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Merged
andreagaede merged 11 commits into from
Apr 4, 2026
Merged

Development #20

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7e4f6aa
Added new terms for Babu lab
jesshaley Mar 30, 2026
a7148ac
Added C. elegans strains
jesshaley Mar 30, 2026
e6f05ae
updated empty terms with Babu terms
andreagaede Mar 30, 2026
37d3eb7
added volatile delivery
andreagaede Mar 30, 2026
29d124b
updating Babu terms
andreagaede Mar 30, 2026
6554a92
Update empty-edit.owl
jesshaley Mar 31, 2026
0f98b7e
Added chemotaxis video term
jesshaley Apr 1, 2026
c975234
Update empty-edit.owl
jesshaley Apr 2, 2026
7f7abae
Update empty-edit.owl
jesshaley Apr 3, 2026
6e4c555
added Babu terms
andreagaede Apr 4, 2026
8a82df7
new release with Babu terms
andreagaede Apr 4, 2026
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493 changes: 435 additions & 58 deletions empty-base.json
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285 changes: 227 additions & 58 deletions empty-base.obo
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415 changes: 357 additions & 58 deletions empty-base.owl
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1,893 changes: 1,400 additions & 493 deletions empty-full.json
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1,012 changes: 697 additions & 315 deletions empty-full.obo
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2,053 changes: 1,512 additions & 541 deletions empty-full.owl
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474 changes: 415 additions & 59 deletions empty-simple.json
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282 changes: 224 additions & 58 deletions empty-simple.obo
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397 changes: 339 additions & 58 deletions empty-simple.owl
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1,893 changes: 1,400 additions & 493 deletions empty.json
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1,012 changes: 697 additions & 315 deletions empty.obo
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2,053 changes: 1,512 additions & 541 deletions empty.owl
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311 changes: 255 additions & 56 deletions src/ontology/empty-edit.owl
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2 changes: 1 addition & 1 deletion src/ontology/empty-edit.properties
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#Thu Feb 12 19:34:43 GMT 2026
#Mon Mar 30 22:06:40 BST 2026
jdbc.password=
jdbc.user=
jdbc.url=
Expand Down
52 changes: 50 additions & 2 deletions src/ontology/imports/ncbitaxon_import.owl
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Expand Up @@ -7,11 +7,13 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/empty/imports/ncbitaxon_import.owl>
<http://purl.obolibrary.org/obo/empty/releases/2026-02-23/imports/ncbitaxon_import.owl>
<http://purl.obolibrary.org/obo/empty/releases/2026-04-04/imports/ncbitaxon_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/ncbitaxon/2025-12-03/ncbitaxon.owl>)
Annotation(owl:versionInfo "2026-02-23")
Annotation(owl:versionInfo "2026-04-04")

Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_1>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_1224>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_1236>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_131209>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_131221>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_131567>))
Expand All @@ -38,6 +40,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_33630>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_33682>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_3372>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_3378>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_3379134>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_3398>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_34346>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_35493>))
Expand All @@ -54,12 +57,17 @@ Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_4895>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_4896>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_4930>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_4932>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_543>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_554915>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_561>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_562>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_5782>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_58023>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_58024>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_637912>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_716545>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_78536>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_91347>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
Declaration(AnnotationProperty(<http://purl.org/dc/terms/description>))
Expand Down Expand Up @@ -88,6 +96,16 @@ AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#has

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_1> "root")

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_1224> (Pseudomonadota)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_1224> "Pseudomonadota")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_1224> <http://purl.obolibrary.org/obo/NCBITaxon_3379134>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_1236> (Gammaproteobacteria)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_1236> "Gammaproteobacteria")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_1236> <http://purl.obolibrary.org/obo/NCBITaxon_1224>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_131209> (Zygnematophyceae)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_131209> "Zygnematophyceae")
Expand Down Expand Up @@ -218,6 +236,11 @@ SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_3372> <http://purl.obolibra
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_3378> "Gnetales")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_3378> <http://purl.obolibrary.org/obo/NCBITaxon_1445966>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_3379134> (Pseudomonadati)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_3379134> "Pseudomonadati")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_3379134> <http://purl.obolibrary.org/obo/NCBITaxon_2>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_3398> (Magnoliopsida)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_3398> "Magnoliopsida")
Expand Down Expand Up @@ -298,11 +321,26 @@ SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_4930> <http://purl.obolibra
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_4932> "Saccharomyces cerevisiae")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_4932> <http://purl.obolibrary.org/obo/NCBITaxon_4930>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_543> (Enterobacteriaceae)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_543> "Enterobacteriaceae")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_543> <http://purl.obolibrary.org/obo/NCBITaxon_91347>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_554915> (Amoebozoa)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_554915> "Amoebozoa")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_554915> <http://purl.obolibrary.org/obo/NCBITaxon_2759>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_561> (Escherichia)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_561> "Escherichia")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_561> <http://purl.obolibrary.org/obo/NCBITaxon_543>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_562> (Escherichia coli)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_562> "Escherichia coli")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_562> <http://purl.obolibrary.org/obo/NCBITaxon_561>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_5782> (Dictyostelium)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_5782> "Dictyostelium")
Expand All @@ -318,6 +356,11 @@ SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_58023> <http://purl.obolibr
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_58024> "Spermatophyta")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_58024> <http://purl.obolibrary.org/obo/NCBITaxon_78536>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_637912> (Escherichia coli OP50)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_637912> "Escherichia coli OP50")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_637912> <http://purl.obolibrary.org/obo/NCBITaxon_562>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_716545> (saccharomyceta)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_716545> "saccharomyceta")
Expand All @@ -328,5 +371,10 @@ SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_716545> <http://purl.obolib
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_78536> "Euphyllophyta")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_78536> <http://purl.obolibrary.org/obo/NCBITaxon_58023>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_91347> (Enterobacterales)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_91347> "Enterobacterales")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_91347> <http://purl.obolibrary.org/obo/NCBITaxon_1236>)


)
55 changes: 52 additions & 3 deletions src/ontology/imports/ncit_import.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/empty/imports/ncit_import.owl>
<http://purl.obolibrary.org/obo/empty/releases/2026-02-23/imports/ncit_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/ncit/releases/2025-08-06/ncit.owl>)
Annotation(owl:versionInfo "2026-02-23")
<http://purl.obolibrary.org/obo/empty/releases/2026-04-04/imports/ncit_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/ncit/releases/2026-03-19/ncit.owl>)
Annotation(owl:versionInfo "2026-04-04")

Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C12219>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C14183>))
Expand All @@ -19,10 +19,15 @@ Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C142485>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C14250>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C14354>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C14376>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C16203>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C16847>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C16853>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C16856>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C17187>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C172272>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C17369>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C179817>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C17995>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C18141>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C18912>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C19160>))
Expand All @@ -37,8 +42,10 @@ Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C25167>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C25180>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C25198>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C25206>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C25218>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C25284>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C25285>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C25294>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C25335>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C25364>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C25365>))
Expand All @@ -62,6 +69,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C69244>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C70663>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C70766>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C73706>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C74957>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C85776>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C85845>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C88206>))
Expand Down Expand Up @@ -138,11 +146,27 @@ SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C14354> <http://purl.obolibrary.
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C14376> "Other Organism Groupings")
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C14376> <http://purl.obolibrary.org/obo/NCIT_C14250>)

# Class: <http://purl.obolibrary.org/obo/NCIT_C16203> (Clinical or Research Activity)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C16203> "Clinical or Research Activity")
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C16203> <http://purl.obolibrary.org/obo/NCIT_C43431>)

# Class: <http://purl.obolibrary.org/obo/NCIT_C16847> (Technique)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C16847> "Technique")
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C16847> <http://purl.obolibrary.org/obo/NCIT_C43431>)

# Class: <http://purl.obolibrary.org/obo/NCIT_C16853> (Microscopy)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C16853> "Microscopy")
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C16853> <http://purl.obolibrary.org/obo/NCIT_C17369>)
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C16853> <http://purl.obolibrary.org/obo/NCIT_C74957>)

# Class: <http://purl.obolibrary.org/obo/NCIT_C16856> (Fluorescence Microscopy)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C16856> "Fluorescence Microscopy")
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C16856> <http://purl.obolibrary.org/obo/NCIT_C17995>)

# Class: <http://purl.obolibrary.org/obo/NCIT_C17187> (Technology)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C17187> "Technology")
Expand All @@ -153,12 +177,22 @@ SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C17187> <http://purl.obolibrary.
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C172272> "Electronic File Content Type")
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C172272> <http://purl.obolibrary.org/obo/NCIT_C25284>)

# Class: <http://purl.obolibrary.org/obo/NCIT_C17369> (Imaging Procedure)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C17369> "Imaging Procedure")
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C17369> <http://purl.obolibrary.org/obo/NCIT_C25218>)

# Class: <http://purl.obolibrary.org/obo/NCIT_C179817> (Velocity)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C179817> "Velocity")
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C179817> <http://purl.obolibrary.org/obo/NCIT_C25447>)
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C179817> <http://purl.obolibrary.org/obo/NCIT_C70766>)

# Class: <http://purl.obolibrary.org/obo/NCIT_C17995> (Light Microscopy)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C17995> "Light Microscopy")
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C17995> <http://purl.obolibrary.org/obo/NCIT_C16853>)

# Class: <http://purl.obolibrary.org/obo/NCIT_C18141> (Computer Sciences)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C18141> "Computer Sciences")
Expand Down Expand Up @@ -231,6 +265,11 @@ SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C25198> <http://purl.obolibrary.
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C25206> "Temperature")
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C25206> <http://purl.obolibrary.org/obo/NCIT_C25447>)

# Class: <http://purl.obolibrary.org/obo/NCIT_C25218> (Clinical Intervention or Procedure)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C25218> "Clinical Intervention or Procedure")
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C25218> <http://purl.obolibrary.org/obo/NCIT_C16203>)

# Class: <http://purl.obolibrary.org/obo/NCIT_C25284> (Type)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C25284> "Type")
Expand All @@ -241,6 +280,11 @@ SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C25284> <http://purl.obolibrary.
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C25285> "Diameter")
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C25285> <http://purl.obolibrary.org/obo/NCIT_C70766>)

# Class: <http://purl.obolibrary.org/obo/NCIT_C25294> (Laboratory Procedure)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C25294> "Laboratory Procedure")
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C25294> <http://purl.obolibrary.org/obo/NCIT_C25218>)

# Class: <http://purl.obolibrary.org/obo/NCIT_C25335> (Volume)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C25335> "Volume")
Expand Down Expand Up @@ -356,6 +400,11 @@ SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C70766> <http://purl.obolibrary.
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C73706> "Spatial Qualifier")
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C73706> <http://purl.obolibrary.org/obo/NCIT_C41009>)

# Class: <http://purl.obolibrary.org/obo/NCIT_C74957> (Mixed Category Laboratory Procedure)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C74957> "Mixed Category Laboratory Procedure")
SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C74957> <http://purl.obolibrary.org/obo/NCIT_C25294>)

# Class: <http://purl.obolibrary.org/obo/NCIT_C85776> (Optical Density Measurement)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCIT_C85776> "Optical Density Measurement")
Expand Down
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