Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Added protein terms_4 #344

Merged
merged 2 commits into from
Sep 12, 2024
Merged

Added protein terms_4 #344

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
74b4889
Added protein terms_4
ar-ibrahim Sep 12, 2024
13666c6
Update dosdp patterns file
ar-ibrahim Sep 12, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
33 changes: 30 additions & 3 deletions src/ontology/imports/merged_import.owl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/oba/imports/merged_import.owl>
<http://purl.obolibrary.org/obo/oba/releases/2024-09-06/imports/merged_import.owl>
Annotation(owl:versionInfo "2024-09-06")
<http://purl.obolibrary.org/obo/oba/releases/2024-09-11/imports/merged_import.owl>
Annotation(owl:versionInfo "2024-09-11")

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
Expand Down Expand Up @@ -29482,6 +29482,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012890>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012891>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012892>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012895>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012896>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012898>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012899>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012901>))
Expand Down Expand Up @@ -35336,6 +35337,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PR_O35955>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_O35969>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_O35988>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_O43150>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_O43157>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_O43173>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_O43175>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_O43181>))
Expand Down Expand Up @@ -41607,6 +41609,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8CJ91>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8CJF9>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8CJG0>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8CJG1>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8CJH3>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8HW98>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8IU57>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8IU80>))
Expand Down Expand Up @@ -55377,7 +55380,7 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0004023> "caus
SubObjectPropertyOf(<http://purl.obolibrary.org/obo/RO_0004023> <http://purl.obolibrary.org/obo/RO_0002410>)
SubObjectPropertyOf(<http://purl.obolibrary.org/obo/RO_0004023> <http://purl.obolibrary.org/obo/RO_0040035>)

# Object Property: <http://purl.obolibrary.org/obo/RO_0004024> (disease causes disruption of)
# Object Property: <http://purl.obolibrary.org/obo/RO_0004024> (disease disrupts)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0004024> "A relationship between a disease and a process where the disease process disrupts the execution of the process.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0004024> "disease causes disruption of")
Expand Down Expand Up @@ -269394,6 +269397,12 @@ AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/PR_000012895> "
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PR_000012895> "plexin-A4")
SubClassOf(<http://purl.obolibrary.org/obo/PR_000012895> <http://purl.obolibrary.org/obo/PR_000000001>)

# Class: <http://purl.obolibrary.org/obo/PR_000012896> (plexin-B1)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/PR_000012896> "Category=gene.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PR_000012896> "plexin-B1")
SubClassOf(<http://purl.obolibrary.org/obo/PR_000012896> <http://purl.obolibrary.org/obo/PR_000000001>)

# Class: <http://purl.obolibrary.org/obo/PR_000012898> (plexin-B3)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/PR_000012898> "Category=gene.")
Expand Down Expand Up @@ -314010,6 +314019,15 @@ SubClassOf(<http://purl.obolibrary.org/obo/PR_O43150> <http://purl.obolibrary.or
SubClassOf(<http://purl.obolibrary.org/obo/PR_O43150> <http://purl.obolibrary.org/obo/PR_000029067>)
SubClassOf(<http://purl.obolibrary.org/obo/PR_O43150> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002160> <http://purl.obolibrary.org/obo/NCBITaxon_9606>))

# Class: <http://purl.obolibrary.org/obo/PR_O43157> (plexin-B1 (human))

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/PR_O43157> "Category=organism-gene.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PR_O43157> "plexin-B1 (human)")
EquivalentClasses(<http://purl.obolibrary.org/obo/PR_O43157> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PR_000012896> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002160> <http://purl.obolibrary.org/obo/NCBITaxon_9606>)))
SubClassOf(<http://purl.obolibrary.org/obo/PR_O43157> <http://purl.obolibrary.org/obo/PR_000012896>)
SubClassOf(<http://purl.obolibrary.org/obo/PR_O43157> <http://purl.obolibrary.org/obo/PR_000029067>)
SubClassOf(<http://purl.obolibrary.org/obo/PR_O43157> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002160> <http://purl.obolibrary.org/obo/NCBITaxon_9606>))

# Class: <http://purl.obolibrary.org/obo/PR_O43173> (sia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase (human))

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/PR_O43173> "Category=organism-gene.")
Expand Down Expand Up @@ -370406,6 +370424,15 @@ SubClassOf(<http://purl.obolibrary.org/obo/PR_Q8CJG1> <http://purl.obolibrary.or
SubClassOf(<http://purl.obolibrary.org/obo/PR_Q8CJG1> <http://purl.obolibrary.org/obo/PR_000029032>)
SubClassOf(<http://purl.obolibrary.org/obo/PR_Q8CJG1> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002160> <http://purl.obolibrary.org/obo/NCBITaxon_10090>))

# Class: <http://purl.obolibrary.org/obo/PR_Q8CJH3> (plexin-B1 (mouse))

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/PR_Q8CJH3> "Category=organism-gene.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PR_Q8CJH3> "plexin-B1 (mouse)")
EquivalentClasses(<http://purl.obolibrary.org/obo/PR_Q8CJH3> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PR_000012896> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002160> <http://purl.obolibrary.org/obo/NCBITaxon_10090>)))
SubClassOf(<http://purl.obolibrary.org/obo/PR_Q8CJH3> <http://purl.obolibrary.org/obo/PR_000012896>)
SubClassOf(<http://purl.obolibrary.org/obo/PR_Q8CJH3> <http://purl.obolibrary.org/obo/PR_000029032>)
SubClassOf(<http://purl.obolibrary.org/obo/PR_Q8CJH3> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002160> <http://purl.obolibrary.org/obo/NCBITaxon_10090>))

# Class: <http://purl.obolibrary.org/obo/PR_Q8HW98> (IgLON family member 5 (mouse))

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/PR_Q8HW98> "Category=organism-gene.")
Expand Down
1 change: 1 addition & 0 deletions src/patterns/data/default/entity_attribute_location.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7055,3 +7055,4 @@ OBA:2051958 level of lymphocyte antigen 75 isoform 4 and LY75-CD302 fusion isofo
OBA:2051959 level of neuroendocrine secretory protein 55 isoform Nesp55 (human) in blood PR:O95467-1 neuroendocrine secretory protein 55 isoform Nesp55 (human) PATO:0000070 amount UBERON:0000178 blood PMID:37794183 https://orcid.org/0000-0001-6757-4744
OBA:2051960 level of immunoglobulin lambda constant 2 (human) in blood PR:P0DOY2 immunoglobulin lambda constant 2 (human) PATO:0000070 amount UBERON:0000178 blood PMID:37794183 https://orcid.org/0000-0001-6757-4744
OBA:2051961 level of progesterone-induced-blocking factor 1 (human) in blood PR:Q8WXW3 progesterone-induced-blocking factor 1 (human) PATO:0000070 amount UBERON:0000178 blood PMID:37794183 https://orcid.org/0000-0001-6757-4744
OBA:2051962 level of plexin-B1 in blood PR:000012896 plexin-B1 PATO:0000070 amount UBERON:0000178 blood PMID:34857772 https://orcid.org/0000-0001-6757-4744
15 changes: 13 additions & 2 deletions src/patterns/definitions.owl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/oba/patterns/definitions.owl>
<http://purl.obolibrary.org/obo/oba/releases/2024-09-09/patterns/definitions.owl>
Annotation(owl:versionInfo "2024-09-09")
<http://purl.obolibrary.org/obo/oba/releases/2024-09-12/patterns/definitions.owl>
Annotation(owl:versionInfo "2024-09-12")

Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10033>))
Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10112>))
Expand Down Expand Up @@ -14192,6 +14192,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2051958>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2051959>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2051960>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2051961>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2051962>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2060000>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2060001>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2060002>))
Expand Down Expand Up @@ -20227,6 +20228,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012890>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012891>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012892>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012895>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012896>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012898>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012899>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012901>))
Expand Down Expand Up @@ -121479,6 +121481,15 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#has
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2051961> "level of progesterone-induced-blocking factor 1 (human) in blood")
EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2051961> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000070> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PR_Q8WXW3> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000178>)))))

# Class: <http://purl.obolibrary.org/obo/OBA_2051962> (level of plexin-B1 in blood)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute_location") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_2051962> "The amount of a plexin-B1 when measured in blood.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_2051962> "https://orcid.org/0000-0001-6757-4744")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/OBA_2051962> "PMID:34857772")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute_location") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_2051962> "blood plexin-B1 amount")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2051962> "level of plexin-B1 in blood")
EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2051962> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000070> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PR_000012896> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000178>)))))

# Class: <http://purl.obolibrary.org/obo/OBA_2060000> (aggressive behavior towards inanimate objects rate)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_2060000> "The rate of a aggressive behavior towards inanimate objects.")
Expand Down