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obophenotype / provisional_cell_ontology

Draft cell type definitions from data - candidates for inclusion in CL
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Errors after Base Import #25

Closed shawntanzk closed 2 years ago

shawntanzk commented 2 years ago

I created a release to check ROBOT report with base file import and a few errors that need to be addressed:

RO and BFO terms have multiplied labels with @en attached, example: (of note: RO:000053 still has old bearer_of label) Not sure where this is coming from cause on RO it seems alright

Level Rule Name Subject Property Value
ERROR multiple_labels BFO:0000063 rdfs:label precedes
ERROR multiple_labels BFO:0000063 rdfs:label precedes@en
ERROR multiple_labels BFO:0000066 rdfs:label occurs in
ERROR multiple_labels BFO:0000066 rdfs:label occurs in@en
ERROR multiple_labels BFO:0000067 rdfs:label contains process
ERROR multiple_labels BFO:0000067 rdfs:label contains process@en
ERROR multiple_labels RO:0000053 rdfs:label bearer of
ERROR multiple_labels RO:0000053 rdfs:label has characteristic@en
ERROR multiple_labels RO:0000056 rdfs:label participates in
ERROR multiple_labels RO:0000056 rdfs:label participates in@en
ERROR multiple_labels RO:0000056 rdfs:label participates_in

UBERON has some multipled_equivalent_classes error - these are accurate in UBERON itself:

Level Rule Name Subject Property Value
ERROR multiple_equivalent_classes UBERON:0000378 owl:equivalentClass d80df3fa-9c13-4d2d-a88d-131d173f5c69genid46142
ERROR multiple_equivalent_classes UBERON:0000378 owl:equivalentClass d80df3fa-9c13-4d2d-a88d-131d173f5c69genid46146
ERROR multiple_equivalent_classes UBERON:0000483 owl:equivalentClass d80df3fa-9c13-4d2d-a88d-131d173f5c69genid46389
ERROR multiple_equivalent_classes UBERON:0000483 owl:equivalentClass d80df3fa-9c13-4d2d-a88d-131d173f5c69genid46393
ERROR multiple_equivalent_classes UBERON:0004451 owl:equivalentClass d80df3fa-9c13-4d2d-a88d-131d173f5c69genid55460
ERROR multiple_equivalent_classes UBERON:0004451 owl:equivalentClass d80df3fa-9c13-4d2d-a88d-131d173f5c69genid55464
ERROR multiple_equivalent_classes UBERON:0015007 owl:equivalentClass d80df3fa-9c13-4d2d-a88d-131d173f5c69genid62199
ERROR multiple_equivalent_classes UBERON:0015007 owl:equivalentClass d80df3fa-9c13-4d2d-a88d-131d173f5c69genid62203
ERROR multiple_equivalent_classes UBERON:0015008 owl:equivalentClass d80df3fa-9c13-4d2d-a88d-131d173f5c69genid62211
ERROR multiple_equivalent_classes UBERON:0015008 owl:equivalentClass d80df3fa-9c13-4d2d-a88d-131d173f5c69genid62215
ERROR multiple_equivalent_classes UBERON:0018142 owl:equivalentClass d80df3fa-9c13-4d2d-a88d-131d173f5c69genid62607
ERROR multiple_equivalent_classes UBERON:0018142 owl:equivalentClass d80df3fa-9c13-4d2d-a88d-131d173f5c69genid62611
shawntanzk commented 2 years ago

Related to #16

matentzn commented 2 years ago

Make sure these are fixe wherever they come from, not just in PCL

also use ROBOT 1.8.2 (latest ODK) for generating the report.

Recommendation: do the report check on the base, not the edit file (neither the full ontology)

shawntanzk commented 2 years ago

on base file, only error (besides the duplicate_label in gene names and old false CL terms) is that CL:0000881 is missing_label -> on checking the full and edit file, the label is there so don't think its a real problem.

matentzn commented 2 years ago

Don't worry about anything else. OBO dashboard looks at base

shawntanzk commented 2 years ago

CL:0000881 is a old pcl term - annotations will get cleared when it gets deleted and robot report will clean

shawntanzk commented 2 years ago

All local errors fixed