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Change has_completed to obo:RO_0002353 #1770

Merged

shawntanzk merged 2 commits into master from remove-has_completed

Jan 19, 2023

Contributor

shawntanzk commented Dec 14, 2022

#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


          Change has_completed to obo:RO_0002353

f8c66c4

#gogoeditdiff
see oborel/obo-relations#574 (comment)

shawntanzk requested review from dosumis, balhoff and addiehl

December 14, 2022 11:52

shawntanzk self-assigned this

github-actions bot commented Dec 14, 2022 •

edited

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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 bot commented Dec 14, 2022 •

edited

Loading

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)

balhoff approved these changes

View reviewed changes

Contributor Author

shawntanzk commented Dec 15, 2022

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


          Merge branch 'master' into remove-has_completed

3279c85

Contributor Author

shawntanzk commented Jan 4, 2023

#gogoeditdiff

Contributor Author

shawntanzk commented Jan 6, 2023

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

Contributor Author

shawntanzk commented Jan 19, 2023

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

shawntanzk merged commit d7ea4ec into master

shawntanzk deleted the remove-has_completed branch

January 19, 2023 11:31

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