Change has_completed to obo:RO_0002353

[shawntanzk]

#gogoeditdiff
see oborel/obo-relations#574 (comment)
Also tagging @bpeters42
Please do see the automated diff (once it comes up) to ensure that changes are accurate.
Thanks

[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/2023-01-04/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/2023-01-04/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

has_completed http://purl.obolibrary.org/obo/cl#has_completed

Removed

• has_completed label "has_completed"

• ObjectProperty: has_completed

[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

Bm4 B cell http://purl.obolibrary.org/obo/CL_0000966

Removed

• Bm4 B cell EquivalentTo germinal center B cell and (has plasma membrane part some ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1) and (has_completed some somatic hypermutation of immunoglobulin genes) and (lacks_plasma_membrane_part some IgD immunoglobulin complex) and (lacks_plasma_membrane_part some lactosylceramide 4-alpha-galactosyltransferase)

Added

• Bm4 B cell EquivalentTo germinal center B cell and (has plasma membrane part some ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1) and (output of some somatic hypermutation of immunoglobulin genes) and (lacks_plasma_membrane_part some IgD immunoglobulin complex) and (lacks_plasma_membrane_part some lactosylceramide 4-alpha-galactosyltransferase)

Bm5 B cell http://purl.obolibrary.org/obo/CL_0000967

Removed

• Bm5 B cell EquivalentTo memory B cell and (has_completed some germinal center B cell differentiation) and (has_completed some somatic hypermutation of immunoglobulin genes) and (lacks_plasma_membrane_part some IgD immunoglobulin complex)

Added

• Bm5 B cell EquivalentTo memory B cell and (output of some germinal center B cell differentiation) and (output of some somatic hypermutation of immunoglobulin genes) and (lacks_plasma_membrane_part some IgD immunoglobulin complex)

CD27-negative gamma-delta T cell http://purl.obolibrary.org/obo/CL_0002125

Removed

• CD27-negative gamma-delta T cell EquivalentTo mature gamma-delta T cell and (has part some nuclear receptor ROR-gamma isoform 2) and (capable of some interleukin-17 production) and (has_completed some T cell differentiation) and (lacks_plasma_membrane_part some CD27 molecule)

Added

• CD27-negative gamma-delta T cell EquivalentTo mature gamma-delta T cell and (has part some nuclear receptor ROR-gamma isoform 2) and (capable of some interleukin-17 production) and (output of some T cell differentiation) and (lacks_plasma_membrane_part some CD27 molecule)

CD27-positive gamma-delta T cell http://purl.obolibrary.org/obo/CL_0002124

Removed

• CD27-positive gamma-delta T cell EquivalentTo mature gamma-delta T cell and (has plasma membrane part some CD27 molecule) and (capable of some type II interferon production) and (has_completed some T cell differentiation)

Added

• CD27-positive gamma-delta T cell EquivalentTo mature gamma-delta T cell and (has plasma membrane part some CD27 molecule) and (capable of some type II interferon production) and (output of some T cell differentiation)

CD4-positive helper T cell http://purl.obolibrary.org/obo/CL_0000492

Removed

• CD4-positive helper T cell SubClassOf has_completed some T cell differentiation

Added

• CD4-positive helper T cell SubClassOf output of some T cell differentiation

CD4-positive, alpha-beta cytotoxic T cell http://purl.obolibrary.org/obo/CL_0000934

Removed

• CD4-positive, alpha-beta cytotoxic T cell EquivalentTo CD4-positive, alpha-beta T cell and (capable of some T cell mediated cytotoxicity) and (has_completed some T cell differentiation)

Added

• CD4-positive, alpha-beta cytotoxic T cell EquivalentTo CD4-positive, alpha-beta T cell and (capable of some T cell mediated cytotoxicity) and (output of some T cell differentiation)

CD4-positive, alpha-beta memory T cell http://purl.obolibrary.org/obo/CL_0000897

Removed

• CD4-positive, alpha-beta memory T cell EquivalentTo CD4-positive, alpha-beta T cell and (bearer of some increased life span) and (has_completed some T cell activation involved in immune response) and (has_completed some memory T cell differentiation)

Added

• CD4-positive, alpha-beta memory T cell EquivalentTo CD4-positive, alpha-beta T cell and (bearer of some increased life span) and (output of some T cell activation involved in immune response) and (output of some memory T cell differentiation)

CD4-positive, alpha-beta memory T cell, CD45RO-positive http://purl.obolibrary.org/obo/CL_0001204

Removed

• CD4-positive, alpha-beta memory T cell, CD45RO-positive EquivalentTo CD4-positive, alpha-beta memory T cell and (has plasma membrane part some receptor-type tyrosine-protein phosphatase C isoform CD45RO) and (has plasma membrane part some interleukin-7 receptor subunit alpha) and (only in taxon some Homo sapiens) and (has high plasma membrane amount some CD44 molecule) and (has high plasma membrane amount some interleukin-2 receptor subunit beta) and (has_completed some memory T cell differentiation) and (lacks_plasma_membrane_part some interleukin-2 receptor subunit alpha)

Added

• CD4-positive, alpha-beta memory T cell, CD45RO-positive EquivalentTo CD4-positive, alpha-beta memory T cell and (has plasma membrane part some receptor-type tyrosine-protein phosphatase C isoform CD45RO) and (has plasma membrane part some interleukin-7 receptor subunit alpha) and (only in taxon some Homo sapiens) and (output of some memory T cell differentiation) and (has high plasma membrane amount some CD44 molecule) and (has high plasma membrane amount some interleukin-2 receptor subunit beta) and (lacks_plasma_membrane_part some interleukin-2 receptor subunit alpha)

CD8-positive, alpha-beta cytokine secreting effector T cell http://purl.obolibrary.org/obo/CL_0000908

Removed

• CD8-positive, alpha-beta cytokine secreting effector T cell EquivalentTo CD8-positive, alpha-beta T cell and (has plasma membrane part some CD69 molecule) and (has plasma membrane part some interleukin-2 receptor subunit alpha) and (capable of some cytokine production) and (has_completed some T cell differentiation) and (lacks_plasma_membrane_part some L-selectin) and (lacks_plasma_membrane_part some interleukin-7 receptor subunit alpha)

Added

• CD8-positive, alpha-beta cytokine secreting effector T cell EquivalentTo CD8-positive, alpha-beta T cell and (has plasma membrane part some CD69 molecule) and (has plasma membrane part some interleukin-2 receptor subunit alpha) and (capable of some cytokine production) and (output of some T cell differentiation) and (lacks_plasma_membrane_part some L-selectin) and (lacks_plasma_membrane_part some interleukin-7 receptor subunit alpha)

CD8-positive, alpha-beta cytotoxic T cell http://purl.obolibrary.org/obo/CL_0000794

Removed

• CD8-positive, alpha-beta cytotoxic T cell EquivalentTo CD8-positive, alpha-beta T cell and (has part some perforin-1) and (has part some granzyme B) and (capable of some T cell mediated cytotoxicity) and (capable of some granzyme B localization to T cell secretory granule) and (has_completed some T cell differentiation)

Added

• CD8-positive, alpha-beta cytotoxic T cell EquivalentTo CD8-positive, alpha-beta T cell and (has part some perforin-1) and (has part some granzyme B) and (capable of some T cell mediated cytotoxicity) and (capable of some granzyme B localization to T cell secretory granule) and (output of some T cell differentiation)

CD8-positive, alpha-beta memory T cell http://purl.obolibrary.org/obo/CL_0000909

Removed

• CD8-positive, alpha-beta memory T cell EquivalentTo CD8-positive, alpha-beta T cell and (bearer of some increased life span) and (has_completed some T cell activation involved in immune response) and (has_completed some memory T cell differentiation)

Added

• CD8-positive, alpha-beta memory T cell EquivalentTo CD8-positive, alpha-beta T cell and (bearer of some increased life span) and (output of some T cell activation involved in immune response) and (output of some memory T cell differentiation)

CD8-positive, alpha-beta memory T cell, CD45RO-positive http://purl.obolibrary.org/obo/CL_0001203

Removed

• CD8-positive, alpha-beta memory T cell, CD45RO-positive EquivalentTo CD8-positive, alpha-beta memory T cell and (has plasma membrane part some receptor-type tyrosine-protein phosphatase C isoform CD45RO) and (has plasma membrane part some interleukin-7 receptor subunit alpha) and (only in taxon some Homo sapiens) and (has high plasma membrane amount some CD44 molecule) and (has high plasma membrane amount some interleukin-2 receptor subunit beta) and (has_completed some memory T cell differentiation) and (lacks_plasma_membrane_part some interleukin-2 receptor subunit alpha)

Added

• CD8-positive, alpha-beta memory T cell, CD45RO-positive EquivalentTo CD8-positive, alpha-beta memory T cell and (has plasma membrane part some receptor-type tyrosine-protein phosphatase C isoform CD45RO) and (has plasma membrane part some interleukin-7 receptor subunit alpha) and (only in taxon some Homo sapiens) and (output of some memory T cell differentiation) and (has high plasma membrane amount some CD44 molecule) and (has high plasma membrane amount some interleukin-2 receptor subunit beta) and (lacks_plasma_membrane_part some interleukin-2 receptor subunit alpha)

class switched memory B cell http://purl.obolibrary.org/obo/CL_0000972

Removed

• class switched memory B cell EquivalentTo memory B cell and (has plasma membrane part some CD27 molecule) and (has_completed some isotype switching) and (lacks_plasma_membrane_part some IgM immunoglobulin complex)

Added

• class switched memory B cell EquivalentTo memory B cell and (has plasma membrane part some CD27 molecule) and (output of some isotype switching) and (lacks_plasma_membrane_part some IgM immunoglobulin complex)

effector T cell http://purl.obolibrary.org/obo/CL_0000911

Removed

• effector T cell EquivalentTo mature T cell and (bearer of some normal life span) and (has_completed some T cell differentiation) and (has_completed some T cell selection)

Added

• effector T cell EquivalentTo mature T cell and (bearer of some normal life span) and (output of some T cell differentiation) and (output of some T cell selection)

effector memory CD4-positive, alpha-beta T cell, terminally differentiated http://purl.obolibrary.org/obo/CL_0001087

Removed

• effector memory CD4-positive, alpha-beta T cell, terminally differentiated EquivalentTo CD4-positive, alpha-beta memory T cell and (has plasma membrane part some receptor-type tyrosine-protein phosphatase C isoform CD45RA) and (in taxon some Homo sapiens) and (has_completed some memory T cell differentiation) and (lacks_plasma_membrane_part some receptor-type tyrosine-protein phosphatase C isoform CD45RO) and (lacks_plasma_membrane_part some C-C chemokine receptor type 7)

Added

• effector memory CD4-positive, alpha-beta T cell, terminally differentiated EquivalentTo CD4-positive, alpha-beta memory T cell and (has plasma membrane part some receptor-type tyrosine-protein phosphatase C isoform CD45RA) and (in taxon some Homo sapiens) and (output of some memory T cell differentiation) and (lacks_plasma_membrane_part some receptor-type tyrosine-protein phosphatase C isoform CD45RO) and (lacks_plasma_membrane_part some C-C chemokine receptor type 7)

effector memory CD8-positive, alpha-beta T cell, terminally differentiated http://purl.obolibrary.org/obo/CL_0001062

Removed

• effector memory CD8-positive, alpha-beta T cell, terminally differentiated EquivalentTo CD8-positive, alpha-beta memory T cell and (has plasma membrane part some receptor-type tyrosine-protein phosphatase C isoform CD45RA) and (in taxon some Homo sapiens) and (has_completed some memory T cell differentiation) and (lacks_plasma_membrane_part some receptor-type tyrosine-protein phosphatase C isoform CD45RO) and (lacks_plasma_membrane_part some C-C chemokine receptor type 7)

Added

• effector memory CD8-positive, alpha-beta T cell, terminally differentiated EquivalentTo CD8-positive, alpha-beta memory T cell and (has plasma membrane part some receptor-type tyrosine-protein phosphatase C isoform CD45RA) and (in taxon some Homo sapiens) and (output of some memory T cell differentiation) and (lacks_plasma_membrane_part some receptor-type tyrosine-protein phosphatase C isoform CD45RO) and (lacks_plasma_membrane_part some C-C chemokine receptor type 7)

has_completed http://purl.obolibrary.org/obo/cl#has_completed

Removed

• has_completed label "has_completed"^^string

• ObjectProperty: has_completed

mature B cell http://purl.obolibrary.org/obo/CL_0000785

Removed

• mature B cell EquivalentTo B cell, CD19-positive and (capable of some antigen processing and presentation of peptide or polysaccharide antigen via MHC class II) and (capable of some B cell activation) and (has_completed some mature B cell differentiation)

Added

• mature B cell EquivalentTo B cell, CD19-positive and (capable of some antigen processing and presentation of peptide or polysaccharide antigen via MHC class II) and (capable of some B cell activation) and (output of some mature B cell differentiation)

mature NK T cell http://purl.obolibrary.org/obo/CL_0000814

Removed

• mature NK T cell EquivalentTo mature alpha-beta T cell and (has plasma membrane part some KLRB1-like protein) and (capable of some MHC class Ib receptor activity) and (capable of some innate immune response) and (has_completed some T cell differentiation)

Added

• mature NK T cell EquivalentTo mature alpha-beta T cell and (has plasma membrane part some KLRB1-like protein) and (capable of some MHC class Ib receptor activity) and (capable of some innate immune response) and (output of some T cell differentiation)

mature T cell http://purl.obolibrary.org/obo/CL_0002419

Removed

• mature T cell EquivalentTo T cell and (has plasma membrane part some T cell receptor complex) and (has_completed some T cell selection)

Added

• mature T cell EquivalentTo T cell and (has plasma membrane part some T cell receptor complex) and (output of some T cell selection)

mature alpha-beta T cell http://purl.obolibrary.org/obo/CL_0000791

Removed

• mature alpha-beta T cell EquivalentTo alpha-beta T cell and (has_completed some T cell selection)

Added

• mature alpha-beta T cell EquivalentTo alpha-beta T cell and (output of some T cell selection)

mature gamma-delta T cell http://purl.obolibrary.org/obo/CL_0000800

Removed

• mature gamma-delta T cell EquivalentTo gamma-delta T cell and (has_completed some T cell selection)

Added

• mature gamma-delta T cell EquivalentTo gamma-delta T cell and (output of some T cell selection)

memory B cell http://purl.obolibrary.org/obo/CL_0000787

Removed

• memory B cell EquivalentTo mature B cell and (has plasma membrane part some MHC class II protein complex) and (has plasma membrane part some membrane-spanning 4-domains subfamily A member 1) and (has_completed some B cell affinity maturation) and (lacks_plasma_membrane_part some syndecan-1)

Added

• memory B cell EquivalentTo mature B cell and (has plasma membrane part some MHC class II protein complex) and (has plasma membrane part some membrane-spanning 4-domains subfamily A member 1) and (output of some B cell affinity maturation) and (lacks_plasma_membrane_part some syndecan-1)

memory T cell http://purl.obolibrary.org/obo/CL_0000813

Removed

• memory T cell EquivalentTo mature T cell and (bearer of some increased life span) and (has_completed some T cell activation involved in immune response) and (has_completed some memory T cell differentiation)

Added

• memory T cell EquivalentTo mature T cell and (bearer of some increased life span) and (output of some T cell activation involved in immune response) and (output of some memory T cell differentiation)

memory regulatory T cell http://purl.obolibrary.org/obo/CL_0002678

Removed

• memory regulatory T cell EquivalentTo CD4-positive, CD25-positive, alpha-beta regulatory T cell and (has_completed some memory T cell differentiation)

Added

• memory regulatory T cell EquivalentTo CD4-positive, CD25-positive, alpha-beta regulatory T cell and (output of some memory T cell differentiation)

mucosal invariant T cell http://purl.obolibrary.org/obo/CL_0000940

Removed

• mucosal invariant T cell EquivalentTo mature alpha-beta T cell and (capable of some innate immune response in mucosa) and (capable of some MHC class Ib receptor activity) and (has_completed some T cell differentiation)

Added

• mucosal invariant T cell EquivalentTo mature alpha-beta T cell and (capable of some innate immune response in mucosa) and (capable of some MHC class Ib receptor activity) and (output of some T cell differentiation)

naive T cell http://purl.obolibrary.org/obo/CL_0000898

Removed

• naive T cell EquivalentTo mature T cell and (has plasma membrane part some receptor-type tyrosine-protein phosphatase C isoform CD45RA) and (has plasma membrane part some C-C chemokine receptor type 7) and (has plasma membrane part some interleukin-7 receptor subunit alpha) and (has high plasma membrane amount some L-selectin) and (has low plasma membrane amount some CD44 molecule) and (has_completed some T cell selection)

Added

• naive T cell EquivalentTo mature T cell and (has plasma membrane part some receptor-type tyrosine-protein phosphatase C isoform CD45RA) and (has plasma membrane part some C-C chemokine receptor type 7) and (has plasma membrane part some interleukin-7 receptor subunit alpha) and (output of some T cell selection) and (has high plasma membrane amount some L-selectin) and (has low plasma membrane amount some CD44 molecule)

non-classical monocyte http://purl.obolibrary.org/obo/CL_0000875

Removed

• non-classical monocyte EquivalentTo monocyte and (bearer of some decreased size) and (capable of some lymphocyte costimulation) and (has high plasma membrane amount some CX3C chemokine receptor 1) and (has_completed some monocyte differentiation) and (lacks_plasma_membrane_part some CD19 molecule) and (lacks_plasma_membrane_part some CD3 epsilon) and (lacks_plasma_membrane_part some membrane-spanning 4-domains subfamily A member 1)

Added

• non-classical monocyte EquivalentTo monocyte and (bearer of some decreased size) and (capable of some lymphocyte costimulation) and (output of some monocyte differentiation) and (has high plasma membrane amount some CX3C chemokine receptor 1) and (lacks_plasma_membrane_part some CD19 molecule) and (lacks_plasma_membrane_part some CD3 epsilon) and (lacks_plasma_membrane_part some membrane-spanning 4-domains subfamily A member 1)

pre-B-II cell http://purl.obolibrary.org/obo/CL_0000955

Removed

• pre-B-II cell EquivalentTo precursor B cell and (has_completed some immunoglobulin heavy chain V-D-J recombination) and (lacks_part some DNA nucleotidylexotransferase) and (lacks_plasma_membrane_part some CD34 molecule)

Added

• pre-B-II cell EquivalentTo precursor B cell and (output of some immunoglobulin heavy chain V-D-J recombination) and (lacks_part some DNA nucleotidylexotransferase) and (lacks_plasma_membrane_part some CD34 molecule)

[shawntanzk]

@addiehl Could you also give a positive review before I merge this, would be more comfortable if you go through this too. Thanks :)

[shawntanzk]

#gogoeditdiff

[shawntanzk]

Not 100% sure why the QC isn't autorunning, but manually triggered it and it passed https:/obophenotype/cell-ontology/actions/runs/3847578786

[shawntanzk]

Merging this given the time has passed, please open a new ticket if there is any issues