Copy link
Collaborator Author

shawntanzk commented Feb 16, 2022 •
edited
Loading

ran sh run.sh make reports/uberon-edit.obo-obo-report.tsv and seems the errors are gone:

Violations: 7899
-----------------
ERROR:      0
WARN:       4894
INFO:       3005

First 5 violations:
WARN	duplicate_definition	UBERON:0000089	IAO:0000115	.
WARN	duplicate_definition	UBERON:0000219	IAO:0000115	.
WARN	duplicate_definition	UBERON:0000444	IAO:0000115	.
WARN	duplicate_definition	UBERON:0001430	IAO:0000115	.
WARN	duplicate_definition	UBERON:0001431	IAO:0000115	.

TSV has not more multiple_equivalent_classes error

@shawntanzk shawntanzk removed the blocked blocked by another issue label Feb 16, 2022
@shawntanzk
Copy link
Collaborator Author

btws related to #2305, heaps of these, a few examples:

<style> </style>
WARN duplicate_scoped_synonym UBERON:0034752 oboInOwl:hasExactSynonym second auditory area
WARN duplicate_scoped_synonym UBERON:0034752 oboInOwl:hasRelatedSynonym second auditory area
WARN duplicate_scoped_synonym UBERON:0034753 oboInOwl:hasExactSynonym inferior occipitofrontal fasciculus
WARN duplicate_scoped_synonym UBERON:0034753 oboInOwl:hasRelatedSynonym inferior occipitofrontal fasciculus
WARN duplicate_scoped_synonym UBERON:0034771 oboInOwl:hasBroadSynonym commissural nucleus of spinal cord
WARN duplicate_scoped_synonym UBERON:0034771 oboInOwl:hasExactSynonym commissural nucleus of spinal cord
WARN duplicate_scoped_synonym UBERON:0034771 oboInOwl:hasRelatedSynonym commissural nucleus of spinal cord
WARN duplicate_scoped_synonym UBERON:0034892 oboInOwl:hasExactSynonym granular insula
WARN duplicate_scoped_synonym UBERON:0034892 oboInOwl:hasRelatedSynonym granular insula
WARN duplicate_scoped_synonym UBERON:0034893 oboInOwl:hasExactSynonym dysgranular insular cortex
WARN duplicate_scoped_synonym UBERON:0034893 oboInOwl:hasRelatedSynonym dysgranular insular cortex
WARN duplicate_scoped_synonym UBERON:0034986 oboInOwl:hasExactSynonym plexus sacralis
WARN duplicate_scoped_synonym UBERON:0034986 oboInOwl:hasRelatedSynonym plexus sacralis
WARN duplicate_scoped_synonym UBERON:0034987 oboInOwl:hasExactSynonym plexus lumbalis
WARN duplicate_scoped_synonym UBERON:0034987 oboInOwl:hasRelatedSynonym plexus lumbalis

@matentzn matentzn mentioned this issue Feb 16, 2022
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@matentzn matentzn

@shawntanzk shawntanzk

Labels
tech
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

Increase severity of QC test obophenotype/uberon
4 participants
@cmungall @anitacaron @matentzn @shawntanzk