Fixes #2251 obsolete increased nucleus size

[aleixpuigb]

Fixes #2251 obsolete increased nucleus size

[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/2024-01-22/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/2024-01-22/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

increased nucleus size http://purl.obolibrary.org/obo/CL_0017505

Removed

• increased nucleus size label "increased nucleus size"

• increased nucleus size definition "A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell."

  • database_cross_reference "GOC:tfm"

Added

• increased nucleus size deprecated true

• increased nucleus size term replaced by PATO_0040072

• increased nucleus size label "obsolete increased nucleus size"

• increased nucleus size definition "OBSOLETE. A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell."

  • database_cross_reference "GOC:tfm"

• increased nucleus size comment "This class was a phenotype, not a cell type."

• increased nucleus size term tracker item "obsolete increased nucleus size #2251"

lymphocyte http://purl.obolibrary.org/obo/CL_0000542

Removed

• lymphocyte SubClassOf has part some increased nucleus size

myeloblast http://purl.obolibrary.org/obo/CL_0000835

Removed

• myeloblast SubClassOf has part some increased nucleus size

proerythroblast http://purl.obolibrary.org/obo/CL_0000547

Removed

• proerythroblast SubClassOf has part some increased nucleus size

promyelocyte http://purl.obolibrary.org/obo/CL_0000836

Removed

• promyelocyte SubClassOf has part some increased nucleus size

[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

increased nucleus size http://purl.obolibrary.org/obo/CL_0017505

Removed

• increased nucleus size label "increased nucleus size"

• increased nucleus size definition "A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell."

  • database_cross_reference "GOC:tfm"

• increased nucleus size EquivalentTo nucleus and (bearer of some increased size)

• increased nucleus size SubClassOf nucleus

Added

• increased nucleus size deprecated true

• increased nucleus size term replaced by high nuclear/cytoplasmic ratio

• increased nucleus size label "obsolete increased nucleus size"

• increased nucleus size definition "OBSOLETE. A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell."

  • database_cross_reference "GOC:tfm"

• increased nucleus size comment "This class was a phenotype, not a cell type."

• increased nucleus size term tracker item "obsolete increased nucleus size #2251"

lymphocyte http://purl.obolibrary.org/obo/CL_0000542

Removed

• lymphocyte EquivalentTo leukocyte and (has part some neutrophillic cytoplasm) and (has part some increased nucleus size) and (has part some heterochromatin) and (bearer of some mononucleate)

Added

• lymphocyte EquivalentTo leukocyte and (has part some neutrophillic cytoplasm) and (has part some heterochromatin) and (bearer of some mononucleate) and (bearer of some high nuclear/cytoplasmic ratio)

myeloblast http://purl.obolibrary.org/obo/CL_0000835

Removed

• myeloblast EquivalentTo granulocytopoietic cell and (has part some basophilic cytoplasm) and (has part some increased nucleus size) and (has part some euchromatin) and (lacks_part some azurophil granule)

Added

• myeloblast EquivalentTo granulocytopoietic cell and (has part some basophilic cytoplasm) and (has part some euchromatin) and (lacks_part some azurophil granule) and (bearer of some high nuclear/cytoplasmic ratio)

proerythroblast http://purl.obolibrary.org/obo/CL_0000547

Removed

• proerythroblast EquivalentTo erythroid lineage cell and (has part some basophilic cytoplasm) and (has part some increased nucleus size) and (has part some nucleolus) and (lacks_plasma_membrane_part some CD19 molecule) and (lacks_plasma_membrane_part some CD4 molecule) and (lacks_plasma_membrane_part some integrin alpha-M) and (lacks_plasma_membrane_part some CD3 epsilon) and (lacks_plasma_membrane_part some neural cell adhesion molecule 1) and (lacks_plasma_membrane_part some CD2 molecule) and (lacks_plasma_membrane_part some T-cell surface glycoprotein CD8 alpha chain) and (lacks_plasma_membrane_part some membrane-spanning 4-domains subfamily A member 1) and (lacks_plasma_membrane_part some T-cell surface glycoprotein CD5) and (lacks_plasma_membrane_part some CD14 molecule) and (lacks_plasma_membrane_part some lymphocyte antigen 6G) and (bearer of some nucleated) and (has plasma membrane part some transferrin receptor protein 1)

Added

• proerythroblast EquivalentTo erythroid lineage cell and (has part some basophilic cytoplasm) and (has part some nucleolus) and (lacks_plasma_membrane_part some CD19 molecule) and (lacks_plasma_membrane_part some CD4 molecule) and (lacks_plasma_membrane_part some integrin alpha-M) and (lacks_plasma_membrane_part some CD3 epsilon) and (lacks_plasma_membrane_part some neural cell adhesion molecule 1) and (lacks_plasma_membrane_part some CD2 molecule) and (lacks_plasma_membrane_part some T-cell surface glycoprotein CD8 alpha chain) and (lacks_plasma_membrane_part some membrane-spanning 4-domains subfamily A member 1) and (lacks_plasma_membrane_part some T-cell surface glycoprotein CD5) and (lacks_plasma_membrane_part some CD14 molecule) and (lacks_plasma_membrane_part some lymphocyte antigen 6G) and (bearer of some nucleated) and (bearer of some high nuclear/cytoplasmic ratio) and (has plasma membrane part some transferrin receptor protein 1)

promyelocyte http://purl.obolibrary.org/obo/CL_0000836

Removed

• promyelocyte EquivalentTo myeloid lineage restricted progenitor cell and (has part some basophilic cytoplasm) and (has part some increased nucleus size) and (has part some nucleolus) and (has part some azurophil granule) and (lacks_plasma_membrane_part some integrin alpha-M) and (lacks_plasma_membrane_part some low affinity immunoglobulin gamma Fc region receptor III) and (lacks_plasma_membrane_part some signal transducer CD24) and (has plasma membrane part some alpha-(1,3)-fucosyltransferase 4) and (has plasma membrane part some CD33 molecule)

Added

• promyelocyte EquivalentTo myeloid lineage restricted progenitor cell and (has part some basophilic cytoplasm) and (has part some nucleolus) and (has part some azurophil granule) and (lacks_plasma_membrane_part some integrin alpha-M) and (lacks_plasma_membrane_part some low affinity immunoglobulin gamma Fc region receptor III) and (lacks_plasma_membrane_part some signal transducer CD24) and (bearer of some high nuclear/cytoplasmic ratio) and (has plasma membrane part some alpha-(1,3)-fucosyltransferase 4) and (has plasma membrane part some CD33 molecule)

[anitacaron]

Please add this URL as IRI.

[dosumis]

Looks good once you've fixed the data type issue Anita found.