Addresses #2259 NTR placental terms

[aleixpuigb]

Addresses #2259 NTR placental terms

[aleixpuigb]

#gogoeditdiff

[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/cl/cl-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-01-09/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-master.owl/cl-simple.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-01-09/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

CL_4033062 http://purl.obolibrary.org/obo/CL_4033062

Added

• CL_4033062 label "interstitial extravillous trophoblast cell"

• CL_4033062 definition "A trophoblast cell that invades the uterine wall to anchor the placenta to the uterus. An interstitial extravillous trophoblast cell differentiates from an extravillous trophoblast cell, becoming hyperchromatic and changing its morphology to a fibroblast-like spindle-shaped cell. In humans, this cell can be distinguished by the expression of placental-specific protein 8, which stimulates migration."

  • database_cross_reference "PMID:37630754"

  • database_cross_reference "doi:10.1007/978-3-030-84725-8"

• CL_4033062 contributor 0000-0001-6677-8489

• CL_4033062 has_related_synonym "iEVT"

  • database_cross_reference "PMID:37630754"

  • has_synonym_type abbreviation

• CL_4033062 has_related_synonym "interstitial extravillous trophoblast"

  • database_cross_reference "PMID:37630754"

• CL_4033062 has exact synonym "invasive interstitial extravillous trophoblast cell"

  • database_cross_reference "doi:10.1007/978-3-030-84725-8"

• CL_4033062 date "2024-01-08T15:43:15Z"^^dateTime

• CL_4033062 has_related_synonym "interstitial trophoblast"

  • database_cross_reference "PMID:11337369"

• Class: CL_4033062

• CL_4033062 SubClassOf trophoblast cell

• CL_4033062 SubClassOf develops from some extravillous trophoblast

CL_4033063 http://purl.obolibrary.org/obo/CL_4033063

Added

• CL_4033063 has_related_synonym "endovascular extravillous trophoblast"

  • database_cross_reference "PMID:37630754"

• CL_4033063 contributor 0000-0001-6677-8489

• CL_4033063 comment "Shortly after implantation, the endovascular extravillous trophoblast cells occlude the maternal spiral arteries, preventing premature oxygen delivery to the placental villi and reducing fetal oxidative stress."

  • database_cross_reference "PMID:37630754"

• CL_4033063 date "2024-01-08T15:43:32Z"^^dateTime

• CL_4033063 definition "A trophoblast cell that invades the maternal spiral arteries and replace the endothelial lining, remodeling the vessels and allowing for adequate blood transport into the placenta. An endovascular extravillous trophoblast cell differentiates from an extravillous trophoblast cell. In humans, this cell can be distinguished by the expression of CD56."

  • database_cross_reference "PMID:37630754"

  • database_cross_reference "doi:10.1007/978-3-030-84725-8"

• CL_4033063 label "endovascular extravillous trophoblast cell"

• CL_4033063 has_related_synonym "endovascular trophoblast"

  • database_cross_reference "PMID:11337369"

• CL_4033063 has_related_synonym "eEVT"

  • database_cross_reference "PMID:37630754"

  • has_synonym_type abbreviation

• Class: CL_4033063

• CL_4033063 SubClassOf trophoblast cell

• CL_4033063 SubClassOf develops from some extravillous trophoblast

CL_4033064 http://purl.obolibrary.org/obo/CL_4033064

Added

• CL_4033064 comment "Uterine macrophages are reported to be evenly distributed throughout the endometrial stroma but with aggregations observed close to the lumen of superficial secretory glands."

  • database_cross_reference "PMID:36113384"

• CL_4033064 has_broad_synonym "uterine macrophage"

  • database_cross_reference "PMID:36113384"

• CL_4033064 label "uterine resident macrophage"

• CL_4033064 date "2024-01-08T16:05:09Z"^^dateTime

• CL_4033064 contributor 0000-0001-6677-8489

• CL_4033064 definition "A tissue-resident macrophage that is part of some uterus."

  • database_cross_reference "PMID:36113384"

• Class: CL_4033064

• CL_4033064 SubClassOf tissue-resident macrophage

[github-actions]

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

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
• Version IRI: None
• Loaded from: file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl

Right

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

Ontology imports

Ontology annotations

CL_4033062 http://purl.obolibrary.org/obo/CL_4033062

Added

• CL_4033062 label "interstitial extravillous trophoblast cell"

• CL_4033062 definition "A trophoblast cell that invades the uterine wall to anchor the placenta to the uterus. An interstitial extravillous trophoblast cell differentiates from an extravillous trophoblast cell, becoming hyperchromatic and changing its morphology to a fibroblast-like spindle-shaped cell. In humans, this cell can be distinguished by the expression of placental-specific protein 8, which stimulates migration."

  • database_cross_reference "PMID:37630754"

  • database_cross_reference "doi:10.1007/978-3-030-84725-8"

• CL_4033062 contributor 0000-0001-6677-8489

• CL_4033062 has_related_synonym "iEVT"

  • database_cross_reference "PMID:37630754"

  • has_synonym_type abbreviation

• CL_4033062 has_related_synonym "interstitial extravillous trophoblast"

  • database_cross_reference "PMID:37630754"

• CL_4033062 has_exact_synonym "invasive interstitial extravillous trophoblast cell"

  • database_cross_reference "doi:10.1007/978-3-030-84725-8"

• CL_4033062 date "2024-01-08T15:43:15Z"^^dateTime

• CL_4033062 has_related_synonym "interstitial trophoblast"

  • database_cross_reference "PMID:11337369"

• Class: CL_4033062

• CL_4033062 SubClassOf trophoblast cell

• CL_4033062 SubClassOf develops from some extravillous trophoblast

CL_4033063 http://purl.obolibrary.org/obo/CL_4033063

Added

• CL_4033063 has_related_synonym "endovascular extravillous trophoblast"

  • database_cross_reference "PMID:37630754"

• CL_4033063 contributor 0000-0001-6677-8489

• CL_4033063 comment "Shortly after implantation, the endovascular extravillous trophoblast cells occlude the maternal spiral arteries, preventing premature oxygen delivery to the placental villi and reducing fetal oxidative stress."

  • database_cross_reference "PMID:37630754"

• CL_4033063 date "2024-01-08T15:43:32Z"^^dateTime

• CL_4033063 definition "A trophoblast cell that invades the maternal spiral arteries and replace the endothelial lining, remodeling the vessels and allowing for adequate blood transport into the placenta. An endovascular extravillous trophoblast cell differentiates from an extravillous trophoblast cell. In humans, this cell can be distinguished by the expression of CD56."

  • database_cross_reference "PMID:37630754"

  • database_cross_reference "doi:10.1007/978-3-030-84725-8"

• CL_4033063 label "endovascular extravillous trophoblast cell"

• CL_4033063 has_related_synonym "endovascular trophoblast"

  • database_cross_reference "PMID:11337369"

• CL_4033063 has_related_synonym "eEVT"

  • database_cross_reference "PMID:37630754"

  • has_synonym_type abbreviation

• Class: CL_4033063

• CL_4033063 SubClassOf trophoblast cell

• CL_4033063 SubClassOf develops from some extravillous trophoblast

CL_4033064 http://purl.obolibrary.org/obo/CL_4033064

Added

• CL_4033064 comment "Uterine macrophages are reported to be evenly distributed throughout the endometrial stroma but with aggregations observed close to the lumen of superficial secretory glands."

  • database_cross_reference "PMID:36113384"

• CL_4033064 has_broad_synonym "uterine macrophage"

  • database_cross_reference "PMID:36113384"

• CL_4033064 label "uterine resident macrophage"

• CL_4033064 date "2024-01-08T16:05:09Z"^^dateTime

• CL_4033064 contributor 0000-0001-6677-8489

• CL_4033064 definition "A tissue-resident macrophage that is part of some uterus."

  • database_cross_reference "PMID:36113384"

• Class: CL_4033064

• CL_4033064 EquivalentTo tissue-resident macrophage and (part_of some uterus)

[dosumis]

Looks good to me. One tiny change suggested 'some uterus' --> 'the uterus'. Biologists find the logical terminology confusing - especially in the context of organs where only one is present per organism.

[aleixpuigb]

Looks good to me. One tiny change suggested 'some uterus' --> 'the uterus'. Biologists find the logical terminology confusing - especially in the context of organs where only one is present per organism.

Thank you for the suggestion, I will change that.