Fixes #3411 to revise 'mesosalpinx' textual/logical definition, synonyms and oviduct synonyms

[aleixpuigb]

Fixes #3411

While I was addressing the ticket I was conflicted if structures related to uterine tubes should have a different term for humans, since many synonyms make reference to fallopian tube. My decision was to keep them as exact synonyms (after all, uterine tube is an exact synonym of fallopian tube).

Therefore, I believe serosa of fallopian tube should be merged into mesosalpinx.

[aleixpuigb]

#gogoeditdiff

[github-actions]

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

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-base.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2024-11-12/uberon-base.owl
• Loaded from: file:/__w/uberon/uberon/src/ontology/uberon-base-main.owl/uberon-base.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-base.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2024-11-12/uberon-base.owl
• Loaded from: file:/__w/uberon/uberon/src/ontology/uberon-base-pr.owl/uberon-base.owl

Ontology imports

Ontology annotations

fallopian tube http://purl.obolibrary.org/obo/UBERON_0003889

Removed

• fallopian tube hasRelatedSynonym "fallopian tubes"

• fallopian tube hasExactSynonym "mammalian oviduct"

  • hasDbXref "https://sourceforge.net/p/geneontology/ontology-requests/8397/"

Added

• fallopian tube hasRelatedSynonym "fallopian tubes"

  • hasSynonymType OMO_0003004

• fallopian tube hasBroadSynonym "mammalian oviduct"

  • hasDbXref "https://sourceforge.net/p/geneontology/ontology-requests/8397/"

mesosalpinx http://purl.obolibrary.org/obo/UBERON_0012331

Removed

• mesosalpinx IAO_0000115 "The mesosalpinx is part of the lining of the abdominal cavity in higher vertebrates, specifically the portion of the broad ligament that stretches from the uterine tube to the level of the ovary."
  • hasDbXref "Wikipedia:Mesosalpinx"

Added

• mesosalpinx IAO_0000115 "A serous layer that is part of the peritoneal lining of the abdominal cavity in higher vertebrates, specifically the portion of the broad ligament that stretches from the uterine (fallopian) tube to the ovary. It is made up of epithelial cells of mesothelium and a mesh of serous membrane lining."

  • hasDbXref "Wikipedia:Mesosalpinx"

  • hasDbXref "PMID:29763118"

• mesosalpinx hasExactSynonym "serous layer of fallopian tube"

  • hasDbXref "doi:10.1016/B978-0-12-801238-3.64401-X"

• mesosalpinx hasExactSynonym "fallopian tube mesosalpinx"

• mesosalpinx hasExactSynonym "mesentery of fallopian tube"

  • hasDbXref "PMID:29763118"

• mesosalpinx hasExactSynonym "mesentery of uterine tube"

  • hasDbXref "PMID:29763118"

• mesosalpinx SubClassOf RO_0002221 some fallopian tube

oviduct http://purl.obolibrary.org/obo/UBERON_0000993

Removed

• oviduct hasExactSynonym "uterine tube"

Added

• oviduct hasNarrowSynonym "uterine tube"

[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:/__w/uberon/uberon/master/src/ontology/uberon-edit.obo

Right

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

Ontology imports

Ontology annotations

fallopian tube http://purl.obolibrary.org/obo/UBERON_0003889

Removed

• fallopian tube has_related_synonym "fallopian tubes"^^string

• fallopian tube has exact synonym "mammalian oviduct"^^string

  • database_cross_reference "https://sourceforge.net/p/geneontology/ontology-requests/8397/"^^[string](http://www.w3.org/2001/XMLSchema#string)

Added

• fallopian tube has_related_synonym "fallopian tubes"^^string

  • has_synonym_type plural form

• fallopian tube has_broad_synonym "mammalian oviduct"^^string

  • database_cross_reference "https://sourceforge.net/p/geneontology/ontology-requests/8397/"^^[string](http://www.w3.org/2001/XMLSchema#string)

mesosalpinx http://purl.obolibrary.org/obo/UBERON_0012331

Removed

• mesosalpinx definition "The mesosalpinx is part of the lining of the abdominal cavity in higher vertebrates, specifically the portion of the broad ligament that stretches from the uterine tube to the level of the ovary."^^string
  • database_cross_reference "Wikipedia:Mesosalpinx"^^string

Added

• mesosalpinx definition "A serous layer that is part of the peritoneal lining of the abdominal cavity in higher vertebrates, specifically the portion of the broad ligament that stretches from the uterine (fallopian) tube to the ovary. It is made up of epithelial cells of mesothelium and a mesh of serous membrane lining."^^string

  • database_cross_reference "PMID:29763118"^^string

  • database_cross_reference "Wikipedia:Mesosalpinx"^^string

• mesosalpinx has exact synonym "serous layer of fallopian tube"^^string

  • database_cross_reference "doi:10.1016/B978-0-12-801238-3.64401-X"^^string

• mesosalpinx has exact synonym "fallopian tube mesosalpinx"^^string

• mesosalpinx has exact synonym "mesentery of fallopian tube"^^string

  • database_cross_reference "PMID:29763118"^^string

• mesosalpinx has exact synonym "mesentery of uterine tube"^^string

  • database_cross_reference "PMID:29763118"^^string

• mesosalpinx SubClassOf serous membrane

• mesosalpinx SubClassOf surrounds some fallopian tube

oviduct http://purl.obolibrary.org/obo/UBERON_0000993

Removed

• oviduct has exact synonym "uterine tube"^^string

Added

• oviduct has narrow synonym "uterine tube"^^string