Fixes #2407 NTR sublumbar lymph node

[ghost]

Fixes #2407 NTR sublumbar lymph node

[ghost]

@shawntanzk, this term is from the robot template you created. I wanted to make some movement on this group of new term requests, so I am starting to manually add them until I get trained on robot. I also find it easier to curate these manually in Protégé instead of in a spreadsheet.
As more are added manually, I'll remove them from the template.

[shawntanzk]

sure totally up to you, but if you want me to just get them all in in a branch using robot template, happy to do so

[ghost]

sure totally up to you, but if you want me to just get them all in in a branch using robot template, happy to do so

Several terms on the present list require some clarifications, so will hold off on a batch addition for now. Once there is a list with straightforward entries, I'd like to learn how to add them via robot commands.

[ghost]

Thanks, @shawntanzk. Does this term seem ready to merge?

[shawntanzk]

your QC failed, so no, I'm running a release atm so I can't help check whats going wrong, but I'm guessing its:

property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-1773-2692
property_value: http://purl.org/dc/elements/1.1/date 2022-05-26T11:59:51Z xsd:dateTime

these should be dc terms instead of dc elements

[ghost]

these should be dc terms instead of dc elements

Yes, now I remember. Can / should we remove the dc elements property values from Protégé if they are not meant to be selected?

[github-actions]

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-05-30/uberon-simple.owl
• Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-simple.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-05-30/uberon-simple.owl
• Loaded from: file:/work/src/ontology/uberon-simple.owl

Ontology imports

Ontology annotations

UBERON_8470001 http://purl.obolibrary.org/obo/UBERON_8470001

Added

• UBERON_8470001 date "2022-05-26T11:59:51Z"^^dateTime

• UBERON_8470001 contributor 0000-0002-1773-2692

• UBERON_8470001 label "sublumbar lymph node"

• UBERON_8470001 has_obo_namespace "uberon"

• UBERON_8470001 id "UBERON:8470001"

• UBERON_8470001 definition "A lymph node with a lymph center located within the caudal abdomen and pelvis, on the ventral side of the lumbar region. Includes the medial iliac, internal iliac (previously termed hypogastric) and sacral lymph nodes."

  • database_cross_reference "PMID:32655159"

  • database_cross_reference "NCIT:C77655"

  • database_cross_reference "https://orcid.org/0000-0002-0819-0473"

• Class: UBERON_8470001

• UBERON_8470001 SubClassOf lymph node

internal iliac lymph node http://purl.obolibrary.org/obo/UBERON_0015881

Added

• internal iliac lymph node SubClassOf UBERON_8470001

medial common iliac lymph node http://purl.obolibrary.org/obo/UBERON_0037532

Added

• medial common iliac lymph node SubClassOf UBERON_8470001

sacral lymph node http://purl.obolibrary.org/obo/UBERON_0002528

Removed

• sacral lymph node SubClassOf lymph node

Added

• sacral lymph node SubClassOf UBERON_8470001

[github-actions]

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/work/src/ontology/uberon-edit.obo

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-edit.obo

Ontology imports

Ontology annotations

internal iliac lymph node http://purl.obolibrary.org/obo/UBERON_0015881

Removed

• internal iliac lymph node SubClassOf sublumbar lymph node

medial common iliac lymph node http://purl.obolibrary.org/obo/UBERON_0037532

Removed

• medial common iliac lymph node SubClassOf sublumbar lymph node

sacral lymph node http://purl.obolibrary.org/obo/UBERON_0002528

Removed

• sacral lymph node SubClassOf sublumbar lymph node

sublumbar lymph node http://purl.obolibrary.org/obo/UBERON_8470001

Removed

• sublumbar lymph node definition "A lymph node with a lymph center located within the caudal abdomen and pelvis, on the ventral side of the lumbar region. Includes the medial iliac, internal iliac (previously termed hypogastric) and sacral lymph nodes."^^string

  • database_cross_reference "PMID:32655159"^^string

  • database_cross_reference "https://orcid.org/0000-0002-0819-0473"^^[string](http://www.w3.org/2001/XMLSchema#string)

  • database_cross_reference "NCIT:C77655"^^string

• sublumbar lymph node contributor 0000-0002-1773-2692

• sublumbar lymph node has_obo_namespace "uberon"^^string

• sublumbar lymph node label "sublumbar lymph node"^^string

• sublumbar lymph node date "2022-05-26T11:59:51Z"^^dateTime

• sublumbar lymph node id "UBERON:8470001"^^string

• Class: sublumbar lymph node

• sublumbar lymph node SubClassOf lymph node

[shawntanzk]

Can / should we remove the dc elements property values from Protégé if they are not meant to be selected?

don't think we can - this rule is specific to the ontologies we care about only, so making a change on protege isn't possible. However, I'm not sure how protege populates the annotations list and which it highlights, think it has something to do with what is declared in the file, though not sure how that works with obo file format. Anyway that's the reason the check is there so that it picks it up before going through :)