Skip to content

Commit

Permalink
Fixes #2480 Refactor multinucleated cells and subclasses (#2501)
Browse files Browse the repository at this point in the history 
* Fixes #2480

- Added a new term (syncytial cell)

* Update cl-edit.owl

* Update cl-edit.owl

* Added supporting references

Added references to support that obliquely striated somatic muscle cell is a mono-nucleated cell.

* updated the classification of multinucleated giant cells

Added multinucleated giant cells under syncytial cell

* Changes made based on feedback

* updated references

* updated syncytial cell ID

* Update cl-edit.owl

* Revert "Update cl-edit.owl"

This reverts commit c46c955.

* Add multiciliated ependymal cell

This cell is merged in the master branch and has been deleted by mistake

---------

Co-authored-by: aleixpuig <[email protected]>
  • Loading branch information
@Caroline-99 @aleixpuigb
Caroline-99 and aleixpuigb authored Aug 20, 2024
1 parent 74b3da8 commit b135731
Showing 1 changed file with 29 additions and 13 deletions.
42 changes: 29 additions & 13 deletions src/ontology/cl-edit.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3059,6 +3059,7 @@ Declaration(Class(obo:CL_4042014))
Declaration(Class(obo:CL_4042015))
Declaration(Class(obo:CL_4042016))
Declaration(Class(obo:CL_4052001))
Declaration(Class(obo:CL_4052002))
Declaration(Class(obo:CP_0000000))
Declaration(Class(obo:CP_0000025))
Declaration(Class(obo:CP_0000027))
Expand Down Expand Up @@ -5624,12 +5625,9 @@ EquivalentClasses(obo:CL_0000227 ObjectIntersectionOf(obo:CL_0000000 ObjectSomeV

# Class: obo:CL_0000228 (multinucleate cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "FB:ma") obo:IAO_0000115 obo:CL_0000228 "A cell with more than one nucleus.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000228 "AEO:0000203")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000228 "WBbt:0008074")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000228 "syncitium")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000228 "syncytial cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000228 "syncytium")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "FB:ma") Annotation(oboInOwl:hasDbXref "Wikipedia:Multinucleate") obo:IAO_0000115 obo:CL_0000228 "A cell with more than one nucleus.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Multinucleate") oboInOwl:hasExactSynonym obo:CL_0000228 "multinucleated cells")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Multinucleate") oboInOwl:hasExactSynonym obo:CL_0000228 "polynuclear cells")
AnnotationAssertion(rdfs:label obo:CL_0000228 "multinucleate cell")
EquivalentClasses(obo:CL_0000228 ObjectIntersectionOf(obo:CL_0000000 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001908)))

Expand Down Expand Up @@ -7033,9 +7031,12 @@ SubClassOf(obo:CL_0000419 obo:CL_0000036)

# Class: obo:CL_0000420 (syncytial epithelial cell)

AnnotationAssertion(obo:IAO_0000115 obo:CL_0000420 "An epithelial cell that forms a syncytium, which is a multinucleated cell resulting from the fusion of multiple cells.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000420 "Wikipedia:Syncytium")
AnnotationAssertion(rdfs:label obo:CL_0000420 "syncytial epithelial cell")
SubClassOf(obo:CL_0000420 obo:CL_0000066)
SubClassOf(obo:CL_0000420 obo:CL_0000228)
SubClassOf(obo:CL_0000420 obo:CL_4052002)

# Class: obo:CL_0000421 (coelomocyte)

Expand Down Expand Up @@ -7859,6 +7860,7 @@ AnnotationAssertion(rdfs:label obo:CL_0000525 "syncytiotrophoblast cell")
AnnotationAssertion(rdfs:seeAlso obo:CL_0000525 "https://github.com/obophenotype/cell-ontology/issues/2100")
EquivalentClasses(obo:CL_0000525 ObjectIntersectionOf(obo:CL_0000351 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001908)))
SubClassOf(obo:CL_0000525 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000371))
SubClassOf(obo:CL_0000525 ObjectSomeValuesFrom(obo:RO_0000056 obo:GO_0000768))

# Class: obo:CL_0000526 (afferent neuron)

Expand Down Expand Up @@ -9022,7 +9024,7 @@ SubClassOf(obo:CL_0000646 obo:CL_0000036)

# Class: obo:CL_0000647 (multinucleated giant cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:add") Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:0702022918") Annotation(oboInOwl:hasDbXref "ISBN:0702024783") obo:IAO_0000115 obo:CL_0000647 "A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:add") Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:0702022918") Annotation(oboInOwl:hasDbXref "ISBN:0702024783") Annotation(oboInOwl:hasDbXref "PMID:33348900") Annotation(oboInOwl:hasDbXref "Wikipedia:Giant_cell") obo:IAO_0000115 obo:CL_0000647 "A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000647 "BTO:0003107")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000647 "FMA:83035")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000647 "MESH:D015726")
Expand All @@ -9031,10 +9033,12 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ISBN:0702022918") Annotation(
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ISBN:0702022918") Annotation(oboInOwl:hasDbXref "ISBN:0702024783") oboInOwl:hasExactSynonym obo:CL_0000647 "macrophage polykaryon")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ISBN:0702022918") Annotation(oboInOwl:hasDbXref "ISBN:0702024783") oboInOwl:hasExactSynonym obo:CL_0000647 "multinucleate giant cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ISBN:0702022918") Annotation(oboInOwl:hasDbXref "ISBN:0702024783") oboInOwl:hasExactSynonym obo:CL_0000647 "syncytial giant cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33348900") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_0000647 "MGC")
AnnotationAssertion(rdfs:comment obo:CL_0000647 "Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this.")
AnnotationAssertion(rdfs:label obo:CL_0000647 "multinucleated giant cell")
EquivalentClasses(obo:CL_0000647 ObjectIntersectionOf(obo:CL_0000766 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001908) ObjectSomeValuesFrom(obo:RO_0000056 obo:GO_0002432) ObjectSomeValuesFrom(obo:RO_0000056 obo:GO_0002544)))
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000647 obo:CL_0000766)
SubClassOf(obo:CL_0000647 ObjectSomeValuesFrom(obo:RO_0000056 obo:GO_0000768))
SubClassOf(obo:CL_0000647 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000235))

# Class: obo:CL_0000648 (kidney granular cell)
Expand Down Expand Up @@ -10179,12 +10183,13 @@ SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000778 obo:CL_0000092

# Class: obo:CL_0000779 (multinuclear osteoclast)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:add") Annotation(oboInOwl:hasDbXref "PMID:12713016") Annotation(oboInOwl:hasDbXref "PMID:9415452") obo:IAO_0000115 obo:CL_0000779 "A specialized multinuclear osteoclast associated with the absorption and removal of bone.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:add") Annotation(oboInOwl:hasDbXref "PMID:12713016") Annotation(oboInOwl:hasDbXref "PMID:29379067") Annotation(oboInOwl:hasDbXref "PMID:38903088") Annotation(oboInOwl:hasDbXref "PMID:9415452") obo:IAO_0000115 obo:CL_0000779 "A specialized multinuclear osteoclast, forming a syncytium through the fusion of mononuclear precursor cells, associated with the absorption and removal of bone.")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000779 "multinucleated osteoclast")
AnnotationAssertion(rdfs:comment obo:CL_0000779 "Morphology: multinucleated, highly vesicular.")
AnnotationAssertion(rdfs:label obo:CL_0000779 "multinuclear osteoclast")
EquivalentClasses(obo:CL_0000779 ObjectIntersectionOf(obo:CL_0000092 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001908)))
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000779 obo:CL_0000092)
SubClassOf(obo:CL_0000779 ObjectSomeValuesFrom(obo:RO_0000056 obo:GO_0000768))
SubClassOf(obo:CL_0000779 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000778))

# Class: obo:CL_0000780 (multinuclear odontoclast)
Expand Down Expand Up @@ -17604,13 +17609,14 @@ AnnotationAssertion(owl:deprecated obo:CL_0002371 "true"^^xsd:boolean)

# Class: obo:CL_0002372 (myotube)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos") Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:0323052908") Annotation(oboInOwl:hasDbXref "PMID:22274696") obo:IAO_0000115 obo:CL_0002372 "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos") Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:0323052908") Annotation(oboInOwl:hasDbXref "PMID:22274696") obo:IAO_0000115 obo:CL_0002372 "A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development.")
AnnotationAssertion(terms:contributor obo:CL_0002372 <https://orcid.org/0000-0003-1980-3228>)
AnnotationAssertion(oboInOwl:creation_date obo:CL_0002372 "2010-09-24T01:13:01Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002372 "myotubule")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002372 "single cell sarcomere")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "FBbt:00005812") oboInOwl:hasExactSynonym obo:CL_0002372 "myofiber")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "FBbt:00005812") oboInOwl:hasExactSynonym obo:CL_0002372 "myofibril")
AnnotationAssertion(rdfs:label obo:CL_0002372 "myotube")
EquivalentClasses(obo:CL_0002372 ObjectIntersectionOf(obo:CL_0000187 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0030017) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001908) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002478)))
SubClassOf(obo:CL_0002372 ObjectSomeValuesFrom(obo:RO_0000056 obo:GO_0000768))

# Class: obo:CL_0002373 (growth hormone releasing hormone secreting cell)

Expand Down Expand Up @@ -22345,9 +22351,9 @@ SubClassOf(obo:CL_0008004 obo:CL_0000187)

# Class: obo:CL_0008005 (obliquely striated somatic muscle cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:8720463") obo:IAO_0000115 obo:CL_0008005 "A somatic muscle cell that is oblquely striated. Examples include the somatic muscles of nematodes.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:8720463") Annotation(oboInOwl:hasDbXref "doi:10.3908/wormatlas.1.7") obo:IAO_0000115 obo:CL_0008005 "A somatic muscle cell that is obliquely striated and mononucleated. Examples include the somatic muscles of nematodes.")
AnnotationAssertion(rdfs:label obo:CL_0008005 "obliquely striated somatic muscle cell")
EquivalentClasses(obo:CL_0008005 ObjectIntersectionOf(obo:CL_0008004 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0030017) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001908) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002479)))
EquivalentClasses(obo:CL_0008005 ObjectIntersectionOf(obo:CL_0008004 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0030017) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001407) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002479)))
SubClassOf(obo:CL_0008005 obo:CL_0008004)

# Class: obo:CL_0008006 (muscle founder cell)
Expand Down Expand Up @@ -32258,6 +32264,16 @@ SubClassOf(obo:CL_4052001 obo:CL_0005012)
SubClassOf(obo:CL_4052001 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005357))
SubClassOf(obo:CL_4052001 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0031514))

# Class: obo:CL_4052002 (syncytial cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20851884") Annotation(oboInOwl:hasDbXref "Wikipedia:Syncytium") obo:IAO_0000115 obo:CL_4052002 "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm.")
AnnotationAssertion(terms:contributor obo:CL_4052002 <https://orcid.org/0009-0000-8480-9277>)
AnnotationAssertion(terms:date obo:CL_4052002 "2024-08-15T10:38:46Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "WBbt:0008074") oboInOwl:hasExactSynonym obo:CL_4052002 "syncytium")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:9067520") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4052002 "SC")
AnnotationAssertion(rdfs:label obo:CL_4052002 "syncytial cell")
EquivalentClasses(obo:CL_4052002 ObjectIntersectionOf(obo:CL_0000000 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001908) ObjectSomeValuesFrom(obo:RO_0000056 obo:GO_0000768)))

# Class: obo:CP_0000000 (obsolete CP:0000000)

AnnotationAssertion(obo:IAO_0100001 obo:CP_0000000 obo:CL_0017500)
Expand Down

0 comments on commit b135731

Please sign in to comment.