Fixes #2646 NTR-lung resident granzyme k-associated CD8 T cell

[Caroline-99]

Fixes #2646 #2677

• Added a new term with textual and logical defs, synonyms and refs
• Imported a PRO term

[aleixpuigb]

Please see inline comments. There are different suggestions that we can discuss.

[Caroline-99]

#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/2024-10-18/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/2024-10-18/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

cycling B cell http://purl.obolibrary.org/obo/CL_4033068

Removed

• cycling B cell contributor 0000-0001-6677-8489

cycling CD4-positive, alpha-beta T cell http://purl.obolibrary.org/obo/CL_4033075

Removed

• cycling CD4-positive, alpha-beta T cell contributor 0000-0001-6677-8489

cycling CD8-positive, alpha-beta T cell http://purl.obolibrary.org/obo/CL_4033074

Removed

• cycling CD8-positive, alpha-beta T cell contributor 0000-0001-6677-8489

cycling T cell http://purl.obolibrary.org/obo/CL_4033069

Removed

• cycling T cell contributor 0000-0001-6677-8489

cycling alveolar macrophage http://purl.obolibrary.org/obo/CL_4033077

Removed

• cycling alveolar macrophage contributor 0000-0001-6677-8489

cycling basal cell http://purl.obolibrary.org/obo/CL_4033082

Removed

• cycling basal cell contributor 0000-0001-6677-8489

cycling dendritic cell http://purl.obolibrary.org/obo/CL_4033070

Removed

• cycling dendritic cell contributor 0000-0001-6677-8489

cycling endothelial cell of lymphatic vessel http://purl.obolibrary.org/obo/CL_4033079

Removed

• cycling endothelial cell of lymphatic vessel contributor 0000-0001-6677-8489

cycling gamma-delta T cell http://purl.obolibrary.org/obo/CL_4033072

Removed

• cycling gamma-delta T cell contributor 0000-0001-6677-8489

cycling glial cell http://purl.obolibrary.org/obo/CL_4047002

Removed

• cycling glial cell contributor 0009-0005-7919-4905

cycling macrophage http://purl.obolibrary.org/obo/CL_4033076

Removed

• cycling macrophage contributor 0000-0001-6677-8489

cycling monocyte http://purl.obolibrary.org/obo/CL_4033073

Removed

• cycling monocyte contributor 0000-0001-6677-8489

cycling mononuclear phagocyte http://purl.obolibrary.org/obo/CL_4033078

Removed

• cycling mononuclear phagocyte contributor 0000-0001-6677-8489

cycling myeloid cell http://purl.obolibrary.org/obo/CL_4033081

Removed

• cycling myeloid cell contributor 0000-0001-6677-8489

cycling natural killer cell http://purl.obolibrary.org/obo/CL_4033071

Removed

• cycling natural killer cell contributor 0000-0001-6677-8489

cycling neuroblast (sensu Vertebrata) http://purl.obolibrary.org/obo/CL_4047005

Removed

• cycling neuroblast (sensu Vertebrata) contributor 0009-0005-7919-4905

cycling plasma cell http://purl.obolibrary.org/obo/CL_4047003

Removed

• cycling plasma cell contributor 0009-0005-7919-4905

cycling pulmonary alveolar type 2 cell http://purl.obolibrary.org/obo/CL_4033080

Removed

• cycling pulmonary alveolar type 2 cell contributor 0000-0001-6677-8489

cycling stromal cell http://purl.obolibrary.org/obo/CL_4047001

Removed

• cycling stromal cell contributor 0009-0005-7919-4905

cycling type EC enteroendocrine cell http://purl.obolibrary.org/obo/CL_4047004

Removed

• cycling type EC enteroendocrine cell contributor 0009-0005-7919-4905

granzyme K-associated CD8 T cell http://purl.obolibrary.org/obo/CL_4052021

Added

• granzyme K-associated CD8 T cell has exact synonym "tissue-enriched expressing GzmK CD8 cell"

  • database_cross_reference "PMID:35704599"

• granzyme K-associated CD8 T cell has_related_synonym "CD8-GZMK cell"

  • has_synonym_type abbreviation

  • database_cross_reference "doi:/10.1101/2022.06.17.496207"

• granzyme K-associated CD8 T cell has narrow synonym "GZMK high CD8+ T effector memory cell"

  • database_cross_reference "PMID:36347862"

• granzyme K-associated CD8 T cell has exact synonym "granzyme K+ CD8 T cell"

  • database_cross_reference "PMID:35704599"

• granzyme K-associated CD8 T cell contributor 0009-0000-8480-9277

• granzyme K-associated CD8 T cell definition "A CD8 T cell characterized by high expression of Granzyme K (GZMK). This cell is enriched in inflamed tissues, including synovial tissue in rheumatoid arthritis, the gut, kidneys, and respiratory tissues during conditions like COVID-19. Unlike highly cytotoxic GZMB+ CD8+ T cell, GZMK+ CD8+ T cell exhibits lower direct cytotoxic potential, and is involved in producing pro-inflammatory cytokines such as IFN-γ and TNF-α."

  • database_cross_reference "PMID:37449888"

  • database_cross_reference "PMID:35704599"

• granzyme K-associated CD8 T cell label "granzyme K-associated CD8 T cell"

• granzyme K-associated CD8 T cell date "2024-10-18T09:51:48Z"^^dateTime

• granzyme K-associated CD8 T cell has exact synonym "TteK CD8 cell"

  • database_cross_reference "PMID:35704599"

• Class: granzyme K-associated CD8 T cell

• granzyme K-associated CD8 T cell SubClassOf CD8-positive, alpha-beta memory T cell

lung resident granzyme K-associated CD8 T cell http://purl.obolibrary.org/obo/CL_4052020

Added

• lung resident granzyme K-associated CD8 T cell label "lung resident granzyme K-associated CD8 T cell"

• lung resident granzyme K-associated CD8 T cell contributor 0009-0000-8480-9277

• lung resident granzyme K-associated CD8 T cell date "2024-10-14T15:42:41Z"^^dateTime

• lung resident granzyme K-associated CD8 T cell has_related_synonym "lung resident CD8-GZMK"

  • has_synonym_type abbreviation

  • database_cross_reference "doi:/10.1101/2022.06.17.496207"

• lung resident granzyme K-associated CD8 T cell definition "A granzyme K-associated CD8 T cell that resides in the lung, characterized by the expression of granzyme K (GZMK), and tissue residency markers CD103 and CD49a. This cell exhibits cytotoxic potential through its expression of multiple granzymes (GZMA, GZMB, GZMH, GZMM) in addition to GZMK."

  • database_cross_reference "doi:/10.1101/2022.06.17.496207"

• lung resident granzyme K-associated CD8 T cell comment "Lung resident granzyme K-associated CD8 T cell represents an intermediate stage of T cell differentiation, with GZMK expression peaking during this phase."

  • database_cross_reference "PMID:28322863"

  • database_cross_reference "doi:/10.1101/2022.06.17.496207"

• lung resident granzyme K-associated CD8 T cell contributor 0000-0002-2336-2552

• Class: lung resident granzyme K-associated CD8 T cell

• lung resident granzyme K-associated CD8 T cell SubClassOf granzyme K-associated CD8 T cell

• lung resident granzyme K-associated CD8 T cell SubClassOf lung resident memory CD8-positive, CD103-positive, alpha-beta T 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

granzyme K http://purl.obolibrary.org/obo/PR_000003472

Added

• Class: granzyme K

granzyme K-associated CD8 T cell http://purl.obolibrary.org/obo/CL_4052021

Added

• granzyme K-associated CD8 T cell has_exact_synonym "tissue-enriched expressing GzmK CD8 cell"

  • database_cross_reference "PMID:35704599"

• granzyme K-associated CD8 T cell has_related_synonym "CD8-GZMK cell"

  • has_synonym_type abbreviation

  • database_cross_reference "doi:/10.1101/2022.06.17.496207"

• granzyme K-associated CD8 T cell has_narrow_synonym "GZMK high CD8+ T effector memory cell"

  • database_cross_reference "PMID:36347862"

• granzyme K-associated CD8 T cell has_exact_synonym "granzyme K+ CD8 T cell"

  • database_cross_reference "PMID:35704599"

• granzyme K-associated CD8 T cell contributor 0009-0000-8480-9277

• granzyme K-associated CD8 T cell definition "A CD8 T cell characterized by high expression of Granzyme K (GZMK). This cell is enriched in inflamed tissues, including synovial tissue in rheumatoid arthritis, the gut, kidneys, and respiratory tissues during conditions like COVID-19. Unlike highly cytotoxic GZMB+ CD8+ T cell, GZMK+ CD8+ T cell exhibits lower direct cytotoxic potential, and is involved in producing pro-inflammatory cytokines such as IFN-γ and TNF-α."

  • database_cross_reference "PMID:37449888"

  • database_cross_reference "PMID:35704599"

• granzyme K-associated CD8 T cell label "granzyme K-associated CD8 T cell"

• granzyme K-associated CD8 T cell date "2024-10-18T09:51:48Z"^^dateTime

• granzyme K-associated CD8 T cell has_exact_synonym "TteK CD8 cell"

  • database_cross_reference "PMID:35704599"

• Class: granzyme K-associated CD8 T cell

• granzyme K-associated CD8 T cell EquivalentTo CD8-positive, alpha-beta memory T cell and (expresses some granzyme K)

lung resident granzyme K-associated CD8 T cell http://purl.obolibrary.org/obo/CL_4052020

Added

• lung resident granzyme K-associated CD8 T cell label "lung resident granzyme K-associated CD8 T cell"

• lung resident granzyme K-associated CD8 T cell contributor 0009-0000-8480-9277

• lung resident granzyme K-associated CD8 T cell date "2024-10-14T15:42:41Z"^^dateTime

• lung resident granzyme K-associated CD8 T cell contributor 0000-0002-2336-2552

• lung resident granzyme K-associated CD8 T cell has_related_synonym "lung resident CD8-GZMK"

  • has_synonym_type abbreviation

  • database_cross_reference "doi:/10.1101/2022.06.17.496207"

• lung resident granzyme K-associated CD8 T cell definition "A granzyme K-associated CD8 T cell that resides in the lung, characterized by the expression of granzyme K (GZMK), and tissue residency markers CD103 and CD49a. This cell exhibits cytotoxic potential through its expression of multiple granzymes (GZMA, GZMB, GZMH, GZMM) in addition to GZMK."

  • database_cross_reference "doi:/10.1101/2022.06.17.496207"

• lung resident granzyme K-associated CD8 T cell comment "Lung resident granzyme K-associated CD8 T cell represents an intermediate stage of T cell differentiation, with GZMK expression peaking during this phase."

  • database_cross_reference "PMID:28322863"

  • database_cross_reference "doi:/10.1101/2022.06.17.496207"

• Class: lung resident granzyme K-associated CD8 T cell

• lung resident granzyme K-associated CD8 T cell EquivalentTo lung resident memory CD8-positive, CD103-positive, alpha-beta T cell and (expresses some granzyme K)

[aleixpuigb]

Thank you for addressing the previous comments and add the new cell type

[aleixpuigb]

The edits look fine.
NOTE: The contributors for cycling cells (added by DOSDP) are removed unintentionally.