Skip to content

Commit

Permalink
#4422, #4421, #4422 ,#4415, #4414 (#4423)
Browse files Browse the repository at this point in the history
  • Loading branch information
@ValWood
ValWood authored Sep 5, 2023
1 parent eabe517 commit 3c315be
Showing 1 changed file with 55 additions and 7 deletions.
62 changes: 55 additions & 7 deletions src/ontology/fypo-edit.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8593,8 +8593,13 @@ Declaration(Class(<http://purl.obolibrary.org/obo/FYPO_0008113>))
Declaration(Class(<http://purl.obolibrary.org/obo/FYPO_0008114>))
Declaration(Class(<http://purl.obolibrary.org/obo/FYPO_0008115>))
Declaration(Class(<http://purl.obolibrary.org/obo/FYPO_0008116>))
Declaration(Class(<http://purl.obolibrary.org/obo/FYPO_0008117>))
Declaration(Class(<http://purl.obolibrary.org/obo/FYPO_0008118>))
Declaration(Class(<http://purl.obolibrary.org/obo/FYPO_0008119>))
Declaration(Class(<http://purl.obolibrary.org/obo/FYPO_0008120>))
Declaration(Class(<http://purl.obolibrary.org/obo/FYPO_0008121>))
Declaration(Class(<http://purl.obolibrary.org/obo/FYPO_0008122>))
Declaration(Class(<http://purl.obolibrary.org/obo/FYPO_0008123>))
Declaration(Class(<http://purl.obolibrary.org/obo/FYPO_0009000>))
Declaration(Class(<http://purl.obolibrary.org/obo/FYPO_0009001>))
Declaration(Class(<http://purl.obolibrary.org/obo/FYPO_0009002>))
Expand Down Expand Up @@ -10259,7 +10264,7 @@ AnnotationAssertion(oboInOwl:id <http://purl.obolibrary.org/obo/BFO_0000050> "pa
AnnotationAssertion(oboInOwl:shorthand <http://purl.obolibrary.org/obo/BFO_0000050> "part_of")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000050> "part_of")

# Object Property: <http://purl.obolibrary.org/obo/BFO_0000051> (has part)
# Object Property: <http://purl.obolibrary.org/obo/BFO_0000051> (has_part)

AnnotationAssertion(<http://purl.obolibrary.org/obo/fypo#usage> <http://purl.obolibrary.org/obo/BFO_0000051> "Used in FYPO to link phenotypes that are collections of features to phenotypes representing the features.")
AnnotationAssertion(oboInOwl:hasDbXref <http://purl.obolibrary.org/obo/BFO_0000051> "BFO:0000051")
Expand Down Expand Up @@ -10314,7 +10319,7 @@ AnnotationAssertion(oboInOwl:id <http://purl.obolibrary.org/obo/GOREL_0000501> "
AnnotationAssertion(oboInOwl:shorthand <http://purl.obolibrary.org/obo/GOREL_0000501> "occurs_at")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GOREL_0000501> "occurs_at")

# Object Property: <http://purl.obolibrary.org/obo/RO_0000052> (characteristic of)
# Object Property: <http://purl.obolibrary.org/obo/RO_0000052> (inheres_in)

AnnotationAssertion(<http://purl.obolibrary.org/obo/fypo#usage> <http://purl.obolibrary.org/obo/RO_0000052> "Used in FYPO as described in PATO best practices; identifies an entity that displays a quality in an entity-quality logical definition. Used only in logical definitions (aka xps).")
AnnotationAssertion(oboInOwl:hasDbXref <http://purl.obolibrary.org/obo/RO_0000052> "RO:0000052")
Expand All @@ -10332,7 +10337,7 @@ AnnotationAssertion(oboInOwl:id <http://purl.obolibrary.org/obo/RO_0001025> "loc
AnnotationAssertion(oboInOwl:shorthand <http://purl.obolibrary.org/obo/RO_0001025> "located_in")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0001025> "located in")

# Object Property: <http://purl.obolibrary.org/obo/RO_0002314> (characteristic of part of)
# Object Property: <http://purl.obolibrary.org/obo/RO_0002314> (inheres in part of)

AnnotationAssertion(<http://purl.obolibrary.org/obo/fypo#usage> <http://purl.obolibrary.org/obo/RO_0002314> "Used in FYPO as described in MP/HP logical definition best practices for processes, and in an analogous manner for cell/cell part structure; identifies an entity that displays a quality in an entity-quality logical definition. Used only in logical definitions (aka xps).")
AnnotationAssertion(oboInOwl:hasDbXref <http://purl.obolibrary.org/obo/RO_0002314> "RO:0002314")
Expand All @@ -10350,7 +10355,7 @@ AnnotationAssertion(oboInOwl:id <http://purl.obolibrary.org/obo/RO_0002503> "tow
AnnotationAssertion(oboInOwl:shorthand <http://purl.obolibrary.org/obo/RO_0002503> "towards")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002503> "towards")

# Object Property: <http://purl.obolibrary.org/obo/RO_0002573> (has modifier)
# Object Property: <http://purl.obolibrary.org/obo/RO_0002573> (qualifier)

AnnotationAssertion(<http://purl.obolibrary.org/obo/fypo#usage> <http://purl.obolibrary.org/obo/RO_0002573> "Used in FYPO as described in PATO best practices; placeholder relation to indicate normality/abnormality.")
AnnotationAssertion(oboInOwl:hasDbXref <http://purl.obolibrary.org/obo/RO_0002573> "RO:0002573")
Expand Down Expand Up @@ -67391,17 +67396,17 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FYPO_0003809> "no
EquivalentClasses(<http://purl.obolibrary.org/obo/FYPO_0003809> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FYPO_0001357> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/BTO_0000316>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002503> <http://purl.obolibrary.org/obo/CHEBI_69136>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002573> <http://purl.obolibrary.org/obo/PATO_0000467>))))
SubClassOf(<http://purl.obolibrary.org/obo/FYPO_0003809> <http://purl.obolibrary.org/obo/FYPO_0001357>)

# Class: <http://purl.obolibrary.org/obo/FYPO_0003810> (small mitochondria present in increased numbers, with normal total mitochondrial volume)
# Class: <http://purl.obolibrary.org/obo/FYPO_0003810> (small fragmented mitochondria present in increased numbers)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FYPO_0003810> "A cell phenotype observed in the vegetative growth phase of the life cycle in which total mitochondrial volume is normal, but mitochondria are smaller and more numerous than normal.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FYPO_0003810> "A cell phenotype observed in the vegetative growth phase of the life cycle in which mitochondria are smaller and more numerous than normal. Total mitochondrial volume is usually similar to normal.")
AnnotationAssertion(oboInOwl:created_by <http://purl.obolibrary.org/obo/FYPO_0003810> "midori")
AnnotationAssertion(oboInOwl:creation_date <http://purl.obolibrary.org/obo/FYPO_0003810> "2014-09-12T14:56:05Z")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasExactSynonym <http://purl.obolibrary.org/obo/FYPO_0003810> "small mitochondria present in increased numbers during vegetative growth")
AnnotationAssertion(oboInOwl:hasOBONamespace <http://purl.obolibrary.org/obo/FYPO_0003810> "fission_yeast_phenotype")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym <http://purl.obolibrary.org/obo/FYPO_0003810> "fragmented mitochondria")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRelatedSynonym <http://purl.obolibrary.org/obo/FYPO_0003810> "small mitochondria present in increased numbers during mitotic cell cycle")
AnnotationAssertion(oboInOwl:id <http://purl.obolibrary.org/obo/FYPO_0003810> "FYPO:0003810")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FYPO_0003810> "small mitochondria present in increased numbers, with normal total mitochondrial volume")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FYPO_0003810> "small fragmented mitochondria present in increased numbers")
SubClassOf(<http://purl.obolibrary.org/obo/FYPO_0003810> <http://purl.obolibrary.org/obo/FYPO_0001322>)
SubClassOf(<http://purl.obolibrary.org/obo/FYPO_0003810> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/FYPO_0007193>))
SubClassOf(<http://purl.obolibrary.org/obo/FYPO_0003810> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/FYPO_0007210>))
Expand Down Expand Up @@ -118412,6 +118417,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PomBase:mah") oboInOwl:hasRel
AnnotationAssertion(oboInOwl:id <http://purl.obolibrary.org/obo/FYPO_0007193> "FYPO:0007193")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FYPO_0007193> "small mitochondria")
EquivalentClasses(<http://purl.obolibrary.org/obo/FYPO_0007193> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000596> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/GOREL_0000032> <http://purl.obolibrary.org/obo/GO_0072690>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/GO_0005739>))))
SubClassOf(<http://purl.obolibrary.org/obo/FYPO_0007193> <http://purl.obolibrary.org/obo/FYPO_0000359>)
SubClassOf(<http://purl.obolibrary.org/obo/FYPO_0007193> <http://purl.obolibrary.org/obo/FYPO_0001322>)

# Class: <http://purl.obolibrary.org/obo/FYPO_0007194> (mitochondria present in increased numbers)
Expand Down Expand Up @@ -130863,6 +130869,15 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FYPO_0008116> "de
EquivalentClasses(<http://purl.obolibrary.org/obo/FYPO_0008116> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000911> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/GO_0004619>))))
SubClassOf(<http://purl.obolibrary.org/obo/FYPO_0008116> <http://purl.obolibrary.org/obo/FYPO_0000663>)

# Class: <http://purl.obolibrary.org/obo/FYPO_0008117> (abnormal de novo SAGA complex assembly)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31748520") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FYPO_0008117> "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which de novo assembly of the SAGA complex is abnormal.")
AnnotationAssertion(oboInOwl:created_by <http://purl.obolibrary.org/obo/FYPO_0008117> "vw")
AnnotationAssertion(oboInOwl:creation_dat <http://purl.obolibrary.org/obo/FYPO_0008117> "2023-09-05T16:22:58Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/FYPO_0008117> "Note that this term refers to the abnormal biogenesis of the complex, i.e. the process of building the complex from individual subunits. For assays identifyion alterations in complex subunit composition use 'abnormal protein complex composition FYPO:0005003' or 'abnormal protein-protein interaction\" (FYPO:0000704) or their descendants.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FYPO_0008117> "abnormal de novo SAGA complex assembly"@en)
SubClassOf(<http://purl.obolibrary.org/obo/FYPO_0008117> <http://purl.obolibrary.org/obo/FYPO_0000447>)

# Class: <http://purl.obolibrary.org/obo/FYPO_0008118> (decreased splicing of introns with branch point-distant 3’-splice site)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36095128") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FYPO_0008118> "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which mRNA splicing via the spliceosome is decreased for specific introns with longer than average (>21 bp) branch site to acceptor distance.")
Expand All @@ -130880,6 +130895,39 @@ AnnotationAssertion(oboInOwl:creation_dat <http://purl.obolibrary.org/obo/FYPO_0
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FYPO_0008119> "normal morphology during phosphate starvation"@en)
SubClassOf(<http://purl.obolibrary.org/obo/FYPO_0008119> <http://purl.obolibrary.org/obo/FYPO_0000672>)

# Class: <http://purl.obolibrary.org/obo/FYPO_0008120> (decreased protein level in SAGA complex)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31748520") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FYPO_0008120> "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of a protein measured in the SAGA complex is lower than normal.")
AnnotationAssertion(oboInOwl:created_by <http://purl.obolibrary.org/obo/FYPO_0008120> "vw")
AnnotationAssertion(oboInOwl:creation_dat <http://purl.obolibrary.org/obo/FYPO_0008120> "2023-09-05T16:37:08Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FYPO_0008120> "decreased protein level in SAGA complex"@en)
SubClassOf(<http://purl.obolibrary.org/obo/FYPO_0008120> <http://purl.obolibrary.org/obo/FYPO_0005003>)

# Class: <http://purl.obolibrary.org/obo/FYPO_0008121> (decreased protein level in NuA4 complex)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31748520") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FYPO_0008121> "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of a protein measured in the NuA4 complex is lower than normal.")
AnnotationAssertion(oboInOwl:created_by <http://purl.obolibrary.org/obo/FYPO_0008121> "vw")
AnnotationAssertion(oboInOwl:creation_dat <http://purl.obolibrary.org/obo/FYPO_0008121> "2023-09-05T16:40:45Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FYPO_0008121> "decreased protein level in NuA4 complex"@en)
SubClassOf(<http://purl.obolibrary.org/obo/FYPO_0008121> <http://purl.obolibrary.org/obo/FYPO_0005003>)

# Class: <http://purl.obolibrary.org/obo/FYPO_0008122> (increased mitochondrial fusion)

AnnotationAssertion(Annotation(<http://purl.obolibrary.org/obo/IAO_0000115> "PMID:37590302") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FYPO_0008122> "A cellular process phenotype in which mitochondrion fusion is increased.")
AnnotationAssertion(oboInOwl:created_by <http://purl.obolibrary.org/obo/FYPO_0008122> "vw")
AnnotationAssertion(oboInOwl:creation_dat <http://purl.obolibrary.org/obo/FYPO_0008122> "2023-09-05T16:53:41Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FYPO_0008122> "increased mitochondrial fusion"@en)
SubClassOf(<http://purl.obolibrary.org/obo/FYPO_0008122> <http://purl.obolibrary.org/obo/FYPO_0008089>)

# Class: <http://purl.obolibrary.org/obo/FYPO_0008123> (loss of viability in stationary phase upon phopshate starvation)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36794724") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FYPO_0008123> "A cell population phenotype in which a smaller than normal proportion of cells in the population remains viable after entering stationary phase, when cells the population are subject to phosphate starvation.")
AnnotationAssertion(oboInOwl:created_by <http://purl.obolibrary.org/obo/FYPO_0008123> "vw")
AnnotationAssertion(oboInOwl:creation_dat <http://purl.obolibrary.org/obo/FYPO_0008123> "2023-09-05T16:57:32Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasExactSynonym <http://purl.obolibrary.org/obo/FYPO_0008123> "decreased chronological lifespan of phosphate-starved cells")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FYPO_0008123> "loss of viability in stationary phase upon phopshate starvation"@en)
SubClassOf(<http://purl.obolibrary.org/obo/FYPO_0008123> <http://purl.obolibrary.org/obo/FYPO_0000245>)

# Class: <http://purl.obolibrary.org/obo/FYPO_0009000> (decreased rate of cytoplasmic microtubule polymerization during mitotic interphase)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36633091") Annotation(oboInOwl:hasDbXref "PomBase:mlr") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FYPO_0009000> "A microtubule cytoskeleton organization phenotype observed during mitotic interphase in which cytoplasmic microtubule polymerization, i.e. the addition of tubulin dimers to the plus end of a microtubule occurs at a lower rate, or speed, than normal.")
Expand Down

0 comments on commit 3c315be

Please sign in to comment.