adding hormion

[meghalithic]

issue #2573

[github-actions[bot]]

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/2022-09-30/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/2022-09-30/uberon-simple.owl
• Loaded from: file:/work/src/ontology/uberon-simple.owl

Ontology imports

Ontology annotations

UBERON_7500106 http://purl.obolibrary.org/obo/UBERON_7500106

Added

• UBERON_7500106 has_obo_namespace "uberon"

• UBERON_7500106 definition "A craniometric point at the junction of the posterior midline border of the vomer with the sphenoid bone on the sphenovomerine suture."

  • database_cross_reference "ISBN:9780873659505"

  • database_cross_reference "https://locatelambda.org/manual"

  • database_cross_reference "https://medical-dictionary.thefreedictionary.com/hormion"

• UBERON_7500106 depicted by "http://locatelambda.org/wp-content/uploads/2018/02/hormion.jpg"

• UBERON_7500106 contributor 0000-0001-8415-4848

• UBERON_7500106 id "UBERON:7500106"

• UBERON_7500106 contributor 0000-0003-2699-3066

• UBERON_7500106 label "hormion"

• Class: UBERON_7500106

• UBERON_7500106 SubClassOf part_of some sphenovomerine suture

• UBERON_7500106 SubClassOf anatomical point

[github-actions[bot]]

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/../../master/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/uberon-edit.obo

Ontology imports

Ontology annotations

UBERON_7500106 http://purl.obolibrary.org/obo/UBERON_7500106

Added

• UBERON_7500106 has_obo_namespace "uberon"^^string

• UBERON_7500106 definition "A craniometric point at the junction of the posterior midline border of the vomer with the sphenoid bone on the sphenovomerine suture."^^string

  • database_cross_reference "ISBN:9780873659505"^^string

  • database_cross_reference "https://medical-dictionary.thefreedictionary.com/hormion"^^string

  • database_cross_reference "https://locatelambda.org/manual"^^string

• UBERON_7500106 depicted by "http://locatelambda.org/wp-content/uploads/2018/02/hormion.jpg"^^string

• UBERON_7500106 contributor 0000-0001-8415-4848

• UBERON_7500106 id "UBERON:7500106"^^string

• UBERON_7500106 contributor 0000-0003-2699-3066

• UBERON_7500106 label "hormion"^^string

• Class: UBERON_7500106

• UBERON_7500106 SubClassOf part_of some sphenovomerine suture

• UBERON_7500106 SubClassOf anatomical point

[shawntanzk]

Error is from term being unsat. Running:

% robot --catalog catalog-v001.xml merge -i tmp/uberon-edit.owl -I http://purl.obolibrary.org/obo/bfo.owl -I http://purl.obolibrary.org/obo/ro.owl -i bridge/uberon-bridge-to-bfo.owl --output test.owl 
shawntan@C02DW26DML87 /Users/shawntan/documents/GitHub/uberon/src/ontology [issue-2573]
% robot explain -i test.owl -M unsatisfiability --unsatisfiable random:10 --explanation unsat.md

Output:

hormion SubClassOf Nothing

• hormion SubClassOf zone of bone organ
  • zone of bone organ SubClassOf composed primarily of some bone tissue
    • composed primarily of Domain material entity
• hormion SubClassOf anatomical point
  • anatomical point SubClassOf immaterial anatomical entity
    • immaterial anatomical entity SubClassOf immaterial entity
• material entity DisjointWith immaterial entity

Axiom Impact

Axioms used 1 times

• immaterial anatomical entity SubClassOf immaterial entity [core.owl]
• zone of bone organ SubClassOf composed primarily of some bone tissue [core.owl]
• anatomical point SubClassOf immaterial anatomical entity [core.owl]
• hormion SubClassOf zone of bone organ [core.owl]
• hormion SubClassOf anatomical point [core.owl]
• material entity DisjointWith immaterial entity [core.owl]
• composed primarily of Domain material entity [core.owl]

Ontologies used:

• core.owl (http://purl.obolibrary.org/obo/uberon/core.owl)

[meghalithic]

@shawntanzk I do not get that same error when I run the reasoner (ELK).

Jugal point (UBERON:0013423) is classified the same way.

[shawntanzk]

The unsat is not from uberon-edit itself but a product that is used for the report tha the QC uses to check something. Seems to merge uberon-edit with bfo, ro, and bfo bridge. Not sure about the other term, will check again next week, but probably still need to fix the unsat

[shawntanzk]

@megbalk

I think this is your offending axiom: UBERON_7500106 SubClassOf zone of bone organ

From my understand of your PR, hormion is a point which is immaterial. However zone of bone organ is a material thing - it refers to an actual bone structure itself.

I assume this axiom would cause issue too:

UBERON_7500106 SubClassOf mesoderm-derived structure

Perhaps consider using 'part of' instead of subclass

[meghalithic]

fixed!

[meghalithic]

@shawntanzk do my changes look ok?

[shawntanzk]

QC checks have passed, I'll leave @bvarner-ebi to review content :) thanks

[meghalithic]

@shawntanzk @bvarner-ebi could one of you review this, please?

[shawntanzk]

@bvarner-ebi - hope its ok if I leave you to do the final review for this. Thanks

[meghalithic]

@bvarner-ebi here is a link to the dbxref: https://www.biblio.com/9780873659505. Let me know if I need to change how I'm reporting as this has been an issue before

I don't mind the definition provided by https://locatelambda.org/manual, but I do want to note that it is on the suture.