Fixing ROBOT report errors before merging ODK branch

[matentzn]

@rays22 Could you try to fix the following robot report errors? I think they are only about 20 errors (not 100), they just keep repeating themselves. Here is what I think:

1. The same class or similar class has been added accidentally. If that is so, you can inspect them in the spreadsheet (also, check out oba and look at oba-edit.owl on the branch).
2. If a trait appears duplicated, you remove one of the two (favour removal of OBA:... classes over OBA:VT... classes). The one you remove, you add it to the src/templates/replaced.tsv table

Fix errors:

Level	Rule Name	Subject	Property	Value
ERROR	duplicate_definition	vocalization behavior quality	definition	The quality of a vocalization behavior.
ERROR	duplicate_definition	vocalization trait	definition	The quality of a vocalization behavior.
ERROR	duplicate_definition	parental behavior quality	definition	The quality of a parental behavior.
ERROR	duplicate_definition	parental behavior trait	definition	The quality of a parental behavior.
ERROR	duplicate_definition	grooming behavior quality	definition	The quality of a grooming behavior.
ERROR	duplicate_definition	grooming behavior trait	definition	The quality of a grooming behavior.
ERROR	duplicate_definition	cilium morphology	definition	The morphology of a cilium.
ERROR	duplicate_definition	cilium morphology	definition	The morphology of a cilium.
ERROR	duplicate_definition	basement membrane morphology	definition	The morphology of a basement membrane.
ERROR	duplicate_definition	basement membrane morphology trait	definition	The morphology of a basement membrane.
ERROR	duplicate_definition	cilium functionality	definition	The functionality of a cilium.
ERROR	duplicate_definition	cilium functionality	definition	The functionality of a cilium.
ERROR	duplicate_definition	protein amount	definition	The amount of a protein.
ERROR	duplicate_definition	protein amount	definition	The amount of a protein.
ERROR	missing_label	OBA:0000001	rdfs:label
ERROR	missing_label	OBA:0000037	rdfs:label
ERROR	missing_label	OBA:0000039	rdfs:label
ERROR	missing_label	OBA:0000069	rdfs:label
ERROR	missing_label	OBA:0000085	rdfs:label
ERROR	missing_label	OBA:0000089	rdfs:label
ERROR	missing_label	OBA:0000121	rdfs:label
ERROR	missing_label	OBA:0000134	rdfs:label
ERROR	missing_label	OBA:0000136	rdfs:label
ERROR	missing_label	OBA:0000140	rdfs:label
ERROR	missing_label	OBA:0000141	rdfs:label
ERROR	missing_label	OBA:0000181	rdfs:label
ERROR	missing_label	OBA:0001001	rdfs:label
ERROR	misused_obsolete_label	obsolete heart contraction rate	rdfs:label	obsolete heart contraction rate
ERROR	misused_obsolete_label	obsolete death onset quality	rdfs:label	obsolete death onset quality
ERROR	misused_obsolete_label	obsolete cell functionality	rdfs:label	obsolete cell functionality
ERROR	misused_obsolete_label	obsolete cell nucleate quality	rdfs:label	obsolete cell nucleate quality
ERROR	misused_obsolete_label	obsolete cell ploidy	rdfs:label	obsolete cell ploidy
ERROR	misused_obsolete_label	obsolete podocyte foot process morphology	rdfs:label	obsolete podocyte foot process morphology
ERROR	misused_obsolete_label	obsolete podocyte foot process amount	rdfs:label	obsolete podocyte foot process amount
ERROR	misused_obsolete_label	obsolete magnocellular neurosecretory cell morphology	rdfs:label	obsolete magnocellular neurosecretory cell morphology
ERROR	misused_obsolete_label	obsolete magnocellular neurosecretory cell altered number of	rdfs:label	obsolete magnocellular neurosecretory cell altered number of
ERROR	misused_obsolete_label	obsolete respiratory system quality	rdfs:label	obsolete respiratory system quality
ERROR	misused_obsolete_label	obsolete reproductive system quality	rdfs:label	obsolete reproductive system quality
ERROR	misused_obsolete_label	obsolete nervous system quality	rdfs:label	obsolete nervous system quality
ERROR	misused_obsolete_label	obsolete glial cell (sensu Vertebrata) quality	rdfs:label	obsolete glial cell (sensu Vertebrata) quality
ERROR	misused_obsolete_label	obsolete cell morphology	rdfs:label	obsolete cell morphology
ERROR	misused_obsolete_label	obsolete paw/hand/foot/hoof morphology trait	rdfs:label	obsolete paw/hand/foot/hoof morphology trait
ERROR	duplicate_label	thymus mass	rdfs:label	thymus mass
ERROR	duplicate_label	thymus mass	rdfs:label	thymus mass
ERROR	duplicate_label	spleen mass	rdfs:label	spleen mass
ERROR	duplicate_label	spleen mass	rdfs:label	spleen mass
ERROR	duplicate_label	protein amount	rdfs:label	protein amount
ERROR	duplicate_label	protein amount	rdfs:label	protein amount
ERROR	duplicate_label	placenta mass	rdfs:label	placenta mass
ERROR	duplicate_label	placenta mass	rdfs:label	placenta mass
ERROR	duplicate_label	ovary mass	rdfs:label	ovary mass
ERROR	duplicate_label	ovary mass	rdfs:label	ovary mass
ERROR	duplicate_label	lung mass	rdfs:label	lung mass
ERROR	duplicate_label	lung mass	rdfs:label	lung mass
ERROR	duplicate_label	liver mass	rdfs:label	liver mass
ERROR	duplicate_label	liver mass	rdfs:label	liver mass
ERROR	duplicate_label	kidney mass	rdfs:label	kidney mass
ERROR	duplicate_label	kidney mass	rdfs:label	kidney mass
ERROR	duplicate_label	heart mass	rdfs:label	heart mass
ERROR	duplicate_label	heart mass	rdfs:label	heart mass
ERROR	duplicate_label	cilium morphology	rdfs:label	cilium morphology
ERROR	duplicate_label	cilium morphology	rdfs:label	cilium morphology
ERROR	duplicate_label	cilium functionality	rdfs:label	cilium functionality
ERROR	duplicate_label	cilium functionality	rdfs:label	cilium functionality
ERROR	duplicate_label	brain mass	rdfs:label	brain mass
ERROR	duplicate_label	brain mass	rdfs:label	brain mass
ERROR	duplicate_label	aorta mass	rdfs:label	aorta mass
ERROR	duplicate_label	aorta mass	rdfs:label	aorta mass
ERROR	duplicate_label	abdominal fat pad mass	rdfs:label	abdominal fat pad mass
ERROR	duplicate_label	abdominal fat pad mass	rdfs:label	abdominal fat pad mass
WARN	duplicate_exact_synonym	vocalization behavior quality	has_exact_synonym	quality of vocalization behavior
WARN	duplicate_exact_synonym	vocalization trait	has_exact_synonym	quality of vocalization behavior
WARN	duplicate_exact_synonym	parental behavior quality	has_exact_synonym	quality of parental behavior
WARN	duplicate_exact_synonym	parental behavior trait	has_exact_synonym	quality of parental behavior
WARN	duplicate_exact_synonym	grooming behavior quality	has_exact_synonym	quality of grooming behavior
WARN	duplicate_exact_synonym	grooming behavior trait	has_exact_synonym	quality of grooming behavior
WARN	duplicate_exact_synonym	cilium morphology	has_exact_synonym	morphology of cilium
WARN	duplicate_exact_synonym	cilium morphology	has_exact_synonym	morphology of cilium
WARN	duplicate_exact_synonym	basement membrane morphology	has_exact_synonym	morphology of basement membrane
WARN	duplicate_exact_synonym	basement membrane morphology trait	has_exact_synonym	morphology of basement membrane
WARN	duplicate_exact_synonym	cilium functionality	has_exact_synonym	functionality of cilium
WARN	duplicate_exact_synonym	cilium functionality	has_exact_synonym	functionality of cilium
WARN	duplicate_exact_synonym	protein amount	has_exact_synonym	amount of protein
WARN	duplicate_exact_synonym	protein amount	has_exact_synonym	amount of protein
WARN	missing_definition	OBA:0000001	definition
WARN	missing_definition	OBA:0000037	definition
WARN	missing_definition	OBA:0000039	definition
WARN	missing_definition	OBA:0000069	definition
WARN	missing_definition	obsolete heart contraction rate	definition
WARN	missing_definition	OBA:0000085	definition
WARN	missing_definition	OBA:0000089	definition
WARN	missing_definition	OBA:0000121	definition
WARN	missing_definition	OBA:0000134	definition
WARN	missing_definition	OBA:0000136	definition
WARN	missing_definition	OBA:0000140	definition
WARN	missing_definition	OBA:0000141	definition
WARN	missing_definition	OBA:0000181	definition
WARN	missing_definition	OBA:0001001	definition

[dosumis]

@matentzn - looks like most of these are imports. Can we turn strict SPARQL checks off for imported terms? There's no accounting for what minor checks might fail in an ontology we import from.

[matentzn]

Which one of these are imports? I only pasted those errors that appear to relate directly to OBA!

[dosumis]

Sorry - misunderstood labels.

Note - looks like more obsolete terms coming through

ERROR	misused_obsolete_label	obsolete cell ploidy	rdfs:label	obsolete cell ploidy

comes from GO:Cell which is now obsolete

[matentzn]

Yes exactly.. My previous strategy to identify these by eye, missed these.

[matentzn]

@rays22 Let me know when you are done with this, so I can proceed to merge :) Thank yoU!

[rays22]

@matentzn , I have pushed a commit with a new src/templates/replaced.tsv that tries to fix the errors. Does it look OK? I was not sure how to deal with the missing_label errors. My plan is to add back the missing labels. I am also trying to obsolete two terms without any replacement terms, it that is OK.

Ontology ID Type    Label   Obsolete    Replacement Term
ID  TYPE    A rdfs:label    AT owl:deprecated^^xsd:boolean  AI IAO:0100001
http://purl.obolibrary.org/obo/OBA_0002455  owl:Class   obsolete death onset quality    TRUE
http://purl.obolibrary.org/obo/OBA_1000873  owl:Class   obsolete glial cell (sensu Vertebrata) quality  TRUE

[rays22]

Update and remaining tasks

Fixed:

• [x] obsolete fillers (misused_obsolete_label) from external ontologies in .../patterns/data/default/attribute_location.tsv, .../patterns/data/default/entity_attribute.tsv, .../patterns/data/default/entity_attribute_location.tsv

• [x] duplicate_definition errors by using ...src/templates/replaced.tsv

• ---

  Remaining tasks:

• [x] fix missing label errors

• [x] fix duplicate_label errors Decided not to add obsolete prefix to duplicate labels.