Fixes #2602 NTR granulosa cells and remake class hierarchy

[aleixpuigb]

Fixes #2602 NTR granulosa cells and remake class hierarchy

[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/2024-09-24/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/2024-09-24/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

cuboidal granulosa cell http://purl.obolibrary.org/obo/CL_4033084

Added

• cuboidal granulosa cell has_related_synonym "cuboidal GC"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:33914868"

• cuboidal granulosa cell definition "A granulosa cell that has a cuboidal morphology and develops from squamous granulosa cell during the transition between primordial follicle to primary follicle. Cuboidal granulosa cells proliferate to form a second layer within secondary follicles."

  • database_cross_reference "PMID:28892263"

• cuboidal granulosa cell label "cuboidal granulosa cell"

• cuboidal granulosa cell date "2024-09-24T13:14:57Z"^^dateTime

• cuboidal granulosa cell has exact synonym "cuboidal epithelial granulosa cell"

  • database_cross_reference "PMID:31849844"

• cuboidal granulosa cell contributor 0000-0001-6677-8489

• cuboidal granulosa cell has exact synonym "columnar granulosa cell"

  • database_cross_reference "PMID:19001500"

• cuboidal granulosa cell has_related_synonym "columnar GC"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:19001500"

• Class: cuboidal granulosa cell

• cuboidal granulosa cell SubClassOf granulosa cell

• cuboidal granulosa cell SubClassOf directly develops from some squamous granulosa cell

cumulus cell http://purl.obolibrary.org/obo/CL_0000711

Removed

• cumulus cell SubClassOf develops from some granulosa cell

• cumulus cell SubClassOf follicular cell of ovary

Added

• cumulus cell SubClassOf develops from some cuboidal granulosa cell

• cumulus cell SubClassOf granulosa cell

follicular cell of ovary http://purl.obolibrary.org/obo/CL_0002174

Added

• follicular cell of ovary SubClassOf ovarian surface epithelial cell

granulosa cell http://purl.obolibrary.org/obo/CL_0000501

Removed

• granulosa cell SubClassOf directly develops from some pre-granulosa cell

Added

• granulosa cell SubClassOf develops from some pre-granulosa cell

mural granulosa cell http://purl.obolibrary.org/obo/CL_4033067

Removed

• mural granulosa cell SubClassOf directly develops from some granulosa cell

• mural granulosa cell SubClassOf ovarian surface epithelial cell

• mural granulosa cell SubClassOf follicular cell of ovary

Added

• mural granulosa cell SubClassOf directly develops from some cuboidal granulosa cell

• mural granulosa cell SubClassOf granulosa cell

pre-granulosa cell http://purl.obolibrary.org/obo/CL_4033066

Removed

• pre-granulosa cell SubClassOf directly develops into some granulosa cell

Added

• pre-granulosa cell SubClassOf directly develops into some squamous granulosa cell

squamous granulosa cell http://purl.obolibrary.org/obo/CL_4033083

Added

• squamous granulosa cell contributor 0000-0001-6677-8489

• squamous granulosa cell has_related_synonym "pre-granulosa cell"

  • database_cross_reference "PMID:33914868"

• squamous granulosa cell definition "A granulosa cell that has a squamous morphology and form a single layer around the oocyte in primordial follicles."

  • database_cross_reference "PMID:28892263"

• squamous granulosa cell date "2024-09-24T13:13:24Z"^^dateTime

• squamous granulosa cell has_related_synonym "squamous GC"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:33914868"

• squamous granulosa cell label "squamous granulosa cell"

• squamous granulosa cell comment "Often in literature squamous granulosa cell and pre-granulosa cell are used as synonyms. However, this term only makes reference to the quiescent granulosa cells that surround the primordial ovarian follicle, while a pre-granulosa cell proliferates to form the primordial follicle (and thus cells become the squamous granulosa cells)."

  • database_cross_reference "https://orcid.org/0000-0001-6677-8489"

• squamous granulosa cell has exact synonym "flattened granulosa cell"

  • database_cross_reference "PMID:22402964"

• Class: squamous granulosa cell

• squamous granulosa cell SubClassOf directly develops into some cuboidal granulosa cell

• squamous granulosa cell SubClassOf directly develops from some pre-granulosa cell

• squamous granulosa cell SubClassOf granulosa cell

[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

cuboidal granulosa cell http://purl.obolibrary.org/obo/CL_4033084

Added

• cuboidal granulosa cell has_related_synonym "cuboidal GC"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:33914868"

• cuboidal granulosa cell definition "A granulosa cell that has a cuboidal morphology and develops from squamous granulosa cell during the transition between primordial follicle to primary follicle. Cuboidal granulosa cells proliferate to form a second layer within secondary follicles."

  • database_cross_reference "PMID:28892263"

• cuboidal granulosa cell label "cuboidal granulosa cell"

• cuboidal granulosa cell date "2024-09-24T13:14:57Z"^^dateTime

• cuboidal granulosa cell has_exact_synonym "cuboidal epithelial granulosa cell"

  • database_cross_reference "PMID:31849844"

• cuboidal granulosa cell contributor 0000-0001-6677-8489

• cuboidal granulosa cell has_exact_synonym "columnar granulosa cell"

  • database_cross_reference "PMID:19001500"

• cuboidal granulosa cell has_related_synonym "columnar GC"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:19001500"

• Class: cuboidal granulosa cell

• cuboidal granulosa cell SubClassOf part of some ovarian follicle

• cuboidal granulosa cell SubClassOf granulosa cell

• cuboidal granulosa cell SubClassOf directly develops from some squamous granulosa cell

cumulus cell http://purl.obolibrary.org/obo/CL_0000711

Removed

• cumulus cell SubClassOf develops from some granulosa cell

• cumulus cell SubClassOf follicular cell of ovary

Added

• cumulus cell SubClassOf develops from some cuboidal granulosa cell

• cumulus cell SubClassOf granulosa cell

follicular cell of ovary http://purl.obolibrary.org/obo/CL_0002174

Added

• follicular cell of ovary SubClassOf part of some ovarian follicle

granulosa cell http://purl.obolibrary.org/obo/CL_0000501

Removed

• granulosa cell SubClassOf directly develops from some pre-granulosa cell

Added

• granulosa cell SubClassOf develops from some pre-granulosa cell

mural granulosa cell http://purl.obolibrary.org/obo/CL_4033067

Removed

• mural granulosa cell SubClassOf directly develops from some granulosa cell

• mural granulosa cell SubClassOf follicular cell of ovary

Added

• mural granulosa cell SubClassOf directly develops from some cuboidal granulosa cell

• mural granulosa cell SubClassOf granulosa cell

pre-granulosa cell http://purl.obolibrary.org/obo/CL_4033066

Removed

• pre-granulosa cell SubClassOf directly develops into some granulosa cell

Added

• pre-granulosa cell SubClassOf directly develops into some squamous granulosa cell

squamous granulosa cell http://purl.obolibrary.org/obo/CL_4033083

Added

• squamous granulosa cell contributor 0000-0001-6677-8489

• squamous granulosa cell has_related_synonym "pre-granulosa cell"

  • database_cross_reference "PMID:33914868"

• squamous granulosa cell definition "A granulosa cell that has a squamous morphology and form a single layer around the oocyte in primordial follicles."

  • database_cross_reference "PMID:28892263"

• squamous granulosa cell date "2024-09-24T13:13:24Z"^^dateTime

• squamous granulosa cell has_related_synonym "squamous GC"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:33914868"

• squamous granulosa cell label "squamous granulosa cell"

• squamous granulosa cell comment "Often in literature squamous granulosa cell and pre-granulosa cell are used as synonyms. However, this term only makes reference to the quiescent granulosa cells that surround the primordial ovarian follicle, while a pre-granulosa cell proliferates to form the primordial follicle (and thus cells become the squamous granulosa cells)."

  • database_cross_reference "https://orcid.org/0000-0001-6677-8489"

• squamous granulosa cell has_exact_synonym "flattened granulosa cell"

  • database_cross_reference "PMID:22402964"

• Class: squamous granulosa cell

• squamous granulosa cell SubClassOf directly develops into some cuboidal granulosa cell

• squamous granulosa cell SubClassOf directly develops from some pre-granulosa cell

• squamous granulosa cell SubClassOf granulosa cell

• squamous granulosa cell SubClassOf part of some primordial ovarian follicle