From 27122c7a8351b5fed4e7eaa161c17d8a043325cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philip=20Str=C3=B6mert?= Date: Tue, 20 Feb 2024 16:42:20 +0100 Subject: [PATCH 1/4] Use current ontology IRI --- docs/odk-workflows/RepoManagement.md | 8 +- docs/odk-workflows/components.md | 6 +- src/ontology/Makefile | 21 +- src/ontology/catalog-v001.xml | 28 +- src/ontology/imports/bfo_import.owl | 8 +- src/ontology/imports/chmo_import.owl | 82 +- src/ontology/imports/iao_import.owl | 521 ++++- src/ontology/imports/obi_import.owl | 2061 ++++++++++++++++- src/ontology/imports/omo_import.owl | 8 +- src/ontology/imports/pato_import.owl | 1956 +++++++++++++++- src/ontology/imports/ro_import.owl | 292 ++- src/ontology/nmrCV-edit.owl | 5 +- src/ontology/nmrCV-odk.yaml | 2 +- src/sparql/inject-subset-declaration.ru | 2 +- src/sparql/inject-synonymtype-declaration.ru | 2 +- src/sparql/iri-range-violation.sparql | 2 +- src/sparql/label-with-iri-violation.sparql | 2 +- src/sparql/nmrCV_terms.sparql | 2 +- .../owldef-self-reference-violation.sparql | 2 +- 19 files changed, 4916 insertions(+), 94 deletions(-) diff --git a/docs/odk-workflows/RepoManagement.md b/docs/odk-workflows/RepoManagement.md index 6559cac..f5b20ba 100644 --- a/docs/odk-workflows/RepoManagement.md +++ b/docs/odk-workflows/RepoManagement.md @@ -45,9 +45,9 @@ Note: our ODK file should only have one `import_group` which can contain multipl 1. Add an import statement to your `src/ontology/nmrCV-edit.owl` file. We suggest to do this using a text editor, by simply copying an existing import declaration and renaming it to the new ontology import, for example as follows: ``` ... - Ontology( - Import() - Import() + Ontology( + Import() + Import() ... ``` 2. Add your imports redirect to your catalog file `src/ontology/catalog-v001.xml`, for example: @@ -68,7 +68,7 @@ Import() in your editors file (the ontology) and ``` - + ``` in your catalog, tools like `robot` or Protégé will recognize the statement diff --git a/docs/odk-workflows/components.md b/docs/odk-workflows/components.md index e4b5f94..26c0724 100644 --- a/docs/odk-workflows/components.md +++ b/docs/odk-workflows/components.md @@ -17,20 +17,20 @@ components: 3) Add the component to your catalog file (src/ontology/catalog-v001.xml) ``` - + ``` 4) Add the component to the edit file (src/ontology/nmrCV-edit.obo) for .obo formats: ``` -import: http://purl.obolibrary.org/obo/nmrCV/components/your-component-name.owl +import: http://nmrML.org/nmrCV/components/your-component-name.owl ``` for .owl formats: ``` -Import() +Import() ``` 5) Refresh your repo by running `sh run.sh make update_repo` - this should create a new file in src/ontology/components. diff --git a/src/ontology/Makefile b/src/ontology/Makefile index bb785ad..d3d13fa 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -16,9 +16,9 @@ # these can be overwritten on the command line OBOBASE= http://purl.obolibrary.org/obo -URIBASE= http://purl.obolibrary.org/obo +URIBASE= http://nmrML.org ONT= nmrCV -ONTBASE= http://purl.obolibrary.org/obo/nmrCV +ONTBASE= http://nmrML.org/nmrCV EDIT_FORMAT= owl SRC = $(ONT)-edit.$(EDIT_FORMAT) MAKE_FAST= $(MAKE) IMP=false PAT=false COMP=false MIR=false @@ -365,8 +365,9 @@ mirror-bfo: | $(TMPDIR) .PHONY: mirror-ro .PRECIOUS: $(MIRRORDIR)/ro.owl mirror-ro: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ro/ro-base.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ro.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: omo @@ -383,8 +384,7 @@ mirror-omo: | $(TMPDIR) .PRECIOUS: $(MIRRORDIR)/iao.owl mirror-iao: | $(TMPDIR) if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/iao.owl --create-dirs -o $(MIRRORDIR)/iao.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/iao.owl -o $@.tmp.owl && \ - $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/IAO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ + $(ROBOT) convert -i $(MIRRORDIR)/iao.owl -o $@.tmp.owl &&\ mv $@.tmp.owl $(TMPDIR)/$@.owl; fi @@ -393,8 +393,7 @@ mirror-iao: | $(TMPDIR) .PRECIOUS: $(MIRRORDIR)/chmo.owl mirror-chmo: | $(TMPDIR) if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/chmo.owl --create-dirs -o $(MIRRORDIR)/chmo.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/chmo.owl -o $@.tmp.owl && \ - $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/CHMO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ + $(ROBOT) convert -i $(MIRRORDIR)/chmo.owl -o $@.tmp.owl &&\ mv $@.tmp.owl $(TMPDIR)/$@.owl; fi @@ -403,8 +402,7 @@ mirror-chmo: | $(TMPDIR) .PRECIOUS: $(MIRRORDIR)/pato.owl mirror-pato: | $(TMPDIR) if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/pato.owl --create-dirs -o $(MIRRORDIR)/pato.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/pato.owl -o $@.tmp.owl && \ - $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/PATO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ + $(ROBOT) convert -i $(MIRRORDIR)/pato.owl -o $@.tmp.owl &&\ mv $@.tmp.owl $(TMPDIR)/$@.owl; fi @@ -413,8 +411,7 @@ mirror-pato: | $(TMPDIR) .PRECIOUS: $(MIRRORDIR)/obi.owl mirror-obi: | $(TMPDIR) if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/obi.owl --create-dirs -o $(MIRRORDIR)/obi.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl && \ - $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/OBI --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ + $(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl &&\ mv $@.tmp.owl $(TMPDIR)/$@.owl; fi diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index 5520e9f..c23e0e0 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -3,26 +3,26 @@ - - + + - - + + - - + + - - + + - - + + - - + + - - + + diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl index d41d48a..e562fce 100644 --- a/src/ontology/imports/bfo_import.owl +++ b/src/ontology/imports/bfo_import.owl @@ -1,4 +1,4 @@ -Prefix(:=) +Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) @@ -6,10 +6,10 @@ Prefix(xsd:=) Prefix(rdfs:=) -Ontology( - +Ontology( + Annotation( ) -Annotation(owl:versionInfo "2023-11-23") +Annotation(owl:versionInfo "2024-02-20") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/chmo_import.owl b/src/ontology/imports/chmo_import.owl index 7fffeec..861c859 100644 --- a/src/ontology/imports/chmo_import.owl +++ b/src/ontology/imports/chmo_import.owl @@ -1,4 +1,4 @@ -Prefix(:=) +Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) @@ -6,17 +6,91 @@ Prefix(xsd:=) Prefix(rdfs:=) -Ontology( - +Ontology( + Annotation( ) -Annotation(owl:versionInfo "2023-11-23") +Annotation(owl:versionInfo "2024-02-20") +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty(rdfs:label)) +############################ +# Annotation Properties +############################ + +# Annotation Property: (definition) + +AnnotationAssertion(rdfs:label "definition") + +# Annotation Property: (database_cross_reference) + +AnnotationAssertion(rdfs:label "database_cross_reference") + +# Annotation Property: (has_exact_synonym) + +AnnotationAssertion(rdfs:label "has_exact_synonym") + +# Annotation Property: (has_obo_format_version) + +AnnotationAssertion(rdfs:label "has_obo_format_version") + + + +############################ +# Classes +############################ + +# Class: (continuant) + +AnnotationAssertion( "BFO:0000002") +AnnotationAssertion(rdfs:label "continuant") + +# Class: (process) + +AnnotationAssertion( "BFO:0000015") +AnnotationAssertion(rdfs:label "process") + +# Class: (realizable_entity) + +AnnotationAssertion( "BFO:0000017") +AnnotationAssertion(rdfs:label "realizable_entity") +SubClassOf( ) + +# Class: (quality) + +AnnotationAssertion( "BFO:0000019") +AnnotationAssertion(rdfs:label "quality") +SubClassOf( ) + +# Class: (specifically dependent continuant) + +AnnotationAssertion( "BFO:0000020") +AnnotationAssertion(rdfs:label "specifically dependent continuant") +SubClassOf( ) + +# Class: (generically dependent continuant) + +AnnotationAssertion( "BFO:0000031") +AnnotationAssertion(rdfs:label "generically dependent continuant") +SubClassOf( ) ) \ No newline at end of file diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl index 1c3f456..fca91e6 100644 --- a/src/ontology/imports/iao_import.owl +++ b/src/ontology/imports/iao_import.owl @@ -1,4 +1,4 @@ -Prefix(:=) +Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) @@ -6,13 +6,25 @@ Prefix(xsd:=) Prefix(rdfs:=) -Ontology( - +Ontology( + Annotation( ) -Annotation(owl:versionInfo "2023-11-23") +Annotation(owl:versionInfo "2024-02-20") Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -20,6 +32,16 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) @@ -39,6 +61,8 @@ Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -47,11 +71,97 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty(rdfs:label)) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: (definition) + +AnnotationAssertion( "definition"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) +AnnotationAssertion( "2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "definition"@en) + +# Annotation Property: (term editor) + +AnnotationAssertion( "term editor"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en) +AnnotationAssertion( "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "term editor"@en) + +# Annotation Property: (definition source) + +AnnotationAssertion( "definition source"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "definition source"@en) + +# Annotation Property: (has broad synonym) + +AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") +AnnotationAssertion(rdfs:label "has broad synonym"@en) +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") + +# Annotation Property: (has exact synonym) + +AnnotationAssertion( "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") +AnnotationAssertion(rdfs:label "has exact synonym"@en) +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") + ############################ # Object Properties @@ -70,6 +180,118 @@ Some currently missing phenomena that should be considered \"about\" are predica AnnotationAssertion( "person:Alan Ruttenberg"@en) AnnotationAssertion( "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en) AnnotationAssertion(rdfs:label "is about"@en) +ObjectPropertyDomain( ) + +# Object Property: (characteristic of) + +AnnotationAssertion( "inheres in"@en) +AnnotationAssertion( "this fragility is a characteristic of this vase"@en) +AnnotationAssertion( "this red color is a characteristic of this apple"@en) +AnnotationAssertion( "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence."@en) +AnnotationAssertion( "inheres_in"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.") +AnnotationAssertion(rdfs:label "characteristic of"@en) +InverseObjectProperties( ) +FunctionalObjectProperty() + +# Object Property: (has characteristic) + +AnnotationAssertion( "bearer of"@en) +AnnotationAssertion( "this apple is bearer of this red color"@en) +AnnotationAssertion( "this vase is bearer of this fragility"@en) +AnnotationAssertion( "Inverse of characteristic_of"@en) +AnnotationAssertion( "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist."@en) +AnnotationAssertion( "bearer_of"@en) +AnnotationAssertion( "is bearer of"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has characteristic"@en) +InverseFunctionalObjectProperty() +ObjectPropertyRange( ) + +# Object Property: (function of) + +AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) +AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists."@en) +AnnotationAssertion( "function_of"@en) +AnnotationAssertion( "is function of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "function of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (quality of) + +AnnotationAssertion( "this red color is a quality of this apple"@en) +AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A quality inheres in its bearer at all times for which the quality exists."@en) +AnnotationAssertion( "is quality of"@en) +AnnotationAssertion( "quality_of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "quality of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (role of) + +AnnotationAssertion( "this investigator role is a role of this person"@en) +AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists."@en) +AnnotationAssertion( "is role of"@en) +AnnotationAssertion( "role_of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "role of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has function) + +AnnotationAssertion( "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists."@en) +AnnotationAssertion( "has_function"@en) +AnnotationAssertion(rdfs:label "has function"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has quality) + +AnnotationAssertion( "this apple has quality this red color"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist."@en) +AnnotationAssertion( "has_quality"@en) +AnnotationAssertion(rdfs:label "has quality"@en) +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (has role) + +AnnotationAssertion( "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists."@en) +AnnotationAssertion( "has_role"@en) +AnnotationAssertion(rdfs:label "has role"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has disposition) + +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) +AnnotationAssertion(rdfs:label "has disposition"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (disposition of) + +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "disposition of"@en) +SubObjectPropertyOf( ) @@ -77,6 +299,281 @@ AnnotationAssertion(rdfs:label "is # Classes ############################ +# Class: (entity) + +AnnotationAssertion( "entity") +AnnotationAssertion( "Entity") +AnnotationAssertion( "Julius Caesar"@en) +AnnotationAssertion( "Verdi’s Requiem"@en) +AnnotationAssertion( "the Second World War"@en) +AnnotationAssertion( "your body mass index"@en) +AnnotationAssertion( "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81"@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") Annotation(rdfs:seeAlso ) "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"@en) +AnnotationAssertion(Annotation( ) "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "entity"@en) + +# Class: (continuant) + +AnnotationAssertion( "continuant") +AnnotationAssertion( "Continuant") +AnnotationAssertion( "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en) +AnnotationAssertion( "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240"@en) +AnnotationAssertion(Annotation( ) "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants"@en) +AnnotationAssertion(Annotation( ) "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])"@en) +AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])"@en) +AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])"@en) +AnnotationAssertion(Annotation( ) "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] ") +AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "continuant"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (occurrent) + +AnnotationAssertion( "occurrent") +AnnotationAssertion( "Occurrent") +AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) +AnnotationAssertion( "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region"@en) +AnnotationAssertion( "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players."@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process."@en) +AnnotationAssertion(Annotation( ) "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.") +AnnotationAssertion(Annotation( ) "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])"@en) +AnnotationAssertion(Annotation( ) "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])"@en) +AnnotationAssertion(Annotation( ) "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "occurrent"@en) +SubClassOf( ) + +# Class: (independent continuant) + +AnnotationAssertion( "ic") +AnnotationAssertion( "IndependentContinuant") +AnnotationAssertion( "a chair"@en) +AnnotationAssertion( "a heart"@en) +AnnotationAssertion( "a leg"@en) +AnnotationAssertion( "a molecule"@en) +AnnotationAssertion( "a spatial region"@en) +AnnotationAssertion( "an atom"@en) +AnnotationAssertion( "an orchestra."@en) +AnnotationAssertion( "an organism"@en) +AnnotationAssertion( "the bottom right portion of a human torso"@en) +AnnotationAssertion( "the interior of your mouth"@en) +AnnotationAssertion(Annotation( ) "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) +AnnotationAssertion(Annotation( ) "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])"@en) +AnnotationAssertion(Annotation( ) "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ") +AnnotationAssertion(Annotation( ) "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] ") +AnnotationAssertion(Annotation( ) "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "independent continuant"@en) +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (process) + +AnnotationAssertion( "process") +AnnotationAssertion( "Process") +AnnotationAssertion( "a process of cell-division, \\ a beating of the heart"@en) +AnnotationAssertion( "a process of meiosis"@en) +AnnotationAssertion( "a process of sleeping"@en) +AnnotationAssertion( "the course of a disease"@en) +AnnotationAssertion( "the flight of a bird"@en) +AnnotationAssertion( "the life of an organism"@en) +AnnotationAssertion( "your process of aging."@en) +AnnotationAssertion(Annotation( ) "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) +AnnotationAssertion( "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)"@en) +AnnotationAssertion(Annotation( ) "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "process"@en) +SubClassOf( ) + +# Class: (disposition) + +AnnotationAssertion( "disposition") +AnnotationAssertion( "Disposition") +AnnotationAssertion( "an atom of element X has the disposition to decay to an atom of element Y"@en) +AnnotationAssertion( "certain people have a predisposition to colon cancer"@en) +AnnotationAssertion( "children are innately disposed to categorize objects in certain ways."@en) +AnnotationAssertion( "the cell wall is disposed to filter chemicals in endocytosis and exocytosis"@en) +AnnotationAssertion( "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type."@en) +AnnotationAssertion(Annotation( ) "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])"@en) +AnnotationAssertion(Annotation( ) "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "disposition"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (realizable entity) + +AnnotationAssertion( "realizable") +AnnotationAssertion( "RealizableEntity") +AnnotationAssertion( "the disposition of this piece of metal to conduct electricity."@en) +AnnotationAssertion( "the disposition of your blood to coagulate"@en) +AnnotationAssertion( "the function of your reproductive organs"@en) +AnnotationAssertion( "the role of being a doctor"@en) +AnnotationAssertion( "the role of this boundary to delineate where Utah and Colorado meet"@en) +AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) +AnnotationAssertion(Annotation( ) "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])"@en) +AnnotationAssertion(Annotation( ) "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "realizable entity"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (quality) + +AnnotationAssertion( "quality") +AnnotationAssertion( "Quality") +AnnotationAssertion( "the ambient temperature of this portion of air"@en) +AnnotationAssertion( "the color of a tomato"@en) +AnnotationAssertion( "the length of the circumference of your waist"@en) +AnnotationAssertion( "the mass of this piece of gold."@en) +AnnotationAssertion( "the shape of your nose"@en) +AnnotationAssertion( "the shape of your nostril"@en) +AnnotationAssertion(Annotation( ) "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])"@en) +AnnotationAssertion(Annotation( ) "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "quality"@en) +SubClassOf( ) + +# Class: (specifically dependent continuant) + +AnnotationAssertion( "sdc") +AnnotationAssertion( "SpecificallyDependentContinuant") +AnnotationAssertion( "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key"@en) +AnnotationAssertion( "of one-sided specifically dependent continuants: the mass of this tomato"@en) +AnnotationAssertion( "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates."@en) +AnnotationAssertion( "the disposition of this fish to decay"@en) +AnnotationAssertion( "the function of this heart: to pump blood"@en) +AnnotationAssertion( "the mutual dependence of proton donors and acceptors in chemical reactions [79"@en) +AnnotationAssertion( "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction"@en) +AnnotationAssertion( "the pink color of a medium rare piece of grilled filet mignon at its center"@en) +AnnotationAssertion( "the role of being a doctor"@en) +AnnotationAssertion( "the shape of this hole."@en) +AnnotationAssertion( "the smell of this portion of mozzarella"@en) +AnnotationAssertion(Annotation( ) "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc."@en) +AnnotationAssertion(Annotation( ) "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (role) + +AnnotationAssertion( "role") +AnnotationAssertion( "Role") +AnnotationAssertion( "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married."@en) +AnnotationAssertion( "the priest role"@en) +AnnotationAssertion( "the role of a boundary to demarcate two neighboring administrative territories"@en) +AnnotationAssertion( "the role of a building in serving as a military target"@en) +AnnotationAssertion( "the role of a stone in marking a property boundary"@en) +AnnotationAssertion( "the role of subject in a clinical trial"@en) +AnnotationAssertion( "the student role"@en) +AnnotationAssertion( "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en) +AnnotationAssertion( "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives."@en) +AnnotationAssertion(Annotation( ) "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "role"@en) +SubClassOf( ) + +# Class: (object) + +AnnotationAssertion( "object") +AnnotationAssertion( "Object") +AnnotationAssertion( "atom"@en) +AnnotationAssertion( "cell"@en) +AnnotationAssertion( "cells and organisms"@en) +AnnotationAssertion( "engineered artifacts"@en) +AnnotationAssertion( "grain of sand"@en) +AnnotationAssertion( "molecule"@en) +AnnotationAssertion( "organelle"@en) +AnnotationAssertion( "organism"@en) +AnnotationAssertion( "planet"@en) +AnnotationAssertion( "solid portions of matter"@en) +AnnotationAssertion( "star"@en) +AnnotationAssertion( "BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting."@en) +AnnotationAssertion( "BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below)."@en) +AnnotationAssertion( "BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47"@en) +AnnotationAssertion( "BFO 2 Reference: an object is a maximal causally unified material entity"@en) +AnnotationAssertion( "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74"@en) +AnnotationAssertion(Annotation( ) "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "object"@en) +SubClassOf( ) + +# Class: (generically dependent continuant) + +AnnotationAssertion( "gdc") +AnnotationAssertion( "GenericallyDependentContinuant") +AnnotationAssertion( "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity."@en) +AnnotationAssertion( "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop"@en) +AnnotationAssertion( "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule."@en) +AnnotationAssertion(Annotation( ) "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) +AnnotationAssertion(Annotation( ) "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "generically dependent continuant"@en) +SubClassOf( ) + +# Class: (function) + +AnnotationAssertion( "function") +AnnotationAssertion( "Function") +AnnotationAssertion( "the function of a hammer to drive in nails"@en) +AnnotationAssertion( "the function of a heart pacemaker to regulate the beating of a heart through electricity"@en) +AnnotationAssertion( "the function of amylase in saliva to break down starch into sugar"@en) +AnnotationAssertion( "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc."@en) +AnnotationAssertion(Annotation( ) "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "function"@en) +SubClassOf( ) + +# Class: (material entity) + +AnnotationAssertion( "material") +AnnotationAssertion( "MaterialEntity") +AnnotationAssertion( "a flame"@en) +AnnotationAssertion( "a forest fire"@en) +AnnotationAssertion( "a human being"@en) +AnnotationAssertion( "a hurricane"@en) +AnnotationAssertion( "a photon"@en) +AnnotationAssertion( "a puff of smoke"@en) +AnnotationAssertion( "a sea wave"@en) +AnnotationAssertion( "a tornado"@en) +AnnotationAssertion( "an aggregate of human beings."@en) +AnnotationAssertion( "an energy wave"@en) +AnnotationAssertion( "an epidemic"@en) +AnnotationAssertion( "the undetached arm of a human being"@en) +AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) +AnnotationAssertion( "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60"@en) +AnnotationAssertion( "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity."@en) +AnnotationAssertion( "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here."@en) +AnnotationAssertion(Annotation( ) "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])"@en) +AnnotationAssertion(Annotation( ) "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])"@en) +AnnotationAssertion(Annotation( ) "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "material entity"@en) +SubClassOf( ) + # Class: (data item) AnnotationAssertion( "data item"@en) @@ -294,5 +791,21 @@ AnnotationAssertion( "requires discussion"@en) ClassAssertion( ) +# Individual: (out of scope) + +AnnotationAssertion( "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not."@en) +AnnotationAssertion( "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease."@en) +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/77") +AnnotationAssertion( "https://orcid.org/0000-0001-5208-3432") +AnnotationAssertion(rdfs:label "out of scope") +ClassAssertion( ) + +DifferentIndividuals( ) +DifferentIndividuals( ) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl index 0399d0c..45c45cb 100644 --- a/src/ontology/imports/obi_import.owl +++ b/src/ontology/imports/obi_import.owl @@ -1,4 +1,4 @@ -Prefix(:=) +Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) @@ -6,41 +6,81 @@ Prefix(xsd:=) Prefix(rdfs:=) -Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2023-11-23") +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2024-02-20") +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -56,6 +96,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -85,6 +126,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -101,7 +143,19 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -109,12 +163,34 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) @@ -331,7 +407,61 @@ Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -345,7 +475,13 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -354,12 +490,206 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty(rdfs:label)) +Declaration(AnnotationProperty()) Declaration(Datatype(xsd:date)) +############################ +# Annotation Properties +############################ + +# Annotation Property: (textual definition) + +AnnotationAssertion( "definition"@en) +AnnotationAssertion( "definition") +AnnotationAssertion( "textual definition") +AnnotationAssertion( ) +AnnotationAssertion( "The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) +AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) +AnnotationAssertion( "2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "definition"@en) +AnnotationAssertion(rdfs:label "definition") +AnnotationAssertion(rdfs:label "textual definition") + +# Annotation Property: (term editor) + +AnnotationAssertion( "term editor"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en) +AnnotationAssertion( "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "term editor"@en) + +# Annotation Property: (definition source) + +AnnotationAssertion( "definition source"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "definition source"@en) + +# Annotation Property: (Contributor) + +AnnotationAssertion( "Examples of a Contributor include a person, an + organisation, or a service. Typically, the name of a + Contributor should be used to indicate the entity."@en-us) +AnnotationAssertion(rdfs:comment "An entity responsible for making contributions to the + content of the resource."@en-us) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "Contributor"@en-us) +AnnotationAssertion(rdfs:label "Contributor") + +# Annotation Property: (Coverage) + +AnnotationAssertion( "Coverage will typically include spatial location (a place name + or geographic coordinates), temporal period (a period label, + date, or date range) or jurisdiction (such as a named + administrative entity). + Recommended best practice is to select a value from a + controlled vocabulary (for example, the Thesaurus of Geographic + Names [TGN]) and that, where appropriate, named places or time + periods be used in preference to numeric identifiers such as + sets of coordinates or date ranges."@en-us) +AnnotationAssertion(rdfs:comment "The extent or scope of the content of the resource."@en-us) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "Coverage"@en-us) +AnnotationAssertion(rdfs:label "Coverage") + +# Annotation Property: (Source) + +AnnotationAssertion( "The present resource may be derived from the Source resource + in whole or in part. Recommended best practice is to reference + the resource by means of a string or number conforming to a + formal identification system."@en-us) +AnnotationAssertion(rdfs:comment "A reference to a resource from which the present resource + is derived."@en-us) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "Source"@en-us) +AnnotationAssertion(rdfs:label "Source") + +# Annotation Property: () + +AnnotationAssertion( "Mark Miller") +AnnotationAssertion( "2018-05-11T13:47:29Z"^^xsd:dateTime) + +# Annotation Property: rdfs:label (label) + +AnnotationAssertion( rdfs:label "label") +AnnotationAssertion(rdfs:label rdfs:label "label") + ############################ # Object Properties ############################ +# Object Property: (part of) + +AnnotationAssertion( "is part of"@en) +AnnotationAssertion( "my brain is part of my body (continuant parthood, two material entities)"@en) +AnnotationAssertion( "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en) +AnnotationAssertion( "this day is part of this year (occurrent parthood)"@en) +AnnotationAssertion( "a core relation that holds between a part and its whole"@en) +AnnotationAssertion( "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other."@en) +AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime"@en) +AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'."@en) +AnnotationAssertion( "part_of"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "part of"@en) +AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (has part) + +AnnotationAssertion( "has part"@en) +AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"@en) +AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en) +AnnotationAssertion( "this year has part this day (occurrent parthood)"@en) +AnnotationAssertion( "a core relation that holds between a whole and its part"@en) +AnnotationAssertion( "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part."@en) +AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime"@en) +AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'."@en) +AnnotationAssertion( "has_part"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has part"@en) +TransitiveObjectProperty() + +# Object Property: (realized in) + +AnnotationAssertion( "realized in"@en) +AnnotationAssertion( "this disease is realized in this disease course"@en) +AnnotationAssertion( "this fragility is realized in this shattering"@en) +AnnotationAssertion( "this investigator role is realized in this investigation"@en) +AnnotationAssertion( "is realized by"@en) +AnnotationAssertion( "realized_in"@en) +AnnotationAssertion( "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])"@en) +AnnotationAssertion(rdfs:comment "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "realized in"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (realizes) + +AnnotationAssertion( "realizes"@en) +AnnotationAssertion( "this disease course realizes this disease"@en) +AnnotationAssertion( "this investigation realizes this investigator role"@en) +AnnotationAssertion( "this shattering realizes this fragility"@en) +AnnotationAssertion( "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])"@en) +AnnotationAssertion(rdfs:comment "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "realizes"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is about) + +AnnotationAssertion( "This document is about information artifacts and their representations"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A (currently) primitive relation that relates an information artifact to an entity."@en) +AnnotationAssertion( "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic."@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en) +AnnotationAssertion(rdfs:label "is about"@en) +ObjectPropertyDomain( ) + # Object Property: (has_specified_input) AnnotationAssertion( "has_specified_input"@en) @@ -376,6 +706,8 @@ AnnotationAssertion( "has_specified_input"@en) EquivalentObjectProperties( ObjectInverseOf()) SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) # Object Property: (is_specified_input_of) @@ -387,6 +719,7 @@ AnnotationAssertion( "PERSON:Bjoern Peters") AnnotationAssertion(rdfs:label "is_specified_input_of"@en) SubObjectPropertyOf( ) +ObjectPropertyRange( ) # Object Property: (has_specified_output) @@ -402,6 +735,8 @@ AnnotationAssertion( "has_specified_output"@en) EquivalentObjectProperties( ObjectInverseOf()) SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) # Object Property: (is_specified_output_of) @@ -414,6 +749,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "is_specified_output_of"@en) SubObjectPropertyOf( ) +ObjectPropertyRange( ) # Object Property: (achieves_planned_objective) @@ -425,6 +761,134 @@ AnnotationAssertion( "PPPB branch derived") AnnotationAssertion( "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch") AnnotationAssertion(rdfs:label "achieves_planned_objective") +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (objective_achieved_by) + +AnnotationAssertion( "objective_achieved_by") +AnnotationAssertion( ) +AnnotationAssertion( "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.") +AnnotationAssertion( "OBI") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "objective_achieved_by") +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (inheres in) + +AnnotationAssertion( "inheres in"@en) +AnnotationAssertion( "this fragility inheres in this vase"@en) +AnnotationAssertion( "this red color inheres in this apple"@en) +AnnotationAssertion( "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A dependent inheres in its bearer at all times for which the dependent exists."@en) +AnnotationAssertion( "inheres_in"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "inheres in"@en) +InverseObjectProperties( ) + +# Object Property: (bearer of) + +AnnotationAssertion( "bearer of"@en) +AnnotationAssertion( "this apple is bearer of this red color"@en) +AnnotationAssertion( "this vase is bearer of this fragility"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist."@en) +AnnotationAssertion( "bearer_of"@en) +AnnotationAssertion( "is bearer of"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "bearer of"@en) +ObjectPropertyRange( ) + +# Object Property: (participates in) + +AnnotationAssertion( "participates in"@en) +AnnotationAssertion( "this blood clot participates in this blood coagulation"@en) +AnnotationAssertion( "this input material (or this output material) participates in this process"@en) +AnnotationAssertion( "this investigator participates in this investigation"@en) +AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion( "participates_in"@en) +AnnotationAssertion(rdfs:label "participates in"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has participant) + +AnnotationAssertion( "has participant"@en) +AnnotationAssertion( "this blood coagulation has participant this blood clot"@en) +AnnotationAssertion( "this investigation has participant this investigator"@en) +AnnotationAssertion( "this process has participant this input material (or this output material)"@en) +AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion( "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) +AnnotationAssertion( "has_participant"@en) +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") +AnnotationAssertion(rdfs:label "has participant"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is concretized as) + +AnnotationAssertion( "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) +AnnotationAssertion( "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) +AnnotationAssertion( "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants."@en) +AnnotationAssertion(rdfs:label "is concretized as"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (concretizes) + +AnnotationAssertion( "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) +AnnotationAssertion( "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) +AnnotationAssertion( "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant."@en) +AnnotationAssertion(rdfs:label "concretizes"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (role of) + +AnnotationAssertion( "this investigator role is a role of this person"@en) +AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists."@en) +AnnotationAssertion( "is role of"@en) +AnnotationAssertion( "role_of"@en) +AnnotationAssertion(rdfs:label "role of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has role) + +AnnotationAssertion( "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists."@en) +AnnotationAssertion( "has_role"@en) +AnnotationAssertion(rdfs:label "has role"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (member of) + +AnnotationAssertion( "An organism that is a member of a population of organisms") +AnnotationAssertion( "is member of is a mereological relation between a item and a collection.") +AnnotationAssertion( "is member of") +AnnotationAssertion( "member part of") +AnnotationAssertion( "SIO") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "member of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has member) + +AnnotationAssertion( "has member is a mereological relation between a collection and an item.") +AnnotationAssertion( "SIO") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has member"@en) +SubObjectPropertyOf( ) +IrreflexiveObjectProperty() @@ -432,6 +896,807 @@ AnnotationAssertion(rdfs:label "ach # Classes ############################ +# Class: (software development) + +AnnotationAssertion( "A planned process that has specified output a software product and that involves the creation of source code."@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "William R. Hogan"@en) +AnnotationAssertion( "http://en.wikipedia.org/wiki/Software_development") +AnnotationAssertion( "A planned process resulting in a software product involving the creation of source code."@en) +AnnotationAssertion(rdfs:label "software development"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectUnionOf( )))) +SubClassOf( ) + +# Class: (dataset creating) + +AnnotationAssertion( "creating a data set"@en) +AnnotationAssertion( "A planned process that has a data set as its specified output."@en) +AnnotationAssertion( "William R. Hogan"@en) +AnnotationAssertion( "data set creation"@en) +AnnotationAssertion( "dataset creation"@en) +AnnotationAssertion(rdfs:label "dataset creating"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (entity) + +AnnotationAssertion( "entity") +AnnotationAssertion( "Entity") +AnnotationAssertion( "Julius Caesar"@en) +AnnotationAssertion( "Verdi’s Requiem"@en) +AnnotationAssertion( "the Second World War"@en) +AnnotationAssertion( "your body mass index"@en) +AnnotationAssertion( "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81"@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") Annotation(rdfs:seeAlso ) "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"@en) +AnnotationAssertion(Annotation( ) "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "entity"@en) + +# Class: (continuant) + +AnnotationAssertion( "continuant") +AnnotationAssertion( "Continuant") +AnnotationAssertion( "continuant"@en) +AnnotationAssertion( "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en) +AnnotationAssertion( "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240"@en) +AnnotationAssertion(Annotation( ) "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants"@en) +AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])"@en) +AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])"@en) +AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])"@en) +AnnotationAssertion(Annotation( ) "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] ") +AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "continuant"@en) +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (occurrent) + +AnnotationAssertion( "occurrent") +AnnotationAssertion( "Occurrent") +AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) +AnnotationAssertion( "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region"@en) +AnnotationAssertion( "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players."@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process."@en) +AnnotationAssertion(Annotation( ) "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.") +AnnotationAssertion(Annotation( ) "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])"@en) +AnnotationAssertion(Annotation( ) "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])"@en) +AnnotationAssertion(Annotation( ) "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "occurrent"@en) +SubClassOf( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (independent continuant) + +AnnotationAssertion( "ic") +AnnotationAssertion( "IndependentContinuant") +AnnotationAssertion( "a chair"@en) +AnnotationAssertion( "a heart"@en) +AnnotationAssertion( "a leg"@en) +AnnotationAssertion( "a molecule"@en) +AnnotationAssertion( "a spatial region"@en) +AnnotationAssertion( "an atom"@en) +AnnotationAssertion( "an orchestra."@en) +AnnotationAssertion( "an organism"@en) +AnnotationAssertion( "the bottom right portion of a human torso"@en) +AnnotationAssertion( "the interior of your mouth"@en) +AnnotationAssertion( "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) +AnnotationAssertion(Annotation( ) "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) +AnnotationAssertion(Annotation( ) "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])"@en) +AnnotationAssertion(Annotation( ) "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ") +AnnotationAssertion(Annotation( ) "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] ") +AnnotationAssertion(Annotation( ) "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "independent continuant"@en) +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (process) + +AnnotationAssertion( "process") +AnnotationAssertion( "Process") +AnnotationAssertion( "a process of cell-division, \\ a beating of the heart"@en) +AnnotationAssertion( "a process of meiosis"@en) +AnnotationAssertion( "a process of sleeping"@en) +AnnotationAssertion( "the course of a disease"@en) +AnnotationAssertion( "the flight of a bird"@en) +AnnotationAssertion( "the life of an organism"@en) +AnnotationAssertion( "your process of aging."@en) +AnnotationAssertion( "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) +AnnotationAssertion(Annotation( ) "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) +AnnotationAssertion( "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)"@en) +AnnotationAssertion(Annotation( ) "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "process"@en) +SubClassOf( ) + +# Class: (realizable entity) + +AnnotationAssertion( "realizable") +AnnotationAssertion( "RealizableEntity") +AnnotationAssertion( "the disposition of this piece of metal to conduct electricity."@en) +AnnotationAssertion( "the disposition of your blood to coagulate"@en) +AnnotationAssertion( "the function of your reproductive organs"@en) +AnnotationAssertion( "the role of being a doctor"@en) +AnnotationAssertion( "the role of this boundary to delineate where Utah and Colorado meet"@en) +AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) +AnnotationAssertion(Annotation( ) "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])"@en) +AnnotationAssertion(Annotation( ) "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "realizable entity"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (quality) + +AnnotationAssertion( "quality") +AnnotationAssertion( "Quality") +AnnotationAssertion( "quality"@en) +AnnotationAssertion( "the ambient temperature of this portion of air"@en) +AnnotationAssertion( "the color of a tomato"@en) +AnnotationAssertion( "the length of the circumference of your waist"@en) +AnnotationAssertion( "the mass of this piece of gold."@en) +AnnotationAssertion( "the shape of your nose"@en) +AnnotationAssertion( "the shape of your nostril"@en) +AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])"@en) +AnnotationAssertion(Annotation( ) "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "quality"@en) +SubClassOf( ) + +# Class: (specifically dependent continuant) + +AnnotationAssertion( "sdc") +AnnotationAssertion( "SpecificallyDependentContinuant") +AnnotationAssertion( "specifically dependent continuant"@en) +AnnotationAssertion( "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key"@en) +AnnotationAssertion( "of one-sided specifically dependent continuants: the mass of this tomato"@en) +AnnotationAssertion( "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates."@en) +AnnotationAssertion( "the disposition of this fish to decay"@en) +AnnotationAssertion( "the function of this heart: to pump blood"@en) +AnnotationAssertion( "the mutual dependence of proton donors and acceptors in chemical reactions [79"@en) +AnnotationAssertion( "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction"@en) +AnnotationAssertion( "the pink color of a medium rare piece of grilled filet mignon at its center"@en) +AnnotationAssertion( "the role of being a doctor"@en) +AnnotationAssertion( "the shape of this hole."@en) +AnnotationAssertion( "the smell of this portion of mozzarella"@en) +AnnotationAssertion( "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) +AnnotationAssertion(Annotation( ) "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])"@en) +AnnotationAssertion(Annotation( ) "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc."@en) +AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] ") +AnnotationAssertion(Annotation( ) "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (role) + +AnnotationAssertion( "role") +AnnotationAssertion( "Role") +AnnotationAssertion( "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married."@en) +AnnotationAssertion( "the priest role"@en) +AnnotationAssertion( "the role of a boundary to demarcate two neighboring administrative territories"@en) +AnnotationAssertion( "the role of a building in serving as a military target"@en) +AnnotationAssertion( "the role of a stone in marking a property boundary"@en) +AnnotationAssertion( "the role of subject in a clinical trial"@en) +AnnotationAssertion( "the student role"@en) +AnnotationAssertion( "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en) +AnnotationAssertion( "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives."@en) +AnnotationAssertion(Annotation( ) "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "role"@en) +SubClassOf( ) + +# Class: (object) + +AnnotationAssertion( "object") +AnnotationAssertion( "Object") +AnnotationAssertion( "atom"@en) +AnnotationAssertion( "cell"@en) +AnnotationAssertion( "cells and organisms"@en) +AnnotationAssertion( "engineered artifacts"@en) +AnnotationAssertion( "grain of sand"@en) +AnnotationAssertion( "molecule"@en) +AnnotationAssertion( "organelle"@en) +AnnotationAssertion( "organism"@en) +AnnotationAssertion( "planet"@en) +AnnotationAssertion( "solid portions of matter"@en) +AnnotationAssertion( "star"@en) +AnnotationAssertion( "BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting."@en) +AnnotationAssertion( "BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below)."@en) +AnnotationAssertion( "BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47"@en) +AnnotationAssertion( "BFO 2 Reference: an object is a maximal causally unified material entity"@en) +AnnotationAssertion( "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74"@en) +AnnotationAssertion(Annotation( ) "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "object"@en) +SubClassOf( ) + +# Class: (generically dependent continuant) + +AnnotationAssertion( "gdc") +AnnotationAssertion( "GenericallyDependentContinuant") +AnnotationAssertion( "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity."@en) +AnnotationAssertion( "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop"@en) +AnnotationAssertion( "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule."@en) +AnnotationAssertion( "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time."@en) +AnnotationAssertion(Annotation( ) "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) +AnnotationAssertion(Annotation( ) "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "generically dependent continuant"@en) +SubClassOf( ) + +# Class: (material entity) + +AnnotationAssertion( "material") +AnnotationAssertion( "MaterialEntity") +AnnotationAssertion( "material entity"@en) +AnnotationAssertion( "a flame"@en) +AnnotationAssertion( "a forest fire"@en) +AnnotationAssertion( "a human being"@en) +AnnotationAssertion( "a hurricane"@en) +AnnotationAssertion( "a photon"@en) +AnnotationAssertion( "a puff of smoke"@en) +AnnotationAssertion( "a sea wave"@en) +AnnotationAssertion( "a tornado"@en) +AnnotationAssertion( "an aggregate of human beings."@en) +AnnotationAssertion( "an energy wave"@en) +AnnotationAssertion( "an epidemic"@en) +AnnotationAssertion( "the undetached arm of a human being"@en) +AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) +AnnotationAssertion( "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60"@en) +AnnotationAssertion( "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity."@en) +AnnotationAssertion( "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here."@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])"@en) +AnnotationAssertion(Annotation( ) "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])"@en) +AnnotationAssertion(Annotation( ) "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "material entity"@en) +SubClassOf( ) + +# Class: (measurement unit label) + +AnnotationAssertion( "measurement unit label"@en) +AnnotationAssertion( "Examples of measurement unit labels are liters, inches, weight per volume."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure."@en) +AnnotationAssertion( "2009-03-16: provenance: a term measurement unit was +proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and +Cristian Cocos, and subsequently moved to IAO where the objective for +which the original term was defined was satisfied with the definition +of this, different, term."@en) +AnnotationAssertion( "2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "measurement unit label"@en) +SubClassOf( ) + +# Class: (objective specification) + +AnnotationAssertion( "objective specification"@en) +AnnotationAssertion( "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved."@en) +AnnotationAssertion( "2009-03-16: original definition when imported from OBI read: \"objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed.\""@en) +AnnotationAssertion( "2014-03-31: In the example of usage (\"In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction\") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that."@en) +AnnotationAssertion( "Answers the question, why did you do this experiment?"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Barry Smith"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Jennifer Fostel"@en) +AnnotationAssertion( "goal specification"@en) +AnnotationAssertion( "OBI Plan and Planned Process/Roles Branch"@en) +AnnotationAssertion( "OBI_0000217"@en) +AnnotationAssertion(rdfs:label "objective specification"@en) +SubClassOf( ) + +# Class: (action specification) + +AnnotationAssertion( "Pour the contents of flask 1 into flask 2"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A directive information entity that describes an action the bearer will take."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "OBI Plan and Planned Process branch"@en) +AnnotationAssertion(rdfs:label "action specification"@en) +SubClassOf( ) + +# Class: (datum label) + +AnnotationAssertion( "datum label"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label"@en) +AnnotationAssertion( "http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n"@en) +AnnotationAssertion( "GROUP: IAO"@en) +AnnotationAssertion( "9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. +") +AnnotationAssertion(rdfs:label "datum label"@en) +SubClassOf( ) + +# Class: (software) + +AnnotationAssertion( "software"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Software is a plan specification composed of a series of instructions that can be +interpreted by or directly executed by a processing unit."@en) +AnnotationAssertion( "see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion( "GROUP: OBI"@en) +AnnotationAssertion(rdfs:label "software"@en) +SubClassOf( ) + +# Class: (information carrier) + +AnnotationAssertion( "information carrier"@en) +AnnotationAssertion( "In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A quality of an information bearer that imparts the information content"@en) +AnnotationAssertion( "12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'."@en) +AnnotationAssertion( "2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en) +AnnotationAssertion(rdfs:label "information carrier"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (data item) + +AnnotationAssertion( "data item"@en) +AnnotationAssertion( "Data items include counts of things, analyte concentrations, and statistical summaries."@en) +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) +AnnotationAssertion( "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers."@en) +AnnotationAssertion( "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum."@en) +AnnotationAssertion( "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en) +AnnotationAssertion( "JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief"@en) +AnnotationAssertion( "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "PERSON: Jonathan Rees"@en) +AnnotationAssertion( "data"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "data item"@en) +SubClassOf( ) + +# Class: (information content entity) + +AnnotationAssertion( "information content entity"@en) +AnnotationAssertion( "Examples of information content entites include journal articles, data, graphical layouts, and graphs."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A generically dependent continuant that is about some thing."@en) +AnnotationAssertion( "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)."@en) +AnnotationAssertion( "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity."@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000142"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "information content entity"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (directive information entity) + +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity whose concretizations indicate to their bearer how to realize them in a process."@en) +AnnotationAssertion( "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be concretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term."@en) +AnnotationAssertion( "2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it."@en) +AnnotationAssertion( "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO"@en) +AnnotationAssertion( "Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion(rdfs:label "directive information entity"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (dot plot) + +AnnotationAssertion( "dot plot"@en) +AnnotationAssertion( "Dot plot of SSC-H and FSC-H."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions."@en) +AnnotationAssertion( "person:Allyson Lister"@en) +AnnotationAssertion( "person:Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000123"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "dot plot"@en) +SubClassOf( ) + +# Class: (graph) + +AnnotationAssertion( "graph"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way."@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "person:Allyson Lister"@en) +AnnotationAssertion( "OBI_0000240"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "graph"@en) +SubClassOf( ) + +# Class: (algorithm) + +AnnotationAssertion( "algorithm"@en) +AnnotationAssertion( "PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata."@en) +AnnotationAssertion( "Philippe Rocca-Serra"@en) +AnnotationAssertion( "PlanAndPlannedProcess Branch"@en) +AnnotationAssertion( "OBI_0000270"@en) +AnnotationAssertion( "adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)"@en) +AnnotationAssertion(rdfs:label "algorithm"@en) +SubClassOf( ) + +# Class: (curation status specification) + +AnnotationAssertion( "curation status specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) +AnnotationAssertion( "PERSON:Bill Bug"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion( "OBI_0000266"@en) +AnnotationAssertion(rdfs:label "curation status specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (source code module) + +AnnotationAssertion( "source code module"@en) +AnnotationAssertion( "The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A source code module is a directive information entity that specifies, using a programming language, some algorithm."@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "person:Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000039"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "source code module"@en) +SubClassOf( ) + +# Class: (data format specification) + +AnnotationAssertion( "data format specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A data format specification is the information content borne by the document published defining the specification. +Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"@en) +AnnotationAssertion( "2009-03-16: provenance: term imported from OBI_0000187, which had original definition \"A data format specification is a plan which organizes +information. Example: The ISO document specifying what encompasses an +XML document; The instructions in a XSD file\""@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PlanAndPlannedProcess Branch"@en) +AnnotationAssertion( "OBI branch derived"@en) +AnnotationAssertion( "OBI_0000187"@en) +AnnotationAssertion(rdfs:label "data format specification"@en) +SubClassOf( ) + +# Class: (data set) + +AnnotationAssertion( "data set"@en) +AnnotationAssertion( "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets."@en) +AnnotationAssertion( "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type"@en) +AnnotationAssertion( "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.") +AnnotationAssertion( "person:Allyson Lister"@en) +AnnotationAssertion( "person:Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000042"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "data set"@en) +SubClassOf( ) + +# Class: (image) + +AnnotationAssertion( "image"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface."@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "person:Allyson"@en) +AnnotationAssertion( "person:Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000030"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "image"@en) +SubClassOf( ) + +# Class: (data about an ontology part) + +AnnotationAssertion( "data about an ontology part"@en) +AnnotationAssertion( "Data about an ontology part is a data item about a part of an ontology, for example a term"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "data about an ontology part"@en) +SubClassOf( ) + +# Class: (plan specification) + +AnnotationAssertion( "plan specification"@en) +AnnotationAssertion( "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified."@en) +AnnotationAssertion( "2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was \" a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan\". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term."@en) +AnnotationAssertion( "2014-03-31: A plan specification can have other parts, such as conditional specifications."@en) +AnnotationAssertion( "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "OBI Plan and Planned Process branch"@en) +AnnotationAssertion( "OBI_0000344"@en) +AnnotationAssertion(rdfs:comment "2/3/2009 Comment from OBI review. + +Action specification not well enough specified. +Conditional specification not well enough specified. +Question whether all plan specifications have objective specifications. + +Request that IAO either clarify these or change definitions not to use them"@en) +AnnotationAssertion(rdfs:label "plan specification"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (material information bearer) + +AnnotationAssertion( "material information bearer"@en) +AnnotationAssertion( "A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier."@en) +AnnotationAssertion( "a brain"@en) +AnnotationAssertion( "a hard drive"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity in which a concretization of an information content entity inheres."@en) +AnnotationAssertion( "GROUP: IAO"@en) +AnnotationAssertion(rdfs:label "material information bearer"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))) +SubClassOf( ) + +# Class: (histogram) + +AnnotationAssertion( "histogram"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A histogram is a report graph which is a statistical description of a +distribution in terms of occurrence frequencies of different event classes."@en) +AnnotationAssertion( "PERSON:Chris Stoeckert"@en) +AnnotationAssertion( "PERSON:James Malone"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion( "GROUP:OBI"@en) +AnnotationAssertion(rdfs:label "histogram"@en) +SubClassOf( ) + +# Class: (heatmap) + +AnnotationAssertion( "heatmap"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A heatmap is a report graph which is a graphical representation of data +where the values taken by a variable(s) are shown as colors in a +two-dimensional map."@en) +AnnotationAssertion( "PERSON:Chris Stoeckert"@en) +AnnotationAssertion( "PERSON:James Malone"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion( "GROUP:OBI"@en) +AnnotationAssertion(rdfs:label "heatmap"@en) +SubClassOf( ) + +# Class: (dendrogram) + +AnnotationAssertion( "dendrogram"@en) +AnnotationAssertion( "Dendrograms are often used in computational biology to +illustrate the clustering of genes."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A dendrogram is a report graph which is a tree diagram +frequently used to illustrate the arrangement of the clusters produced by a +clustering algorithm."@en) +AnnotationAssertion( "PERSON:Chris Stoeckert"@en) +AnnotationAssertion( "PERSON:James Malone"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Dendrogram"@en) +AnnotationAssertion(rdfs:label "dendrogram"@en) +SubClassOf( ) + +# Class: (scatter plot) + +AnnotationAssertion( "scatter plot"@en) +AnnotationAssertion( "Comparison of gene expression values in two samples can be displayed in a scatter plot"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis."@en) +AnnotationAssertion( "PERSON:Chris Stoeckert"@en) +AnnotationAssertion( "PERSON:James Malone"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion( "scattergraph"@en) +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Scatterplot"@en) +AnnotationAssertion(rdfs:label "scatter plot"@en) +SubClassOf( ) + +# Class: (obsolescence reason specification) + +AnnotationAssertion( "obsolescence reason specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "obsolescence reason specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (figure) + +AnnotationAssertion( "figure"@en) +AnnotationAssertion( "Any picture, diagram or table"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something."@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion(rdfs:label "figure"@en) +SubClassOf( ) + +# Class: (diagram) + +AnnotationAssertion( "diagram"@en) +AnnotationAssertion( "A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A figure that expresses one or more propositions"@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion(rdfs:label "diagram"@en) +SubClassOf( ) + +# Class: (document) + +AnnotationAssertion( "document"@en) +AnnotationAssertion( "A journal article, patent application, laboratory notebook, or a book"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A collection of information content entities intended to be understood together as a whole"@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion(rdfs:label "document"@en) +SubClassOf( ) + +# Class: (denotator type) + +AnnotationAssertion( "denotator type"@en) +AnnotationAssertion( "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities."@en) +AnnotationAssertion( "A denotator type indicates how a term should be interpreted from an ontological perspective."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "Barry Smith, Werner Ceusters"@en) +AnnotationAssertion(rdfs:label "denotator type"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (Viruses) + +AnnotationAssertion( "Viruses") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Viruses") +SubClassOf( ) + +# Class: (Euteleostomi) + +AnnotationAssertion( "Euteleostomi") +AnnotationAssertion( "bony vertebrates") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Euteleostomi") +SubClassOf( ) + +# Class: (Bacteria) + +AnnotationAssertion( "Bacteria") +AnnotationAssertion( "eubacteria") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Bacteria") +SubClassOf( ) + +# Class: (Archaea) + +AnnotationAssertion( "Archaea") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Archaea") +SubClassOf( ) + +# Class: (Eukaryota) + +AnnotationAssertion( "Eukaryota") +AnnotationAssertion( "eucaryotes") +AnnotationAssertion( "eukaryotes") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Eukaryota") +SubClassOf( ) + +# Class: (Euarchontoglires) + +AnnotationAssertion( "Euarchontoglires") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Euarchontoglires") +SubClassOf( ) + +# Class: (Tetrapoda) + +AnnotationAssertion( "Tetrapoda") +AnnotationAssertion( "tetrapods") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Tetrapoda") +SubClassOf( ) + +# Class: (Amniota) + +AnnotationAssertion( "Amniota") +AnnotationAssertion( "amniotes") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Amniota") +SubClassOf( ) + +# Class: (Opisthokonta) + +AnnotationAssertion( "Opisthokonta") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Opisthokonta") +SubClassOf( ) + +# Class: (Metazoa) + +AnnotationAssertion( "Metazoa") +AnnotationAssertion( "metazoans") +AnnotationAssertion( "multicellular animals") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Metazoa") +SubClassOf( ) + +# Class: (Bilateria) + +AnnotationAssertion( "Bilateria") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Bilateria") +SubClassOf( ) + +# Class: (Mammalia) + +AnnotationAssertion( "Mammalia") +AnnotationAssertion( "mammals") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Mammalia") +SubClassOf( ) + +# Class: (Vertebrata ) + +AnnotationAssertion( "Vertebrata ") +AnnotationAssertion( "Vertebrata") +AnnotationAssertion( "vertebrates") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Vertebrata ") +SubClassOf( ) + +# Class: (Homo sapiens) + +AnnotationAssertion( "Homo sapiens") +AnnotationAssertion( "human") +AnnotationAssertion( "human being") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Homo sapiens") +SubClassOf( ) + # Class: (planned process) AnnotationAssertion( "planned process"@en) @@ -500,6 +1765,36 @@ AnnotationAssertion(rdfs:label "cla EquivalentClasses( ObjectSomeValuesFrom( )) SubClassOf( ) +# Class: (processed material) + +AnnotationAssertion( "processed material"@en) +AnnotationAssertion( "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Is a material entity that is created or changed during material processing."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "processed material"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (material processing) + +AnnotationAssertion( "material processing") +AnnotationAssertion( "A cell lysis, production of a cloning vector, creating a buffer.") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process which results in physical changes in a specified input material"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON: Philippe Rocca Serra") +AnnotationAssertion( "material transformation"@en) +AnnotationAssertion( "OBI branch derived"@en) +AnnotationAssertion(rdfs:label "material processing"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + # Class: (specimen role) AnnotationAssertion( "specimen role") @@ -574,6 +1869,56 @@ AnnotationAssertion(rdfs:label "reg EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (material transformation objective) + +AnnotationAssertion( "material transformation objective") +AnnotationAssertion( "The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.") +AnnotationAssertion( ) +AnnotationAssertion( "an objective specifiction that creates an specific output object from input materials."@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "artifact creation objective"@en) +AnnotationAssertion( "GROUP: OBI PlanAndPlannedProcess Branch") +AnnotationAssertion(rdfs:label "material transformation objective"@en) +SubClassOf( ) + +# Class: (manufacturing) + +AnnotationAssertion( "manufacturing") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process with the objective to produce a processed material which will have a function for future use."@en) +AnnotationAssertion( "This includes a single scientist making a processed material for personal use."@en) +AnnotationAssertion( "A person or organization (having manufacturer role) is a participant in this process") +AnnotationAssertion( "Manufacturing implies reproducibility and responsibility AR") +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "GROUP: OBI PlanAndPlannedProcess Branch") +AnnotationAssertion(rdfs:label "manufacturing"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (manufacturing objective) + +AnnotationAssertion( "manufacturing objective") +AnnotationAssertion( ) +AnnotationAssertion( "is the objective to manufacture a material of a certain function (device)"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "GROUP: OBI PlanAndPlannedProcess Branch") +AnnotationAssertion(rdfs:label "manufacturing objective"@en) +SubClassOf( ) + # Class: (manufacturer role) AnnotationAssertion( "manufacturer role") @@ -585,6 +1930,7 @@ AnnotationAssertion( "manufacturer role") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) +SubClassOf( ObjectAllValuesFrom( )) # Class: (clustered data set) @@ -757,6 +2103,22 @@ AnnotationAssertion( "service provider role") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (processed specimen) + +AnnotationAssertion( "processed specimen") +AnnotationAssertion( "A tissue sample that has been sliced and stained for a histology study. +A blood specimen that has been centrifuged to obtain the white blood cells.") +AnnotationAssertion( ) +AnnotationAssertion( "A specimen that has been intentionally physically modified.") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion(rdfs:comment "A tissue sample that has been sliced and stained for a histology study.") +AnnotationAssertion(rdfs:label "processed specimen") +EquivalentClasses( ObjectIntersectionOf( )) +SubClassOf( ) +SubClassOf( ) # Class: (categorical label) @@ -1101,6 +2463,25 @@ AnnotationAssertion(rdfs:label "mat EquivalentClasses( ObjectIntersectionOf(ObjectUnionOf( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (organism) + +AnnotationAssertion( "organism"@en) +AnnotationAssertion( "animal"@en) +AnnotationAssertion( "fungus"@en) +AnnotationAssertion( "plant"@en) +AnnotationAssertion( "virus"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en) +AnnotationAssertion( "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')") +AnnotationAssertion( "13-02-2009: +OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. +This issue is outside the scope of OBI.") +AnnotationAssertion( "GROUP: OBI Biomaterial Branch") +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Organism"@en) +AnnotationAssertion(rdfs:label "organism"@en) +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + # Class: (specimen) AnnotationAssertion( "specimen"@en) @@ -1339,11 +2720,213 @@ SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) SubClassOf( ObjectAllValuesFrom( )) +# Class: (length unit) + +AnnotationAssertion( "length unit") +AnnotationAssertion( "A unit which is a standard measure of the distance between two points.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "length unit") +SubClassOf( ) + +# Class: (mass unit) + +AnnotationAssertion( "mass unit") +AnnotationAssertion( "A unit which is a standard measure of the amount of matter/energy of a physical object.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "mass unit") +SubClassOf( ) + +# Class: (time unit) + +AnnotationAssertion( "time unit") +AnnotationAssertion( "A unit which is a standard measure of the dimension in which events occur in sequence.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "time unit") +SubClassOf( ) + +# Class: (temperature unit) + +AnnotationAssertion( "temperature unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "temperature unit") +SubClassOf( ) + +# Class: (substance unit) + +AnnotationAssertion( "substance unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "substance unit") +SubClassOf( ) + +# Class: (concentration unit) + +AnnotationAssertion( "concentration unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "concentration unit") +SubClassOf( ) + +# Class: (volume unit) + +AnnotationAssertion( "volume unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "volume unit") +SubClassOf( ) + +# Class: (frequency unit) + +AnnotationAssertion( "frequency unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "frequency unit") +SubClassOf( ) + +# Class: (volumetric flow rate unit) + +AnnotationAssertion( "volumetric flow rate unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "volumetric flow rate unit") +SubClassOf( ) + +# Class: (rate unit) + +AnnotationAssertion( "rate unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "rate unit") +SubClassOf( ) + ############################ # Named Individuals ############################ +# Individual: (example to be eventually removed) + +AnnotationAssertion( "example to be eventually removed"@en) +AnnotationAssertion(rdfs:label "example to be eventually removed"@en) +ClassAssertion( ) + +# Individual: (failed exploratory term) + +AnnotationAssertion( "failed exploratory term"@en) +AnnotationAssertion( "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "failed exploratory term"@en) +ClassAssertion( ) + +# Individual: (metadata complete) + +AnnotationAssertion( "metadata complete"@en) +AnnotationAssertion( "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en) +AnnotationAssertion(rdfs:label "metadata complete"@en) +ClassAssertion( ) + +# Individual: (organizational term) + +AnnotationAssertion( "organizational term"@en) +AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) +AnnotationAssertion( "PERSON:Alan Ruttenberg") +AnnotationAssertion(rdfs:label "organizational term"@en) +ClassAssertion( ) + +# Individual: (ready for release) + +AnnotationAssertion( "ready for release"@en) +AnnotationAssertion( "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en) +AnnotationAssertion(rdfs:label "ready for release"@en) +ClassAssertion( ) + +# Individual: (metadata incomplete) + +AnnotationAssertion( "metadata incomplete"@en) +AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) +AnnotationAssertion(rdfs:label "metadata incomplete"@en) +ClassAssertion( ) + +# Individual: (uncurated) + +AnnotationAssertion( "uncurated"@en) +AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) +AnnotationAssertion(rdfs:label "uncurated"@en) +ClassAssertion( ) + +# Individual: (pending final vetting) + +AnnotationAssertion( "pending final vetting"@en) +AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) +AnnotationAssertion(rdfs:label "pending final vetting"@en) +ClassAssertion( ) + +# Individual: (placeholder removed) + +AnnotationAssertion( "placeholder removed"@en) +AnnotationAssertion(rdfs:label "placeholder removed"@en) +ClassAssertion( ) + +# Individual: (terms merged) + +AnnotationAssertion( "terms merged"@en) +AnnotationAssertion( "An editor note should explain what were the merged terms and the reason for the merge."@en) +AnnotationAssertion(rdfs:label "terms merged"@en) +ClassAssertion( ) + +# Individual: (term imported) + +AnnotationAssertion( "term imported"@en) +AnnotationAssertion( "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."@en) +AnnotationAssertion(rdfs:label "term imported"@en) +ClassAssertion( ) + +# Individual: (term split) + +AnnotationAssertion( "term split"@en) +AnnotationAssertion( "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."@en) +AnnotationAssertion(rdfs:label "term split"@en) +ClassAssertion( ) + +# Individual: (universal) + +AnnotationAssertion( "universal"@en) +AnnotationAssertion( "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf"@en) +AnnotationAssertion(rdfs:label "universal"@en) +ClassAssertion( ) + +# Individual: (defined class) + +AnnotationAssertion( "defined class"@en) +AnnotationAssertion( "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal"@en) +AnnotationAssertion( "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "defined class"@en) +ClassAssertion( ) + +# Individual: (named class expression) + +AnnotationAssertion( "named class expression"@en) +AnnotationAssertion( "A named class expression is a logical expression that is given a name. The name can be used in place of the expression."@en) +AnnotationAssertion( "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "named class expression"@en) +ClassAssertion( ) + +# Individual: (to be replaced with external ontology term) + +AnnotationAssertion( "to be replaced with external ontology term"@en) +AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) +ClassAssertion( ) + +# Individual: (requires discussion) + +AnnotationAssertion( "requires discussion"@en) +AnnotationAssertion( "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "requires discussion"@en) +ClassAssertion( ) + # Individual: (Transformation-ML) AnnotationAssertion( "Transformation-ML"@en) @@ -3636,5 +5219,471 @@ AnnotationAssertion( "InBios") ClassAssertion( ) - +# Individual: (meter) + +AnnotationAssertion( "meter") +AnnotationAssertion( "A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.") +AnnotationAssertion( "m") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "meter") +ClassAssertion( ) + +# Individual: (kilogram) + +AnnotationAssertion( "kilogram") +AnnotationAssertion( "A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.") +AnnotationAssertion( "kg") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "kilogram") +ClassAssertion( ) + +# Individual: (second) + +AnnotationAssertion( "second") +AnnotationAssertion( "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.") +AnnotationAssertion( "s") +AnnotationAssertion( "sec") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "second") +ClassAssertion( ) + +# Individual: (centimeter) + +AnnotationAssertion( "centimeter") +AnnotationAssertion( "A length unit which is equal to one hundredth of a meter or 10^[-2] m.") +AnnotationAssertion( "cm") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "centimeter") +ClassAssertion( ) + +# Individual: (millimeter) + +AnnotationAssertion( "millimeter") +AnnotationAssertion( "A length unit which is equal to one thousandth of a meter or 10^[-3] m.") +AnnotationAssertion( "mm") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "millimeter") +ClassAssertion( ) + +# Individual: (micrometer) + +AnnotationAssertion( "micrometer") +AnnotationAssertion( "A length unit which is equal to one millionth of a meter or 10^[-6] m.") +AnnotationAssertion( "um") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "micrometer") +ClassAssertion( ) + +# Individual: (nanometer) + +AnnotationAssertion( "nanometer") +AnnotationAssertion( "A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.") +AnnotationAssertion( "nm") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "nanometer") +ClassAssertion( ) + +# Individual: (angstrom) + +AnnotationAssertion( "angstrom") +AnnotationAssertion( "A length unit which is equal to 10 [-10] m.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "angstrom") +ClassAssertion( ) + +# Individual: (gram) + +AnnotationAssertion( "gram") +AnnotationAssertion( "A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.") +AnnotationAssertion( "g") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "gram") +ClassAssertion( ) + +# Individual: (milligram) + +AnnotationAssertion( "milligram") +AnnotationAssertion( "A mass unit which is equal to one thousandth of a gram or 10^[-3] g.") +AnnotationAssertion( "mg") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "milligram") +ClassAssertion( ) + +# Individual: (microgram) + +AnnotationAssertion( "microgram") +AnnotationAssertion( "A mass unit which is equal to one millionth of a gram or 10^[-6] g.") +AnnotationAssertion( "ug") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "microgram") +ClassAssertion( ) + +# Individual: (nanogram) + +AnnotationAssertion( "nanogram") +AnnotationAssertion( "A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.") +AnnotationAssertion( "ng") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "nanogram") +ClassAssertion( ) + +# Individual: (picogram) + +AnnotationAssertion( "picogram") +AnnotationAssertion( "A mass unit which is equal to 10^[-12] g.") +AnnotationAssertion( "pg") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "picogram") +ClassAssertion( ) + +# Individual: (degree Celsius) + +AnnotationAssertion( "degree Celsius") +AnnotationAssertion( "A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.") +AnnotationAssertion( "C") +AnnotationAssertion( "degree C") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "degree Celsius") +ClassAssertion( ) + +# Individual: (minute) + +AnnotationAssertion( "minute") +AnnotationAssertion( "A time unit which is equal to 60 seconds.") +AnnotationAssertion( "min") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "minute") +ClassAssertion( ) + +# Individual: (hour) + +AnnotationAssertion( "hour") +AnnotationAssertion( "A time unit which is equal to 3600 seconds or 60 minutes.") +AnnotationAssertion( "h") +AnnotationAssertion( "hr") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "hour") +ClassAssertion( ) + +# Individual: (day) + +AnnotationAssertion( "day") +AnnotationAssertion( "A time unit which is equal to 24 hours.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "day") +ClassAssertion( ) + +# Individual: (week) + +AnnotationAssertion( "week") +AnnotationAssertion( "A time unit which is equal to 7 days.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "week") +ClassAssertion( ) + +# Individual: (month) + +AnnotationAssertion( "month") +AnnotationAssertion( "A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "month") +ClassAssertion( ) + +# Individual: (year) + +AnnotationAssertion( "year") +AnnotationAssertion( "A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "year") +ClassAssertion( ) + +# Individual: (micromole) + +AnnotationAssertion( "micromole") +AnnotationAssertion( "A substance unit equal to a millionth of a mol or 10^[-6] mol.") +AnnotationAssertion( "umol") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "micromole") +ClassAssertion( ) + +# Individual: (nanomole) + +AnnotationAssertion( "nanomole") +AnnotationAssertion( "A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.") +AnnotationAssertion( "nmol") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "nanomole") +ClassAssertion( ) + +# Individual: (picomole) + +AnnotationAssertion( "picomole") +AnnotationAssertion( "A substance unit equal to 10^[-12] mol.") +AnnotationAssertion( "pmol") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "picomole") +ClassAssertion( ) + +# Individual: (molar) + +AnnotationAssertion( "molar") +AnnotationAssertion( "A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).") +AnnotationAssertion( "M") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "molar") +ClassAssertion( ) + +# Individual: (millimolar) + +AnnotationAssertion( "millimolar") +AnnotationAssertion( "A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.") +AnnotationAssertion( "mM") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "millimolar") +ClassAssertion( ) + +# Individual: (micromolar) + +AnnotationAssertion( "micromolar") +AnnotationAssertion( "A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.") +AnnotationAssertion( "uM") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "micromolar") +ClassAssertion( ) + +# Individual: (nanomolar) + +AnnotationAssertion( "nanomolar") +AnnotationAssertion( "A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.") +AnnotationAssertion( "nM") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "nanomolar") +ClassAssertion( ) + +# Individual: (picomolar) + +AnnotationAssertion( "picomolar") +AnnotationAssertion( "A unit of molarity which is equal to 10^[-12] M.") +AnnotationAssertion( "pM") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "picomolar") +ClassAssertion( ) + +# Individual: (cubic centimeter) + +AnnotationAssertion( "cubic centimeter") +AnnotationAssertion( "A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.") +AnnotationAssertion( "cc") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cubic centimeter") +ClassAssertion( ) + +# Individual: (milliliter) + +AnnotationAssertion( "milliliter") +AnnotationAssertion( "A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.") +AnnotationAssertion( "ml") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "milliliter") +ClassAssertion( ) + +# Individual: (liter) + +AnnotationAssertion( "liter") +AnnotationAssertion( "A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.") +AnnotationAssertion( "L") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "liter") +ClassAssertion( ) + +# Individual: (cubic decimeter) + +AnnotationAssertion( "cubic decimeter") +AnnotationAssertion( "A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cubic decimeter") +ClassAssertion( ) + +# Individual: (microliter) + +AnnotationAssertion( "microliter") +AnnotationAssertion( "A volume unit which is equal to one millionth of a liter or 10^[-6] L.") +AnnotationAssertion( "ul") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "microliter") +ClassAssertion( ) + +# Individual: (nanoliter) + +AnnotationAssertion( "nanoliter") +AnnotationAssertion( "A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.") +AnnotationAssertion( "nl") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "nanoliter") +ClassAssertion( ) + +# Individual: (picoliter) + +AnnotationAssertion( "picoliter") +AnnotationAssertion( "A volume unit which is equal to 10^[-12] L.") +AnnotationAssertion( "pl") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "picoliter") +ClassAssertion( ) + +# Individual: (hertz) + +AnnotationAssertion( "hertz") +AnnotationAssertion( "A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "hertz") +ClassAssertion( ) + +# Individual: (mass percentage) + +AnnotationAssertion( "mass percentage") +AnnotationAssertion( "A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.") +AnnotationAssertion( "% w/w") +AnnotationAssertion( "percent weight pr weight") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "mass percentage") +ClassAssertion( ) + +# Individual: (mass volume percentage) + +AnnotationAssertion( "mass volume percentage") +AnnotationAssertion( "A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.") +AnnotationAssertion( "% w/v") +AnnotationAssertion( "percent vol per vol") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "mass volume percentage") +ClassAssertion( ) + +# Individual: (volume percentage) + +AnnotationAssertion( "volume percentage") +AnnotationAssertion( "A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.") +AnnotationAssertion( "% v/v") +AnnotationAssertion( "percent vol per vol") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "volume percentage") +ClassAssertion( ) + +# Individual: (gram per liter) + +AnnotationAssertion( "gram per liter") +AnnotationAssertion( "A mass unit density which is equal to mass of an object in grams divided by the volume in liters.") +AnnotationAssertion( "g per L") +AnnotationAssertion( "g/L") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "gram per liter") +ClassAssertion( ) + +# Individual: (milligram per milliliter) + +AnnotationAssertion( "milligram per milliliter") +AnnotationAssertion( "A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.") +AnnotationAssertion( "mg per ml") +AnnotationAssertion( "mg/ml") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "milligram per milliliter") +ClassAssertion( ) + +# Individual: (degree Fahrenheit) + +AnnotationAssertion( "degree Fahrenheit") +AnnotationAssertion( "A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "degree Fahrenheit") +ClassAssertion( ) + +# Individual: (pH) + +AnnotationAssertion( "pH") +AnnotationAssertion( "A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "pH") +ClassAssertion( ) + +# Individual: (milliliter per liter) + +AnnotationAssertion( "milliliter per liter") +AnnotationAssertion( "A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.") +AnnotationAssertion( "ml per L") +AnnotationAssertion( "ml/l") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "milliliter per liter") +ClassAssertion( ) + +# Individual: (gram per deciliter) + +AnnotationAssertion( "gram per deciliter") +AnnotationAssertion( "A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.") +AnnotationAssertion( "g/dl") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "gram per deciliter") +ClassAssertion( ) + +# Individual: (colony forming unit per volume) + +AnnotationAssertion( "colony forming unit per volume") +AnnotationAssertion( "A concentration unit which a measure of viable bacterial numbers in a given volume.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "colony forming unit per volume") +ClassAssertion( ) + +# Individual: (microliters per minute) + +AnnotationAssertion( "microliters per minute") +AnnotationAssertion( "A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "microliters per minute") +ClassAssertion( ) + +# Individual: (count per nanomolar second) + +AnnotationAssertion( "count per nanomolar second") +AnnotationAssertion( "A rate unit which is equal to one over one nanomolar second.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "count per nanomolar second") +ClassAssertion( ) + +# Individual: (count per molar second) + +AnnotationAssertion( "count per molar second") +AnnotationAssertion( "A rate unit which is equal to one over one molar second.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "count per molar second") +ClassAssertion( ) + +# Individual: (count per nanomolar) + +AnnotationAssertion( "count per nanomolar") +AnnotationAssertion( "A rate unit which is equal to one over one nanomolar.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "count per nanomolar") +ClassAssertion( ) + +# Individual: (count per molar) + +AnnotationAssertion( "count per molar") +AnnotationAssertion( "A rate unit which is equal to one over one molar.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "count per molar") +ClassAssertion( ) + +# Individual: (microgram per liter) + +AnnotationAssertion( "microgram per liter") +AnnotationAssertion( "A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.") +AnnotationAssertion( "ng/ml") +AnnotationAssertion( "ug/L") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "microgram per liter") +ClassAssertion( ) + + +DisjointClasses( ) +DifferentIndividuals( ) +DifferentIndividuals( ) ) \ No newline at end of file diff --git a/src/ontology/imports/omo_import.owl b/src/ontology/imports/omo_import.owl index 20e3e28..dcf743a 100644 --- a/src/ontology/imports/omo_import.owl +++ b/src/ontology/imports/omo_import.owl @@ -1,4 +1,4 @@ -Prefix(:=) +Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) @@ -6,10 +6,10 @@ Prefix(xsd:=) Prefix(rdfs:=) -Ontology( - +Ontology( + Annotation( ) -Annotation(owl:versionInfo "2023-11-23") +Annotation(owl:versionInfo "2024-02-20") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index 1e5cbd0..8704e8d 100644 --- a/src/ontology/imports/pato_import.owl +++ b/src/ontology/imports/pato_import.owl @@ -1,4 +1,4 @@ -Prefix(:=) +Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) @@ -6,18 +6,1966 @@ Prefix(xsd:=) Prefix(rdfs:=) -Ontology( - +Ontology( + Annotation( ) -Annotation(owl:versionInfo "2023-11-23") +Annotation(owl:versionInfo "2024-02-20") +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty(rdfs:comment)) +Declaration(AnnotationProperty(rdfs:label)) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ +# Annotation Property: (definition) +AnnotationAssertion(rdfs:label "definition") + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: (is a defining property chain axiom) + +AnnotationAssertion( "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL") +AnnotationAssertion(rdfs:label "is a defining property chain axiom") + +# Annotation Property: (is a defining property chain axiom where second argument is reflexive) + +AnnotationAssertion( "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.") +AnnotationAssertion(rdfs:label "is a defining property chain axiom where second argument is reflexive") + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: (license) + +AnnotationAssertion( "http://purl.org/dc/terms/license") +AnnotationAssertion( "uberon") +AnnotationAssertion( "dcterms-license") +AnnotationAssertion( "true"^^xsd:boolean) +AnnotationAssertion( "dcterms-license") +AnnotationAssertion(rdfs:label "license") + +# Annotation Property: (consider) + +AnnotationAssertion(rdfs:label "consider") + +# Annotation Property: (has_broad_synonym) + +AnnotationAssertion(rdfs:label "has_broad_synonym") + +# Annotation Property: (database_cross_reference) + +AnnotationAssertion(rdfs:label "database_cross_reference") + +# Annotation Property: (has_exact_synonym) + +AnnotationAssertion(rdfs:label "has_exact_synonym") + +# Annotation Property: (has_obo_format_version) + +AnnotationAssertion(rdfs:label "has_obo_format_version") + +# Annotation Property: (has_obo_namespace) + +AnnotationAssertion(rdfs:label "has_obo_namespace") + + +############################ +# Object Properties +############################ + +# Object Property: (part_of) + +AnnotationAssertion( "is part of"@en) +AnnotationAssertion( "my brain is part of my body (continuant parthood, two material entities)"@en) +AnnotationAssertion( "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en) +AnnotationAssertion( "this day is part of this year (occurrent parthood)"@en) +AnnotationAssertion( "a core relation that holds between a part and its whole"@en) +AnnotationAssertion( "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other."@en) +AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) +AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'."@en) +AnnotationAssertion( "part_of"@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "BFO:0000050") +AnnotationAssertion( "external") +AnnotationAssertion( "quality") +AnnotationAssertion( "uberon") +AnnotationAssertion( "part_of") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "part_of") +AnnotationAssertion(rdfs:label "part of"@en) +AnnotationAssertion(rdfs:label "part of") +AnnotationAssertion(rdfs:label "part_of") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (has part) + +AnnotationAssertion( "has part"@en) +AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"@en) +AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en) +AnnotationAssertion( "this year has part this day (occurrent parthood)"@en) +AnnotationAssertion( "a core relation that holds between a whole and its part"@en) +AnnotationAssertion( "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part."@en) +AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) +AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'."@en) +AnnotationAssertion( "has_part"@en) +AnnotationAssertion( ) +AnnotationAssertion( "BFO:0000051") +AnnotationAssertion( "external") +AnnotationAssertion( "quality") +AnnotationAssertion( "uberon") +AnnotationAssertion( "has_part") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "has_part") +AnnotationAssertion(rdfs:label "has part"@en) +AnnotationAssertion(rdfs:label "has part") +AnnotationAssertion(rdfs:label "has_part") +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (preceded by) + +AnnotationAssertion( "preceded by"@en) +AnnotationAssertion( "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) +AnnotationAssertion( "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other."@en) +AnnotationAssertion( "is preceded by"@en) +AnnotationAssertion( "preceded_by"@en) +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") +AnnotationAssertion( "BFO:0000062") +AnnotationAssertion( "external") +AnnotationAssertion( "uberon") +AnnotationAssertion( "preceded_by") +AnnotationAssertion( ) +AnnotationAssertion( "preceded_by") +AnnotationAssertion(rdfs:label "preceded by"@en) +AnnotationAssertion(rdfs:label "preceded by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (precedes) + +AnnotationAssertion( "precedes"@en) +AnnotationAssertion( "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) +AnnotationAssertion( "BFO:0000063") +AnnotationAssertion( "external") +AnnotationAssertion( "uberon") +AnnotationAssertion( "precedes") +AnnotationAssertion( ) +AnnotationAssertion( "precedes") +AnnotationAssertion(rdfs:label "precedes"@en) +AnnotationAssertion(rdfs:label "precedes") +SubObjectPropertyOf( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (characteristic of) + +AnnotationAssertion( "inheres in"@en) +AnnotationAssertion( "this fragility is a characteristic of this vase"@en) +AnnotationAssertion( "this red color is a characteristic of this apple"@en) +AnnotationAssertion( "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence."@en) +AnnotationAssertion( "inheres_in"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.") +AnnotationAssertion(rdfs:label "characteristic of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +FunctionalObjectProperty() + +# Object Property: (bearer of) + +AnnotationAssertion( "bearer of"@en) +AnnotationAssertion( "this apple is bearer of this red color"@en) +AnnotationAssertion( "this vase is bearer of this fragility"@en) +AnnotationAssertion( "Inverse of characteristic_of"@en) +AnnotationAssertion( "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist."@en) +AnnotationAssertion( "bearer_of"@en) +AnnotationAssertion( "is bearer of"@en) +AnnotationAssertion( ) +AnnotationAssertion( "RO:0000053") +AnnotationAssertion( "external") +AnnotationAssertion( "bearer_of") +AnnotationAssertion( "bearer_of") +AnnotationAssertion(rdfs:label "has characteristic"@en) +AnnotationAssertion(rdfs:label "bearer of") +InverseFunctionalObjectProperty() +ObjectPropertyRange( ) + +# Object Property: (participates in) + +AnnotationAssertion( "participates in"@en) +AnnotationAssertion( "this blood clot participates in this blood coagulation"@en) +AnnotationAssertion( "this input material (or this output material) participates in this process"@en) +AnnotationAssertion( "this investigator participates in this investigation"@en) +AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion( "participates_in"@en) +AnnotationAssertion( "RO:0000056") +AnnotationAssertion( "external") +AnnotationAssertion( "uberon") +AnnotationAssertion( "participates_in") +AnnotationAssertion( "participates_in") +AnnotationAssertion(rdfs:label "participates in"@en) +AnnotationAssertion(rdfs:label "participates in") +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has participant) + +AnnotationAssertion( "has participant"@en) +AnnotationAssertion( "this blood coagulation has participant this blood clot"@en) +AnnotationAssertion( "this investigation has participant this investigator"@en) +AnnotationAssertion( "this process has participant this input material (or this output material)"@en) +AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion( "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) +AnnotationAssertion( "has_participant"@en) +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") +AnnotationAssertion( "RO:0000057") +AnnotationAssertion( "external") +AnnotationAssertion( "has_participant") +AnnotationAssertion( "has_participant") +AnnotationAssertion(rdfs:label "has participant"@en) +AnnotationAssertion(rdfs:label "has participant") +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (function of) + +AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) +AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists."@en) +AnnotationAssertion( "function_of"@en) +AnnotationAssertion( "is function of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "function of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (quality of) + +AnnotationAssertion( "this red color is a quality of this apple"@en) +AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A quality inheres in its bearer at all times for which the quality exists."@en) +AnnotationAssertion( "is quality of"@en) +AnnotationAssertion( "quality_of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "quality of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (role of) + +AnnotationAssertion( "this investigator role is a role of this person"@en) +AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists."@en) +AnnotationAssertion( "is role of"@en) +AnnotationAssertion( "role_of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "role of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has function) + +AnnotationAssertion( "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists."@en) +AnnotationAssertion( "has_function"@en) +AnnotationAssertion(rdfs:label "has function"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has quality) + +AnnotationAssertion( "this apple has quality this red color"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist."@en) +AnnotationAssertion( "has_quality"@en) +AnnotationAssertion( "RO:0000086") +AnnotationAssertion( "uberon") +AnnotationAssertion( "has_quality") +AnnotationAssertion( "has_quality") +AnnotationAssertion(rdfs:label "has quality"@en) +AnnotationAssertion(rdfs:label "has quality") +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (has role) + +AnnotationAssertion( "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists."@en) +AnnotationAssertion( "has_role"@en) +AnnotationAssertion(rdfs:label "has role"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has disposition) + +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) +AnnotationAssertion(rdfs:label "has disposition"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (disposition of) + +AnnotationAssertion( "inverse of has disposition") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "disposition of"@en) +SubObjectPropertyOf( ) + +# Object Property: (has regulatory component activity) + +AnnotationAssertion( "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-05-24T09:30:46Z"^^xsd:dateTime) +AnnotationAssertion( "RO:0002013") +AnnotationAssertion( "external") +AnnotationAssertion( "has_regulatory_component_activity") +AnnotationAssertion( "has_regulatory_component_activity") +AnnotationAssertion(rdfs:label "has regulatory component activity") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has negative regulatory component activity) + +AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-05-24T09:31:01Z"^^xsd:dateTime) +AnnotationAssertion( "RO:0002014") +AnnotationAssertion( "external") +AnnotationAssertion( "has_negative_regulatory_component_activity") +AnnotationAssertion( "has_negative_regulatory_component_activity") +AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.") +AnnotationAssertion(rdfs:label "has negative regulatory component activity") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has positive regulatory component activity) + +AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-05-24T09:31:17Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.") +AnnotationAssertion(rdfs:label "has positive regulatory component activity") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has component activity) + +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-05-24T09:44:33Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") +AnnotationAssertion(rdfs:label "has component activity") +SubObjectPropertyOf( ) + +# Object Property: (has component process) + +AnnotationAssertion( "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-05-24T09:49:21Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "has component process") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly regulated by) + +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) +AnnotationAssertion(Annotation( "GOC:dos") rdfs:comment "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") +AnnotationAssertion(rdfs:label "directly regulated by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (directly negatively regulated by) + +AnnotationAssertion(Annotation( "GOC:dos") "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-09-17T13:52:38Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "directly negatively regulated by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (directly positively regulated by) + +AnnotationAssertion(Annotation( "GOC:dos") "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-09-17T13:52:47Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "directly positively regulated by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has effector activity) + +AnnotationAssertion(Annotation( "GOC:dos") "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-09-22T14:14:36Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.") +AnnotationAssertion(rdfs:label "has effector activity") +SubObjectPropertyOf( ) +FunctionalObjectProperty() + +# Object Property: (ends after) + +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)"@en) +AnnotationAssertion(rdfs:label "ends after"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (immediately preceded by) + +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( "starts_at_end_of") +AnnotationAssertion( "RO:0002087") +AnnotationAssertion( "external") +AnnotationAssertion( "uberon") +AnnotationAssertion( "immediately_preceded_by") +AnnotationAssertion( "immediately_preceded_by") +AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) +AnnotationAssertion(rdfs:label "immediately preceded by"@en) +AnnotationAssertion(rdfs:label "immediately preceded by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (immediately precedes) + +AnnotationAssertion( ) +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( "ends_at_start_of") +AnnotationAssertion( "meets") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002090") +AnnotationAssertion( "external") +AnnotationAssertion( "immediately_precedes") +AnnotationAssertion( ) +AnnotationAssertion( "immediately_precedes") +AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en) +AnnotationAssertion(rdfs:label "immediately precedes"@en) +AnnotationAssertion(rdfs:label "immediately precedes") +SubObjectPropertyOf( ) + +# Object Property: (overlaps) + +AnnotationAssertion( ) +AnnotationAssertion( "x overlaps y if and only if there exists some z such that x has part z and z part of y") +AnnotationAssertion( "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002131") +AnnotationAssertion( "external") +AnnotationAssertion( "uberon") +AnnotationAssertion( "overlaps") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "overlaps") +AnnotationAssertion(rdfs:label "overlaps"@en) +AnnotationAssertion(rdfs:label "overlaps") +SubObjectPropertyOf( ) +SymmetricObjectProperty() + +# Object Property: (has component) + +AnnotationAssertion( ) +AnnotationAssertion( "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") +AnnotationAssertion( "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.") +AnnotationAssertion( "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit."@en) +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002180") +AnnotationAssertion( "external") +AnnotationAssertion( "uberon") +AnnotationAssertion( "has_component") +AnnotationAssertion( ) +AnnotationAssertion( "has_component") +AnnotationAssertion(rdfs:label "has component"@en) +AnnotationAssertion(rdfs:label "has component") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (regulates) + +AnnotationAssertion( "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "GO") +AnnotationAssertion( "Regulation precludes parthood; the regulatory process may not be within the regulated process.") +AnnotationAssertion( "regulates (processual)") +AnnotationAssertion( "false"^^xsd:boolean) +AnnotationAssertion( "RO:0002211") +AnnotationAssertion( "external") +AnnotationAssertion( "regulates") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "regulates") +AnnotationAssertion(rdfs:label "regulates"@en) +AnnotationAssertion(rdfs:label "regulates") +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (negatively regulates) + +AnnotationAssertion( "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "negatively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002212") +AnnotationAssertion( "external") +AnnotationAssertion( "negatively_regulates") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "negatively_regulates") +AnnotationAssertion(rdfs:label "negatively regulates"@en) +AnnotationAssertion(rdfs:label "negatively regulates") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (positively regulates) + +AnnotationAssertion( "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "positively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002213") +AnnotationAssertion( "external") +AnnotationAssertion( "positively_regulates") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "positively_regulates") +AnnotationAssertion(rdfs:label "positively regulates"@en) +AnnotationAssertion(rdfs:label "positively regulates") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (capable of) + +AnnotationAssertion( "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)") +AnnotationAssertion( "osteoclast SubClassOf 'capable of' some 'bone resorption'") +AnnotationAssertion( "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. ") +AnnotationAssertion( ) +AnnotationAssertion( "has function realized in") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\".") +AnnotationAssertion( "RO:0002215") +AnnotationAssertion( "external") +AnnotationAssertion( "uberon") +AnnotationAssertion( "capable_of") +AnnotationAssertion( ) +AnnotationAssertion( "capable_of") +AnnotationAssertion(rdfs:label "capable of"@en) +AnnotationAssertion(rdfs:label "capable of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (capable of part of) + +AnnotationAssertion( "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.") +AnnotationAssertion( ) +AnnotationAssertion( "has function in") +AnnotationAssertion( "RO:0002216") +AnnotationAssertion( "external") +AnnotationAssertion( "uberon") +AnnotationAssertion( "capable_of_part_of") +AnnotationAssertion( "capable_of_part_of") +AnnotationAssertion(rdfs:label "capable of part of"@en) +AnnotationAssertion(rdfs:label "capable of part of") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (temporally related to) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.") +AnnotationAssertion( "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1"^^xsd:anyURI) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.") +AnnotationAssertion(rdfs:label "temporally related to"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has input) + +AnnotationAssertion( ) +AnnotationAssertion( "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.") +AnnotationAssertion( ) +AnnotationAssertion( "consumes") +AnnotationAssertion( "RO:0002233") +AnnotationAssertion( "external") +AnnotationAssertion( "has_input") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "has_input") +AnnotationAssertion(rdfs:label "has input"@en) +AnnotationAssertion(rdfs:label "has input") +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (acts upstream of) + +AnnotationAssertion( "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.") +AnnotationAssertion( "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within) + +AnnotationAssertion( "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.") +AnnotationAssertion( "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.") +AnnotationAssertion( "affects") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of or within") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of, positive effect) + +AnnotationAssertion( "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002304") +AnnotationAssertion( "external") +AnnotationAssertion( "causally_upstream_of,_positive_effect") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "causally_upstream_of,_positive_effect") +AnnotationAssertion(rdfs:comment "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y") +AnnotationAssertion(rdfs:label "causally upstream of, positive effect") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of, negative effect) + +AnnotationAssertion( "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002305") +AnnotationAssertion( "external") +AnnotationAssertion( "causally_upstream_of,_negative_effect") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "causally_upstream_of,_negative_effect") +AnnotationAssertion(rdfs:label "causally upstream of, negative effect") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (characteristic of part of) + +AnnotationAssertion( "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.") +AnnotationAssertion( "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of") +AnnotationAssertion( ) +AnnotationAssertion( "inheres in part of") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "characteristic of part of"@en) +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (mereotopologically related to) + +AnnotationAssertion( "A mereological relationship or a topological relationship") +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "mereotopologically related to"@en) + +# Object Property: (enables) + +AnnotationAssertion( "a particular instances of akt-2 enables some instance of protein kinase activity") +AnnotationAssertion( "c enables p iff c is capable of p and c acts to execute p.") +AnnotationAssertion( ) +AnnotationAssertion( "catalyzes") +AnnotationAssertion( "executes") +AnnotationAssertion( "has") +AnnotationAssertion( "is catalyzing") +AnnotationAssertion( "is executing") +AnnotationAssertion( "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "enables"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (functionally related to) + +AnnotationAssertion( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") +AnnotationAssertion( ) +AnnotationAssertion( "This is a grouping relation that collects relations used for the purpose of connecting structure and function") +AnnotationAssertion( "RO:0002328") +AnnotationAssertion( "uberon") +AnnotationAssertion( "functionally_related_to") +AnnotationAssertion( "functionally_related_to") +AnnotationAssertion(rdfs:label "functionally related to"@en) +AnnotationAssertion(rdfs:label "functionally related to") + +# Object Property: (part of structure that is capable of) + +AnnotationAssertion( "this relation holds between c and p when c is part of some c', and c' is capable of p.") +AnnotationAssertion( ) +AnnotationAssertion( "false"^^xsd:boolean) +AnnotationAssertion(rdfs:label "part of structure that is capable of"@en) +SubObjectPropertyOf( ) + +# Object Property: (involved in) + +AnnotationAssertion( "c involved_in p if and only if c enables some process p', and p' is part of p") +AnnotationAssertion( ) +AnnotationAssertion( "actively involved in") +AnnotationAssertion( "enables part of") +AnnotationAssertion(rdfs:label "involved in"@en) +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (enabled by) + +AnnotationAssertion( "inverse of enables") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "enabled by"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (regulated by) + +AnnotationAssertion( "inverse of regulates") +AnnotationAssertion( ) +AnnotationAssertion( "regulated by (processual)") +AnnotationAssertion( "RO:0002334") +AnnotationAssertion( "external") +AnnotationAssertion( "regulated_by") +AnnotationAssertion( ) +AnnotationAssertion( "regulated_by") +AnnotationAssertion(rdfs:label "regulated by"@en) +AnnotationAssertion(rdfs:label "regulated by") +SubObjectPropertyOf( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (negatively regulated by) + +AnnotationAssertion( "inverse of negatively regulates") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002335") +AnnotationAssertion( "external") +AnnotationAssertion( "negatively_regulated_by") +AnnotationAssertion( ) +AnnotationAssertion( "negatively_regulated_by") +AnnotationAssertion(rdfs:label "negatively regulated by"@en) +AnnotationAssertion(rdfs:label "negatively regulated by") +SubObjectPropertyOf( ) + +# Object Property: (positively regulated by) + +AnnotationAssertion( "inverse of positively regulates") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002336") +AnnotationAssertion( "external") +AnnotationAssertion( "positively_regulated_by") +AnnotationAssertion( ) +AnnotationAssertion( "positively_regulated_by") +AnnotationAssertion(rdfs:label "positively regulated by"@en) +AnnotationAssertion(rdfs:label "positively regulated by") +SubObjectPropertyOf( ) + +# Object Property: (input of) + +AnnotationAssertion( "inverse of has input") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002352") +AnnotationAssertion( "uberon") +AnnotationAssertion( "input_of") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "input_of") +AnnotationAssertion(rdfs:label "input of"@en) +AnnotationAssertion(rdfs:label "input of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally downstream of) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of upstream of") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002404") +AnnotationAssertion( "external") +AnnotationAssertion( "causally_downstream_of") +AnnotationAssertion( "causally_downstream_of") +AnnotationAssertion(rdfs:label "causally downstream of"@en) +AnnotationAssertion(rdfs:label "causally downstream of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (immediately causally downstream of) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002405") +AnnotationAssertion( "external") +AnnotationAssertion( "immediately_causally_downstream_of") +AnnotationAssertion( "immediately_causally_downstream_of") +AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) +AnnotationAssertion(rdfs:label "immediately causally downstream of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (indirectly positively regulates) + +AnnotationAssertion( "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "indirectly activates") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (indirectly negatively regulates) + +AnnotationAssertion( "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "indirectly inhibits") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (causally related to) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Causality") "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.") +AnnotationAssertion( "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. + +To define causal relations in an activity-flow type network, we make use of 3 primitives: + + * Temporal: how do the intervals of the two occurrents relate? + * Is the causal relation regulatory? + * Is the influence positive or negative? + +The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. + +For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. + +For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. + +Each of these 3 primitives can be composed to yield a cross-product of different relation types.") +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:label "causally related to"@en) + +# Object Property: (causally upstream of) + +AnnotationAssertion( "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002411") +AnnotationAssertion( "external") +AnnotationAssertion( "causally_upstream_of") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "causally_upstream_of") +AnnotationAssertion(rdfs:label "causally upstream of"@en) +AnnotationAssertion(rdfs:label "causally upstream of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (immediately causally upstream of) + +AnnotationAssertion( "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002412") +AnnotationAssertion( "external") +AnnotationAssertion( "immediately_causally_upstream_of") +AnnotationAssertion( "immediately_causally_upstream_of") +AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) +AnnotationAssertion(rdfs:label "immediately causally upstream of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of or within) + +AnnotationAssertion( "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.") +AnnotationAssertion( "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2") +AnnotationAssertion( ) +AnnotationAssertion( "influences (processual)") +AnnotationAssertion( "RO:0002418") +AnnotationAssertion( "external") +AnnotationAssertion( "affects") +AnnotationAssertion( "causally_upstream_of_or_within") +AnnotationAssertion( "causally_upstream_of_or_within") +AnnotationAssertion(rdfs:label "causally upstream of or within") +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (causally downstream of or within) + +AnnotationAssertion( "inverse of causally upstream of or within") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002427") +AnnotationAssertion( "external") +AnnotationAssertion( "causally_downstream_of_or_within") +AnnotationAssertion( ) +AnnotationAssertion( "causally_downstream_of_or_within") +AnnotationAssertion(rdfs:label "causally downstream of or within") +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (involved in regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' regulates some p") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "involved in regulation of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (involved in positive regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' positively regulates some p") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "involved in positive regulation of") +SubObjectPropertyOf( ) + +# Object Property: (involved in negative regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "involved in negative regulation of") +SubObjectPropertyOf( ) + +# Object Property: (involved in or involved in regulation of) + +AnnotationAssertion( "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p") +AnnotationAssertion( "OWL does not allow defining object properties via a Union") +AnnotationAssertion( ) +AnnotationAssertion( "involved in or reguates") +AnnotationAssertion(rdfs:label "involved in or involved in regulation of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (interacts with) + +AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") +AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) +AnnotationAssertion( "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") +AnnotationAssertion( ) +AnnotationAssertion( "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") +AnnotationAssertion( "in pairwise interaction with") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "interacts with") +AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) +AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0914"^^xsd:anyURI) +SymmetricObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (molecularly interacts with) + +AnnotationAssertion( "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.") +AnnotationAssertion( ) +AnnotationAssertion( "binds") +AnnotationAssertion( "molecularly binds with") +AnnotationAssertion(rdfs:label "molecularly interacts with") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0915"^^xsd:anyURI) +SubObjectPropertyOf( ) +SymmetricObjectProperty() + +# Object Property: (phosphorylates) + +AnnotationAssertion( "Axiomatization to GO to be added later") +AnnotationAssertion( ) +AnnotationAssertion( "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.") +AnnotationAssertion(rdfs:label "phosphorylates") +SubObjectPropertyOf( ) + +# Object Property: (directly regulates activity of) + +AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "molecularly controls") +AnnotationAssertion(rdfs:label "directly regulates activity of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly negatively regulates activity of) + +AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly inhibits") +AnnotationAssertion( "molecularly decreases activity of") +AnnotationAssertion(rdfs:label "directly negatively regulates activity of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly positively regulates activity of) + +AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly activates") +AnnotationAssertion( "molecularly increases activity of") +AnnotationAssertion(rdfs:label "directly positively regulates activity of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (helper property (not for use in curation)) + +AnnotationAssertion( ) +AnnotationAssertion( "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.") +AnnotationAssertion(rdfs:label "helper property (not for use in curation)") + +# Object Property: (is kinase activity) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "is kinase activity") +SubObjectPropertyOf( ) + +# Object Property: (causal agent in process) + +AnnotationAssertion( "A relationship between a material entity and a process where the material entity has some causal role that influences the process") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causal agent in process") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (causal relation between processes) + +AnnotationAssertion( "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:label "causal relation between processes") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (depends on) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "depends on") +AnnotationAssertion(rdfs:seeAlso ) + +# Object Property: (causal relation between entities) + +AnnotationAssertion( "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:label "causal relation between entities") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (causally influenced by) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "causally influenced by (entity-centric)") +AnnotationAssertion(rdfs:label "causally influenced by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (interaction relation helper property) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "interaction relation helper property") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) +SubObjectPropertyOf( ) + +# Object Property: (molecular interaction relation helper property) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "molecular interaction relation helper property") +SubObjectPropertyOf( ) + +# Object Property: (causally influences) + +AnnotationAssertion( "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "causally influences (entity-centric)") +AnnotationAssertion(rdfs:label "causally influences") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly regulates) + +AnnotationAssertion( "p directly regulates q iff p is immediately causally upstream of q and p regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly regulates (processual)") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002578") +AnnotationAssertion( "external") +AnnotationAssertion( "directly_regulates") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly_regulates") +AnnotationAssertion(rdfs:label "directly regulates") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has part structure that is capable of) + +AnnotationAssertion( "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'") +AnnotationAssertion( "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has part structure that is capable of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causal relation between material entity and a process) + +AnnotationAssertion( "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.") +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causal relation between material entity and a process") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (capable of regulating) + +AnnotationAssertion( "pyrethroid -> growth") +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of regulating") +SubObjectPropertyOf( ) + +# Object Property: (capable of negatively regulating) + +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of negatively regulating") +SubObjectPropertyOf( ) + +# Object Property: (capable of positively regulating) + +AnnotationAssertion( "renin -> arteriolar smooth muscle contraction") +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of positively regulating") +SubObjectPropertyOf( ) + +# Object Property: (process has causal agent) + +AnnotationAssertion( "Inverse of 'causal agent in process'") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002608") +AnnotationAssertion( "external") +AnnotationAssertion( "process_has_causal_agent") +AnnotationAssertion( "process_has_causal_agent") +AnnotationAssertion(rdfs:label "process has causal agent") +SubObjectPropertyOf( ) + +# Object Property: (directly positively regulates) + +AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "directly positively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002629") +AnnotationAssertion( "external") +AnnotationAssertion( "directly_positively_regulates") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly_positively_regulates") +AnnotationAssertion(rdfs:label "directly positively regulates") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (directly negatively regulates) + +AnnotationAssertion( "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "directly negatively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002630") +AnnotationAssertion( "external") +AnnotationAssertion( "directly_negatively_regulates") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly_negatively_regulates") +AnnotationAssertion(rdfs:label "directly negatively regulates") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (enables subfunction) + +AnnotationAssertion( "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.") +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-25T23:20:13Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "enables subfunction") +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within, positive effect) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within, negative effect) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of, positive effect) + +AnnotationAssertion( "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of, positive effect") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of, negative effect) + +AnnotationAssertion( "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of, negative effect") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of or within, negative effect) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-03-13T23:55:05Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of or within, positive effect) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") +SubObjectPropertyOf( ) + +# Object Property: (regulates activity of) + +AnnotationAssertion( "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulates activity of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (indirectly causally upstream of) + +AnnotationAssertion( "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.") +AnnotationAssertion( "pg") +AnnotationAssertion( "2022-09-26T06:07:17Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "indirectly causally upstream of"@en) +SubObjectPropertyOf( ) + +# Object Property: (indirectly regulates) + +AnnotationAssertion( "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") +AnnotationAssertion( "pg") +AnnotationAssertion( "2022-09-26T06:08:01Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "indirectly regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (device utilizes material) + +AnnotationAssertion( "A diagnostic testing device utilizes a specimen.") +AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") +AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") +AnnotationAssertion( "2021-11-08T12:00:00Z") +AnnotationAssertion( "utilizes") +AnnotationAssertion(rdfs:label "device utilizes material"@en) + +# Object Property: (regulates characteristic) + +AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0019000") +AnnotationAssertion( "gene_ontology") +AnnotationAssertion( "regulates_characteristic") +AnnotationAssertion( "regulates_characteristic") +AnnotationAssertion(rdfs:label "regulates characteristic") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (positively regulates characteristic) + +AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0019001") +AnnotationAssertion( "gene_ontology") +AnnotationAssertion( "positively_regulates_characteristic") +AnnotationAssertion( "positively_regulates_characteristic") +AnnotationAssertion(rdfs:label "positively regulates characteristic") +SubObjectPropertyOf( ) + +# Object Property: (negatively regulates characteristic) + +AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0019002") +AnnotationAssertion( "gene_ontology") +AnnotationAssertion( "negatively_regulates_characteristic") +AnnotationAssertion( "negatively_regulates_characteristic") +AnnotationAssertion(rdfs:label "negatively regulates characteristic") +SubObjectPropertyOf( ) + + + +############################ +# Classes +############################ + +# Class: (continuant) + +AnnotationAssertion( "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en) +AnnotationAssertion(rdfs:label "continuant"@en) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (occurrent) + +AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) +AnnotationAssertion(rdfs:label "occurrent"@en) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (independent continuant) + +AnnotationAssertion( "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) +AnnotationAssertion(rdfs:label "independent continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) + +# Class: (process) + +AnnotationAssertion( "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) +AnnotationAssertion(rdfs:label "process"@en) +SubClassOf( ) + +# Class: (disposition) + +AnnotationAssertion(rdfs:label "disposition"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (realizable entity) + +AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) +AnnotationAssertion(rdfs:label "realizable entity"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) + +# Class: (quality) + +AnnotationAssertion(rdfs:label "quality"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (specifically dependent continuant) + +AnnotationAssertion( "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) +AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (role) + +AnnotationAssertion( "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en) +AnnotationAssertion(rdfs:label "role"@en) +EquivalentClasses( ) +SubClassOf( ) + +# Class: (function) + +AnnotationAssertion(rdfs:label "function"@en) +SubClassOf( ) + +# Class: (material entity) + +AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) +AnnotationAssertion(rdfs:label "material entity"@en) +SubClassOf( ) + +# Class: (role) + +AnnotationAssertion( "A role is particular behaviour which a material entity may exhibit.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion( "CHEBI:50906") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "role") +SubClassOf( ) + +# Class: (molecular_function) + +AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") +AnnotationAssertion( "GO:0005554") +AnnotationAssertion( "molecular function") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0003674") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") +AnnotationAssertion(rdfs:label "molecular_function") +SubClassOf( ) +DisjointClasses( ) + +# Class: (catalytic activity) + +AnnotationAssertion(Annotation( "GOC:vw") Annotation( "ISBN:0198506732") "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.") +AnnotationAssertion( "Wikipedia:Enzyme") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "enzyme activity") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0003824") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "catalytic activity") +SubClassOf( ) + +# Class: (biological_process) + +AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24968"^^xsd:anyURI) +AnnotationAssertion( "jl") +AnnotationAssertion( "2012-09-19T15:05:24Z") +AnnotationAssertion( "GO:0000004") +AnnotationAssertion( "GO:0007582") +AnnotationAssertion( "GO:0044699") +AnnotationAssertion( "Wikipedia:Biological_process") +AnnotationAssertion( "biological process") +AnnotationAssertion( "physiological process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "single organism process") +AnnotationAssertion( "single-organism process") +AnnotationAssertion( "GO:0008150") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") +AnnotationAssertion(rdfs:label "biological_process") +SubClassOf( ) + +# Class: (kinase activity) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") +AnnotationAssertion(Annotation(rdfs:label "FN3KRP phosphorylates PsiAm, RibAm") "Reactome:R-HSA-6788855") +AnnotationAssertion(Annotation(rdfs:label "FN3K phosphorylates ketosamines") "Reactome:R-HSA-6788867") +AnnotationAssertion( "phosphokinase activity") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0016301") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.") +AnnotationAssertion(rdfs:label "kinase activity") +SubClassOf( ) +SubClassOf( ObjectHasSelf()) + +# Class: (transferase activity) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.") +AnnotationAssertion( "EC:2.-.-.-") +AnnotationAssertion(Annotation(rdfs:label "PE is converted to PS by PTDSS2") "Reactome:R-HSA-1483089") +AnnotationAssertion(Annotation(rdfs:label "PC is converted to PS by PTDSS1") "Reactome:R-HSA-1483186") +AnnotationAssertion(Annotation(rdfs:label "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK") "Reactome:R-HSA-5668414") +AnnotationAssertion(Annotation(rdfs:label "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248") "Reactome:R-HSA-8868783") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0016740") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "transferase activity") +SubClassOf( ) + +# Class: (transferase activity, transferring phosphorus-containing groups) + +AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).") +AnnotationAssertion( "EC:2.7.-.-") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0016772") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.") +AnnotationAssertion(rdfs:label "transferase activity, transferring phosphorus-containing groups") +SubClassOf( ) + +# Class: (quality) + +AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities") +AnnotationAssertion( "PATO:0000072") +AnnotationAssertion( "quality") +AnnotationAssertion( "PATO:0000001") +AnnotationAssertion(rdfs:label "quality") +SubClassOf( ) + + +SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index f025490..4b26ca5 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -1,4 +1,4 @@ -Prefix(:=) +Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) @@ -6,10 +6,10 @@ Prefix(xsd:=) Prefix(rdfs:=) -Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2023-11-23") +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2024-02-20") Declaration(Class()) Declaration(Class()) @@ -20,11 +20,13 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -130,6 +132,15 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -139,6 +150,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -156,8 +168,8 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -165,13 +177,18 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:comment)) Declaration(AnnotationProperty(rdfs:label)) @@ -181,6 +198,56 @@ Declaration(AnnotationProperty()) # Annotation Properties ############################ +# Annotation Property: (definition) + +AnnotationAssertion( "definition"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) +AnnotationAssertion( "2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "definition"@en) +AnnotationAssertion(rdfs:label "definition") + +# Annotation Property: (term editor) + +AnnotationAssertion( "term editor"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en) +AnnotationAssertion( "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "term editor"@en) + +# Annotation Property: (definition source) + +AnnotationAssertion( "definition source"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "definition source"@en) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -215,6 +282,32 @@ SubAnnotationPropertyOf( ) +# Annotation Property: (has_broad_synonym) + +AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") +AnnotationAssertion(rdfs:label "has broad synonym"@en) +AnnotationAssertion(rdfs:label "has_broad_synonym") +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") + +# Annotation Property: (database_cross_reference) + +AnnotationAssertion(rdfs:label "database_cross_reference") + +# Annotation Property: (has exact synonym) + +AnnotationAssertion( "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") +AnnotationAssertion(rdfs:label "has exact synonym"@en) +AnnotationAssertion(rdfs:label "has_exact_synonym") +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") + +# Annotation Property: (has_obo_format_version) + +AnnotationAssertion(rdfs:label "has_obo_format_version") + ############################ # Object Properties @@ -246,6 +339,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "part of"@en) +AnnotationAssertion(rdfs:label "part of") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) @@ -272,6 +366,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has part"@en) +AnnotationAssertion(rdfs:label "has part") SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -327,6 +422,8 @@ AnnotationAssertion( "is bearer of"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has characteristic"@en) +AnnotationAssertion(rdfs:label "has characteristic") +AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") InverseFunctionalObjectProperty() ObjectPropertyRange( ) @@ -354,7 +451,9 @@ AnnotationAssertion( "has_participant"@en) AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") AnnotationAssertion(rdfs:label "has participant"@en) +AnnotationAssertion(rdfs:label "has participant") ObjectPropertyDomain( ) +ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (function of) @@ -802,6 +901,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enabled by"@en) +AnnotationAssertion(rdfs:label "enabled by") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1397,6 +1497,7 @@ AnnotationAssertion(rdfs:label "ind SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) DisjointClasses( ) +DisjointClasses( ) # Class: (process) @@ -1404,6 +1505,7 @@ AnnotationAssertion( "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) AnnotationAssertion(rdfs:label "process"@en) SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) # Class: (disposition) @@ -1414,6 +1516,7 @@ DisjointClasses( (realizable entity) AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) +AnnotationAssertion(rdfs:label "realizable"@en) AnnotationAssertion(rdfs:label "realizable entity"@en) SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) @@ -1425,13 +1528,18 @@ AnnotationAssertion(rdfs:label "qua SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) -# Class: (specifically dependent continuant) +# Class: (characteristic) AnnotationAssertion( "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) AnnotationAssertion(rdfs:comment "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) +AnnotationAssertion(rdfs:label "characteristic"@en) AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +AnnotationAssertion(rdfs:seeAlso "https://github.com/OBOFoundry/COB/issues/65") +AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) # Class: (role) @@ -1439,6 +1547,14 @@ AnnotationAssertion( "role"@en) SubClassOf( ) +# Class: (generically dependent continuant) + +AnnotationAssertion( "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) +AnnotationAssertion(rdfs:comment "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time."@en) +AnnotationAssertion(rdfs:label "generically dependent continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) + # Class: (function) AnnotationAssertion(rdfs:label "function"@en) @@ -1450,12 +1566,138 @@ AnnotationAssertion( "material entity"@en) SubClassOf( ) -# Class: () - +# Class: (molecular_function) + +AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") +AnnotationAssertion( "molecular function") +AnnotationAssertion( "GO:0003674") +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") +AnnotationAssertion(rdfs:comment "This is the same as GO molecular function") +AnnotationAssertion(rdfs:label "gene product or complex activity"@en) +AnnotationAssertion(rdfs:label "molecular_function") +SubClassOf( ) +DisjointClasses( ) + +# Class: (biological_process) + +AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") +AnnotationAssertion( "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.") +AnnotationAssertion( "jl") +AnnotationAssertion( "2012-09-19T15:05:24Z") +AnnotationAssertion( "Wikipedia:Biological_process") +AnnotationAssertion( "biological process") +AnnotationAssertion( "physiological process") +AnnotationAssertion( "single organism process") +AnnotationAssertion( "single-organism process") +AnnotationAssertion( "GO:0008150") +AnnotationAssertion(rdfs:comment "A biological process is an evolved process") +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") +AnnotationAssertion(rdfs:label "biological process"@en) +AnnotationAssertion(rdfs:label "biological_process") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (kinase activity) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") +AnnotationAssertion(Annotation(rdfs:label "FN3KRP phosphorylates PsiAm, RibAm") "Reactome:R-HSA-6788855") +AnnotationAssertion(Annotation(rdfs:label "FN3K phosphorylates ketosamines") "Reactome:R-HSA-6788867") +AnnotationAssertion( "phosphokinase activity") +AnnotationAssertion( "GO:0016301") +AnnotationAssertion(rdfs:comment "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.") +AnnotationAssertion(rdfs:label "kinase activity") +SubClassOf( ) SubClassOf( ObjectHasSelf()) +# Class: (curation status specification) + +AnnotationAssertion( "curation status specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) +AnnotationAssertion( "PERSON:Bill Bug"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion( "OBI_0000266"@en) +AnnotationAssertion(rdfs:label "curation status specification"@en) +EquivalentClasses( ObjectOneOf( )) + +# Class: (quality) + +AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities") +AnnotationAssertion( "PATO:0000001") +AnnotationAssertion(rdfs:label "quality") +SubClassOf( ) + + +############################ +# Named Individuals +############################ + +# Individual: (example to be eventually removed) + +AnnotationAssertion( "example to be eventually removed"@en) +AnnotationAssertion(rdfs:label "example to be eventually removed"@en) + +# Individual: (metadata complete) + +AnnotationAssertion( "metadata complete"@en) +AnnotationAssertion( "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en) +AnnotationAssertion(rdfs:label "metadata complete"@en) + +# Individual: (organizational term) + +AnnotationAssertion( "organizational term"@en) +AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) +AnnotationAssertion(rdfs:label "organizational term"@en) + +# Individual: (ready for release) + +AnnotationAssertion( "ready for release"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en) +AnnotationAssertion(rdfs:label "ready for release"@en) + +# Individual: (metadata incomplete) + +AnnotationAssertion( "metadata incomplete"@en) +AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) +AnnotationAssertion(rdfs:label "metadata incomplete"@en) + +# Individual: (uncurated) + +AnnotationAssertion( "uncurated"@en) +AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) +AnnotationAssertion(rdfs:label "uncurated"@en) + +# Individual: (pending final vetting) + +AnnotationAssertion( "pending final vetting"@en) +AnnotationAssertion( ) +AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) +AnnotationAssertion(rdfs:label "pending final vetting"@en) +ClassAssertion( ) + +# Individual: (to be replaced with external ontology term) + +AnnotationAssertion( "to be replaced with external ontology term"@en) +AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) + +# Individual: (requires discussion) + +AnnotationAssertion( "requires discussion"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "requires discussion"@en) +ClassAssertion( ) + SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) +DifferentIndividuals( ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -1508,30 +1750,30 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/nmrCV-edit.owl b/src/ontology/nmrCV-edit.owl index dc5de0d..59289a2 100644 --- a/src/ontology/nmrCV-edit.owl +++ b/src/ontology/nmrCV-edit.owl @@ -1,5 +1,4 @@ - -Prefix(:=) +Prefix(:=) Prefix(dce:=) Prefix(owl:=) Prefix(rdf:=) @@ -9,7 +8,7 @@ Prefix(rdfs:=) Prefix(dcterms:=) -Ontology( +Ontology( Import() diff --git a/src/ontology/nmrCV-odk.yaml b/src/ontology/nmrCV-odk.yaml index 4c904f5..e6979f8 100644 --- a/src/ontology/nmrCV-odk.yaml +++ b/src/ontology/nmrCV-odk.yaml @@ -11,7 +11,7 @@ license: https://creativecommons.org/publicdomain/mark/1.0/ ## general ODK Settings ## -uribase: http://purl.obolibrary.org/obo +uribase: http://nmrML.org repo: nmrCV git_main_branch: main github_org: nmrML diff --git a/src/sparql/inject-subset-declaration.ru b/src/sparql/inject-subset-declaration.ru index 788313b..34c4248 100644 --- a/src/sparql/inject-subset-declaration.ru +++ b/src/sparql/inject-subset-declaration.ru @@ -7,5 +7,5 @@ INSERT { ?y rdfs:subPropertyOf ?y . FILTER(isIRI(?y)) - FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(http://purl.obolibrary.org/obo)")) + FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(http://nmrML.org)")) } \ No newline at end of file diff --git a/src/sparql/inject-synonymtype-declaration.ru b/src/sparql/inject-synonymtype-declaration.ru index cad57ed..860cb43 100644 --- a/src/sparql/inject-synonymtype-declaration.ru +++ b/src/sparql/inject-synonymtype-declaration.ru @@ -7,5 +7,5 @@ INSERT { ?y rdfs:subPropertyOf ?y . FILTER(isIRI(?y)) - FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(http://purl.obolibrary.org/obo)")) + FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(http://nmrML.org)")) } \ No newline at end of file diff --git a/src/sparql/iri-range-violation.sparql b/src/sparql/iri-range-violation.sparql index 156ea77..ad168b0 100644 --- a/src/sparql/iri-range-violation.sparql +++ b/src/sparql/iri-range-violation.sparql @@ -13,7 +13,7 @@ WHERE { oboInOwl:inSubset dcterms:contributor } ?term ?property ?value . - FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/NMRCV_"))) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://nmrML.org/NMRCV_"))) FILTER (!isIRI(?value)) } diff --git a/src/sparql/label-with-iri-violation.sparql b/src/sparql/label-with-iri-violation.sparql index bace00b..206bed1 100644 --- a/src/sparql/label-with-iri-violation.sparql +++ b/src/sparql/label-with-iri-violation.sparql @@ -4,6 +4,6 @@ SELECT ?term ?value WHERE { ?term rdfs:label ?value . FILTER (REGEX(?value, "http[s]?[:]")) - FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/NMRCV_"))) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://nmrML.org/NMRCV_"))) } diff --git a/src/sparql/nmrCV_terms.sparql b/src/sparql/nmrCV_terms.sparql index 4a45430..baaa55d 100644 --- a/src/sparql/nmrCV_terms.sparql +++ b/src/sparql/nmrCV_terms.sparql @@ -3,5 +3,5 @@ WHERE { { ?s1 ?p1 ?term . } UNION { ?term ?p2 ?o2 . } - FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/NMRCV_"))) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://nmrML.org/NMRCV_"))) } diff --git a/src/sparql/owldef-self-reference-violation.sparql b/src/sparql/owldef-self-reference-violation.sparql index 6a8407b..6d55235 100644 --- a/src/sparql/owldef-self-reference-violation.sparql +++ b/src/sparql/owldef-self-reference-violation.sparql @@ -7,6 +7,6 @@ SELECT ?term WHERE { { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?term ] ] } UNION { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?term ] ] ] } - FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/NMRCV_"))) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://nmrML.org/NMRCV_"))) } From 37005e6901bbc72f4a6efcfaeefd43fb89becb42 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philip=20Str=C3=B6mert?= Date: Tue, 20 Feb 2024 16:43:22 +0100 Subject: [PATCH 2/4] Copy nmrCV.owl 1.1. classes into nmrCV-edit.owl --- src/ontology/nmrCV-edit.owl | 5656 ++++++++++++++++++++++++++++++++++- 1 file changed, 5643 insertions(+), 13 deletions(-) diff --git a/src/ontology/nmrCV-edit.owl b/src/ontology/nmrCV-edit.owl index 59289a2..086a6a6 100644 --- a/src/ontology/nmrCV-edit.owl +++ b/src/ontology/nmrCV-edit.owl @@ -1,56 +1,5686 @@ Prefix(:=) Prefix(dce:=) +Prefix(obo:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) Prefix(xsd:=) +Prefix(doap:=) +Prefix(foaf:=) Prefix(rdfs:=) +Prefix(skos:=) Prefix(dcterms:=) +Prefix(oboInOwl:=) Ontology( +Import() +Import() +Import() +Import() +Import() +Import() +Import() +Annotation(dce:contributor "Annick Moing") +Annotation(dce:contributor "Catherine Deborde") +Annotation(dce:contributor "Daniel Jacob") +Annotation(dce:contributor "Daniel Schober") +Annotation(dce:contributor "Joseph Cruz") +Annotation(dce:contributor "Michael Wilson") +Annotation(dce:contributor "Philippe Rocca-Serra") +Annotation(dce:contributor "Reza Salek") +Annotation(dce:contributor "Since this is a prolonged effort spanning a larger time period, there naturally were many people involved in the creation over the years and during different times. -Import() +People involved in the term creation from ID >1400000 : -Import() +This part of the NMR ontology was originally developed by the ontology working group (http://msi-ontology.sourceforge.net/) of the msi-metabolomicssociety (msi-workgroups.sf.net): -Import() +Daniel Schober (EBI) +Chris Taylor (EBI and HUPO-PSI) +Dennis Rubtsov (Un of Cambridge, UK) +Helen Jenkins (Un of Wales, Aberystwyth, UK) +Irena Spasic (Center for Integrative Systems Biology, Manchester, UK) +Larissa Soldatova (University of Wales, Aberystwyth, UK) +Philippe Rocca-Serra (EBI and MGED Society) +Susanna-Assunta Sansone (EBI) -Import() +People involved in the term creation from ID<1400000: -Import() +Joseph Cruz +Daniel Schober +Michael Wilson +Reza Salek +Daniel Jacob +David Wishart -Import() +Terms with IDs ID<1400000 that were NOT asserted in the original Wishart obo file were created by Daniel Schober (COSMOS WP2). Its IDs were autogenerated with the Protege ID generator. -Import() +Other people that substantially helped in revising the latest and Cosmos governed CV additions were: +Michael Wilson, Wishart Group, Edmonton, Alberta, Canada +Daniel Jacob, INRA, Bordeaux, France +Annick Moing, INRA, Bordeaux, France +Catherine Deborde, INRA, Bordeaux, France +Reza Salek, EBI, Hinxton, UK +Philippe Rocca-Serra, University of Oxford, Oxford, UK +Andrea Porzel, IPB-Halle, Germany +and the COSMOS WP2 team +A paper describing the overall nmrML data standard and CV has been accepted by Analytical Chemistry (Manuscript ID: ac-2017-02795f.R1), title +`nmrML: a community supported open data standard for the description, storage, and exchange of NMR data`, author(s): Schober, Daniel; Jacob, Daniel; Wilson, Michael; Cruz, Joseph; Marcu, Ana; Grant, Jason; Moing, Annick; Deborde, Catherine; de Figueiredo, Luis; Haug, Kenneth; Rocca-Serra, Philippe; Easton, John; Ebbels, Timothy; Hao, Jie; Ludwig, Christian; Günther, Ulrich; Rosato, Antonio; Klein, Matthias; Lewis, Ian; Luchinat, Claudio; Jones, Andrew; Grauslys, Arturas; Larralde, Martin; Yokochi, Masashi; Kobayashi, Naohiro; Porzel, Andrea; Griffin, Julian; Viant, Mark; Wishart, David; Steinbeck, Christoph; Salek, Reza; Neumann, Steffen") +Annotation(dce:contributor "Steffen Neumann") +Annotation(dce:coverage "Nuclear magnetic resonance (NMR) data annotation as required by the msi sanctioned open +access nmrML XML format developed by the COSMOS EU project.") Annotation(dcterms:description "This artefact is an MSI-approved controlled vocabulary primarily developed under COSMOS EU and PhenoMeNal EU governance. The nmrCV is supporting the nmrML XML format with standardized terms. nmrML is a vendor agnostic open access NMR raw data standard. Its primaly role is analogous to the mzCV for the PSI-approved mzML XML format. It uses BFO2.0 as its Top level. This CV was derived from two predecessors (The NMR CV from the David Wishart Group, developed by Joseph Cruz) and the MSI nmr CV developed by Daniel Schober at the EBI. This simple taxonomy of terms (no DL semantics used) serves the nuclear magnetic resonance markup language (nmrML) with meaningful descriptors to amend the nmrML xml file with CV terms. Metabolomics scientists are encouraged to use this CV to annotrate their raw and experimental context data, i.e. within nmrML. The approach to have an exchange syntax mixed of an xsd and CV stems from the PSI mzML effort. The reason to branch out from an xsd into a CV is, that in areas where the terminology is likely to change faster than the nmrML xsd could be updated and aligned, an externally and decentrallised maintained CV can accompensate for such dynamics in a more flexible way. A second reason for this set-up is that semantic validity of CV terms used in an nmrML XML instance (allowed CV terms, position/relation to each other, cardinality) can be validated by rule-based proprietary validators: By means of cardinality specifications and XPath expressions defined in an XML mapping file (an instances of the CvMappingRules.xsd ), one can define what ontology terms are allowed in a specific location of the data model.") Annotation(dcterms:license ) Annotation(dcterms:title "nuclear magnetic resonance CV") +Annotation(doap:audience "This CV is to be used by metabolomics researchers, or basically any chenomics or proteomics researchers who apply the nmrML xml to store their NMRraw data in a vendor agnostic manner. But nmrML can also be used to capture experimental results and (limited) basic metadata like molecule to spectral feature assignments.") +Annotation(doap:bug-database "https://github.com/nmrML/nmrML/issues") +Annotation(doap:documenter "Daniel Schober") +Annotation(doap:implements "https://github.com/nmrML/nmrML") +Annotation(doap:location "https://github.com/nmrML/nmrCV") +Annotation(doap:mailing-list "https://groups.google.com/forum/?hl=en#!forum/nmrml/join") +Annotation(doap:maintainer "https://www.wikidata.org/wiki/Q96678459") +Annotation(owl:deprecated "http://www.metabolomicscentre.ca/nmrML/msi-nmr.obo") +Annotation(owl:versionInfo "2.0_alpha") - -Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) 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+Declaration(AnnotationProperty(oboInOwl:auto-generated-by)) +Declaration(AnnotationProperty(oboInOwl:consider)) +Declaration(AnnotationProperty(oboInOwl:created_by)) +Declaration(AnnotationProperty(oboInOwl:creation_date)) +Declaration(AnnotationProperty(oboInOwl:date)) +Declaration(AnnotationProperty(oboInOwl:default-namespace)) +Declaration(AnnotationProperty(oboInOwl:hasBroadSynonym)) +Declaration(AnnotationProperty(oboInOwl:hasDbXref)) +Declaration(AnnotationProperty(oboInOwl:hasExactSynonym)) +Declaration(AnnotationProperty(oboInOwl:hasOBOFormatVersion)) +Declaration(AnnotationProperty(oboInOwl:hasOBONamespace)) +Declaration(AnnotationProperty(oboInOwl:id)) +Declaration(AnnotationProperty(oboInOwl:saved-by)) +Declaration(AnnotationProperty(rdfs:label)) +Declaration(AnnotationProperty(skos:altLabel)) +Declaration(AnnotationProperty(skos:definition)) +Declaration(AnnotationProperty(skos:editorialNote)) +Declaration(AnnotationProperty(skos:example)) +Declaration(AnnotationProperty(skos:scopeNote)) +Declaration(AnnotationProperty(foaf:homepage)) ############################ # Annotation Properties ############################ +# Annotation Property: dcterms:description (description) + AnnotationAssertion(rdfs:label dcterms:description "description") + +# Annotation Property: dcterms:license (license) + AnnotationAssertion(rdfs:label dcterms:license "license") + +# Annotation Property: dcterms:title (title) + AnnotationAssertion(rdfs:label dcterms:title "title") + + ############################ # Classes ############################ -# Class: (root node) +# Class: (integer32) + +AnnotationAssertion(dce:coverage "For 1r/1i spectra and for Bruker, this term describe an array of integers (32bits).") +AnnotationAssertion(rdfs:label "integer32"@en) +SubClassOf( ) + +# Class: (sample number) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A reference number relevant to the sample under study.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000001") +AnnotationAssertion(rdfs:label "sample number") +SubClassOf( ) + +# Class: (long64) + +AnnotationAssertion(dce:coverage "For 1r/1i spectra and for Bruker, this term describe an array of longs (64bits).") +AnnotationAssertion(rdfs:label "long64"@en) +SubClassOf( ) + +# Class: (sample state information) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "The chemical phase of a pure sample, or the state of a mixed sample.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000003") +AnnotationAssertion(rdfs:label "sample state information") +SubClassOf( ) + +# Class: (sample mass information) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Total mass of sample used.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:float") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000004") +AnnotationAssertion(rdfs:label "sample mass information") +SubClassOf( ) + +# Class: (sample volume) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Total volume of solution used.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:float") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000005") +AnnotationAssertion(rdfs:label "sample volume") +SubClassOf( ) + +# Class: (sample concentration) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:float") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000006") +AnnotationAssertion(rdfs:label "sample concentration") +SubClassOf( ) + +# Class: (quadrature detection) + +AnnotationAssertion(rdfs:comment "One of the problems that should be apparent after observing the spectrum and the FID is that it is not possible +to determine if the frequency is positive or negative. The instrument uses a spectrometer +frequency and all signal frequencies are measured relative to the spectrometer frequency. If a molecule +produces two signals, one at 300,000,001 Hz and another at 299,999,999 Hz, and the spectrometer frequency +is 300,000,000 Hz, the first signal is at +1 Hz and the second is at -1 Hz. Electronically the lower frequency +signals are very easy frequency to detect, transmit, amplify and sample. +The complication with this rotating frame of reference is that a single detector can not distinguish positive and +negative frequencies. This problem is why quadrature detection is important. Quadrature detection uses two detector channels +separated by 90 degrees. These are referred to as the real channel and the imaginary channel. Using these +two channels, it is possible to distinguish positive and negative frequencies. This section shows how the +quadrature signal is processed to obtain an NMR spectrum. +The Fourier transform produces a complex number with a real and an imaginary component. The Re function +extracts the real spectrum and the Im function extracts the imaginary spectrum from the complex number.") +AnnotationAssertion(rdfs:label "quadrature detection"@en) +SubClassOf( ) + +# Class: (contact role) + +AnnotationAssertion(rdfs:label "contact role"@en) +SubClassOf( ) + +# Class: (data file attribute) + +AnnotationAssertion(rdfs:label "data file attribute"@en) +SubClassOf( obo:BFO_0000031) + +# Class: (NMR instrument type) + +AnnotationAssertion(rdfs:label "NMR instrument type"@en) +SubClassOf( ) + +# Class: (1D spectrum coordinate system descriptor) + +AnnotationAssertion(rdfs:label "1D spectrum coordinate system descriptor"@en) +SubClassOf( ) + +# Class: (pre-acquisition solvent suppression) + +AnnotationAssertion(rdfs:label "pre-acquisition solvent suppression"@en) +SubClassOf( ) + +# Class: (peak processing) + +AnnotationAssertion(rdfs:label "peak processing"@en) +SubClassOf( ) + +# Class: (Hexafluorobenzene) + +AnnotationAssertion(rdfs:label "Hexafluorobenzene"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (Chloroform-d) + +AnnotationAssertion(oboInOwl:hasExactSynonym "CDCl3") +AnnotationAssertion(rdfs:label "Chloroform-d"@en) +SubClassOf( ) + +# Class: (heavy water) + +AnnotationAssertion(oboInOwl:consider "CHEBI:41981") +AnnotationAssertion(oboInOwl:hasExactSynonym "D2O") +AnnotationAssertion(rdfs:label "heavy water"@en) +SubClassOf( ) + +# Class: (sample pH) + +AnnotationAssertion(rdfs:label "sample pH"@en) +SubClassOf( ) + +# Class: (post buffer pH) + +AnnotationAssertion(rdfs:label "post buffer pH"@en) +SubClassOf( ) + +# Class: (apodization) + +AnnotationAssertion(obo:IAO_0000117 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 "http://www.scs.illinois.edu/nmr/handouts/general_pdf/ugi034.pdf") +AnnotationAssertion(rdfs:label "apodization") +AnnotationAssertion(skos:definition "Apodization is an umbrella term that is used to refer to signal processing covering the manipulation of the FID to either increase signal-to-noise (S/N) or resolution. it is usually possible to gain either S/N or resolution, but not both. +Apodization is usually performed by applying a window function to the FID") +SubClassOf( ) + +# Class: (metabolomics database identifier) + +AnnotationAssertion(dce:source "http://www.metabolomicssociety.org/databases") +AnnotationAssertion(rdfs:comment "PRS: rename 'reference' to 'identifier'"@en) +AnnotationAssertion(rdfs:label "metabolomics database identifier"@en) +SubClassOf( ) + +# Class: (Metabolights identifier) + +AnnotationAssertion(rdfs:label "Metabolights identifier"@en) +SubClassOf( ) + +# Class: (acetonitrile) + +AnnotationAssertion(rdfs:label "acetonitrile"@en) +SubClassOf( ) + +# Class: (1,4-Dioxane) + +AnnotationAssertion(rdfs:label "1,4-Dioxane"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (1H spectrum reference compound) + +AnnotationAssertion(rdfs:label "1H spectrum reference compound"@en) +SubClassOf( ) + +# Class: (2,2-Dimethyl-2-silapentane-5-sulfonate) + +AnnotationAssertion(oboInOwl:hasExactSynonym "DSS") +AnnotationAssertion(rdfs:label "2,2-Dimethyl-2-silapentane-5-sulfonate"@en) +SubClassOf( ) + +# Class: (sodium acetate) + +AnnotationAssertion(rdfs:label "sodium acetate"@en) +SubClassOf( ) + +# Class: (tetramethylsilane) + +AnnotationAssertion(oboInOwl:hasExactSynonym "TMS") +AnnotationAssertion(rdfs:label "tetramethylsilane"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (13C spectrum reference compound) + +AnnotationAssertion(rdfs:label "13C spectrum reference compound"@en) +SubClassOf( ) + +# Class: (NMR instrument model) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Instrument model name not including the vendor's name.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000031") +AnnotationAssertion(rdfs:label "NMR instrument model") +SubClassOf( ) + +# Class: (instrument customization) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Free text description of a single customization made to the instrument; for several modifications, use several entries.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000032") +AnnotationAssertion(rdfs:label "instrument customization") +SubClassOf( ) + +# Class: (Chloroform-d1) + +AnnotationAssertion(rdfs:label "Chloroform-d1"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (keyword) + +AnnotationAssertion(rdfs:label "keyword") +SubClassOf( ) + +# Class: (tetramethylammonium bromide) + +AnnotationAssertion(rdfs:label "tetramethylammonium bromide"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (15N spectrum reference compound) + +AnnotationAssertion(rdfs:label "15N spectrum reference compound"@en) +SubClassOf( ) + +# Class: (ammonia (liquid)) + +AnnotationAssertion(rdfs:label "ammonia (liquid)"@en) +SubClassOf( ) + +# Class: (ammonium bromide) + +AnnotationAssertion(rdfs:label "ammonium bromide"@en) +SubClassOf( ) + +# Class: (1,4-morpholine) + +AnnotationAssertion(rdfs:label "1,4-morpholine"@en) +SubClassOf( ) + +# Class: (nitromethane) + +AnnotationAssertion(rdfs:label "nitromethane"@en) +SubClassOf( ) + +# Class: (pyridine) + +AnnotationAssertion(rdfs:label "pyridine"@en) +SubClassOf( ) + +# Class: (sodium nitrate) + +AnnotationAssertion(rdfs:label "sodium nitrate"@en) +SubClassOf( ) + +# Class: (post-acquisition solvent suppression) + +AnnotationAssertion(oboInOwl:hasExactSynonym "solvent filtering") +AnnotationAssertion(rdfs:label "post-acquisition solvent suppression"@en) +SubClassOf( ) + +# Class: (decoupling method) + +AnnotationAssertion(obo:IAO_0000115 "Nuclear magnetic resonance decoupling (NMR decoupling for short) is a special method used in nuclear magnetic resonance (NMR) spectroscopy where a sample to be analyzed is irradiated at a certain frequency or frequency range to eliminate fully or partially the effect of coupling between certain nuclei. NMR coupling refers to the effect of nuclei on each other in atoms within a couple of bonds distance of each other in molecules. This effect causes NMR signals in a spectrum to be split into multiple peaks which are up to several hertz frequency from each other. Decoupling fully or partially eliminates splitting of the signal between the nuclei irradiated and other nuclei such as the nuclei being analyzed in a certain spectrum. NMR spectroscopy and sometimes decoupling can help determine structures of chemical compounds.") +AnnotationAssertion(dce:source "http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_decoupling") +AnnotationAssertion(rdfs:label "decoupling method"@en) +SubClassOf( ) + +# Class: (homonuclear decoupling) + +AnnotationAssertion(rdfs:label "homonuclear decoupling"@en) +SubClassOf( ) + +# Class: (heteronuclear decoupling) + +AnnotationAssertion(rdfs:label "heteronuclear decoupling"@en) +SubClassOf( ) + +# Class: (emulsion) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "State if the sample is in emulsion form.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000047") +AnnotationAssertion(rdfs:label "emulsion") +SubClassOf( ) + +# Class: (gas) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "State if the sample is in gaseous form.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000048") +AnnotationAssertion(rdfs:label "gas") +SubClassOf( ) + +# Class: (liquid) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "State if the sample is in liquid form.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000049") +AnnotationAssertion(rdfs:label "liquid") +SubClassOf( ) + +# Class: (solid) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "State if the sample is in solid form.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000050") +AnnotationAssertion(rdfs:label "solid") +SubClassOf( ) + +# Class: (solution) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "State if the sample is in solution form.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000051") +AnnotationAssertion(rdfs:label "solution") +SubClassOf( ) + +# Class: (suspension) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "State if the sample is in suspension form.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000052") +AnnotationAssertion(rdfs:label "suspension") +SubClassOf( ) + +# Class: (sample batch information) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Sample batch lot identifier.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000053") +AnnotationAssertion(rdfs:label "sample batch information") +SubClassOf( ) + +# Class: (broad band decoupling) + +AnnotationAssertion(rdfs:label "broad band decoupling"@en) +SubClassOf( ) + +# Class: (off resonance decoupling) + +AnnotationAssertion(rdfs:label "off resonance decoupling"@en) +SubClassOf( ) + +# Class: (specific decoupling) + +AnnotationAssertion(oboInOwl:hasExactSynonym "band-selective decoupling") +AnnotationAssertion(oboInOwl:hasExactSynonym "narowband decoupling") +AnnotationAssertion(rdfs:label "specific decoupling"@en) +SubClassOf( ) + +# Class: (angle of sinusoid) + +AnnotationAssertion(rdfs:label "angle of sinusoid"@en) +SubClassOf( ) + +# Class: (31P spectrum reference compound) + +AnnotationAssertion(rdfs:label "31P spectrum reference compound"@en) +SubClassOf( ) + +# Class: (phosphoric acid) + +AnnotationAssertion(oboInOwl:hasExactSynonym "H3PO4") +AnnotationAssertion(rdfs:label "phosphoric acid"@en) +SubClassOf( ) + +# Class: (phosphorus) + +AnnotationAssertion(oboInOwl:hasExactSynonym "P4") +AnnotationAssertion(rdfs:label "phosphorus"@en) +SubClassOf( ) + +# Class: (trimethyl phosphate) + +AnnotationAssertion(oboInOwl:hasExactSynonym "(CH3O)3PO") +AnnotationAssertion(rdfs:label "trimethyl phosphate"@en) +SubClassOf( ) + +# Class: (triphenylphosphine) + +AnnotationAssertion(oboInOwl:hasExactSynonym "P(C6H5)3") +AnnotationAssertion(rdfs:label "triphenylphosphine"@en) +SubClassOf( ) + +# Class: (triphenylphosphine oxide) + +AnnotationAssertion(oboInOwl:hasExactSynonym "O=P(C6H5)3") +AnnotationAssertion(rdfs:label "triphenylphosphine oxide"@en) +SubClassOf( ) + +# Class: (co-dissolved internal reference) + +AnnotationAssertion(rdfs:label "co-dissolved internal reference"@en) +SubClassOf( ) + +# Class: (synthetic reference signal) + +AnnotationAssertion(rdfs:label "synthetic reference signal"@en) +SubClassOf( ) + +# Class: (residual solvent signal) + +AnnotationAssertion(rdfs:label "residual solvent signal"@en) +SubClassOf( ) + +# Class: (FID zero filling) + +AnnotationAssertion(rdfs:label "FID zero filling"@en) +SubClassOf( ) + +# Class: (data extrapolation using linear prediction) + +AnnotationAssertion(rdfs:label "data extrapolation using linear prediction"@en) +SubClassOf( ) + +# Class: (multiplying FID by window function) + +AnnotationAssertion(rdfs:label "multiplying FID by window function"@en) +SubClassOf( ) + +# Class: (FID fourier transformation) + +AnnotationAssertion(rdfs:label "FID fourier transformation"@en) +AnnotationAssertion(skos:definition "The mathematical conversion of time-resolved FID raw data into frequency resolved NMR spectra (frequency-resolved NMR data) by means of fourier transformation of coordinate systems.") +SubClassOf( ) + +# Class: (phase correction) + +AnnotationAssertion(oboInOwl:hasExactSynonym "phasing") +AnnotationAssertion(oboInOwl:hasExactSynonym "spectral phasing") +AnnotationAssertion(rdfs:label "phase correction"@en) +SubClassOf( ) + +# Class: (peak integration) + +AnnotationAssertion(rdfs:label "peak integration"@en) +SubClassOf( ) + +# Class: (peak alignment) + +AnnotationAssertion(rdfs:label "peak alignment"@en) +SubClassOf( ) + +# Class: (peak shape fitting) + +AnnotationAssertion(rdfs:label "peak shape fitting"@en) +SubClassOf( ) + +# Class: (spectral referencing) + +AnnotationAssertion(rdfs:label "spectral referencing"@en) +SubClassOf( ) + +# Class: (sodium trimethylsilyl-propionate) + +AnnotationAssertion(dce:source "Pohl, L.; Eckle, M. (1969). \"Sodium 3-(trimethylsilyl)tetradeuteriopropionate, a new water-soluble standard for 1H.N.M.R.\". Angewandte Chemie, International Edition in English 8 (5): 381. doi:10.1002/anie.196903811") +AnnotationAssertion(oboInOwl:hasExactSynonym "TMSP") +AnnotationAssertion(oboInOwl:hasExactSynonym "trimethylsilyl propanoic acid") +AnnotationAssertion(rdfs:label "sodium trimethylsilyl-propionate"@en) +SubClassOf( ) + +# Class: (linear scaling) + +AnnotationAssertion(rdfs:comment "used to be 'linear scaling algorithm'") +AnnotationAssertion(rdfs:label "linear scaling"@en) +SubClassOf( ) + +# Class: (scaling) + +AnnotationAssertion(rdfs:comment "used to be called 'scaling algorithm'") +AnnotationAssertion(rdfs:label "scaling"@en) +SubClassOf( ) + +# Class: (non-linear scaling) + +AnnotationAssertion(rdfs:comment "used to be postfixed with algorithm") +AnnotationAssertion(rdfs:label "non-linear scaling"@en) +SubClassOf( ) + +# Class: (total spectral area scaling) + +AnnotationAssertion(rdfs:label "total spectral area scaling"@en) +SubClassOf( ) + +# Class: (probabilistic quotient normalization) + +AnnotationAssertion(dce:source "Dieterle F, Ross A, Schlotterbeck G, Senn H: Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics. Anal Chem 2006, 78(13):4281-90.") +AnnotationAssertion(rdfs:label "probabilistic quotient normalization"@en) +SubClassOf( ) + +# Class: (scaling by generalized logarithmic transformation) + +AnnotationAssertion(oboInOwl:hasExactSynonym "glog scaling") +AnnotationAssertion(rdfs:label "scaling by generalized logarithmic transformation"@en) +SubClassOf( ) + +# Class: (pareto scaling) + +AnnotationAssertion(rdfs:label "pareto scaling"@en) +SubClassOf( ) + +# Class: (autoscaling) + +AnnotationAssertion(rdfs:label "autoscaling"@en) +SubClassOf( ) + +# Class: (2D J-resolved spectrum) + +AnnotationAssertion(oboInOwl:hasExactSynonym "JRES spectrum") +AnnotationAssertion(rdfs:label "2D J-resolved spectrum"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (MetaboLab software) + +AnnotationAssertion(dce:source "http://www.biomedcentral.com/1471-2105/12/366#B2") +AnnotationAssertion(rdfs:label "MetaboLab software"@en) +SubClassOf( ) + +# Class: (Metaboquant software) + +AnnotationAssertion(rdfs:label "Metaboquant software"@en) +SubClassOf( ) + +# Class: (rNMR software) + +AnnotationAssertion(rdfs:label "rNMR software"@en) +SubClassOf( ) + +# Class: (open source NMR software) + +AnnotationAssertion(rdfs:label "open source NMR software"@en) +SubClassOf( ) + +# Class: (commercial NMR software) + +AnnotationAssertion(rdfs:label "commercial NMR software"@en) +SubClassOf( ) + +# Class: (NMRLab software) + +AnnotationAssertion(dce:source "Günther U, Ludwig C, Rüterjans H: NMRLAB - advanced NMR data processing in Matlab., J Magn Reson 2000, 145(2):201-208.") +AnnotationAssertion(rdfs:label "NMRLab software"@en) +SubClassOf( ) + +# Class: (NMRPipe software) + +AnnotationAssertion(dce:source "Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A: NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 1995, 6(3):277-293.") +AnnotationAssertion(rdfs:label "NMRPipe software"@en) +SubClassOf( ) + +# Class: (matNMR software) + +AnnotationAssertion(dce:source "van Beek JD: matNMR: a flexible toolbox for processing, analyzing and visualizing magnetic resonance data in Matlab. J Magn Reson 2007, 187:19-26. ") +AnnotationAssertion(rdfs:label "matNMR software"@en) +SubClassOf( ) + +# Class: (concentration of chemical compound) + +AnnotationAssertion(rdfs:label "concentration of chemical compound"@en) +SubClassOf( ) + +# Class: (manual phase correction) + +AnnotationAssertion(rdfs:label "manual phase correction"@en) +SubClassOf( ) + +# Class: (automatic phase correction) + +AnnotationAssertion(rdfs:label "automatic phase correction"@en) +SubClassOf( ) + +# Class: (DC offset correction) + +AnnotationAssertion(rdfs:label "DC offset correction"@en) +SubClassOf( ) + +# Class: (Gibbs multiplication) + +AnnotationAssertion(dce:source "http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-366") +AnnotationAssertion(rdfs:label "Gibbs multiplication"@en) +SubClassOf( ) + +# Class: (skyline projection) + +AnnotationAssertion(rdfs:label "skyline projection"@en) +SubClassOf( ) + +# Class: (shifted sine window function) + +AnnotationAssertion(oboInOwl:hasExactSynonym "shifted sine apodization") +AnnotationAssertion(rdfs:label "shifted sine window function"@en) +SubClassOf( ) + +# Class: (sinc window multiplication of FID (1D)) + +AnnotationAssertion(oboInOwl:hasExactSynonym "SINC") +AnnotationAssertion(oboInOwl:hasExactSynonym "Sinc window multiplication") +AnnotationAssertion(rdfs:label "sinc window multiplication of FID (1D)"@en) +SubClassOf( ) + +# Class: (SEM window function) + +AnnotationAssertion(dce:source "http://www.sciencedirect.com/science/article/pii/S0003267008000950") +AnnotationAssertion(doap:bug-database "https://github.com/nmrML/nmrML/issues/36") +AnnotationAssertion(oboInOwl:hasExactSynonym "combined sine-bell–exponential window function") +AnnotationAssertion(rdfs:label "SEM window function"@en) +SubClassOf( ) + +# Class: (trapezoid window function) + +AnnotationAssertion(oboInOwl:hasExactSynonym "TRAP") +AnnotationAssertion(oboInOwl:hasExactSynonym "trapezoid apodization") +AnnotationAssertion(rdfs:comment "Functional form ( 0:t1 linear increase from 0.0 to 1.0, t1:size-t2 1.0 + -t2: linear decrease from 1.0 to 0.0 / Parameters ( * data Array of spectral data., * t1 Left ramp length., * t2 Right ramp length., * inv Set True for inverse apodization.") +AnnotationAssertion(rdfs:label "trapezoid window function"@en) +SubClassOf( ) + +# Class: (shifted gaussian window function) + +AnnotationAssertion(rdfs:label "shifted gaussian window function"@en) +SubClassOf( ) + +# Class: (baseline correction using spline function) + +AnnotationAssertion(rdfs:label "baseline correction using spline function"@en) +SubClassOf( ) + +# Class: (heteronuclear single quantum coherence spectrum) + +AnnotationAssertion(oboInOwl:hasExactSynonym "HSQC NMR spectrum") +AnnotationAssertion(rdfs:label "heteronuclear single quantum coherence spectrum"@en) +SubClassOf( ) + +# Class: (Zangger-Sterk pulse sequence) + +AnnotationAssertion(rdfs:label "Zangger-Sterk pulse sequence"@en) +SubClassOf( ) + +# Class: (pure shift 1D Zangger-Sterk pulse sequence) + +AnnotationAssertion(dce:source "http://nmr.chemistry.manchester.ac.uk/?q=node/256") +AnnotationAssertion(rdfs:label "pure shift 1D Zangger-Sterk pulse sequence"@en) +SubClassOf( ) + +# Class: (oneshot pulse sequence) + +AnnotationAssertion(dce:source "http://nmr.chemistry.manchester.ac.uk/?q=node/264") +AnnotationAssertion(rdfs:label "oneshot pulse sequence"@en) +SubClassOf( ) + +# Class: (pure shift oneshot pulse sequence) + +AnnotationAssertion(dce:source "http://nmr.chemistry.manchester.ac.uk/?q=node/265") +AnnotationAssertion(rdfs:label "pure shift oneshot pulse sequence"@en) +SubClassOf( ) + +# Class: (perfect echo watergate pulse sequence) + +AnnotationAssertion(dce:source "http://nmr.chemistry.manchester.ac.uk/?q=node/285") +AnnotationAssertion(oboInOwl:hasExactSynonym "PE Watergate pulse sequence") +AnnotationAssertion(rdfs:label "perfect echo watergate pulse sequence"@en) +SubClassOf( ) + +# Class: (NMR Star 3.1 file format) + +AnnotationAssertion(rdfs:label "NMR Star 3.1 file format"@en) +SubClassOf( ) + +# Class: (NMR Star 2.1 file format) + +AnnotationAssertion(rdfs:label "NMR Star 2.1 file format"@en) +SubClassOf( ) + +# Class: (3D spectrum) + +AnnotationAssertion(oboInOwl:hasExactSynonym "three dimensional spectrum") +AnnotationAssertion(rdfs:label "3D spectrum"@en) +SubClassOf( ) + +# Class: (4D spectrum) + +AnnotationAssertion(oboInOwl:hasExactSynonym "four dimensional spectrum") +AnnotationAssertion(rdfs:label "4D spectrum"@en) +SubClassOf( ) + +# Class: (NMR spectrum by dimensionality) + +AnnotationAssertion(rdfs:label "NMR spectrum by dimensionality"@en) +SubClassOf( ) + +# Class: (homonuclear chemical shift spectrum) + +AnnotationAssertion(rdfs:label "homonuclear chemical shift spectrum"@en) +SubClassOf( ) + +# Class: (heteronuclear chemical shift spectrum) + +AnnotationAssertion(rdfs:label "heteronuclear chemical shift spectrum"@en) +SubClassOf( ) + +# Class: (Bruker instrument model) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Bruker instrument model.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000122") +AnnotationAssertion(rdfs:label "Bruker instrument model") +SubClassOf( ) + +# Class: (homonuclear exchange spectroscopy spectrum) + +AnnotationAssertion(rdfs:label "homonuclear exchange spectroscopy spectrum"@en) +SubClassOf( ) + +# Class: (heteronuclear exchange spectroscopy spectrum) + +AnnotationAssertion(rdfs:label "heteronuclear exchange spectroscopy spectrum"@en) +SubClassOf( ) + +# Class: (homonuclear J-resolved spectrum) + +AnnotationAssertion(rdfs:label "homonuclear J-resolved spectrum"@en) +SubClassOf( ) + +# Class: (heteronuclear J-resolved spectrum) + +AnnotationAssertion(rdfs:label "heteronuclear J-resolved spectrum"@en) +SubClassOf( ) + +# Class: (calibration test spectrum) + +AnnotationAssertion(rdfs:label "calibration test spectrum"@en) +SubClassOf( ) + +# Class: (NMR star software) + +AnnotationAssertion(rdfs:label "NMR star software"@en) +SubClassOf( ) + +# Class: (Felix software) + +AnnotationAssertion(dce:source "http://www.felixnmr.com/") +AnnotationAssertion(rdfs:label "Felix software"@en) +SubClassOf( ) + +# Class: (PIPP software) + +AnnotationAssertion(rdfs:label "PIPP software"@en) +SubClassOf( ) + +# Class: (TALOS+ software) + +AnnotationAssertion(rdfs:label "TALOS+ software"@en) +SubClassOf( ) + +# Class: (CYANA software) + +AnnotationAssertion(dce:source "http://www.cyana.org/wiki/index.php/Main_Page") +AnnotationAssertion(rdfs:label "CYANA software"@en) +SubClassOf( ) + +# Class: (XPLOR-NIH software) + +AnnotationAssertion(dce:source "http://nmr.cit.nih.gov/xplor-nih/") +AnnotationAssertion(rdfs:label "XPLOR-NIH software"@en) +SubClassOf( ) + +# Class: (computed concentration) + +AnnotationAssertion(rdfs:label "computed concentration"@en) +AnnotationAssertion(skos:editorialNote "request these in UO ?") +SubClassOf( ) + +# Class: (XEASY software) + +AnnotationAssertion(dce:source "http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/XEASY") +AnnotationAssertion(rdfs:label "XEASY software"@en) +SubClassOf( ) + +# Class: (sparky software) + +AnnotationAssertion(rdfs:label "sparky software"@en) +SubClassOf( ) + +# Class: (CARA software) + +AnnotationAssertion(dce:source "http://nmr-software.blogspot.de/2007/04/cara.html") +AnnotationAssertion(rdfs:label "CARA software"@en) +SubClassOf( ) + +# Class: (Wattos software) + +AnnotationAssertion(rdfs:label "Wattos software"@en) +SubClassOf( ) + +# Class: (MADNMR software) + +AnnotationAssertion(rdfs:label "MADNMR software"@en) +SubClassOf( ) + +# Class: (Pronto software) + +AnnotationAssertion(rdfs:label "Pronto software"@en) +SubClassOf( ) + +# Class: (TRIAD NMR software) + +AnnotationAssertion(rdfs:label "TRIAD NMR software"@en) +SubClassOf( ) + +# Class: (library based computed concentration) + +AnnotationAssertion(rdfs:label "library based computed concentration"@en) +SubClassOf( ) + +# Class: (Lorenzian estimated concentration) + +AnnotationAssertion(oboInOwl:hasExactSynonym "Lorenzian (-Integration) (Modeled Area) Estimated Concentration") +AnnotationAssertion(rdfs:comment "https://docs.google.com/spreadsheets/d/1egsLQWoQuCxAYPr9MIo-F0A5K9RCbJSC8yWZyYq_fiQ/edit?usp=sharing") +AnnotationAssertion(rdfs:label "Lorenzian estimated concentration"@en) +SubClassOf( ) + +# Class: (measured area based concentration) + +AnnotationAssertion(oboInOwl:hasExactSynonym "Measured Area (Integration) based Concentration") +AnnotationAssertion(rdfs:label "measured area based concentration"@en) +SubClassOf( ) + +# Class: (time-domain amplitude computed concentration) + +AnnotationAssertion(rdfs:label "time-domain amplitude computed concentration"@en) +SubClassOf( ) + +# Class: (group time delay compensation) + +AnnotationAssertion(rdfs:label "group time delay compensation"@en) +AnnotationAssertion(rdfs:seeAlso "http://nmr-analysis.blogspot.fr/2008/02/why-arent-bruker-fids-time-corrected.html") +AnnotationAssertion(skos:definition "This is independent of the bruker acquisition parameter named \"GRPDLY\" (Group Delay), but this is a \"shift\" applied on the fid to calibrate its zero") +SubClassOf( ) + +# Class: (scaling by forward linear prediction) + +AnnotationAssertion(rdfs:label "scaling by forward linear prediction"@en) +SubClassOf( ) + +# Class: (back calculation of first points by linear-prediction) + +AnnotationAssertion(rdfs:label "back calculation of first points by linear-prediction"@en) +SubClassOf( ) + +# Class: (scaling by mirror image linear prediction) + +AnnotationAssertion(rdfs:label "scaling by mirror image linear prediction"@en) +SubClassOf( ) + +# Class: (digital filtering) + +AnnotationAssertion(rdfs:label "digital filtering"@en) +SubClassOf( ) + +# Class: (3D strip plot generation) + +AnnotationAssertion(obo:IAO_0000119 "Daniel Schober") +AnnotationAssertion(dce:source "http://jjhelmus.github.io/nmrglue/current/jbnmr_examples/s11_strip_plots.html") +AnnotationAssertion(rdfs:label "3D strip plot generation"@en) +AnnotationAssertion(skos:definition "A spectrum vizualization method for 3D nmr spectra, assisting assignments for large sequential molecules, i.e. Proteins. +The first two axis in the plot represent the ppms along the two acquisition nuclei, and a third dimension captures the sequential molecule order for the third nucleus.") +SubClassOf( ) + +# Class: (Batman software) + +AnnotationAssertion(rdfs:label "Batman software"@en) +SubClassOf( ) + +# Class: (JEOL instrument model) + +AnnotationAssertion(rdfs:label "JEOL instrument model"@en) +SubClassOf( ) + +# Class: (tecmag instrument model) + +AnnotationAssertion(rdfs:label "tecmag instrument model"@en) +SubClassOf( ) + +# Class: (automatic baseline recognition) + +AnnotationAssertion(dce:source "Bao et al. (2013) A new automatic baseline correction method based on iterative method, J. Magn. Res. 218:35-43") +AnnotationAssertion(dce:source "Golotvin & Williams (2000), Improved baseline recognition and modeling of FT NMR spectra, J. Magn. Res. 146:122-125") +AnnotationAssertion(rdfs:label "automatic baseline recognition"@en) +SubClassOf( ) + +# Class: (Trimethylsilyl propionate) + +AnnotationAssertion(oboInOwl:hasExactSynonym "TSP") +AnnotationAssertion(rdfs:label "Trimethylsilyl propionate"@en) +SubClassOf( ) + +# Class: (TMIC lab pulse sequence) + +AnnotationAssertion(oboInOwl:hasExactSynonym "pulse sequence from Wishart lab library") +AnnotationAssertion(rdfs:label "TMIC lab pulse sequence"@en) +SubClassOf( ) + +# Class: (probe gradient strength) + +AnnotationAssertion(rdfs:label "probe gradient strength"@en) +SubClassOf( ) + +# Class: (NMR acquisition computer operating system) + +AnnotationAssertion(dce:coverage "e.g. Linux or Windows, ...") +AnnotationAssertion(rdfs:label "NMR acquisition computer operating system"@en) +SubClassOf( ) + +# Class: (NMR autosampler software) + +AnnotationAssertion(dce:coverage "e.g. Bruker Biospin ICON-NMR") +AnnotationAssertion(rdfs:label "NMR autosampler software"@en) +SubClassOf( ) + +# Class: (Bruker Biospin ICON-NMR software) + +AnnotationAssertion(rdfs:label "Bruker Biospin ICON-NMR software"@en) +AnnotationAssertion(rdfs:seeAlso "http://www.bruker.com/products/mr/nmr/nmr-software/software/iconnmr/overview.html") +SubClassOf( ) + +# Class: (buffer pH) + +AnnotationAssertion(rdfs:label "buffer pH"@en) +SubClassOf( ) + +# Class: (field frequency lock) + +AnnotationAssertion(dce:coverage "e.g. heavy water (D2O)") +AnnotationAssertion(oboInOwl:hasExactSynonym "lock frequency") +AnnotationAssertion(rdfs:label "field frequency lock"@en) +SubClassOf( ) + +# Class: (concentration standard) + +AnnotationAssertion(oboInOwl:hasExactSynonym "quantitation standard") +AnnotationAssertion(rdfs:label "concentration standard"@en) +SubClassOf( ) + +# Class: (NMR acquisition software) + +AnnotationAssertion(rdfs:label "NMR acquisition software"@en) +SubClassOf( ) + +# Class: (CIMR MI standard) + +AnnotationAssertion(rdfs:label "CIMR MI standard"@en) +SubClassOf( ) + +# Class: (signal line width check) + +AnnotationAssertion(rdfs:label "signal line width check"@en) +SubClassOf( ) + +# Class: (signal line width at five percent intensity check) + +AnnotationAssertion(rdfs:label "signal line width at five percent intensity check"@en) +SubClassOf( ) + +# Class: (NMR spectrum descriptor) + +AnnotationAssertion(rdfs:label "NMR spectrum descriptor"@en) +SubClassOf( obo:BFO_0000031) + +# Class: (pulse width) + +AnnotationAssertion(rdfs:label "pulse width"@en) +SubClassOf( ) + +# Class: (hard pulse width) + +AnnotationAssertion(rdfs:label "hard pulse width"@en) +SubClassOf( ) + +# Class: (sweep width) + +AnnotationAssertion(oboInOwl:hasExactSynonym "spectrum width") +AnnotationAssertion(rdfs:label "sweep width"@en) +SubClassOf( ) + +# Class: (number of data points) + +AnnotationAssertion(oboInOwl:hasExactSynonym "number of data points in spectrum") +AnnotationAssertion(oboInOwl:hasExactSynonym "number of first dimension data points") +AnnotationAssertion(rdfs:label "number of data points"@en) +SubClassOf( ) + +# Class: (x end value) + +AnnotationAssertion(obo:IAO_0000115 "tempdef: The end value for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum.") +AnnotationAssertion(rdfs:label "x end value"@en) +SubClassOf( ) + +# Class: (y-axis type) + +AnnotationAssertion(rdfs:label "y-axis type"@en) +SubClassOf( ) + +# Class: (center of bin on x-axis) + +AnnotationAssertion(oboInOwl:hasExactSynonym "bucket x center") +AnnotationAssertion(rdfs:label "center of bin on x-axis"@en) +SubClassOf( ) + +# Class: (spectral quantitation algorithm) + +AnnotationAssertion(oboInOwl:hasExactSynonym "NMR spectrum quantification method") +AnnotationAssertion(rdfs:label "spectral quantitation algorithm"@en) +SubClassOf( ) + +# Class: (NMRProcFlow software) + +AnnotationAssertion(obo:IAO_0000115 "The NMRProcFlow open source software provides a complete set of tools for processing (e.g. Bucketing) and visualization of 1D NMR data, the whole within an interactive interface based on a spectra visualization."@en) +AnnotationAssertion(rdfs:label "NMRProcFlow software"@en) +AnnotationAssertion(foaf:homepage "http://www.nmrprocflow.org/"@en) +SubClassOf( ) + +# Class: (Bayesil software) + +AnnotationAssertion(obo:IAO_0000115 "Bayesil is a web system that automatically identifies and quantifies metabolites using 1D 1H NMR spectra of ultra-filtered plasma, serum or cerebrospinal fluid. The NMR spectra must be collected in a standardized fashion for Bayesil to perform optimally. Bayesil first performs all spectral processing steps, including Fourier transformation, phasing, solvent filtering, chemical shift referencing, baseline correction and reference line shape convolution automatically. It then deconvolutes the resulting NMR spectrum using a reference spectral library, which here contains the signatures of more than 60 metabolites. This deconvolution process determines both the identity and quantity of the compounds in the biofluid mixture."@en) +AnnotationAssertion(dce:source "Ravanbakhsh S, Liu P, Bjorndahl TC, Mandal R, Grant JR, Wilson M, Eisner R, Sinelnikov I, Hu X, Luchinat C, Greiner R, Wishart DS. (2015) Accurate, Fully-Automated NMR Spectral Profiling for Metabolomics. PLoS ONE 10(5): e0124219.") +AnnotationAssertion(rdfs:label "Bayesil software"@en) +AnnotationAssertion(foaf:homepage "http://bayesil.ca/") +SubClassOf( ) + +# Class: (nmrML Assign) + +AnnotationAssertion(obo:IAO_0000115 "nmrML-Assign is a web server for creating an nmrML file from a FID and a structure. The FID is first automatically processed with Bayesil. The resulting interactive spectrum allows assigning peaks to specific atoms in the structure and the assignments are saved in the nmrML format. For more information about nmrML please visit nmrML.org. nmrML-Assign works with 1H and 13C NMR spectra in Bruker or Agilent/Varian format."@en) +AnnotationAssertion(rdfs:comment "Uses JspectraView Software"@en) +AnnotationAssertion(rdfs:label "nmrML Assign"@en) +AnnotationAssertion(foaf:homepage "http://nmrml.bayesil.ca/"@en) +SubClassOf( ) + +# Class: (doublet feature) + +AnnotationAssertion(oboInOwl:hasExactSynonym "d") +AnnotationAssertion(rdfs:label "doublet feature"@en) +SubClassOf( ) + +# Class: (triplet feature) + +AnnotationAssertion(oboInOwl:hasExactSynonym "t") +AnnotationAssertion(rdfs:label "triplet feature"@en) +SubClassOf( ) + +# Class: (quatruplet feature) + +AnnotationAssertion(oboInOwl:hasExactSynonym "q") +AnnotationAssertion(rdfs:label "quatruplet feature"@en) +SubClassOf( ) + +# Class: (cluster of peaks across samples) + +AnnotationAssertion(obo:IAO_0000115 "a set of peaks that are highly correlated in a series of samples") +AnnotationAssertion(dce:coverage "a feature request by Daniel Jacob inserted at IBP hackathon") +AnnotationAssertion(rdfs:label "cluster of peaks across samples"@en) +SubClassOf( ) + +# Class: (simulated spectrum) + +AnnotationAssertion(rdfs:label "simulated spectrum"@en) +SubClassOf( ) + +# Class: (pulse parameter) + +AnnotationAssertion(rdfs:label "pulse parameter"@en) +SubClassOf( ) + +# Class: (JEOL FID format) + +AnnotationAssertion(rdfs:label "JEOL FID format"@en) +SubClassOf( ) + +# Class: (doublet of doublets feature) + +AnnotationAssertion(oboInOwl:hasExactSynonym "dd") +AnnotationAssertion(rdfs:label "doublet of doublets feature"@en) +SubClassOf( ) + +# Class: (ABX multiplet pattern) + +AnnotationAssertion(rdfs:label "ABX multiplet pattern"@en) +AnnotationAssertion(skos:definition "AMX, ABX and ABC patterns, and various related spin systems are very common in Proton NMR of organic molecules.When two of the protons of an AMX pattern approach each other to form an ABX pattern, the characteristic changes in intensities of a strongly coupled system (leaning) are seen, and, as the size of J approaches the value of νAB more complicated changes arise, so that the pattern can no longer be analyzed correctly by first order methods.") +AnnotationAssertion(foaf:homepage "http://www.chem.wisc.edu/areas/reich/nmr/05-hmr-12-abx.htm") +SubClassOf( ) + +# Class: (singlet feature) + +AnnotationAssertion(oboInOwl:hasExactSynonym "s") +AnnotationAssertion(rdfs:label "singlet feature"@en) +SubClassOf( ) + +# Class: (quintet feature) + +AnnotationAssertion(oboInOwl:hasExactSynonym "qi") +AnnotationAssertion(rdfs:label "quintet feature"@en) +SubClassOf( ) + +# Class: (doublet of triplets) + +AnnotationAssertion(oboInOwl:hasExactSynonym "dt") +AnnotationAssertion(rdfs:label "doublet of triplets"@en) +SubClassOf( ) + +# Class: (triplet of douplets) + +AnnotationAssertion(oboInOwl:hasExactSynonym "td") +AnnotationAssertion(rdfs:label "triplet of douplets"@en) +SubClassOf( ) + +# Class: (triplet of triplets) + +AnnotationAssertion(oboInOwl:hasExactSynonym "tt") +AnnotationAssertion(rdfs:label "triplet of triplets"@en) +SubClassOf( ) + +# Class: (NMR spectrum by pulse sequence) + +AnnotationAssertion(rdfs:label "NMR spectrum by pulse sequence"@en) +SubClassOf( ) + +# Class: (NMR spectrum by processing step) + +AnnotationAssertion(rdfs:label "NMR spectrum by processing step"@en) +SubClassOf( ) + +# Class: (2D spectrum coordinate system descriptor) + +AnnotationAssertion(rdfs:label "2D spectrum coordinate system descriptor"@en) +SubClassOf( ) + +# Class: (y-axis value type) + +AnnotationAssertion(rdfs:label "y-axis value type"@en) +AnnotationAssertion(rdfs:seeAlso "the subclasses come from the Rubtsov specification") +SubClassOf( ) + +# Class: (power value type) + +AnnotationAssertion(rdfs:label "power value type"@en) +SubClassOf( ) + +# Class: (magnitude value type) + +AnnotationAssertion(rdfs:label "magnitude value type"@en) +SubClassOf( ) + +# Class: (real value type) + +AnnotationAssertion(rdfs:label "real value type"@en) +SubClassOf( ) + +# Class: (imaginary value type) + +AnnotationAssertion(rdfs:label "imaginary value type"@en) +SubClassOf( ) + +# Class: (complex value types) + +AnnotationAssertion(rdfs:label "complex value types"@en) +SubClassOf( ) + +# Class: (spectral projection axis) + +AnnotationAssertion(rdfs:label "spectral projection axis"@en) +SubClassOf( ) + +# Class: (f1 axis) + +AnnotationAssertion(rdfs:label "f1 axis"@en) +SubClassOf( ) + +# Class: (f2 axis) + +AnnotationAssertion(rdfs:label "f2 axis"@en) +SubClassOf( ) + +# Class: (NMR Format converter) + +AnnotationAssertion(rdfs:label "NMR Format converter"@en) +SubClassOf( ) + +# Class: (BML-NMR identifier) + +AnnotationAssertion(rdfs:label "BML-NMR identifier"@en) +SubClassOf( ) + +# Class: (creatinine) + +AnnotationAssertion(rdfs:comment "will be further specified via a concentration value") +AnnotationAssertion(rdfs:label "creatinine"@en) +SubClassOf( ) + +# Class: (2D pulse sequence) + +AnnotationAssertion(rdfs:label "2D pulse sequence"@en) +SubClassOf( ) + +# Class: (data simulation) + +AnnotationAssertion(rdfs:comment "used to be labeled 'NMR spectrum simulation'") +AnnotationAssertion(rdfs:label "data simulation"@en) +SubClassOf( ) + +# Class: (dynamic nuclear polarization NMR) + +AnnotationAssertion(oboInOwl:hasExactSynonym "DNP NMR") +AnnotationAssertion(oboInOwl:hasExactSynonym "dynamic nuclear polarization enhanced NMR system") +AnnotationAssertion(rdfs:label "dynamic nuclear polarization NMR"@en) +SubClassOf( ) + +# Class: (chemical shift) + +AnnotationAssertion(obo:IAO_0000115 "Chemical shift is the resonance frequency of a nucleus related to a chemical shift standard. in ppm along x-axis") +AnnotationAssertion(dce:source "http://en.wikipedia.org/wiki/Chemical_shift") +AnnotationAssertion(rdfs:label "chemical shift"@en) +SubClassOf( ) + +# Class: (nmr signal intensity) + +AnnotationAssertion(obo:IAO_0000115 "an information object that describes the strength of the NMR signal") +AnnotationAssertion(rdfs:label "nmr signal intensity"@en) +SubClassOf( ) + +# Class: (baseline correction using polynomial function) + +AnnotationAssertion(rdfs:label "baseline correction using polynomial function"@en) +SubClassOf( ) + +# Class: (first transient of the tnnoesy-presaturation pulse sequence) + +AnnotationAssertion(rdfs:label "first transient of the tnnoesy-presaturation pulse sequence"@en) +SubClassOf( ) + +# Class: (Varian acquisition parameter file) + +AnnotationAssertion(rdfs:label "Varian acquisition parameter file"@en) +SubClassOf( ) + +# Class: (procpar) + +AnnotationAssertion(rdfs:label "procpar"@en) +SubClassOf( ) + +# Class: (acqus) + +AnnotationAssertion(rdfs:label "acqus"@en) +SubClassOf( ) + +# Class: (Bruker acquisition parameter file) + +AnnotationAssertion(rdfs:label "Bruker acquisition parameter file"@en) +SubClassOf( ) + +# Class: (peak feature) + +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000231") +AnnotationAssertion(rdfs:label "peak feature") +SubClassOf( ) + +# Class: (global) + +AnnotationAssertion(rdfs:label "global"@en) +SubClassOf( ) + +# Class: (Varian autosampler) + +AnnotationAssertion(rdfs:label "Varian autosampler"@en) +SubClassOf( ) + +# Class: (Varian SMS 50) + +AnnotationAssertion(rdfs:label "Varian SMS 50"@en) +SubClassOf( ) + +# Class: (Varian probe) + +AnnotationAssertion(rdfs:label "Varian probe"@en) +SubClassOf( ) + +# Class: (5mm HCN probe) + +AnnotationAssertion(rdfs:label "5mm HCN probe"@en) +SubClassOf( ) + +# Class: (Varian liquid cold probe) + +AnnotationAssertion(rdfs:label "Varian liquid cold probe"@en) +SubClassOf( ) + +# Class: (reference compound NMR spectrum) + +AnnotationAssertion(rdfs:comment "e.g as in HMDB") +AnnotationAssertion(rdfs:label "reference compound NMR spectrum"@en) +SubClassOf( ) + +# Class: (Mestrelab software) + +AnnotationAssertion(rdfs:label "Mestrelab software"@en) +SubClassOf( ) + +# Class: (ACD spectrus software) + +AnnotationAssertion(rdfs:label "ACD spectrus software"@en) +SubClassOf( ) + +# Class: (Mat NMR 3 software) + +AnnotationAssertion(rdfs:label "Mat NMR 3 software"@en) +SubClassOf( ) + +# Class: (NMRLab software) + +AnnotationAssertion(rdfs:label "NMRLab software"@en) +SubClassOf( ) + +# Class: (Spinworks NMR software) + +AnnotationAssertion(rdfs:label "Spinworks NMR software"@en) +SubClassOf( ) + +# Class: (NMR software vendor) + +AnnotationAssertion(rdfs:label "NMR software vendor"@en) +SubClassOf( ) + +# Class: (Spinworks) + +AnnotationAssertion(rdfs:label "Spinworks"@en) +SubClassOf( ) + +# Class: (iNMR software) + +AnnotationAssertion(rdfs:label "iNMR software"@en) +SubClassOf( ) + +# Class: (NMR pipe) + +AnnotationAssertion(rdfs:label "NMR pipe"@en) +SubClassOf( ) + +# Class: (cule NMR software) + +AnnotationAssertion(rdfs:label "cule NMR software"@en) +SubClassOf( ) + +# Class: (Matlab to nmrML converter) + +AnnotationAssertion(dce:source "Git: nmrML\\tools\\Parser_and_Converters\\Matlab"@en) +AnnotationAssertion(rdfs:comment "By Batman/ Tim Ebbels Group"@en) +AnnotationAssertion(rdfs:label "Matlab to nmrML converter"@en) +SubClassOf( ) + +# Class: (Bruker processing parameter file) + +AnnotationAssertion(rdfs:label "Bruker processing parameter file"@en) +SubClassOf( ) + +# Class: (procs) + +AnnotationAssertion(rdfs:label "procs"@en) +SubClassOf( ) + +# Class: (Varian processing parameter file) + +AnnotationAssertion(rdfs:label "Varian processing parameter file"@en) +SubClassOf( ) + +# Class: (Madison Metabolomics Consortium Database MMCD identifier) + +AnnotationAssertion(dce:source "http://mmcd.nmrfam.wisc.edu/") +AnnotationAssertion(rdfs:comment "PRS: rename 'identifyer' to 'identifier'"@en) +AnnotationAssertion(rdfs:label "Madison Metabolomics Consortium Database MMCD identifier"@en) +SubClassOf( ) + +# Class: (Bigg metabolomics database identifier) + +AnnotationAssertion(dce:source "http://bigg.ucsd.edu/") +AnnotationAssertion(rdfs:label "Bigg metabolomics database identifier"@en) +SubClassOf( ) + +# Class: (Lorentz Gaussian window function) + +AnnotationAssertion(oboInOwl:hasExactSynonym "Lorentz-to-Gauss apodization") +AnnotationAssertion(rdfs:comment "Functional form: + gm(x_i) = exp(e - g*g) + Where: e = pi*i*g1 + g = 0.6*pi*g2*(g3*(size-1)-i) + Parameters: + * data Array of spectral data. + * g1 Inverse exponential width. + * g2 Gaussian broaden width. + * g3 Location of gauss maximum. + * inv Set True for inverse apodization.") +AnnotationAssertion(rdfs:label "Lorentz Gaussian window function"@en) +SubClassOf( ) + +# Class: (traf window function) + +AnnotationAssertion(oboInOwl:hasExactSynonym "TRAF") +AnnotationAssertion(oboInOwl:hasExactSynonym "Transform of Reverse Added FIDs") +AnnotationAssertion(rdfs:label "traf window function"@en) +AnnotationAssertion(skos:definition "A Window function described by Daniel Traficante in their original paper.") +SubClassOf( ) + +# Class: (trafs window function) + +AnnotationAssertion(oboInOwl:hasExactSynonym "TRAFS") +AnnotationAssertion(rdfs:label "trafs window function"@en) +SubClassOf( ) + +# Class: (peak fitting) + +AnnotationAssertion(rdfs:label "peak fitting"@en) +SubClassOf( ) + +# Class: (peak assignment) + +AnnotationAssertion(rdfs:label "peak assignment"@en) +SubClassOf( ) + +# Class: (deconvolution) + +AnnotationAssertion(rdfs:label "deconvolution"@en) +SubClassOf( ) + +# Class: (chemical shift sorting) + +AnnotationAssertion(obo:IAO_0000115 "A method of sorting multiple spectra by position of chemical shift peaks. This method is used in Batman and improves the fit for shifted/overlapped peaks.") +AnnotationAssertion(rdfs:label "chemical shift sorting"@en) +SubClassOf( ) + +# Class: (fid file) + +AnnotationAssertion(rdfs:label "fid file"@en) +SubClassOf( ) + +# Class: (Varian FID file) + +AnnotationAssertion(rdfs:label "Varian FID file"@en) +SubClassOf( ) + +# Class: (Bruker FID file) + +AnnotationAssertion(rdfs:label "Bruker FID file"@en) +SubClassOf( ) + +# Class: (ERVA-based bucketing) + +AnnotationAssertion(dce:source "Jacob D. et al (2013) Analytical and Bioanalytical Chemistry, 405, 5049-5061") +AnnotationAssertion(rdfs:comment "Taking advantage of the concentration variability of each compound in a series of samples, buckets are linked together into clusters based on significant correlations.This is done i.g. in ERVA-based bucketing") +AnnotationAssertion(rdfs:label "ERVA-based bucketing"@en) +SubClassOf( ) + +# Class: (cluster of peaks) + +AnnotationAssertion(rdfs:label "cluster of peaks"@en) +SubClassOf( ) + +# Class: (Match NMR tube) + +AnnotationAssertion(rdfs:label "Match NMR tube"@en) +SubClassOf( ) + +# Class: (shaped tube) + +AnnotationAssertion(rdfs:label "shaped tube"@en) +SubClassOf( ) + +# Class: (Shigemi tube) + +AnnotationAssertion(rdfs:label "Shigemi tube"@en) +SubClassOf( ) + +# Class: (standard tube) + +AnnotationAssertion(rdfs:label "standard tube"@en) +SubClassOf( ) + +# Class: (Bruker tube) + +AnnotationAssertion(rdfs:label "Bruker tube"@en) +SubClassOf( ) + +# Class: (JEOL magnet) + +AnnotationAssertion(rdfs:label "JEOL magnet"@en) +AnnotationAssertion(foaf:homepage "http://www.jeolusa.com/PRODUCTS/Nuclear-Magnetic-Resonance/Magnets") +SubClassOf( ) + +# Class: (JEOL ECS magnet) + +AnnotationAssertion(rdfs:label "JEOL ECS magnet"@en) +SubClassOf( ) + +# Class: (JEOL ECA magnet) + +AnnotationAssertion(rdfs:label "JEOL ECA magnet"@en) +SubClassOf( ) + +# Class: (JEOL ECX magnet) + +AnnotationAssertion(rdfs:label "JEOL ECX magnet"@en) +SubClassOf( ) + +# Class: (Varian NMR software) + +AnnotationAssertion(rdfs:label "Varian NMR software"@en) +SubClassOf( ) + +# Class: (VnmrJ software) + +AnnotationAssertion(rdfs:label "VnmrJ software"@en) +SubClassOf( ) + +# Class: (Wilmad tube) + +AnnotationAssertion(rdfs:label "Wilmad tube"@en) +SubClassOf( ) + +# Class: (4mm Match tube) + +AnnotationAssertion(rdfs:label "4mm Match tube"@en) +SubClassOf( ) + +# Class: (2.5mm Match tube) + +AnnotationAssertion(rdfs:label "2.5mm Match tube"@en) +SubClassOf( ) + +# Class: (3mm Match tube) + +AnnotationAssertion(rdfs:label "3mm Match tube"@en) +SubClassOf( ) + +# Class: (5mm Match tube) + +AnnotationAssertion(rdfs:label "5mm Match tube"@en) +SubClassOf( ) + +# Class: (1mm Match tube) + +AnnotationAssertion(rdfs:label "1mm Match tube"@en) +SubClassOf( ) + +# Class: (1.7mm Match tube) + +AnnotationAssertion(rdfs:label "1.7mm Match tube"@en) +SubClassOf( ) + +# Class: (2mm Match tube) + +AnnotationAssertion(rdfs:label "2mm Match tube"@en) +SubClassOf( ) + +# Class: (4.25mm Match tube) + +AnnotationAssertion(rdfs:label "4.25mm Match tube"@en) +SubClassOf( ) + +# Class: (3mm standard tube) + +AnnotationAssertion(rdfs:label "3mm standard tube"@en) +SubClassOf( ) + +# Class: (5mm standard tube) + +AnnotationAssertion(rdfs:label "5mm standard tube"@en) +SubClassOf( ) + +# Class: (1mm standard tube) + +AnnotationAssertion(rdfs:label "1mm standard tube"@en) +SubClassOf( ) + +# Class: (1.7mm standard tube) + +AnnotationAssertion(rdfs:label "1.7mm standard tube"@en) +SubClassOf( ) + +# Class: (Wilmad economy tube) + +AnnotationAssertion(rdfs:label "Wilmad economy tube"@en) +SubClassOf( ) + +# Class: (Wilmad precision tube) + +AnnotationAssertion(rdfs:label "Wilmad precision tube"@en) +SubClassOf( ) + +# Class: (Norell tube) + +AnnotationAssertion(rdfs:label "Norell tube"@en) +SubClassOf( ) + +# Class: (JEOL FID file) + +AnnotationAssertion(rdfs:label "JEOL FID file"@en) +SubClassOf( ) + +# Class: (nmRIO) + +AnnotationAssertion(dce:source "Git: nmrML\\tools\\Parser_and_Converters\\R"@en) +AnnotationAssertion(rdfs:comment "R statistics to nmrML. Developed by Steffen Neumann, IPB-Halle.de"@en) +AnnotationAssertion(rdfs:label "nmRIO"@en) +SubClassOf( ) + +# Class: (rNMR-IO) + +AnnotationAssertion(dce:source "Git: nmrML\\tools\\Parser_and_Converters\\R\\rNMR-IO"@en) +AnnotationAssertion(rdfs:label "rNMR-IO"@en) +SubClassOf( ) + +# Class: (Vendor2nmrML_Java) + +AnnotationAssertion(obo:IAO_0000115 "Based on both nmrML.xsd (XML Schema Definition) and CV params (such as ontologies nmrCV, UO, CHEBI ...), a converter written in Java was developed that automatically generates nmrML files, from raw files of the major NMR vendors. The choice of Java was guided by i) the JAXB framework (Java Architecture for XML Binding), ii) its OS-platform independence and iii) strengthened by the existence of a useful java library (i.e [nmr-fid-tool](https://github.com/LuisFF/nmr-fid-tool)) for further processing and visualisation of the resulting nmrML data. +As nmrML intents to gather and integrate several types of data and corresponding metadata in a single file, it is necessary to process each data source separately. Thus, two command tools were developed. + +The first one, nmrMLcreate allows to create a new nmrML file, based on available Bruker or Varian/Agilent raw files. + +The second one, nmrMLproc allows to add and fill in additional sections corresponding to the data processing step."@en) +AnnotationAssertion(dce:source "Git: nmrML\\tools\\Parser_and_Converters\\Java\\converter"@en) +AnnotationAssertion(rdfs:comment "Developed by Daniel Jacob at INRA Bordeaux. The recommended converter for Bruker and Varian/Agilent vendor format conversion."@en) +AnnotationAssertion(rdfs:label "Vendor2nmrML_Java"@en) +SubClassOf( ) + +# Class: (Varian magnet) + +AnnotationAssertion(oboInOwl:hasExactSynonym "Agilent magnet") +AnnotationAssertion(rdfs:label "Varian magnet"@en) +SubClassOf( ) + +# Class: (premium compact narrow bore magnet) + +AnnotationAssertion(rdfs:label "premium compact narrow bore magnet"@en) +SubClassOf( ) + +# Class: (premium shielded narrow bore magnet) + +AnnotationAssertion(rdfs:label "premium shielded narrow bore magnet"@en) +SubClassOf( ) + +# Class: (premium shielded wide bore magnet) + +AnnotationAssertion(rdfs:label "premium shielded wide bore magnet"@en) +SubClassOf( ) + +# Class: (modified Gaussian window function) + +AnnotationAssertion(oboInOwl:hasExactSynonym "modified gaussian apodization") +AnnotationAssertion(rdfs:comment "Functional form: + gmb(x_i) = exp(-a*i - b*i*i) + Parameters: + * data Array of spectral data. + * a Exponential term. + * b Gaussian term. + * inv Set True for inverse apodization.") +AnnotationAssertion(rdfs:label "modified Gaussian window function"@en) +SubClassOf( ) + +# Class: (exponentially damped J-modulation window function) + +AnnotationAssertion(oboInOwl:hasExactSynonym "exponentially damped J-modulation apodization") +AnnotationAssertion(rdfs:comment "Functional form: + jmod(x_i) = exp(-e)*sin( pi*off + pi*(end-off)*i/(size-1)) + Parameters: + * data Array of spectral data. + * e Exponential term. + * off Start of modulation in fraction of pi radians. + * end End of modulation in fraction of pi radians. + * inv Set True for inverse apodization") +AnnotationAssertion(rdfs:label "exponentially damped J-modulation window function"@en) +SubClassOf( ) + +# Class: (shifted sine bell window function) + +AnnotationAssertion(oboInOwl:hasExactSynonym "shifted sine-bell apodization") +AnnotationAssertion(rdfs:comment "Functional form: + sp(x_i) = sin( (pi*off + pi*(end-off)*i/(size-1) )**pow + Parameters: + * data Array of spectral data. + * start Start of Sine-Bell as percent of vector (0.0 -> 1.0) + * end End of Sine-Bell as percent of vector (0.0 -> 1.0 ) + * pow Power of Sine-Bell + * inv Set True for inverse apodization.") +AnnotationAssertion(rdfs:label "shifted sine bell window function"@en) +SubClassOf( ) + +# Class: (triangle window function) + +AnnotationAssertion(oboInOwl:hasExactSynonym "triangle apodization") +AnnotationAssertion(rdfs:comment "Functional form: + 0:loc linear increase/decrease from lHi to 1.0 + loc: linear increase/decrease from 1.0 to rHi + + Parameters: + * data Array of spectral data. + * loc Location of apex, \"auto\" sets to middle. + * lHi Left side starting height. + * rHi Right side starting height. + * inv Set True for inverse apodization.") +AnnotationAssertion(rdfs:label "triangle window function"@en) +SubClassOf( ) + +# Class: (acquisition log file) + +AnnotationAssertion(obo:IAO_0000115 "The acquisition log file is a created during an acquisition and could useful for debugging an acquisition that has gone awry.") +AnnotationAssertion(rdfs:label "acquisition log file"@en) +SubClassOf( ) + +# Class: (PynmrML) + +AnnotationAssertion(dce:source "Git: nmrML\\tools\\Parser_and_Converters\\python"@en) +AnnotationAssertion(rdfs:comment "A Python based vendor to nmrML converter developed by MIchael Wilson at TMIC Edmonton."@en) +AnnotationAssertion(rdfs:label "PynmrML"@en) +SubClassOf( ) + +# Class: (MetaboAnalyst software) + +AnnotationAssertion(obo:IAO_0000115 "A web server designed to permit comprehensive metabolomic data analysis, visualization and interpretation. It supports a wide range of complex statistical calculations and high quality graphical rendering functions that require significant computational resources."@en) +AnnotationAssertion(rdfs:comment " Jianguo Xia, Igor V. Sinelnikov, Beomsoo Han and David S. Wishart, MetaboAnalyst 3.0—making metabolomics more meaningful, Nucl. Acids Res. (1 July 2015) 43 (W1): W251-W257. doi: 10.1093/nar/gkv380 "@en) +AnnotationAssertion(rdfs:label "MetaboAnalyst software"@en) +AnnotationAssertion(foaf:homepage "www.metaboanalyst.ca"@en) +SubClassOf( ) + +# Class: (acqu2s) + +AnnotationAssertion(rdfs:label "acqu2s"@en) +SubClassOf( ) + +# Class: (acqu3s) + +AnnotationAssertion(rdfs:label "acqu3s"@en) +SubClassOf( ) + +# Class: (proc2s) + +AnnotationAssertion(rdfs:label "proc2s"@en) +SubClassOf( ) + +# Class: (proc3s) + +AnnotationAssertion(rdfs:label "proc3s"@en) +SubClassOf( ) + +# Class: (NMR spectrum file) + +AnnotationAssertion(rdfs:label "NMR spectrum file"@en) +SubClassOf( ) + +# Class: (Bruker NMR spectrum file) + +AnnotationAssertion(rdfs:label "Bruker NMR spectrum file"@en) +SubClassOf( ) + +# Class: (1R file) + +AnnotationAssertion(rdfs:label "1R file"@en) +SubClassOf( ) + +# Class: (title file) + +AnnotationAssertion(rdfs:label "title file"@en) +SubClassOf( ) + +# Class: (XEASY software) + +AnnotationAssertion(obo:IAO_0000115 "A new program package, XEASY, was written for interactive computer support of the analysis of NMR spectra for three-dimensional structure determination of biological macromolecules. XEASY was developed for work with 2D, 3D and 4D NMR data sets. It includes all the functions performed by the precursor program EASY, which was designed for the analysis of 2D NMR spectra, i.e., peak picking and support of sequence-specific resonance assignments, cross-peak assignments, cross-peak integration and rate constant determination for dynamic processes."@en) +AnnotationAssertion(dce:source "Christian Bartels, Tai-he Xia, Martin Billeter, Peter Güntert, Kurt Wüthrich, The program XEASY for computer-supported NMR spectral analysis of biological macromolecules, J Biomol NMR (1995) 6: 1. doi:10.1007/BF00417486"@en) +AnnotationAssertion(rdfs:label "XEASY software"@en) +SubClassOf( ) + +# Class: (NMR spectrum vizualisation software) + +AnnotationAssertion(rdfs:label "NMR spectrum vizualisation software"@en) +SubClassOf( ) + +# Class: (JspectraView software) + +AnnotationAssertion(rdfs:comment "Used in NMR Assign tool for Baysil"@en) +AnnotationAssertion(rdfs:label "JspectraView software"@en) +SubClassOf( ) + +# Class: (cryoprobe) + +AnnotationAssertion(rdfs:label "cryoprobe"@en) +SubClassOf( ) + +# Class: (inverse detection NMR probe) + +AnnotationAssertion(rdfs:label "inverse detection NMR probe"@en) +SubClassOf( ) + +# Class: (5mm inverse detection cryoprobe) + +AnnotationAssertion(rdfs:label "5mm inverse detection cryoprobe"@en) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (NMRViewer software) + +AnnotationAssertion(dce:source "Git: nmrML\\tools\\Visualizers\\PMB_NMRviewer"@en) +AnnotationAssertion(rdfs:comment "Developed by Daniel Jacob, INRA Bordeaux"@en) +AnnotationAssertion(rdfs:label "NMRViewer software"@en) +AnnotationAssertion(skos:example "http://services.cbib.u-bordeaux2.fr/SPECNMR/examples"@en) +SubClassOf( ) + +# Class: (material processing) + +AnnotationAssertion(rdfs:label "material processing"@en) +SubClassOf( obo:BFO_0000015) + +# Class: (AB multiplet pattern) + +AnnotationAssertion(dce:source "http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm") +AnnotationAssertion(rdfs:label "AB multiplet pattern"@en) +SubClassOf( ) + +# Class: (NMR solvent) + +AnnotationAssertion(rdfs:comment "Use Chebi entities here.") +AnnotationAssertion(rdfs:label "NMR solvent"@en) +SubClassOf( obo:BFO_0000030) + +# Class: (NMR buffer) + +AnnotationAssertion(rdfs:comment "Use Chebi entities here.") +AnnotationAssertion(rdfs:label "NMR buffer"@en) +SubClassOf( obo:BFO_0000030) + +# Class: (presat water suppression) + +AnnotationAssertion(rdfs:label "presat water suppression"@en) +SubClassOf( ) + +# Class: (Varian VNMRS 600) + +AnnotationAssertion(rdfs:label "Varian VNMRS 600"@en) +SubClassOf( ) + +# Class: (data content encoding) + +AnnotationAssertion(rdfs:label "data content encoding"@en) +SubClassOf( ) + +# Class: (data compression scheme) + +AnnotationAssertion(rdfs:label "data compression scheme"@en) +SubClassOf( ) + +# Class: (byte format) + +AnnotationAssertion(rdfs:label "byte format"@en) +SubClassOf( ) + +# Class: (zlib) + +AnnotationAssertion(rdfs:label "zlib"@en) +SubClassOf( ) + +# Class: (complex64) + +AnnotationAssertion(rdfs:label "complex64"@en) +AnnotationAssertion(skos:definition "This byte format uses a consecutive array of two 32bit float numbers to represent the real and imaginary part of the complex values.") +SubClassOf( ) + +# Class: (complex128) + +AnnotationAssertion(rdfs:label "complex128"@en) +AnnotationAssertion(skos:definition "This byte format uses a consecutive array of two 64bit double precision values to represent the real and imaginary part of the complex values.") +SubClassOf( ) + +# Class: (binary data compression type) + +AnnotationAssertion(rdfs:label "binary data compression type"@en) +SubClassOf( ) + +# Class: (AB2 multiplet pattern) + +AnnotationAssertion(dce:source "http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm") +AnnotationAssertion(rdfs:label "AB2 multiplet pattern"@en) +SubClassOf( ) + +# Class: (data encoding parameter) + +AnnotationAssertion(rdfs:label "data encoding parameter"@en) +SubClassOf( ) + +# Class: (uncompressed data) + +AnnotationAssertion(rdfs:label "uncompressed data"@en) +SubClassOf( ) + +# Class: (digital signal processing firmware version) + +AnnotationAssertion(obo:IAO_0000115 "DSPFVS - DSP (Digital signal processing) firmware version corresponds to the version of the digital filter, a hardware component used by the spectrometer") +AnnotationAssertion(oboInOwl:hasExactSynonym "DSPFVS") +AnnotationAssertion(rdfs:label "digital signal processing firmware version"@en) +SubClassOf( ) + +# Class: (decimation factor) + +AnnotationAssertion(obo:IAO_0000115 "DECIM - decimation factor is a (bruker) acquisition parameter that captures the number of raw analog points that are averaged in order to obtain a digital signal recorded in the fid.") +AnnotationAssertion(oboInOwl:hasExactSynonym "DECIM") +AnnotationAssertion(rdfs:label "decimation factor"@en) +SubClassOf( ) + +# Class: (group time delay) + +AnnotationAssertion(obo:IAO_0000115 "GRPDLY - is the time delay (in number of points?) between acquiring the analog signal and producing the digital signal (i.e. \"The group delay is the time necessary for the digital filter function to “walk into” the raw FID and start generating significant intensity.\")") +AnnotationAssertion(oboInOwl:hasExactSynonym "GRPDLY") +AnnotationAssertion(rdfs:label "group time delay"@en) +SubClassOf( ) + +# Class: (NMR sampling strategy) + +AnnotationAssertion(rdfs:label "NMR sampling strategy"@en) +AnnotationAssertion(skos:definition "a type of data acquisition parameter (when recording the FID) which can be continuous/uniform or sparse/non-uniform signal acquisition.") +SubClassOf( ) + +# Class: (uniform sampling) + +AnnotationAssertion(oboInOwl:hasExactSynonym "continuous sampling") +AnnotationAssertion(rdfs:label "uniform sampling"@en) +AnnotationAssertion(skos:definition "With uniform sampling, each sample is separated by the \"dwell time\".") +AnnotationAssertion(skos:editorialNote "With uniform sampling we don't need to record the time points because we know the dwell time. We may add named strategies to the CV over time that are more specific than non-uniform") +SubClassOf( ) + +# Class: (non-uniform sampling) + +AnnotationAssertion(dce:source "http://link.springer.com/chapter/10.1007%2F1-4020-3910-7_142#page-1") +AnnotationAssertion(oboInOwl:hasExactSynonym "sparse sampling") +AnnotationAssertion(rdfs:label "non-uniform sampling"@en) +AnnotationAssertion(skos:definition "with non-uniform, some samples are skipped, there are different strategies for which to skip, but we can simply record the time point as well as the complex data point in order to represent this type of data.") +AnnotationAssertion(skos:editorialNote "Non-uniform sampling is something likely to become more important in the future, because it allows you to capture higher dimension spectra much more quickly") +SubClassOf( ) + +# Class: (Bruker XWIN-NMR software) + +AnnotationAssertion(rdfs:label "Bruker XWIN-NMR software"@en) +SubClassOf( ) + +# Class: (software attribute) + +AnnotationAssertion(rdfs:label "software attribute"@en) +SubClassOf( obo:BFO_0000031) + +# Class: (NMR software version) + +AnnotationAssertion(rdfs:label "NMR software version"@en) +SubClassOf( ) + +# Class: (ABX3 multiplet pattern) + +AnnotationAssertion(dce:source "http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm") +AnnotationAssertion(rdfs:label "ABX3 multiplet pattern"@en) +SubClassOf( ) + +# Class: (AA'BB' multiplet pattern) + +AnnotationAssertion(dce:source "http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm") +AnnotationAssertion(rdfs:label "AA'BB' multiplet pattern"@en) +SubClassOf( ) + +# Class: (AA'XX' multiplet pattern) + +AnnotationAssertion(dce:source "http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm") +AnnotationAssertion(rdfs:label "AA'XX' multiplet pattern"@en) +SubClassOf( ) + +# Class: (variable size bucketing) + +AnnotationAssertion(rdfs:label "variable size bucketing"@en) +SubClassOf( ) + +# Class: (uniform bucketing) + +AnnotationAssertion(rdfs:label "uniform bucketing"@en) +SubClassOf( ) + +# Class: (intelligent bucketing) + +AnnotationAssertion(rdfs:label "intelligent bucketing"@en) +SubClassOf( ) + +# Class: (bucket importing) + +AnnotationAssertion(rdfs:label "bucket importing"@en) +SubClassOf( ) + +# Class: (bucket resetting) + +AnnotationAssertion(rdfs:comment "put in as reqired by NMRProcFlow tool") +AnnotationAssertion(rdfs:label "bucket resetting"@en) +SubClassOf( ) + +# Class: (global baseline correction) + +AnnotationAssertion(rdfs:comment "as needed for nmrProcFlow") +AnnotationAssertion(rdfs:label "global baseline correction"@en) +SubClassOf( ) + +# Class: (local baseline correction) + +AnnotationAssertion(rdfs:comment "as needed for nmrProcFlow") +AnnotationAssertion(rdfs:label "local baseline correction"@en) +SubClassOf( ) + +# Class: (bucket fusioning) + +AnnotationAssertion(rdfs:label "bucket fusioning"@en) +SubClassOf( ) + +# Class: (JNM-ECX Series FT NMR instrument) + +AnnotationAssertion(rdfs:label "JNM-ECX Series FT NMR instrument"@en) +SubClassOf( ) + +# Class: (JNM-ECZR Series FT NMR instrument) + +AnnotationAssertion(rdfs:label "JNM-ECZR Series FT NMR instrument"@en) +AnnotationAssertion(skos:definition "JNM-ECZR series is a new system that fully incorporates the latest digital and high frequency technologies. +Improved reliability and a more compact size make possible by incorporating more advanced integrated circuits, it supports even greater expandability options than current models for multi-channel operation, high power amplifiers and other accessories. +The bus line for control of attachments has been upgraded to high speed and enables highly accurate and rapid control. +400 MHz - 1 GHz") +SubClassOf( ) + +# Class: (JNM-ECZS Series FT NMR instrument) + +AnnotationAssertion(rdfs:label "JNM-ECZS Series FT NMR instrument"@en) +AnnotationAssertion(skos:definition "The entry model ECZS spectrometer has the same basic functions, performance and capability of high-end model. The main console is amazingly small, less than 1/2 that of the current ECS series spectrometer. +Coupling the use of advanced software with highly reliable automation, all routine daily measurements can be automated, while the use of the autotune Supercool probe realizes the world’s highest sensitivity in its class. +Whatever your application field ECZS can demonstrate its power. +400 MHz") +SubClassOf( ) + +# Class: (AVANCE III HD) + +AnnotationAssertion(rdfs:label "AVANCE III HD"@en) +SubClassOf( ) + +# Class: (NanoBay400 MHz) + +AnnotationAssertion(rdfs:label "NanoBay400 MHz"@en) +SubClassOf( ) + +# Class: (Fourier 300HD) + +AnnotationAssertion(rdfs:label "Fourier 300HD"@en) +SubClassOf( ) + +# Class: (DNP-NMR) + +AnnotationAssertion(rdfs:label "DNP-NMR"@en) +SubClassOf( ) + +# Class: (LC-NMR instrument) + +AnnotationAssertion(rdfs:label "LC-NMR instrument"@en) +SubClassOf( ) + +# Class: (LC-NMR/MS instrument) + +AnnotationAssertion(rdfs:label "LC-NMR/MS instrument"@en) +SubClassOf( ) + +# Class: (Food-Screener instrument) + +AnnotationAssertion(rdfs:label "Food-Screener instrument"@en) +SubClassOf( ) + +# Class: (AVANCE IVDr) + +AnnotationAssertion(rdfs:label "AVANCE IVDr"@en) +SubClassOf( ) + +# Class: (JEOL Resonance 400MHz YH magnet) + +AnnotationAssertion(rdfs:label "JEOL Resonance 400MHz YH magnet"@en) +SubClassOf( ) + +# Class: (JEOL Resonance 500MHz magnet) + +AnnotationAssertion(rdfs:label "JEOL Resonance 500MHz magnet"@en) +SubClassOf( ) + +# Class: (JEOL Resonance 600MHz magnet) + +AnnotationAssertion(rdfs:label "JEOL Resonance 600MHz magnet"@en) +SubClassOf( ) + +# Class: (JEOL Resonance 700MHz magnet) + +AnnotationAssertion(rdfs:label "JEOL Resonance 700MHz magnet"@en) +SubClassOf( ) + +# Class: (JEOL Resonance 800MHz magnet) + +AnnotationAssertion(rdfs:label "JEOL Resonance 800MHz magnet"@en) +SubClassOf( ) + +# Class: (single peak feature) + +AnnotationAssertion(rdfs:label "single peak feature"@en) +SubClassOf( ) + +# Class: (NMR instrument vendor) + +AnnotationAssertion(rdfs:label "NMR instrument vendor"@en) +AnnotationAssertion(skos:definition "Any organisation ort person that sells NMR instruments to customers.") +SubClassOf( ) + +# Class: (Avance I spectrometer) + +AnnotationAssertion(rdfs:label "Avance I spectrometer"@en) +SubClassOf( ) + +# Class: (Oxford Instruments) + +AnnotationAssertion(rdfs:label "Oxford Instruments"@en) +SubClassOf( ) + +# Class: (Spinlock SRL) + +AnnotationAssertion(rdfs:label "Spinlock SRL"@en) +SubClassOf( ) + +# Class: (General Electric) + +AnnotationAssertion(rdfs:label "General Electric"@en) +SubClassOf( ) + +# Class: (Kimble Chase) + +AnnotationAssertion(rdfs:label "Kimble Chase"@en) +SubClassOf( ) + +# Class: (Phillips) + +AnnotationAssertion(rdfs:label "Phillips"@en) +SubClassOf( ) + +# Class: (Siemens AG) + +AnnotationAssertion(rdfs:label "Siemens AG"@en) +SubClassOf( ) + +# Class: (Varian Inova 500) + +AnnotationAssertion(rdfs:label "Varian Inova 500"@en) +SubClassOf( ) + +# Class: (Varian VNMRS instrument) + +AnnotationAssertion(rdfs:label "Varian VNMRS instrument"@en) +SubClassOf( ) + +# Class: (Varian Mercury plus) + +AnnotationAssertion(rdfs:label "Varian Mercury plus"@en) +SubClassOf( ) + +# Class: (Varian UnityInova instrument) + +AnnotationAssertion(rdfs:label "Varian UnityInova instrument"@en) +SubClassOf( ) + +# Class: (Varian 400-MR NMR instrument) + +AnnotationAssertion(rdfs:label "Varian 400-MR NMR instrument"@en) +SubClassOf( ) + +# Class: (Varian DDR2 instrument) + +AnnotationAssertion(rdfs:label "Varian DDR2 instrument"@en) +SubClassOf( ) + +# Class: (Agilent NMR instrument) + +AnnotationAssertion(rdfs:label "Agilent NMR instrument"@en) +SubClassOf( ) + +# Class: (Agilent 400-MR NMR instrument) + +AnnotationAssertion(rdfs:label "Agilent 400-MR NMR instrument"@en) +SubClassOf( ) + +# Class: (Varian Mercury 400) + +AnnotationAssertion(rdfs:label "Varian Mercury 400"@en) +SubClassOf( ) + +# Class: (Agilent Au 400 (DDR2 Console)) + +AnnotationAssertion(rdfs:label "Agilent Au 400 (DDR2 Console)"@en) +SubClassOf( ) + +# Class: (Agilent DDR 2 w/ HCN cryoprobe) + +AnnotationAssertion(rdfs:label "Agilent DDR 2 w/ HCN cryoprobe"@en) +SubClassOf( ) + +# Class: (BMRB identifier) + +AnnotationAssertion(rdfs:label "BMRB identifier"@en) +SubClassOf( ) + +# Class: (left trapezoid limit) + +AnnotationAssertion(oboInOwl:hasExactSynonym "TM1") +AnnotationAssertion(rdfs:comment " 0 "left trapezoid limit"@en) +SubClassOf( ) + +# Class: (trapezoid window function parameter) + +AnnotationAssertion(rdfs:label "trapezoid window function parameter"@en) +SubClassOf( ) + +# Class: (complex64 Integer) + +AnnotationAssertion(rdfs:label "complex64 Integer"@en) +AnnotationAssertion(skos:definition "This byte format uses a consecutive array of two 32bit integer numbers to represent the real and imaginary part of the complex values (2x32bits=>2x4bytes=> 2 integers) for the FID datatype.") +SubClassOf( ) + +# Class: (complex128 Integer) + +AnnotationAssertion(rdfs:label "complex128 Integer"@en) +AnnotationAssertion(skos:definition "This byte format uses a consecutive array of two 64bit long integer numbers to represent the real and imaginary part of the complex values (2x64bits => 2x8bytes => 2 longs) for the FID datatype.") +SubClassOf( ) + +# Class: (right trapezoid limit) + +AnnotationAssertion(oboInOwl:hasExactSynonym "TM2") +AnnotationAssertion(rdfs:comment "0 "right trapezoid limit"@en) +SubClassOf( ) + +# Class: (thirty degree pulse duration) + +AnnotationAssertion(oboInOwl:hasExactSynonym "30 degree pulse duration") +AnnotationAssertion(rdfs:label "thirty degree pulse duration"@en) +AnnotationAssertion(skos:definition "The duration of the excitation pulse needed to rotate the magnetisation vector by 30 degrees.") +SubClassOf( ) + +# Class: (InChi) + +AnnotationAssertion(rdfs:label "InChi"@en) +SubClassOf( ) + +# Class: (inchikey) + +AnnotationAssertion(rdfs:label "inchikey"@en) +SubClassOf( ) + +# Class: (Wiswesser Line Notation) + +AnnotationAssertion(oboInOwl:hasExactSynonym "WLN") +AnnotationAssertion(rdfs:label "Wiswesser Line Notation"@en) +SubClassOf( ) + +# Class: (ROSDAL) + +AnnotationAssertion(rdfs:label "ROSDAL"@en) +SubClassOf( ) + +# Class: (SLN-Tripos) + +AnnotationAssertion(rdfs:label "SLN-Tripos"@en) +SubClassOf( ) + +# Class: (smarts) + +AnnotationAssertion(rdfs:label "smarts"@en) +SubClassOf( ) + +# Class: (line representation) + +AnnotationAssertion(rdfs:label "line representation"@en) +SubClassOf( ) + +# Class: (2D topological molecule representation) + +AnnotationAssertion(rdfs:label "2D topological molecule representation"@en) +SubClassOf( ) + +# Class: (2D bond line structure) + +AnnotationAssertion(rdfs:label "2D bond line structure"@en) +SubClassOf( ) + +# Class: (3D geometrical molecule representation) + +AnnotationAssertion(rdfs:label "3D geometrical molecule representation"@en) +SubClassOf( ) + +# Class: (3D bond line structure) + +AnnotationAssertion(rdfs:label "3D bond line structure"@en) +SubClassOf( ) + +# Class: (CAS number) + +AnnotationAssertion(rdfs:label "CAS number"@en) +SubClassOf( ) + +# Class: (fingerprint model) + +AnnotationAssertion(rdfs:label "fingerprint model"@en) +SubClassOf( ) + +# Class: (molfile) + +AnnotationAssertion(rdfs:label "molfile"@en) +SubClassOf( ) + +# Class: (compound similarity measure) + +AnnotationAssertion(rdfs:label "compound similarity measure"@en) +SubClassOf( ) + +# Class: (Tanimoto similarity) + +AnnotationAssertion(rdfs:label "Tanimoto similarity"@en) +SubClassOf( ) + +# Class: (Gaussian window function parameter) + +AnnotationAssertion(rdfs:label "Gaussian window function parameter"@en) +SubClassOf( ) + +# Class: ( 2,2-Dimethyl-2-silapentane-5-sulfonate) + +AnnotationAssertion(oboInOwl:hasExactSynonym "DSS") +AnnotationAssertion(rdfs:label " 2,2-Dimethyl-2-silapentane-5-sulfonate"@en) +SubClassOf( ) + +# Class: (Gaussian maximum position) + +AnnotationAssertion(rdfs:label "Gaussian maximum position"@en) +SubClassOf( ) + +# Class: (2H spectrum reference compound) + +AnnotationAssertion(rdfs:label "2H spectrum reference compound"@en) +SubClassOf( ) + +# Class: (ABX2 multiplet pattern) + +AnnotationAssertion(rdfs:label "ABX2 multiplet pattern"@en) +SubClassOf( ) + +# Class: (DRX 600 instrument) + +AnnotationAssertion(rdfs:label "DRX 600 instrument"@en) +SubClassOf( ) + +# Class: (plot and graph generation) + +AnnotationAssertion(rdfs:label "plot and graph generation"@en) +SubClassOf( ) + +# Class: (reference deconvolution) + +AnnotationAssertion(rdfs:label "reference deconvolution"@en) +AnnotationAssertion(skos:definition "vertical alignment of on and offset of the peak of the reference compound.") +SubClassOf( ) + +# Class: (spectral smoothing) + +AnnotationAssertion(rdfs:label "spectral smoothing"@en) +AnnotationAssertion(skos:definition "the process of removing noisy jitters in a spectral curve to get clearer and more meaningful signals and peaks.") +SubClassOf( ) + +# Class: (NMR database format) + +AnnotationAssertion(rdfs:label "NMR database format"@en) +SubClassOf( ) + +# Class: (BMRB/XML file format) + +AnnotationAssertion(dce:source "M. Yokochi, N. Kobayashi, E. L. Ulrich, A. R. Kinjo, T. Iwata, Y. E. Ioannidis, M. Livny, J. L. Markley, H. Nakamura, C. Kojima, T. Fujiwara, “Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins,” Journal of Biomedical Semantics, 5:7:16 (2016)") +AnnotationAssertion(rdfs:label "BMRB/XML file format"@en) +SubClassOf( ) + +# Class: (nD spectrum) + +AnnotationAssertion(rdfs:label "nD spectrum"@en) +SubClassOf( ) + +# Class: (NMR data conversion) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Terms used to describe types of data processing.") +AnnotationAssertion(oboInOwl:hasExactSynonym "data processing") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000452") +AnnotationAssertion(rdfs:label "NMR data conversion") +SubClassOf( ) + +# Class: (sample) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "tempdef: A sample is a role that is played by an object of interest in an investigation used to obtain generalizable information about the sample source. + defprov: Daniel Schober") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000457") +AnnotationAssertion(rdfs:label "sample") +SubClassOf( obo:BFO_0000030) + +# Class: (instrument) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Description of the instrument or the mass spectrometer.") +AnnotationAssertion(oboInOwl:hasExactSynonym "instrument configuration") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000463") +AnnotationAssertion(rdfs:label "instrument") +SubClassOf( obo:BFO_0000030) + +# Class: (Varian/Agilent instrument model) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Varian instrument model.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000489") +AnnotationAssertion(rdfs:label "Varian/Agilent instrument model") +SubClassOf( ) + +# Class: (instrument attribute) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Instrument properties that are associated with a value.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000496") +AnnotationAssertion(rdfs:label "instrument attribute") +SubClassOf( ) + +# Class: (data file content) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Describes the data content on the file.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000524") +AnnotationAssertion(rdfs:label "data file content") +SubClassOf( ) + +# Class: (instrument serial number) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Serial Number of the instrument.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000529") +AnnotationAssertion(rdfs:label "instrument serial number") +SubClassOf( ) + +# Class: (file format conversion) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Conversion of one file format to another.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000530") +AnnotationAssertion(rdfs:label "file format conversion") +SubClassOf( ) + +# Class: (software) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Software related to the recording or transformation of spectra.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000531") +AnnotationAssertion(rdfs:label "software") +SubClassOf( obo:BFO_0000017) + +# Class: (object attribute) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Object Attribute.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000547") +AnnotationAssertion(rdfs:label "object attribute") +SubClassOf( obo:BFO_0000031) + +# Class: (sample attribute) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Sample properties that are associated with a value.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000548") +AnnotationAssertion(rdfs:label "sample attribute") +SubClassOf( ) + +# Class: (data file checksum type) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000561") +AnnotationAssertion(rdfs:label "data file checksum type") +SubClassOf( ) + +# Class: (MD5) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "MD5 (Message-Digest algorithm 5) is a cryptographic hash function with a 128-bit hash value used to check the integrity of files.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000568") +AnnotationAssertion(rdfs:label "MD5") +SubClassOf( ) + +# Class: (SHA-1) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000569") +AnnotationAssertion(rdfs:label "SHA-1") +SubClassOf( ) + +# Class: (NMR raw data file format) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Describes the type of file and its content.") +AnnotationAssertion(oboInOwl:hasExactSynonym "source file") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000577") +AnnotationAssertion(rdfs:label "NMR raw data file format") +SubClassOf( ) + +# Class: (contact attribute) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Details about a person or organization to contact in case of concern or discussion about the file.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000585") +AnnotationAssertion(rdfs:label "contact attribute") +SubClassOf( ) + +# Class: (contact name) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Name of the contact person or organization.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000586") +AnnotationAssertion(rdfs:label "contact name") +SubClassOf( ) + +# Class: (contact address) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Postal address of the contact person or organization.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000587") +AnnotationAssertion(rdfs:label "contact address") +SubClassOf( ) + +# Class: (contact URL) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Uniform Resource Locator related to the contact person or organization.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000588") +AnnotationAssertion(rdfs:label "contact URL") +SubClassOf( ) + +# Class: (contact email) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Email address of the contact person or organization.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000589") +AnnotationAssertion(rdfs:label "contact email") +SubClassOf( ) + +# Class: (contact organization) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Home institution of the contact person.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000590") +AnnotationAssertion(rdfs:label "contact organization") +SubClassOf( ) + +# Class: (data processing parameter) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Data processing parameter used in the data processing performed on the data file.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000630") +AnnotationAssertion(rdfs:label "data processing parameter") +SubClassOf( ) + +# Class: (data processing completion time) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "The time that a data processing action was finished.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:date") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000747") +AnnotationAssertion(rdfs:label "data processing completion time") +SubClassOf( obo:BFO_0000019) + +# Class: (FID format) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Describes how the native spectrum identifiers are formated.") +AnnotationAssertion(oboInOwl:hasExactSynonym "nativeID format") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000767") +AnnotationAssertion(rdfs:label "FID format") +SubClassOf( ) + +# Class: (Bruker FID format) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "file=xsd:IDREF.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000773") +AnnotationAssertion(rdfs:comment "The nativeID must be the same as the source file ID.") +AnnotationAssertion(rdfs:label "Bruker FID format") +SubClassOf( ) + +# Class: (custom unreleased software) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the MSI-NMR working group in order to have another CV term added.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000799") +AnnotationAssertion(rdfs:label "custom unreleased software") +SubClassOf( ) + +# Class: (sample preparation information) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Description of the preparation steps which took place before the measurement was performed.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000831") +AnnotationAssertion(rdfs:label "sample preparation information") +SubClassOf( ) + +# Class: (molecule) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A molecules is a fundamental component of a chemical compound that is the smallest part of the compound that can participate in a chemical reaction.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000859") +AnnotationAssertion(rdfs:label "molecule") +SubClassOf( ) + +# Class: (peptide) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A compound of low molecular weight that is composed of two or more amino acids.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000860") +AnnotationAssertion(rdfs:label "peptide") +SubClassOf( ) + +# Class: (chemical compound attribute) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A describable property of a chemical compound.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000861") +AnnotationAssertion(rdfs:label "chemical compound attribute") +SubClassOf( ) + +# Class: (isoelectric point) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "The pH of a solution at which a charged molecule does not migrate in an electric field.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:float") +AnnotationAssertion(oboInOwl:hasExactSynonym "pI") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000862") +AnnotationAssertion(rdfs:label "isoelectric point") +SubClassOf( ) + +# Class: (predicted isoelectric point) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:float") +AnnotationAssertion(oboInOwl:hasExactSynonym "predicted pI") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000863") +AnnotationAssertion(rdfs:label "predicted isoelectric point") +SubClassOf( ) + +# Class: (chemical compound formula) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A combination of symbols used to express the chemical composition of a compound.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000864") +AnnotationAssertion(rdfs:label "chemical compound formula") +SubClassOf( ) + +# Class: (empirical formula) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A chemical formula which expresses the proportions of the elements present in a substance.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000865") +AnnotationAssertion(rdfs:label "empirical formula") +SubClassOf( ) + +# Class: (molecular formula) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000866") +AnnotationAssertion(rdfs:label "molecular formula") +SubClassOf( ) + +# Class: (structural formula) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000867") +AnnotationAssertion(rdfs:label "structural formula") +SubClassOf( ) + +# Class: (SMILES string) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000868") +AnnotationAssertion(rdfs:label "SMILES string") +SubClassOf( ) + +# Class: (external reference identifier) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "An identifier/accession number to an external reference database.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000878") +AnnotationAssertion(rdfs:label "external reference identifier") +SubClassOf( ) + +# Class: (PubMed identifier) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A unique identifier for a publication in the PubMed database (MIR:00000015).") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:integer") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000879") +AnnotationAssertion(rdfs:label "PubMed identifier") +SubClassOf( ) + +# Class: (chemical compound) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A substance formed by chemical union of two or more elements or ingredients in definite proportion by weight.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000881") +AnnotationAssertion(rdfs:comment "Use Chebi entities here.") +AnnotationAssertion(rdfs:label "chemical compound") +SubClassOf( obo:BFO_0000030) + +# Class: (protein) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA coding for the protein.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000882") +AnnotationAssertion(rdfs:label "protein") +SubClassOf( ) + +# Class: (protein short name) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN).") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000883") +AnnotationAssertion(rdfs:label "protein short name") +SubClassOf( ) + +# Class: (protein attribute) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "An nonphysical attribute describing a specific protein.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000884") +AnnotationAssertion(rdfs:label "protein attribute") +SubClassOf( ) + +# Class: (protein accession) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Accession number for a specific protein in a database.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000885") +AnnotationAssertion(rdfs:label "protein accession") +SubClassOf( ) + +# Class: (protein name) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A long name describing the function of the protein.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000886") +AnnotationAssertion(rdfs:label "protein name") +SubClassOf( ) + +# Class: (peptide attribute) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "An nonphysical attribute that can be used to describe a peptide.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000887") +AnnotationAssertion(rdfs:label "peptide attribute") +SubClassOf( ) + +# Class: (unmodified peptide sequence) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A sequence of letter symbols denoting the order of amino acids that compose the peptide, without encoding any amino acid mass modifications that might be present.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000888") +AnnotationAssertion(rdfs:label "unmodified peptide sequence") +SubClassOf( ) + +# Class: (modified peptide sequence) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A sequence of letter symbols denoting the order of amino acids that compose the peptide plus the encoding any amino acid mass modifications that are present using the notation where the total mass of the modified amino acid is specified in square bracketed numbers following the letter (e.g. R[162.10111] indicates an arginine whose final modified mass is 162.10111 amu).") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000889") +AnnotationAssertion(rdfs:label "modified peptide sequence") +SubClassOf( ) + +# Class: (peptide labeling state) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A state description of how a peptide might be isotopically or isobarically labelled.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000890") +AnnotationAssertion(rdfs:label "peptide labeling state") +SubClassOf( ) + +# Class: (heavy labeled peptide) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A peptide that has been created or labeled with some heavier-than-usual isotopes.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000891") +AnnotationAssertion(rdfs:label "heavy labeled peptide") +SubClassOf( ) + +# Class: (unlabeled peptide) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A peptide that has not been labeled with heavier-than-usual isotopes. This is often referred to as \"light\" to distinguish from \"heavy\".") +AnnotationAssertion(oboInOwl:hasExactSynonym "light labeled peptide") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000892") +AnnotationAssertion(rdfs:label "unlabeled peptide") +SubClassOf( ) + +# Class: (peptide group label) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000893") +AnnotationAssertion(rdfs:label "peptide group label") +SubClassOf( ) + +# Class: (data standard) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000898") +AnnotationAssertion(rdfs:label "data standard") +SubClassOf( obo:BFO_0000031) + +# Class: (de facto standard) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard.") +AnnotationAssertion(oboInOwl:hasDbXref "MS_1000899") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000899") +AnnotationAssertion(rdfs:label "de facto standard") +SubClassOf( ) + +# Class: (minimum information standard) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result.") +AnnotationAssertion(oboInOwl:hasDbXref "MS_1000899") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000900") +AnnotationAssertion(rdfs:label "minimum information standard") +SubClassOf( ) + +# Class: (tab delimited text file) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A file that has two or more columns of tabular data where each column is separated by a TAB character.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000914") +AnnotationAssertion(rdfs:label "tab delimited text file") +SubClassOf( ) + +# Class: (protein modification) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000933") +AnnotationAssertion(rdfs:label "protein modification") +SubClassOf( ) + +# Class: (gene name) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Name of the gene from which the protein is translated.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1000934") +AnnotationAssertion(rdfs:label "gene name") +SubClassOf( ) + +# Class: (intermediate analysis format) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:MI") obo:IAO_0000115 "Type of the source file, the nmrIdentML was created from.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001040") +AnnotationAssertion(rdfs:label "intermediate analysis format") +SubClassOf( ) + +# Class: (data stored in database) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:MI") obo:IAO_0000115 "Source file for this nmrIdentML was a data set in a database.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001107") +AnnotationAssertion(rdfs:label "data stored in database") +AnnotationAssertion(skos:editorialNote "retire? Consider: \"NMR database format\" ?") +SubClassOf( ) + +# Class: (software vendor) + +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001267") +AnnotationAssertion(rdfs:label "software vendor") +SubClassOf( ) + +# Class: (programmer) + +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001268") +AnnotationAssertion(rdfs:label "programmer") +SubClassOf( ) + +# Class: (instrument vendor) + +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001269") +AnnotationAssertion(rdfs:label "instrument vendor") +SubClassOf( ) + +# Class: (lab personnel) + +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001270") +AnnotationAssertion(rdfs:label "lab personnel") +SubClassOf( ) + +# Class: (researcher) + +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001271") +AnnotationAssertion(rdfs:label "researcher") +SubClassOf( ) + +# Class: (analysis software) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Analysis software.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001456") +AnnotationAssertion(rdfs:label "analysis software") +SubClassOf( ) + +# Class: (data processing software) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Conversion software.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001457") +AnnotationAssertion(rdfs:label "data processing software") +SubClassOf( ) + +# Class: (data file format) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Format of data files.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001459") +AnnotationAssertion(rdfs:label "data file format") +SubClassOf( ) + +# Class: (contact phone number) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Phone number of the contact person or organization.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001755") +AnnotationAssertion(rdfs:label "contact phone number") +SubClassOf( ) + +# Class: (contact fax number) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Fax number for the contact person or organization.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001756") +AnnotationAssertion(rdfs:label "contact fax number") +SubClassOf( ) + +# Class: (contact toll-free phone number) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Toll-free phone number of the contact person or organization.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001757") +AnnotationAssertion(rdfs:label "contact toll-free phone number") +SubClassOf( ) + +# Class: (Digital Object Identifier (DOI)) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:MI") obo:IAO_0000115 "DOI unique identifier.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001922") +AnnotationAssertion(rdfs:label "Digital Object Identifier (DOI)") +SubClassOf( ) + +# Class: (external reference keyword) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:MI") obo:IAO_0000115 "Free text attribute that can enrich the information about an entity.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001923") +AnnotationAssertion(rdfs:label "external reference keyword") +SubClassOf( ) + +# Class: (journal article keyword) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:MI") obo:IAO_0000115 "Keyword present in a scientific publication.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001924") +AnnotationAssertion(rdfs:label "journal article keyword") +SubClassOf( ) + +# Class: (submitter keyword) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:MI") obo:IAO_0000115 "Keyword assigned by the data submitter.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001925") +AnnotationAssertion(rdfs:label "submitter keyword") +SubClassOf( ) + +# Class: (curator keyword) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:MI") obo:IAO_0000115 "Keyword assigned by a data curator.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001926") +AnnotationAssertion(rdfs:label "curator keyword") +SubClassOf( ) + +# Class: (NMR acquisition parameter) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Parameters used in the NMR spectrometry acquisition.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1001954") +AnnotationAssertion(rdfs:label "NMR acquisition parameter") +SubClassOf( ) + +# Class: (HMDB identifier) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A unique identifier for a metabolite in the HMDB database (HMDB00001).") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:integer") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002000") +AnnotationAssertion(rdfs:label "HMDB identifier") +SubClassOf( ) + +# Class: (Chenomx software) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Chenomx software for data acquisition and analysis.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002001") +AnnotationAssertion(rdfs:label "Chenomx software") +SubClassOf( ) + +# Class: (Chenomx NMR Suite software) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Chenomx software for data analysis.") +AnnotationAssertion(dce:source "http://www.chenomx.com/software/") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002002") +AnnotationAssertion(rdfs:label "Chenomx NMR Suite software") +SubClassOf( ) + +# Class: (Varian FID format) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "file=xsd:IDREF.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002003") +AnnotationAssertion(rdfs:comment "The nativeID must be the same as the source file ID.") +AnnotationAssertion(rdfs:label "Varian FID format") +SubClassOf( ) + +# Class: (NMR spectrometer file format) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002004") +AnnotationAssertion(rdfs:label "NMR spectrometer file format") +SubClassOf( ) + +# Class: (text file) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:PI") obo:IAO_0000115 "Simple text file of peaks.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002005") +AnnotationAssertion(rdfs:label "text file") +SubClassOf( ) + +# Class: (acquisition parameter file) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Parameter file used to configure the acquisition of raw data on the instrument.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002006") +AnnotationAssertion(rdfs:label "acquisition parameter file") +SubClassOf( ) + +# Class: (NMR spectrum) + +AnnotationAssertion(obo:IAO_0000115 "tempdef: A frequency sorted array of the NMR signal frequency components. Nuclei with different resonance frequencies will show up as peaks at different corresponding frequencies in the spectrum, or 'lines'. + def: A NMR spectrum is a set of chemical shifts representing a chemical analysis. + synonym: NMR spectrum") +AnnotationAssertion(dce:source "as designated Experiment type on http://www.bmrb.wisc.edu/tools/choose_pulse_info.php ") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002007") +AnnotationAssertion(rdfs:label "NMR spectrum") +SubClassOf( ) + +# Class: (conversion to nmrML) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Conversion of a file format to Metabolomics Standards Initiative nmrData file format.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002008") +AnnotationAssertion(rdfs:label "conversion to nmrML") +SubClassOf( ) + +# Class: (conversion to JCAMP-DX) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Conversion of a file format to JCAMP-DX file format.") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002009") +AnnotationAssertion(rdfs:label "conversion to JCAMP-DX") +SubClassOf( ) + +# Class: (NMR solvent information) + +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002010") +AnnotationAssertion(rdfs:label "NMR solvent information") +SubClassOf( ) + +# Class: (pH) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "pH.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002011") +AnnotationAssertion(rdfs:label "pH") +SubClassOf( ) + +# Class: (chemical shift reference) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Chemical shift reference is a run attribute to designate the parts-per-million value of the peak used to reference a spectrum. It points to a fix chemical shift number, for examples 0 ppm for DSS or TSP. It can also have a calculated concentration, for examples 0.1 mM.") +AnnotationAssertion(doap:bug-database "https://github.com/nmrML/nmrML/issues/29#issue") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002013") +AnnotationAssertion(rdfs:label "chemical shift reference") +SubClassOf( ) + +# Class: (binned spectrum descriptor) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "A bin for a spectrum.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasExactSynonym "bucketed spectrum descriptor") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002014") +AnnotationAssertion(rdfs:label "binned spectrum descriptor") +SubClassOf( ) + +# Class: (bin label) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Bin label.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002015") +AnnotationAssertion(rdfs:label "bin label") +SubClassOf( ) + +# Class: (bin start) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Bin start.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:decimal") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002016") +AnnotationAssertion(rdfs:label "bin start") +SubClassOf( ) + +# Class: (bin end) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Bin end.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:decimal") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002017") +AnnotationAssertion(rdfs:label "bin end") +SubClassOf( ) + +# Class: (bin area) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Bin area.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:decimal") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002018") +AnnotationAssertion(rdfs:label "bin area") +SubClassOf( ) + +# Class: (assigned chemical compound name) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Name of metabolite.") +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:string") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002020") +AnnotationAssertion(rdfs:label "assigned chemical compound name") +SubClassOf( ) + +# Class: (assigned chemical compound concentration) + +AnnotationAssertion(Annotation(rdfs:label "The allowed value-type for this CV term.") oboInOwl:hasDbXref "value-type:xsd:decimal") +AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") +AnnotationAssertion(oboInOwl:id "NMR:1002021") +AnnotationAssertion(rdfs:label "assigned chemical compound concentration") +SubClassOf( ) + +# Class: (Hilbert transformation based scaling) + +AnnotationAssertion(rdfs:label "Hilbert transformation based scaling"@en) +SubClassOf( ) + +# Class: (optional part of NMR instrument) + +AnnotationAssertion(rdfs:comment "def: Part of an NMR instrument which is not cardinally important and hence optional / facultative for the proper intended function of the instrument. + synonym: optional part of NMR instrument + clsdel: ontologically there is no such universal which characteristic is a possible (!) state of being a part of something...") +AnnotationAssertion(rdfs:label "optional part of NMR instrument") +AnnotationAssertion(owl:versionInfo "TODO: Discuss \"obligatory_part_of\".") +SubClassOf( ) + +# Class: (autosampler) + +AnnotationAssertion(rdfs:comment "def: An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. + altdef: The autosampler is an automatic sample changer.") +AnnotationAssertion(rdfs:label "autosampler") +SubClassOf( ) + +# Class: (multiplicity feature) + +AnnotationAssertion(obo:IAO_0000119 "http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm") +AnnotationAssertion(oboInOwl:hasExactSynonym "multiplicity") +AnnotationAssertion(rdfs:label "multiplicity feature") +SubClassOf( ) + +# Class: (projected spectrum) + +AnnotationAssertion(rdfs:comment "tempdef: The data matrix a spectrum consists of can be projected from a higher dimension onto a lower dimension, e.g. a 3D NMR spectrum can be converted (projected) into a 2D NMR spectrum. + defprov: Daniel Schober") +AnnotationAssertion(rdfs:label "projected spectrum") +SubClassOf( ) + +# Class: (bucketed spectrum) + +AnnotationAssertion(oboInOwl:hasExactSynonym "binned spectrum") +AnnotationAssertion(rdfs:comment "def: A post-processed NMR spectrum in which the y-values of the datapoints have been summed based on periodic ranges of the x-axis values.") +AnnotationAssertion(rdfs:label "bucketed spectrum") +AnnotationAssertion(owl:versionInfo "TODO: has spectral post processing parameter") +SubClassOf( ) + +# Class: (peak-picked spectrum) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "peak-picked spectrum") +AnnotationAssertion(owl:versionInfo "TODO: has spectral post processing parameter.") +SubClassOf( ) + +# Class: (cardinal part of NMR instrument) + +AnnotationAssertion(rdfs:comment "def: A part of an NMR instrument which is cardinally important and hence obligatory and compulsatory for the proper intended function of the instrument. + synonym: cardinal part of NMR instrument") +AnnotationAssertion(rdfs:label "cardinal part of NMR instrument") +SubClassOf( ) + +# Class: (acquisition computer) + +AnnotationAssertion(rdfs:comment "def: A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers.") +AnnotationAssertion(rdfs:label "acquisition computer") +SubClassOf( ) + +# Class: (NMR probe) + +AnnotationAssertion(rdfs:comment "def: Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile “single point of failure” that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency. + altdef: The instrument that transmits and recieves radiofrequency to and from the NMR sample.") +AnnotationAssertion(rdfs:label "NMR probe") +SubClassOf( ) + +# Class: (console) + +AnnotationAssertion(rdfs:comment "def: A component of an NMR instrument that controls the activities of the other components.") +AnnotationAssertion(rdfs:label "console") +AnnotationAssertion(owl:versionInfo "TODO: same as or part of acquisition computer?") +SubClassOf( ) + +# Class: (number of acquisition data points) + +AnnotationAssertion(rdfs:comment "tempdef: The number of data points in a data set.") +AnnotationAssertion(rdfs:label "number of acquisition data points") +SubClassOf( ) + +# Class: (hadamard frequency) + +AnnotationAssertion(rdfs:comment "def: A frequency used during Hadamard encoding.") +AnnotationAssertion(rdfs:label "hadamard frequency") +SubClassOf( ) + +# Class: (projection axis) + +AnnotationAssertion(rdfs:comment "def: The axis onto which the spectrum was projected.") +AnnotationAssertion(rdfs:label "projection axis") +SubClassOf( ) + +# Class: (ninety degree pulse duration) + +AnnotationAssertion(oboInOwl:hasExactSynonym "90 degree pulse duration") +AnnotationAssertion(rdfs:label "ninety degree pulse duration") +AnnotationAssertion(skos:definition "The duration of the excitation pulse needed to rotate the magnetisation vector by 90 degrees.") +SubClassOf( ) + +# Class: (dwell time) + +AnnotationAssertion(rdfs:comment "def: A digital sampling interval. + alsprcls: time interval") +AnnotationAssertion(rdfs:label "dwell time") +SubClassOf( ) + +# Class: (sample temperature in autosampler) + +AnnotationAssertion(rdfs:comment "def: The temperature of an item of analysis material whilst in an autosampler.") +AnnotationAssertion(rdfs:label "sample temperature in autosampler") +SubClassOf( ) + +# Class: (sample temperature in magnet) + +AnnotationAssertion(rdfs:comment "def: The temperature of an NMR sample whilst in the magnet of an NMR instrument.") +AnnotationAssertion(rdfs:label "sample temperature in magnet") +SubClassOf( ) + +# Class: (irradiation frequency) + +AnnotationAssertion(rdfs:comment "def: The frequency of the RF radiation used to irradiate an NMR sample.") +AnnotationAssertion(rdfs:label "irradiation frequency") +SubClassOf( ) + +# Class: (field strength) + +AnnotationAssertion(rdfs:comment "def: The intensity of an electric, magnetic, or other field.") +AnnotationAssertion(rdfs:label "field strength") +SubClassOf( ) + +# Class: (spinning rate) + +AnnotationAssertion(rdfs:comment "def: The rate at which an item of analysis material is spun.") +AnnotationAssertion(rdfs:label "spinning rate") +SubClassOf( ) + +# Class: (decoupled nucleus flag) + +AnnotationAssertion(rdfs:comment "def: An indication of whether the nucleus being studied is the acquitsition nucleus.") +AnnotationAssertion(rdfs:label "decoupled nucleus flag") +SubClassOf( ) + +# Class: (buffer information) + +AnnotationAssertion(rdfs:comment "def: A compound added to a sample to alter its pH value.") +AnnotationAssertion(rdfs:label "buffer information") +SubClassOf( ) + +# Class: (calibration compound) + +AnnotationAssertion(oboInOwl:hasExactSynonym "reference compound") +AnnotationAssertion(oboInOwl:hasExactSynonym "reference standard") +AnnotationAssertion(rdfs:comment "def: The compound that produced the peak used to reference a spectrum during data pre-processing.") +AnnotationAssertion(rdfs:label "calibration compound") +SubClassOf( ) + +# Class: (chemical shift standard) + +AnnotationAssertion(dce:source "http://www.nmrnotes.org/NMRPages/refcomps.html") +AnnotationAssertion(doap:bug-database "https://github.com/nmrML/nmrML/issues/31") +AnnotationAssertion(doap:bug-database "https://github.com/nmrML/nmrML/issues/33") +AnnotationAssertion(oboInOwl:hasExactSynonym "chemical shift reference compound") +AnnotationAssertion(rdfs:comment "def: A compound that is added to an NMR sample to enable the alignment of spectra. The power of NMR is that for most nuclei the NMR frequency changes very slightly with different molecular environment or chemical bonding. These shifts are very small, on the order of 1 part in 10+9. This is referred to as \"Chemical Shift.\" Tables of chemical shifts are tabulated and used to determine molecular structure. Combining NMR chemical shift information with other NMR information such as peak integration, coupling constants and Nuclear Overhauser Enhancement (NOE) can result in complete three-dimensional molecular structures of molecules in solution without using X-ray crystallography.") +AnnotationAssertion(rdfs:label "chemical shift standard") +SubClassOf( ) + +# Class: (quality check compound signal) + +AnnotationAssertion(rdfs:comment "def: The compound that produced a peak that is measured to assess the quality of a data set.") +AnnotationAssertion(rdfs:label "quality check compound signal") +SubClassOf( ) + +# Class: (NMR pulse sequence) + +AnnotationAssertion(dce:source "http://www.bmrb.wisc.edu/tools/choose_pulse_info.php") +AnnotationAssertion(doap:bug-database "https://github.com/nmrML/nmrML/issues/40") +AnnotationAssertion(rdfs:comment "def: A sequence of excitation pulses.") +AnnotationAssertion(rdfs:label "NMR pulse sequence") +AnnotationAssertion(skos:editorialNote "May later import from + +http://purl.obolibrary.org/obo/CHMO_0001841") +AnnotationAssertion(skos:editorialNote "See also http://www.jcamp-dx.org/protocols/NMR%20Pulse%20Sequences%20PAC%2079(11)%20pp1748-1764%202001.pdf") +SubClassOf( ) + +# Class: (frequency domain data processing) + +AnnotationAssertion(oboInOwl:hasExactSynonym "nmr-spectrum data processing") +AnnotationAssertion(oboInOwl:hasExactSynonym "post-FT data processing") +AnnotationAssertion(rdfs:comment "def: Automatic or manual procedures performed upon pre-processed NMR data sets that aim to summarise them or annotate them with speculative values.") +AnnotationAssertion(rdfs:label "frequency domain data processing"@en) +SubClassOf( ) + +# Class: (time domain data processing) + +AnnotationAssertion(oboInOwl:hasExactSynonym "pre-FT data processing") +AnnotationAssertion(rdfs:comment "def: The post acquisition process of producing or refining a spectrum from raw data. + defprov: Daniel Schober") +AnnotationAssertion(rdfs:label "time domain data processing"@en) +SubClassOf( ) + +# Class: (NMR data processing) + +AnnotationAssertion(rdfs:comment "def: A data transformation that converts an NMR input data set into an output data set in a tracable and useful manner.") +AnnotationAssertion(rdfs:label "NMR data processing") +SubClassOf( ) + +# Class: (non-fourier FID transformation) + +AnnotationAssertion(rdfs:comment "tempdef: A non FT based method for converting from the time to the frequency domain.") +AnnotationAssertion(rdfs:label "non-fourier FID transformation") +AnnotationAssertion(owl:versionInfo "TODO:Exclusion guided definition.") +SubClassOf( ) + +# Class: (data encoding) + +AnnotationAssertion(doap:bug-database "https://github.com/nmrML/nmrML/issues/37") +AnnotationAssertion(rdfs:comment "tempdef: A data processing which alteres a data file for a specific purpose. + defprov: Daniel Schober") +AnnotationAssertion(rdfs:label "data encoding") +SubClassOf( ) + +# Class: (G matrix fourier transform projection) + +AnnotationAssertion(rdfs:comment "tempdef:GFT NMR allows for rapid multidimensional FT NMR spectral information gathering, avoiding sampling limitations without compromising on the precision of chemicalshift. + defprov: ttp://www.nsm.buffalo.edu/Research/GFT/szyperski_publications_1st_page/Szyperski%2067.pdf + synonym: GFT-projection") +AnnotationAssertion(rdfs:label "G matrix fourier transform projection") +SubClassOf( ) + +# Class: (time proportional phase incrementation) + +AnnotationAssertion(rdfs:comment "defneed + synonym: TPPI") +AnnotationAssertion(rdfs:label "time proportional phase incrementation") +SubClassOf( ) + +# Class: (states-time proportional phase incrementation) + +AnnotationAssertion(rdfs:comment "def: A method for quadrature detection. + synonym: S-TPPI") +AnnotationAssertion(rdfs:label "states-time proportional phase incrementation") +SubClassOf( ) + +# Class: (Hadamard encoding) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "Hadamard encoding") +SubClassOf( ) + +# Class: (Frydman encoding) + +AnnotationAssertion(dce:source "http://www.magnet.fsu.edu/library/publications/NHMFL_Publication-6859.pdf") +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "Frydman encoding") +SubClassOf( ) + +# Class: (echo anti-echo coherence selection) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "echo anti-echo coherence selection") +SubClassOf( ) + +# Class: (NMR instrument) + +AnnotationAssertion(rdfs:comment "def: An Instrument which is used to carry out a NMR analysis of some sample. + synonym: NMR instrument") +AnnotationAssertion(rdfs:label "NMR instrument") +SubClassOf( ) + +# Class: (NMR instrument acquisition parameter set) + +AnnotationAssertion(rdfs:comment "def: The list of parameters that describe the instrument settings used for the acquisition of a spectrum. + altdef: The set of variables dependent on a given pulse sequence that will be optimised in order to acquire a spectrum. + synonym: NMR instrument acquisition parameter set") +AnnotationAssertion(rdfs:label "NMR instrument acquisition parameter set") +SubClassOf( ) + +# Class: (data transformation) + +AnnotationAssertion(oboInOwl:hasBroadSynonym "method") +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "data transformation"@en) +AnnotationAssertion(owl:versionInfo "altspcls: process ???") +SubClassOf( obo:BFO_0000015) + +# Class: (normalisation) + +AnnotationAssertion(obo:IAO_0000117 "Philippe Rocca Serra") +AnnotationAssertion(obo:IAO_0000119 "http://pubs.acs.org/doi/pdf/10.1021/ac0519312 + +10.1021/ac0519312 + +Scaling and Normalization Effects in NMR Spectroscopic Metabonomic Data Sets + +Andrew Craig , Olivier Cloarec , Elaine Holmes , Jeremy K. Nicholson , and John C. Lindon * +Biological Chemistry, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ U.K.") +AnnotationAssertion(obo:IAO_0000119 "http://stats.stackexchange.com/questions/35591/normalization-vs-scaling") +AnnotationAssertion(rdfs:label "normalisation") +AnnotationAssertion(skos:definition "normalization is a data transformation process which aims at making data seem roughly normally distributied by applying a mathematical function, which is most of time a continuous function. +This is a row operation that is applied to the data from each sample and comprises methods to make the data from all samples directly comparable with each other. A common use is to remove or minimize the effects of variable dilution of the samples.") +SubClassOf( ) + +# Class: (pre-acquisition water suppression) + +AnnotationAssertion(rdfs:comment "tempdef: A technique used to suppress the water resonance peak in a spectrum. Suppression of the strong solvent signal is necessary in order to obtain high signal to noise for the peaks of the sample under investiogation, e.g. protein peaks. + defprov: Daniel Schober") +AnnotationAssertion(rdfs:label "pre-acquisition water suppression") +SubClassOf( ) + +# Class: (window function for apodization) + +AnnotationAssertion(obo:IAO_0000115 "A function applied to a FID to increase the signal-to-noise ratio or the resolution.") +AnnotationAssertion(dce:source "http://www.uwyo.edu/wheelernmr/nmr/window_functions.pdf") +AnnotationAssertion(doap:bug-database "https://github.com/nmrML/nmrML/issues/39") +AnnotationAssertion(doap:bug-database "https://github.com/nmrML/nmrML/issues/67") +AnnotationAssertion(oboInOwl:hasExactSynonym "apodization function") +AnnotationAssertion(rdfs:label "window function for apodization") +SubClassOf( ) + +# Class: (exponential multiplication window function) + +AnnotationAssertion(obo:IAO_0000115 "The exponential function used to multiply a FID by to produce a desitred amount of line broadening.") +AnnotationAssertion(oboInOwl:hasExactSynonym "exponential apodization") +AnnotationAssertion(rdfs:comment "Functional form: + em(x_i) = exp(-pi*i*lb) + Parameters: + * data Array of spectral data. + * lp Exponential line broadening. + * inv Set True for inverse apodization.") +AnnotationAssertion(rdfs:label "exponential multiplication window function") +SubClassOf( ) + +# Class: (Gaussian window function) + +AnnotationAssertion(oboInOwl:hasExactSynonym "gaussian broadening") +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "Gaussian window function") +SubClassOf( ) + +# Class: (sine window function) + +AnnotationAssertion(oboInOwl:hasExactSynonym "sine") +AnnotationAssertion(oboInOwl:hasExactSynonym "sine bell window function") +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "sine window function") +SubClassOf( ) + +# Class: (sine squared window) + +AnnotationAssertion(oboInOwl:hasExactSynonym "QSINE") +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "sine squared window") +SubClassOf( ) + +# Class: (spectral denoising) + +AnnotationAssertion(rdfs:comment "def: A method for eliminating or reducing the noise in a spectrum.") +AnnotationAssertion(rdfs:label "spectral denoising") +SubClassOf( ) + +# Class: (baseline correction) + +AnnotationAssertion(rdfs:comment "def: A method of flattening the baseline of a spectrum.") +AnnotationAssertion(rdfs:label "baseline correction") +SubClassOf( ) + +# Class: (spectral projection) + +AnnotationAssertion(rdfs:comment "A method of spectral projection.") +AnnotationAssertion(rdfs:label "spectral projection") +SubClassOf( ) + +# Class: (maximum intensity projection) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "maximum intensity projection") +SubClassOf( ) + +# Class: (summation projection) + +AnnotationAssertion(rdfs:comment "def: .A projection method that sums the intensities of a pre-processed 2D J-resolved NMR spectrum to obtain a projected spectrum. + altdef: The adding of spectra together to produce a composite avergaed spectrum.") +AnnotationAssertion(rdfs:label "summation projection") +SubClassOf( ) + +# Class: (zero order phase correction) + +AnnotationAssertion(rdfs:comment "def: A parameter used to mix real and imaginary part of an NMR spectrum that the real part of the spectrum is in pure absorption mode. + altdef: The number of degrees that a central peak must be moved in order to achieve an absorptive mode line width.") +AnnotationAssertion(rdfs:label "zero order phase correction") +SubClassOf( ) + +# Class: (first order phase correction) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "first order phase correction") +SubClassOf( ) + +# Class: (symmetrisation) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "symmetrisation") +SubClassOf( ) + +# Class: (acquisition nucleus) + +AnnotationAssertion(rdfs:comment "def: The nucleus of an element or isotope that is being studied during an NMR analysis. Common NMR requirements include direct 1D and 2D proton-only NMR, direct observation of 13C NMR with 1H decoupling, direct observation of other nuclei such as 19F, 31P, 29Si, 31P, 27Al, and 15N (with or without 1H decoupling), triple resonance NMR (especially inverse triple resonance such as 1H observe, 13C and 15N decouple), and inverse 2D and 3D experiments such as HMQC and HMBC.") +AnnotationAssertion(rdfs:label "acquisition nucleus") +SubClassOf( obo:BFO_0000030) + +# Class: (quality check peak feature) + +AnnotationAssertion(rdfs:comment "def: A feature of a peak that is measured to assess the quality of a data set.") +AnnotationAssertion(rdfs:label "quality check peak feature") +SubClassOf( ) + +# Class: (number of scans) + +AnnotationAssertion(rdfs:comment "def: The number of repeat scans performed and summed to create the data set for an NMR sample.") +AnnotationAssertion(rdfs:label "number of scans") +SubClassOf( ) + +# Class: (number of steady state scans) + +AnnotationAssertion(rdfs:comment "def: The number of scans whose data is not summed to create the data set for an NMR sample, but that are carried out to establish the steady-state of relaxation for the nuclei.") +AnnotationAssertion(rdfs:label "number of steady state scans") +SubClassOf( ) + +# Class: (atom environment encoding) + +AnnotationAssertion(rdfs:comment "def: A scheme for producing a numerical representation of the environment of an atom.") +AnnotationAssertion(rdfs:label "atom environment encoding") +SubClassOf( ) + +# Class: (relaxation delay) + +AnnotationAssertion(rdfs:comment "def: The delay between repeat scans to allow nuclei to relax back to their steady state.") +AnnotationAssertion(rdfs:label "relaxation delay") +SubClassOf( ) + +# Class: (x-axis unit) + +AnnotationAssertion(rdfs:comment "def: The units of measure for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum. + altdef: The units used to represent either time domain (for a FID) or the frequency domain (for a spectrum).") +AnnotationAssertion(rdfs:label "x-axis unit") +SubClassOf( ) + +# Class: (y-axis unit) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "y-axis unit") +SubClassOf( ) + +# Class: (additional axis unit) + +AnnotationAssertion(rdfs:comment "def: The unit of measurement of the second dimension of a 2D NMR dataset.") +AnnotationAssertion(rdfs:label "additional axis unit") +SubClassOf( ) + +# Class: (x start value) + +AnnotationAssertion(rdfs:comment "def: The starting value for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum. + altdef: The initial time or frequency a FID or spectrum is recorded from.") +AnnotationAssertion(rdfs:label "x start value") +SubClassOf( ) + +# Class: (x end value) + +AnnotationAssertion(rdfs:comment "tempdef: The end value for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum.") +AnnotationAssertion(rdfs:label "x end value") +SubClassOf( ) + +# Class: (window function parameter) + +AnnotationAssertion(rdfs:comment "def: A parameter to a window function.") +AnnotationAssertion(rdfs:label "window function parameter") +SubClassOf( ) + +# Class: (line broadening) + +AnnotationAssertion(obo:IAO_0000117 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 "http://www.chem.wisc.edu/areas/reich/nmr/08-tech-01-relax.htm. + +Hans J. Reich 2015, University of Wisconsin") +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "line broadening") +AnnotationAssertion(skos:definition "line broadening is a process resulting in spectral peak signal becoming hard to interpret and analysed. Line broadening is affected by spin-spin relaxation and/or spin-lattice relaxation processes. +When relaxation is very fast, NMR lines are broad, J-coupling may not be resolved or the signal may even be difficult or impossible to detect. +The maximum repetition rate during acquisition of an NMR signal is governed by T1 - short T1 means the magnetization recovers more rapidly, and a spectrum can be acquired in less time. +Line broadening may be caused by: +Sample inhomogeneity (poor mixing. solid particles), Temperature gradients across sample, Paramagnetic impurities.") +SubClassOf( ) + +# Class: (line sharpening) + +AnnotationAssertion(obo:IAO_0000117 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 "http://www.chem.wisc.edu/areas/reich/nmr/08-tech-01-relax.htm. + +Hans J. Reich 2015, University of Wisconsin") +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "line sharpening") +AnnotationAssertion(skos:definition "line sharpening is a data transformation process inverse to that of line broadening, which aims to improve the quality of the signal being acquired and being analyzed in order to obtain clear, sharp peaks, in turn making interpretation easier. +Line sharpening can be optimized during data acquisition or performed during data analysis by applied digital processing and filtering.") +SubClassOf( ) + +# Class: (parameter) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "parameter") +SubClassOf( obo:BFO_0000031) + +# Class: (NMR spectral projection parameter set) + +AnnotationAssertion(rdfs:comment "def: The data processing parameters that describe a method of translating a 2D NMR pre-processed spectrum into a 1D NMR spectrum. + synonym: NMR spectral projection parameter set") +AnnotationAssertion(rdfs:label "NMR spectral projection parameter set") +SubClassOf( ) + +# Class: (NMR data post-processing parameter set) + +AnnotationAssertion(rdfs:comment "def: A description of the post-processing strategy used to convert a pre-processed NMR spectrum into a suitable data format for chemometric analysis. + synonym: NMR spectrum post-processing parameter set") +AnnotationAssertion(rdfs:label "NMR data post-processing parameter set") +AnnotationAssertion(owl:versionInfo "TODO: altsprcls: process, not clear wether set is plural (list) or process.") +SubClassOf( ) + +# Class: (NMR quality check parameter set) + +AnnotationAssertion(rdfs:comment "tempdef: A nuclear magnetic resonance spectroscopy quality check parameter set is a parameter set used for the quality check method for an NMR analysis + synonym: NMR quality check parameter set") +AnnotationAssertion(rdfs:label "NMR quality check parameter set") +SubClassOf( ) + +# Class: (post-acquisition water suppression) + +AnnotationAssertion(oboInOwl:hasExactSynonym "excitation sculpting") +AnnotationAssertion(rdfs:comment "tempdef: A data processing technique used to suppress the water peak in a spectrum in order to get clearer results. + defprov: Daniel Schober") +AnnotationAssertion(rdfs:label "post-acquisition water suppression") +SubClassOf( ) + +# Class: (hankel singular value decomposition) + +AnnotationAssertion(rdfs:comment "def: This Method removes the residual water and its side lobes, thereby reducing the baseline for the metabolites of interest and allowing subsequent data analysis using more sophisticated nonlinear least squares algorithms. + synonym: HSVD") +AnnotationAssertion(rdfs:label "hankel singular value decomposition") +SubClassOf( ) + +# Class: (convolution) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "convolution") +SubClassOf( ) + +# Class: (polynomial fitting) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "polynomial fitting") +SubClassOf( ) + +# Class: (WaveWat) + +AnnotationAssertion(rdfs:comment "def: A computational method that archieves water suppression via wavlet multi resolution analysis.") +AnnotationAssertion(rdfs:label "WaveWat") +SubClassOf( ) + +# Class: (NMR data pre-processing parameter set) + +AnnotationAssertion(rdfs:comment "defneed + synonym: NMR data pre-processing parameter set") +AnnotationAssertion(rdfs:label "NMR data pre-processing parameter set") +SubClassOf( ) + +# Class: (NMR quality check) + +AnnotationAssertion(rdfs:comment "def: The process of ensuring the quality of the raw data that results from an NMR analysis. + synonym: NMR quality check") +AnnotationAssertion(rdfs:label "NMR quality check") +SubClassOf( ) + +# Class: (reference) + +AnnotationAssertion(rdfs:comment "def: A reference is a label which refers to data elsewhere, as opposed to containing the data itself. Accessing the value that a reference refers to is called dereferencing it. References are fundamental in constructing many data structures and in exchanging information between different parts of programs and databases.") +AnnotationAssertion(rdfs:label "reference") +SubClassOf( obo:BFO_0000031) + +# Class: (FID file) + +AnnotationAssertion(oboInOwl:hasExactSynonym "FID file reference") +AnnotationAssertion(rdfs:comment "def: A reference to a file containing the raw FID. + synonym: FID file reference") +AnnotationAssertion(rdfs:label "FID file") +SubClassOf( ) + +# Class: (pulse sequence literature reference) + +AnnotationAssertion(rdfs:comment "def: A reference to a description of a pulse sequence in the literature.") +AnnotationAssertion(rdfs:label "pulse sequence literature reference") +SubClassOf( ) + +# Class: (shaped pulse file) + +AnnotationAssertion(rdfs:comment "def: A reference to a file containing a specfication of the shape of an excitation pulse.") +AnnotationAssertion(rdfs:label "shaped pulse file") +SubClassOf( ) + +# Class: (pulse sequence file) + +AnnotationAssertion(rdfs:comment "def: A reference to a file containing a specification of a pulse sequence.") +AnnotationAssertion(rdfs:label "pulse sequence file") +SubClassOf( ) + +# Class: (processing parameter file) + +AnnotationAssertion(rdfs:comment "def: A reference to a file of data pre-processing parameters produced by the machine.") +AnnotationAssertion(rdfs:label "processing parameter file") +SubClassOf( ) + +# Class: (NMR sample identifier) + +AnnotationAssertion(rdfs:comment "PRS: rename 'reference' to 'identifier'"@en) +AnnotationAssertion(rdfs:comment "def: A reference to information on the provenance of the NMR sample. + synonym: NMR sample reference") +AnnotationAssertion(rdfs:label "NMR sample identifier") +SubClassOf( ) + +# Class: (NMR quality check descriptor) + +AnnotationAssertion(rdfs:comment "def: A result of an NMR quality check. + synonym: NMR quality check result") +AnnotationAssertion(rdfs:label "NMR quality check descriptor") +SubClassOf( ) + +# Class: (NMR sample) + +AnnotationAssertion(rdfs:comment "def: A sample that has been prepared for chemical analysis by NMR. NMR samples are usually liquid solutions contained in glass tubes. NMR solution sample volume ranges from 50ul to 5ml depending on the NMR probe. Sample concentrations of solute for 1H NMR are usually in the range of 100ug to 5g, with 10 to 50mg being typical. NMR is not a chemical trace analysis technique. The NMR signal of solids and gases can be recorded but to measure solid-state NMR additional specialized hardware is required. + synonym: NMR sample") +AnnotationAssertion(rdfs:label "NMR sample") +SubClassOf( ) + +# Class: (sample introduction parameter) + +AnnotationAssertion(rdfs:comment "tempdef: A sample introduction parameter is a parameter that describes the particular method of introducing the sample under investigation into the NMR instrument.") +AnnotationAssertion(rdfs:label "sample introduction parameter") +SubClassOf( ) + +# Class: (magic angle spinning rotor) + +AnnotationAssertion(rdfs:comment "defneed + synonym: MAS rotor") +AnnotationAssertion(rdfs:label "magic angle spinning rotor") +SubClassOf( ) + +# Class: (flow probe) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "flow probe") +SubClassOf( ) + +# Class: (NMR sample tube) + +AnnotationAssertion(obo:IAO_0000115 "The sample-tube holds the NMR sample and sits in the NMR probe. It is usually a glass tube of 5-20mm diameter.") +AnnotationAssertion(dce:source "http://en.wikipedia.org/wiki/NMR_tube") +AnnotationAssertion(doap:bug-database "https://github.com/nmrML/nmrML/issues/54") +AnnotationAssertion(oboInOwl:hasExactSynonym "sample tube") +AnnotationAssertion(rdfs:comment "sortal dimensions are Vendor, Size (Diameter, length), Material (glass, quarz, pyrex ...), Frequency, Concentricity, OD and ID") +AnnotationAssertion(rdfs:label "NMR sample tube") +SubClassOf( ) + +# Class: (spectrum pre-processing software) + +AnnotationAssertion(rdfs:comment "def: A software artifact used during data pre-processing.") +AnnotationAssertion(rdfs:label "spectrum pre-processing software") +SubClassOf( ) + +# Class: (spectrum post-processing software) + +AnnotationAssertion(rdfs:comment "def: A software artifact used during spectral post-processing.") +AnnotationAssertion(rdfs:label "spectrum post-processing software") +SubClassOf( ) + +# Class: (peak picking) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "peak picking") +SubClassOf( ) + +# Class: (bucketing) + +AnnotationAssertion(oboInOwl:hasExactSynonym "binning") +AnnotationAssertion(rdfs:comment "def: A post-processing method that divides a pre-processed NMR spectrum into a series of buckets (or bins) along the x-axis, and then integrates the spectral intensity within each bucket. + altdef: A type of automated integration which occurs across pre-defined regions for a spectrum.") +AnnotationAssertion(rdfs:comment "for bucket parameters see 'binned spectrum descriptor'") +AnnotationAssertion(rdfs:label "bucketing") +SubClassOf( ) + +# Class: (presat pulse sequence) + +AnnotationAssertion(oboInOwl:hasExactSynonym "presaturation of the solvent resonance") +AnnotationAssertion(rdfs:comment "defneed + synonym: presaturation") +AnnotationAssertion(rdfs:label "presat pulse sequence") +SubClassOf( ) + +# Class: (water suppression enhanced through T1 effects) + +AnnotationAssertion(rdfs:comment "tempdef: An improved water-suppression technique called WET (water suppression enhanced through T1 effects), developed from a Bloch equation analysis of the longitudinal magnetization over the T1 and B1 ranges of interest, achieves T1- and B1-insensitive suppression with four RF pulses, each having a numerically optimized flip angle. Once flip angles have been optimized for a given sequence, time-consuming flip-angle adjustments during clinical examinations are eliminated. + defprov: Daniel Schober + synonym: WET") +AnnotationAssertion(rdfs:label "water suppression enhanced through T1 effects") +AnnotationAssertion(skos:altLabel "WET"@en) +SubClassOf( ) + +# Class: (nuclear overhauser and exchange spectroscopy-presat) + +AnnotationAssertion(oboInOwl:hasExactSynonym "NOESY presat") +AnnotationAssertion(rdfs:comment "tempdef: The presat for an nuclear overhauser and exchange spectroscopy experiment. A 2D method used to map NOE correlations between protons within a molecule. The nuclear Overhauser effect (NOE) causes changes in peak areas, as a secondary effect of decoupling. + defprov: Daniel Schober + synonym: NOESY-presat") +AnnotationAssertion(rdfs:label "nuclear overhauser and exchange spectroscopy-presat") +SubClassOf( ) + +# Class: (watergate) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "watergate") +SubClassOf( ) + +# Class: (coherence pathway rejection) + +AnnotationAssertion(rdfs:comment "tempdef: A water suppression method which is used to suppress the natural water signal in a gradient selection experiment (e.g. echo/antiecho), where the water coherence is not \"refocused\" by the refocus gradient (therefore, is not selected). + defprov: Daniel Schober") +AnnotationAssertion(rdfs:label "coherence pathway rejection") +SubClassOf( ) + +# Class: (flip-back watergate) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "flip-back watergate") +SubClassOf( ) + +# Class: (jump and return pulse sequence) + +AnnotationAssertion(rdfs:comment "tempdef: A jump and return pulse sequence method is a water suppression method that uses a defined pulse sequence to make fast exchanging protons visible.") +AnnotationAssertion(rdfs:label "jump and return pulse sequence") +SubClassOf( ) + +# Class: (jump and return 1-1) + +AnnotationAssertion(rdfs:comment "tempdef: A jump and return 1-1 pulse sequence method is a jump and return method that uses one 90 degree pulse and one 90 degree return puls to make fast exchanging protons visible, first described by Plateau,P. and Gueron,M. (1982) J. Am. Chem. Soc., 104, 7310–7311. Compared to the 1-3-3-1 method it has a lower receiver gain and the dispersive tail of water interferes with the signals of interest.") +AnnotationAssertion(rdfs:label "jump and return 1-1") +SubClassOf( ) + +# Class: (jump and return 1-3-3-1) + +AnnotationAssertion(rdfs:comment "tempdef:A jump and return 1-3-3-1 pulse sequence method is a jump and return method that uses a 1-3-3-1 pulse sequence to make fast exchanging protons visible. Compared to the 1-1 method it has better water suppression (higher receiver gain) capabilities, but with offset-dependent phase distortion (unsuitable for 2D).") +AnnotationAssertion(rdfs:label "jump and return 1-3-3-1") +SubClassOf( ) + +# Class: (1D spectrum) + +AnnotationAssertion(rdfs:comment "defneed + synonym: 1D spectrum") +AnnotationAssertion(rdfs:label "1D spectrum") +SubClassOf( ) + +# Class: (2D spectrum) + +AnnotationAssertion(rdfs:comment "defneed + synonym: 2D spectrum") +AnnotationAssertion(rdfs:label "2D spectrum") +SubClassOf( ) + +# Class: (1D NMR acquisition parameter set) + +AnnotationAssertion(rdfs:comment "defneed + synonym: 1D NMR acquisition parameter set") +AnnotationAssertion(rdfs:label "1D NMR acquisition parameter set") +SubClassOf( ) + +# Class: (2D NMR acquisition parameter set) + +AnnotationAssertion(rdfs:comment "defneed + synonym: 2D NMR acquisition parameter set") +AnnotationAssertion(rdfs:label "2D NMR acquisition parameter set") +SubClassOf( ) + +# Class: (carr purcell meiboom gill pulse sequence) + +AnnotationAssertion(rdfs:comment "tempdef: A modification of Carr-Purcell RF pulse sequence with 90° phase shift in the rotating frame of reference between the 90° pulse and the subsequent 180° pulses to reduce accumulating effects of imperfections in the 180° pulses. Suppression of effects of pulse error accumulation can alternatively be achieved by alternating phases of the 180° pulses by 180°. + defprov: Daniel Schober + synonym: 1D CPMG") +AnnotationAssertion(rdfs:label "carr purcell meiboom gill pulse sequence") +AnnotationAssertion(skos:altLabel "CPMG"@en) +SubClassOf( ) + +# Class: ( total correlation spectroscopy pulse sequence) + +AnnotationAssertion(oboInOwl:hasExactSynonym "TCOSY pulse sequence") +AnnotationAssertion(rdfs:comment "tempdef: Total Correlation Spectroscopy. A 2D homonuclear correlation experiment used to analyse scalar (J) coupling networks between protons. TOCSY is able to relay magnetisation between spins, A-B-C-D.., and can therefore show correlations amongst spins that are not directly coupled (eg A-C and A-D) but exist within the same spin system. + defprov: Daniel Schober + synonym:2D TOCSY pulse sequence") +AnnotationAssertion(rdfs:label " total correlation spectroscopy pulse sequence") +SubClassOf( ) + +# Class: (1D pulse sequence) + +AnnotationAssertion(rdfs:comment "def: One dimensional (referring to a FID, pre-processed spectrum, or post-processed spectrum). + synonym: 1D") +AnnotationAssertion(rdfs:label "1D pulse sequence") +SubClassOf( ) + +# Class: (J-resolved pulse sequence) + +AnnotationAssertion(rdfs:comment "tempdef: In 1D NMR, as the multiplets from different chemically shifted nuclei overlap, spectral assignments become too difficult. In order to resolve the chemical shift and spin-spin coupling parameters along the different axis, 2D and 3D J-resolved NMR spectroscopies are used. + defprov: Daniel Schober + synonym: 2D J-resolved") +AnnotationAssertion(rdfs:label "J-resolved pulse sequence") +SubClassOf( ) + +# Class: (hadamard total correlation spectroscopy pulse sequence) + +AnnotationAssertion(rdfs:comment "defneed + synonym: 2D hadamard TOCSY") +AnnotationAssertion(rdfs:label "hadamard total correlation spectroscopy pulse sequence") +SubClassOf( ) + +# Class: (diffusion edited pulse sequence) + +AnnotationAssertion(rdfs:comment "defneed + synonym: 1D diffusion edited") +AnnotationAssertion(rdfs:label "diffusion edited pulse sequence") +SubClassOf( ) + +# Class: (NMR magnet) + +AnnotationAssertion(rdfs:comment "def: A magnet which induces a certain frequency (MHz) and which has a certain bore diameter. + altdef: The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss.") +AnnotationAssertion(rdfs:label "NMR magnet") +SubClassOf( ) + +# Class: (Bruker NMR magnet) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "Bruker NMR magnet") +SubClassOf( ) + +# Class: (UltraShield) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "UltraShield") +SubClassOf( ) + +# Class: (Ultrastabilized) + +AnnotationAssertion(rdfs:label "Ultrastabilized") +SubClassOf( ) + +# Class: (US 2) + +AnnotationAssertion(rdfs:label "US 2") +AnnotationAssertion(owl:versionInfo "??? How to model \"hoch 2\"?") +SubClassOf( ) + +# Class: (UltraShield Plus) + +AnnotationAssertion(rdfs:label "UltraShield Plus") +SubClassOf( ) + +# Class: (Bruker CryoProbe) + +AnnotationAssertion(rdfs:comment "def: The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis: + Significant S/N gains (with moderately salty samples also) + Short pulse widths + Short ring down times + Linear behavior in power response + Gradient capability + CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and higher + All high resolution probes have a lock circuit + All high resolution probes have Z-gradient + defprov: Bruker website") +AnnotationAssertion(rdfs:label "Bruker CryoProbe") +SubClassOf( ) +SubClassOf( ) + +# Class: (high resolution magic angle spin probe) + +AnnotationAssertion(rdfs:comment "def: Samples that are neither solid nor liquid, being of biological, chemical, and/or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Bruker’s high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject/insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g., 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used. + defprov: Bruker website + altdef: High resolution MAS (hr-MAS) provides an easy means of obtaining high resolution spectra for a variety of samples that would otherwise result in poorly resolved spectra. The addition of an hr-MAS probe and a MAS pneumatic unit to a standard high resolution spectrometer is all that is needed to open the gate to the world of hr-MAS spectroscopy and gain access to a vast amount of highly interesting samples. + synonyms: High resolution MAS, hr-MAS") +AnnotationAssertion(rdfs:label "high resolution magic angle spin probe") +SubClassOf( ) + +# Class: (solid magic angle spinning probe) + +AnnotationAssertion(rdfs:comment "def: Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei. + defprov: Bruker website + synonym: solid MAS probe") +AnnotationAssertion(rdfs:label "solid magic angle spinning probe") +SubClassOf( ) + +# Class: (1mm MicroProbe) + +AnnotationAssertion(rdfs:comment "def: Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include: + up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount) + excellent solvent suppression properties + virtually no salt effect + discrete samples in tubes that can be sealed and stored + automation accessory for sample preparation and handling available + defprov: Bruker website") +AnnotationAssertion(rdfs:label "1mm MicroProbe") +SubClassOf( ) + +# Class: (flow high resolution probe) + +AnnotationAssertion(rdfs:comment "def: Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes. + defprov: Bruker website + synonym: flow HR-probe") +AnnotationAssertion(rdfs:label "flow high resolution probe") +SubClassOf( ) + +# Class: (NMR instrument parameter set) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "NMR instrument parameter set") +SubClassOf( ) + +# Class: (AVANCE II spectrometer) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "AVANCE II spectrometer") +AnnotationAssertion(owl:versionInfo "TODO: May need no definition") +SubClassOf( ) + +# Class: (Bruker NMR instrument) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "Bruker NMR instrument") +AnnotationAssertion(foaf:homepage "https://www.bruker.com/de/products/mr/nmr.html") +SubClassOf( ) + +# Class: (Metabolic Profiler instrument) + +AnnotationAssertion(rdfs:comment "For metabolism studies, and analysis of complex mixtures.") +AnnotationAssertion(rdfs:label "Metabolic Profiler instrument") +SubClassOf( ) + +# Class: (Hyphenated NMR instrument) + +AnnotationAssertion(rdfs:comment "NMR Instruments using hyphenated analytical techniques combining mass spectrometry and chromatograph.") +AnnotationAssertion(rdfs:label "Hyphenated NMR instrument") +SubClassOf( ) + +# Class: (Capillary LC-NMR) + +AnnotationAssertion(rdfs:label "Capillary LC-NMR") +SubClassOf( ) + +# Class: (NMR Case) + +AnnotationAssertion(rdfs:comment "def: The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats. + defprov: Bruker website") +AnnotationAssertion(rdfs:label "NMR Case") +SubClassOf( ) + +# Class: (NMR tube washing system) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "NMR tube washing system") +SubClassOf( ) + +# Class: (Bruker AutoClean) + +AnnotationAssertion(rdfs:comment "def: In today's fast-paced research environment, NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean™ system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material. + defprov: Bruker website") +AnnotationAssertion(rdfs:label "Bruker AutoClean") +SubClassOf( ) + +# Class: (Bruker BEST NMR) + +AnnotationAssertion(rdfs:comment "def: The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data. + defprov: Bruker website + synonym: Bruker Efficient Sample Transfer NMR") +AnnotationAssertion(rdfs:label "Bruker BEST NMR") +SubClassOf( ) + +# Class: (SampleRail) + +AnnotationAssertion(rdfs:comment "def: This system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. + The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back + defprov: website") +AnnotationAssertion(rdfs:label "SampleRail") +SubClassOf( ) + +# Class: (SampleJet) + +AnnotationAssertion(rdfs:comment "def: Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation. + The SampleJet utilizes the modern-day industry standard for sample arrangements—the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement. + defprov: Bruker website") +AnnotationAssertion(rdfs:label "SampleJet") +SubClassOf( ) + +# Class: (Bruker autosampler) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "Bruker autosampler") +SubClassOf( ) + +# Class: (B-ACS) + +AnnotationAssertion(rdfs:comment "def: The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit. + defprov: Bruker website") +AnnotationAssertion(rdfs:label "B-ACS") +SubClassOf( ) + +# Class: (Bruker MATCH) + +AnnotationAssertion(rdfs:comment "def: The Bruker Multiple Adjustable Tube Clamp Holder MATCH™ system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications. + The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube. + defprov: Bruker website + synonym: Bruker Multiple Adjustable Tube Clamp Holder") +AnnotationAssertion(rdfs:label "Bruker MATCH") +SubClassOf( ) + +# Class: (NMR sample holder) + +AnnotationAssertion(rdfs:comment "def: A NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the NMR sample.") +AnnotationAssertion(rdfs:label "NMR sample holder") +SubClassOf( ) + +# Class: (NMR software) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "NMR software") +SubClassOf( ) + +# Class: (Bruker NMR software) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "Bruker NMR software") +AnnotationAssertion(owl:versionInfo "TODO: May need no definition.") +SubClassOf( ) + +# Class: (Bruker TopSpin software) + +AnnotationAssertion(rdfs:label "Bruker TopSpin software") +SubClassOf( ) + +# Class: (SampleTrack software) + +AnnotationAssertion(rdfs:label "SampleTrack software") +SubClassOf( ) + +# Class: (Paravision software) + +AnnotationAssertion(rdfs:label "Paravision software") +SubClassOf( ) + +# Class: (AURELIA software) + +AnnotationAssertion(rdfs:label "AURELIA software") +SubClassOf( ) + +# Class: (AUREMOL software) + +AnnotationAssertion(rdfs:label "AUREMOL software") +SubClassOf( ) + +# Class: (AMIX VIEWER & AMIX-TOOLS) + +AnnotationAssertion(rdfs:label "AMIX VIEWER & AMIX-TOOLS") +SubClassOf( ) + +# Class: (high resolution probe) + +AnnotationAssertion(rdfs:comment "def:BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features. + defprov: Bruker website + synonym: HR Probe") +AnnotationAssertion(rdfs:label "high resolution probe") +SubClassOf( ) + +# Class: (high resolution probe with ATM) + +AnnotationAssertion(rdfs:comment "def: The ATM option for AVANCE spectrometers is available for: + Double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90° pulsewidths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems. + defprov: Bruker website + synonym: High Resolution Probes with Automatic Tuning and Matching, HR probe with ATM") +AnnotationAssertion(rdfs:label "high resolution probe with ATM") +SubClassOf( ) + +# Class: (micro imaging probe) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "micro imaging probe") +SubClassOf( ) + +# Class: (JEOL NMR instrument) + +AnnotationAssertion(rdfs:label "JEOL NMR instrument") +SubClassOf( ) + +# Class: (JNM-ECX Series FT NMR instrument) + +AnnotationAssertion(rdfs:label "JNM-ECX Series FT NMR instrument") +AnnotationAssertion(skos:definition "The JNM-ECX series is an FT NMR spectrometer developed making full use of the latest digital and high frequency technology. This high performance, sophisticated spectrometer designed to take advantage of high field magnet development to include 1GHz. Innovative features to support not only the conventional NMR applications such as structural analysis of molecules and evaluation of materials but also future progress of science and technologies including research for development of new drugs, postgenome research and development of new materials.") +SubClassOf( ) + +# Class: (JNM-ECA Series FT NMR instrument) + +AnnotationAssertion(rdfs:label "JNM-ECA Series FT NMR instrument") +AnnotationAssertion(skos:definition "The JNM-ECA series is an FT NMR spectrometer developed making full use of the latest digital and high frequency technology. This high performance, sophisticated spectrometer designed to take advantage of high field magnet development to include 1GHz. Innovative features to support not only the conventional NMR applications such as structural analysis of molecules and evaluation of materials but also future progress of science and technologies including research for development of new drugs, postgenome research and development of new materials.") +SubClassOf( ) + +# Class: (JEOL NMR software) + +AnnotationAssertion(rdfs:label "JEOL NMR software") +SubClassOf( ) + +# Class: (Delta NMR software) + +AnnotationAssertion(rdfs:label "Delta NMR software") +SubClassOf( ) + +# Class: (Bruker NMR probe) + +AnnotationAssertion(rdfs:comment "https://www.bruker.com/products/mr/nmr/probes/probes.html") +AnnotationAssertion(rdfs:label "Bruker NMR probe") +SubClassOf( ) + +# Class: (JEOL NMR probe) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "JEOL NMR probe") +SubClassOf( ) + +# Class: (CapNMR probe) + +AnnotationAssertion(rdfs:label "CapNMR probe") +SubClassOf( ) + +# Class: (Varian NMR instrument) + +AnnotationAssertion(rdfs:label "Varian NMR instrument") +SubClassOf( ) + +# Class: (Varian MERCURY) + +AnnotationAssertion(rdfs:label "Varian MERCURY") +SubClassOf( ) + +# Class: (Varian INOVA) + +AnnotationAssertion(rdfs:label "Varian INOVA") +SubClassOf( ) + +# Class: (Varian UNITY) + +AnnotationAssertion(rdfs:label "Varian UNITY") +SubClassOf( ) + +# Class: (Varian VXR) + +AnnotationAssertion(rdfs:label "Varian VXR") +SubClassOf( ) + +# Class: (Varian GEMINI) + +AnnotationAssertion(rdfs:label "Varian GEMINI") +SubClassOf( ) + +# Class: (AMX instrument) + +AnnotationAssertion(rdfs:label "AMX instrument") +SubClassOf( ) + +# Class: (AC instrument) + +AnnotationAssertion(rdfs:label "AC instrument") +SubClassOf( ) + +# Class: (liquid NMR probe) + +AnnotationAssertion(rdfs:label "liquid NMR probe") +SubClassOf( ) + +# Class: (solid NMR probe) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "solid NMR probe") +SubClassOf( ) + +# Class: (NMR imaging probe) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "NMR imaging probe") +SubClassOf( ) + +# Class: (tecmag console) + +AnnotationAssertion(rdfs:label "tecmag console") +SubClassOf( ) + +# Class: (DISCOVERY console) + +AnnotationAssertion(rdfs:comment "def: The Discovery™ is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network + defprov: tecmag website") +AnnotationAssertion(rdfs:label "DISCOVERY console") +SubClassOf( ) + +# Class: (tecmag EAGLE probe) + +AnnotationAssertion(rdfs:comment "def: The Eagle™ is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz widebore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers. + defprov: website") +AnnotationAssertion(rdfs:label "tecmag EAGLE probe") +SubClassOf( ) + +# Class: (APOLLO console) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "APOLLO console") +SubClassOf( ) + +# Class: (tecmag NMR instrument) + +AnnotationAssertion(rdfs:label "tecmag NMR instrument") +SubClassOf( ) + +# Class: (CAT) + +AnnotationAssertion(rdfs:label "CAT") +SubClassOf( ) + +# Class: (magnetic field strength) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "magnetic field strength") +SubClassOf( ) + +# Class: (vendor) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "vendor") +AnnotationAssertion(owl:versionInfo "TODO: Belongs in Ref Ontol.") +SubClassOf( ) + +# Class: (NMR instrument manufacturer) + +AnnotationAssertion(rdfs:comment "A manufacturer that produces (and eventually sells) NMR instruments.") +AnnotationAssertion(rdfs:label "NMR instrument manufacturer") +SubClassOf( ) + +# Class: (Bruker) + +AnnotationAssertion(rdfs:comment "defneed") +AnnotationAssertion(rdfs:label "Bruker") +AnnotationAssertion(owl:versionInfo "TODO: May not need definition due to its instance character.") +SubClassOf( ) + +# Class: (Varian) + +AnnotationAssertion(rdfs:label "Varian") +SubClassOf( ) + +# Class: (JEOL) + +AnnotationAssertion(rdfs:label "JEOL") +SubClassOf( ) + +# Class: (MR Resources) + +AnnotationAssertion(rdfs:label "MR Resources") +SubClassOf( ) + +# Class: (tecmag) + +AnnotationAssertion(rdfs:label "tecmag") +SubClassOf( ) + +# Class: (sample temperature information) + +AnnotationAssertion(rdfs:comment "def: In some cases, it is necessary or advisable to control the temperature of the sample at some value other than ambient. The sample may be only slightly solubility at room temperatures, or it may be desirable to control some aspect of the dynamics of the system. In such cases, a default temperature, or some means of selecting this parameter, can be built into the experiment.") +AnnotationAssertion(rdfs:label "sample temperature information") +SubClassOf( ) + +# Class: (Doty Scientific) + +AnnotationAssertion(rdfs:label "Doty Scientific") +SubClassOf( ) + +# Class: (Wilmad) + +AnnotationAssertion(rdfs:label "Wilmad") +SubClassOf( ) + +# Class: (JS Research) + +AnnotationAssertion(rdfs:label "JS Research") +SubClassOf( ) + +# Class: (data file) + +AnnotationAssertion(rdfs:label "data file") +AnnotationAssertion(skos:altLabel "file") +AnnotationAssertion(skos:definition "Any data file as generated by some acquisition computer or console.") +AnnotationAssertion(skos:editorialNote "This is a class annotation exemplifying skos usage. We assume the rdfs:label to capture the skos:preferedLabel.") +AnnotationAssertion(skos:example "an FID raw data file") +AnnotationAssertion(skos:scopeNote "In the NMR case a file generated by an NMR acquisition computer, console or NMR processing software.") +SubClassOf( obo:BFO_0000031) + +# Class: (Acorn NMR Inc) + +AnnotationAssertion(rdfs:label "Acorn NMR Inc") +SubClassOf( ) + +# Class: (liquid chromatography NMR) + +AnnotationAssertion(oboInOwl:hasExactSynonym "LC NMR") +AnnotationAssertion(rdfs:label "liquid chromatography NMR") +SubClassOf( ) + +# Class: (LC MS NMR) + +AnnotationAssertion(rdfs:comment "Includes the connection to a high-resolution TOF-LC-MS system.") +AnnotationAssertion(rdfs:label "LC MS NMR") +SubClassOf( ) + +# Class: (solid phase extraction NMR) + +AnnotationAssertion(oboInOwl:hasExactSynonym "SPE NMR") +AnnotationAssertion(rdfs:comment "A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE™ NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra.") +AnnotationAssertion(rdfs:label "solid phase extraction NMR") +SubClassOf( ) + +# Class: (Capillary LC-NMR) + +AnnotationAssertion(rdfs:comment "Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume.") +AnnotationAssertion(rdfs:label "Capillary LC-NMR") +SubClassOf( ) + +# Class: (direct detection probe) + +AnnotationAssertion(rdfs:label "direct detection probe") +SubClassOf( ) + +# Class: (indirect detection probe) + +AnnotationAssertion(rdfs:label "indirect detection probe") +SubClassOf( ) + +# Class: (continuous wave NMR) + +AnnotationAssertion(rdfs:comment "Continuous wave NMR spectrometers are similar in principle to optical spectrometers. The sample is held in a strong magnetic field, and the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned). + Defprov: http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm") +AnnotationAssertion(rdfs:label "continuous wave NMR") +SubClassOf( ) + +# Class: (fourier transformation NMR instrument) + +AnnotationAssertion(rdfs:comment "In FT-NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation. + Defprov: http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm") +AnnotationAssertion(rdfs:label "fourier transformation NMR instrument") +SubClassOf( ) + +# Class: (NMR software data format) + +AnnotationAssertion(rdfs:label "NMR software data format") +SubClassOf( ) + +# Class: (ChemMagnetics format) + +AnnotationAssertion(rdfs:label "ChemMagnetics format") +SubClassOf( ) + +# Class: (GE Omega format) + +AnnotationAssertion(rdfs:label "GE Omega format") +SubClassOf( ) + +# Class: (JEOL Lambda format) + +AnnotationAssertion(rdfs:label "JEOL Lambda format") +SubClassOf( ) + +# Class: (JEOL Alpha format) + +AnnotationAssertion(rdfs:label "JEOL Alpha format") +SubClassOf( ) + +# Class: (Jeol Delta format) + +AnnotationAssertion(rdfs:label "Jeol Delta format") +SubClassOf( ) + +# Class: (JEOL generic format) + +AnnotationAssertion(rdfs:label "JEOL generic format") +SubClassOf( ) + +# Class: (JEOL AL95 format) + +AnnotationAssertion(rdfs:label "JEOL AL95 format") +SubClassOf( ) + +# Class: (JEOL EX format) + +AnnotationAssertion(rdfs:label "JEOL EX format") +SubClassOf( ) + +# Class: (TecMag format) + +AnnotationAssertion(rdfs:label "TecMag format") +SubClassOf( ) + +# Class: (Varian VNMR format) + +AnnotationAssertion(rdfs:label "Varian VNMR format") +SubClassOf( ) + +# Class: (Galactic format) + +AnnotationAssertion(rdfs:label "Galactic format") +SubClassOf( ) + +# Class: (Felix format) + +AnnotationAssertion(rdfs:label "Felix format") +SubClassOf( ) + +# Class: (JCAMP DX format) + +AnnotationAssertion(rdfs:label "JCAMP DX format") +SubClassOf( ) + +# Class: (Lybrics format) + +AnnotationAssertion(rdfs:label "Lybrics format") +SubClassOf( ) + +# Class: (Nuts format) + +AnnotationAssertion(rdfs:label "Nuts format") +SubClassOf( ) + +# Class: (MACNMR format) + +AnnotationAssertion(rdfs:label "MACNMR format") +SubClassOf( ) + +# Class: (Nicolet GE/QE-300 format) + +AnnotationAssertion(rdfs:label "Nicolet GE/QE-300 format") +SubClassOf( ) + +# Class: (multiplet feature) + +AnnotationAssertion(oboInOwl:hasExactSynonym "m") +AnnotationAssertion(rdfs:comment "J-coupler") +AnnotationAssertion(rdfs:label "multiplet feature") +SubClassOf( ) + +# Class: (ThermoMattson) + +AnnotationAssertion(rdfs:label "ThermoMattson") +SubClassOf( ) + +# Class: (FOSS) + +AnnotationAssertion(rdfs:label "FOSS") +SubClassOf( ) + +# Class: (Jasco) + +AnnotationAssertion(rdfs:label "Jasco") +SubClassOf( ) + +# Class: (Agilent Technologies) + +AnnotationAssertion(rdfs:label "Agilent Technologies") +SubClassOf( ) + +# Class: (micromass) + +AnnotationAssertion(rdfs:label "micromass") +SubClassOf( ) + +# Class: (Waters) + +AnnotationAssertion(rdfs:label "Waters") +SubClassOf( ) + +# Class: (ThermoNicolet) + +AnnotationAssertion(rdfs:label "ThermoNicolet") +SubClassOf( ) + +# Class: (Perkin Elmer) + +AnnotationAssertion(rdfs:label "Perkin Elmer") +SubClassOf( ) + +# Class: (OceanOptics) + +AnnotationAssertion(rdfs:label "OceanOptics") +SubClassOf( ) + +# Class: (ThermoFinnigan) + +AnnotationAssertion(rdfs:label "ThermoFinnigan") +SubClassOf( ) + +# Class: (Applied Biosystems) + +AnnotationAssertion(rdfs:label "Applied Biosystems") +SubClassOf( ) + +# Class: (TX) + +AnnotationAssertion(rdfs:label "TX") +SubClassOf( ) + +# Class: (Net CDF format) + +AnnotationAssertion(rdfs:label "Net CDF format") +SubClassOf( ) + +# Class: (Bruker DISNMR format) + +AnnotationAssertion(rdfs:label "Bruker DISNMR format") +SubClassOf( ) + +# Class: (Bruker UXNMR/XWIN-NMR format) + +AnnotationAssertion(rdfs:label "Bruker UXNMR/XWIN-NMR format") +SubClassOf( ) + +# Class: (Bruker WIN NMR format) + +AnnotationAssertion(rdfs:label "Bruker WIN NMR format") +SubClassOf( ) -AnnotationAssertion(rdfs:label "root node"@en) +# Class: (acdlabs) +AnnotationAssertion(rdfs:label "acdlabs") +SubClassOf( ) -) +) \ No newline at end of file From bae89a076418dbd09a1044bb4cfbb9e96b4a3855 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philip=20Str=C3=B6mert?= Date: Tue, 20 Feb 2024 16:43:56 +0100 Subject: [PATCH 3/4] Deactivate using base import modules for now --- src/ontology/nmrCV-odk.yaml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/src/ontology/nmrCV-odk.yaml b/src/ontology/nmrCV-odk.yaml index e6979f8..261f5d0 100644 --- a/src/ontology/nmrCV-odk.yaml +++ b/src/ontology/nmrCV-odk.yaml @@ -39,15 +39,11 @@ import_group: - id: bfo module_type: mirror - id: ro - use_base: true - id: omo module_type: mirror - id: iao - make_base: true - id: chmo - make_base: true - id: pato - make_base: true - id: obi - make_base: true + From 5a4cf0ec22ee25f396ddb26f91d23b7d718cc882 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philip=20Str=C3=B6mert?= Date: Tue, 20 Feb 2024 16:44:11 +0100 Subject: [PATCH 4/4] Update .gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 6dd431a..7add119 100644 --- a/.gitignore +++ b/.gitignore @@ -45,3 +45,4 @@ src/patterns/all_pattern_terms.txt .idea/inspectionProfiles/profiles_settings.xml .idea/vcs.xml .idea/workspace.xml +.idea/misc.xml