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Fixes #1266 populate mononuclear phagocyte #2208

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merged 6 commits into from
Nov 13, 2023

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Fixes #1266 populate mononuclear phagocyte

Fixes #1266 populate mononuclear phagocyte
@aleixpuigb
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#gogoeditdiff

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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/2023-10-27/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/2023-10-27/cl-simple.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

bone marrow macrophage http://purl.obolibrary.org/obo/CL_0002476

Removed

Added

macrophage http://purl.obolibrary.org/obo/CL_0000235

Removed

Added

mononuclear osteoclast http://purl.obolibrary.org/obo/CL_0000778

Removed

Added

mononuclear phagocyte http://purl.obolibrary.org/obo/CL_0000113

Removed

Added

multinuclear osteoclast http://purl.obolibrary.org/obo/CL_0000779

Removed

Added

osteoclast http://purl.obolibrary.org/obo/CL_0000092

Added

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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

macrophage http://purl.obolibrary.org/obo/CL_0000235

Added

mononuclear phagocyte http://purl.obolibrary.org/obo/CL_0000113

Added

osteoclast http://purl.obolibrary.org/obo/CL_0000092

Added

@aleixpuigb aleixpuigb requested a review from a user November 9, 2023 10:05
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Edits do not appear to match tasks described in linked ticket.

This comment suggests 'dendritic cell' and monocyte will be classified as children of 'mononuclear phagocyte'.
See also inline comment.

@@ -4300,6 +4300,7 @@ AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0000092 "chondroclast")
AnnotationAssertion(rdfs:comment obo:CL_0000092 "Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid.")
AnnotationAssertion(rdfs:label obo:CL_0000092 "osteoclast")
EquivalentClasses(obo:CL_0000092 ObjectIntersectionOf(obo:CL_0000766 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001474) ObjectSomeValuesFrom(obo:BFO_0000051 obo:PR_000001850) ObjectSomeValuesFrom(obo:BFO_0000051 obo:PR_000001937) ObjectSomeValuesFrom(obo:BFO_0000051 obo:PR_000001944) ObjectSomeValuesFrom(obo:BFO_0000051 obo:PR_000007597) ObjectSomeValuesFrom(obo:BFO_0000051 obo:PR_000011178) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001954) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000002062) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0045453)))
SubClassOf(obo:CL_0000092 obo:CL_0000518)
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Did not see this edit reflected in tasks of related ticket.

@aleixpuigb aleixpuigb merged commit f362518 into master Nov 13, 2023
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@aleixpuigb aleixpuigb deleted the 1266_mononuclear_phagocyte branch November 13, 2023 15:01
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[Typo/Bug] mononuclear & multinucleate phagocyte have no children!
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