@prefix : <http://purl.org/cbio/> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix up: <http://purl.uniprot.org/core/> .
@prefix efo: <http://www.ebi.ac.uk/efo/> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix pav: <http://purl.org/pav/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix bgee: <http://bgee.org/#> .
@prefix lscr: <http://purl.org/lscr#> .
@prefix obda: <https://w3id.org/obda/vocabulary#> .
@prefix orth: <http://purl.org/net/orth#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix swrl: <http://www.w3.org/2003/11/swrl#> .
@prefix genex: <http://purl.org/genex#> .
@prefix swrla: <http://swrl.stanford.edu/ontologies/3.3/swrla.owl#> .
@prefix swrlb: <http://www.w3.org/2003/11/swrlb#> .
@prefix terms: <http://purl.org/dc/terms/> .
@prefix uberon: <http://purl.obolibrary.org/obo/uberon#> .
@prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> .
@prefix  mondo: <http://purl.obolibrary.org/obo/mondo#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix voag: <http://voag.linkedmodel.org/schema/voag#> .
@prefix npg: <http://ns.nature.com/terms/> .
@prefix chebi: <http://purl.obolibrary.org/obo/chebi/> .
@prefix faldo: <http://biohackathon.org/resource/faldo#> .
@base <http://purl.org/cbio>.

####Some entities and relations extracted from 
#RO core : <http://purl.obolibrary.org/obo/ro/core.owl>
#foaf: <http://xmlns.com/foaf/0.1/>
#EFO (with a few modifications - removed some class restrictions): <http://www.ebi.ac.uk/efo/>
#Genex: <http://purl.org/genex>
#NCI thesaurus: <>
#Dcterms (provenance specialised as an owl:AnnotationProperty rather than its superclass rdf:Property): <http://purl.org/dc/terms/>
#dc elements: <http://purl.org/dc/elements/1.1/>
#VOAG: http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl
#OBI .
#SIO
#ERO eagle-i resource ontology http://purl.obolibrary.org/obo/ero.owl
#SO Sequences and features ontology
#FALDO ontology
####
<http://purl.org/cbio> rdf:type owl:Ontology ;
                        owl:versionIRI <http://purl.org/cbio/0.4> ;
                        owl:imports <https://raw.githubusercontent.com/qfo/OrthologyOntology/master/lscr.ttl> , <http://biohackathon.org/resource/faldo> ;
                        owl:versionInfo "Cancer biomarker ontology (CBIO)."@en ;
                        dc:creator <http://purl.org/query/tarcisiomf> ;
                        terms:modified "2022-03-15"^^<http://www.w3.org/2001/XMLSchema#date> .

#################################################################
#    Annotation properties
#################################################################

###  http://purl.obolibrary.org/obo/IAO_0000112
obo:IAO_0000112 rdf:type owl:AnnotationProperty ;
                rdfs:label "example of usage" .


###  http://purl.obolibrary.org/obo/IAO_0000115
obo:IAO_0000115 rdf:type owl:AnnotationProperty ;
                rdfs:label "definition"^^xsd:string .


###  http://purl.obolibrary.org/obo/IAO_0000116
obo:IAO_0000116 rdf:type owl:AnnotationProperty ;
                rdfs:isDefinedBy obo:iao.owl ;
                rdfs:label "editor note"@en .


###  http://purl.obolibrary.org/obo/IAO_0000232
obo:IAO_0000232 rdf:type owl:AnnotationProperty ;
                rdfs:isDefinedBy obo:iao.owl ;
                rdfs:label "curator note"@en .


###  http://purl.obolibrary.org/obo/IAO_0000600
obo:IAO_0000600 rdf:type owl:AnnotationProperty ;
                rdfs:isDefinedBy obo:iao.owl ;
                rdfs:label "elucidation"@en .


###  http://purl.org/dc/terms/description
terms:description rdf:type rdf:Property ;
                  terms:description "Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource."@en ;
                  rdfs:comment "An account of the resource."@en ;
                  rdfs:isDefinedBy terms: ;
                  rdfs:label "Description"@en .


###  http://purl.org/net/orth#inDatabase
orth:inDatabase rdf:type owl:AnnotationProperty ;
                rdfs:comment "A property to define the database an orthology dataset belongs to."@en ;
                rdfs:label "in database"@en ;
                rdfs:domain orth:OrthologyDataset .


###  http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation
efo:NCI_Thesaurus_definition_citation rdf:type owl:AnnotationProperty ;
                                      obo:IAO_0000115 "http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation is an annotation property that is drawn from NCI_Thesaurus"^^xsd:string ;
                                      efo:NCI_Thesaurus_definition_citation "http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation is an annotation property that is drawn from NCI_Thesaurus"^^xsd:string ;
                                      rdfs:subPropertyOf efo:definition_citation .


###  http://www.ebi.ac.uk/efo/alternative_term
efo:alternative_term rdf:type owl:AnnotationProperty ;
                     obo:IAO_0000115 "An alternative label for a given entity such as a commonly used abbreviation or synonym. " ;
                     rdfs:label "alternative_term"^^xsd:string .


###  http://www.ebi.ac.uk/efo/definition_citation
efo:definition_citation rdf:type owl:AnnotationProperty ;
                        obo:IAO_0000115 "A definition citation is a document, ontology class, person or organization from which the definition of the class is derived. It is used in the same sense as a citation in literature, in that the definition may have been derived from these sources or that this definition is related to these source." .


###  http://www.ebi.ac.uk/efo/source_definition
efo:source_definition rdf:type owl:AnnotationProperty .


###  http://www.geneontology.org/formats/oboInOwl#id
oboInOwl:id rdf:type owl:AnnotationProperty .


###  http://www.geneontology.org/formats/oboInOwl#inSubset
oboInOwl:inSubset rdf:type owl:AnnotationProperty .


###  http://www.w3.org/2004/02/skos/core#altLabel
skos:altLabel rdf:type owl:AnnotationProperty ;
              rdfs:comment "The range of skos:altLabel is the class of RDF plain literals."@en ,
                           "skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties."@en ;
              rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
              rdfs:label "alternative label"@en ;
              skos:definition "An alternative lexical label for a resource."@en ;
              skos:example "Acronyms, abbreviations, spelling variants, and irregular plural/singular forms may be included among the alternative labels for a concept. Mis-spelled terms are normally included as hidden labels (see skos:hiddenLabel)."@en ;
              rdfs:subPropertyOf rdfs:label .


###  http://www.w3.org/2004/02/skos/core#definition
skos:definition rdf:type owl:AnnotationProperty ;
                rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
                rdfs:label "definition"@en ;
                skos:definition "A statement or formal explanation of the meaning of a concept."@en ;
                rdfs:subPropertyOf skos:note .


###  http://www.w3.org/2004/02/skos/core#example
skos:example rdf:type owl:AnnotationProperty ;
             rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
             rdfs:label "example"@en ;
             skos:definition "An example of the use of a concept."@en ;
             rdfs:subPropertyOf skos:note .


###  http://www.w3.org/2004/02/skos/core#note
skos:note rdf:type owl:AnnotationProperty ;
          rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
          rdfs:label "note"@en ;
          skos:definition "A general note, for any purpose."@en ;
          skos:scopeNote "This property may be used directly, or as a super-property for more specific note types."@en .


###  http://www.w3.org/2004/02/skos/core#scopeNote
skos:scopeNote rdf:type owl:AnnotationProperty ;
               rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
               rdfs:label "scope note"@en ;
               skos:definition "A note that helps to clarify the meaning and/or the use of a concept."@en ;
               rdfs:subPropertyOf skos:note .


#################################################################
#    Object Properties
#################################################################

###  http://purl.obolibrary.org/obo/CDAO_0000194
obo:CDAO_0000194 rdf:type owl:ObjectProperty ;
				 owl:inverseOf  obo:BFO_0000051 ;
                 rdfs:label "part_of"^^xsd:string .


###  http://purl.obolibrary.org/obo/RO_0001018
obo:RO_0001018 rdf:type owl:ObjectProperty ;
               rdfs:label "contained in"@en .


###  http://purl.obolibrary.org/obo/RO_0002162
obo:RO_0002162 rdf:type owl:ObjectProperty ;
               rdfs:comment "Connects a biological entity to its taxon of origin."@en ;
               rdfs:label "in taxon"@en .


###  http://purl.obolibrary.org/obo/RO_0002206
obo:RO_0002206 rdf:type owl:ObjectProperty ;
               rdfs:subPropertyOf obo:RO_0002330 ;
               owl:inverseOf obo:RO_0002292 ;
               rdfs:domain obo:BFO_0000002 ;
               rdfs:range obo:BFO_0000004 ;
               obo:IAO_0000112 "'neural crest cell'  SubClassOf expresses some 'Wnt1 gene'" ;
               obo:IAO_0000115 "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" ;
               rdfs:label "expressed in"@en .


###  http://purl.obolibrary.org/obo/RO_0002245
obo:RO_0002245 rdf:type owl:ObjectProperty ;
               rdfs:subPropertyOf genex:isExpressedIn ;
               obo:IAO_0000115 "g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background." ;
               rdfs:label "over-expressed in" ;
               skos:altLabel "highly expressed in"@en .


###  http://purl.obolibrary.org/obo/RO_0002246
obo:RO_0002246 rdf:type owl:ObjectProperty ;
               rdfs:subPropertyOf genex:isExpressedIn ;
               obo:IAO_0000115 "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background." ;
               rdfs:label "under-expressed in" .


###  http://purl.obolibrary.org/obo/RO_0002291
obo:RO_0002291 rdf:type owl:ObjectProperty ;
               rdfs:subPropertyOf genex:isExpressedIn ;
               owl:inverseOf obo:RO_0002293 ;
               obo:IAO_0000115 "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" ;
               obo:IAO_0000116 "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." ;
               rdfs:label "ubiquitously expressed in"@en .


###  http://purl.obolibrary.org/obo/RO_0002292
obo:RO_0002292 rdf:type owl:ObjectProperty ;
               rdfs:subPropertyOf obo:RO_0002330 ;
               obo:IAO_0000115 "Inverse of 'expressed in'" ;
               rdfs:label "expresses"@en .


###  http://purl.obolibrary.org/obo/RO_0002293
obo:RO_0002293 rdf:type owl:ObjectProperty ;
               rdfs:subPropertyOf obo:RO_0002292 ;
               obo:IAO_0000115 "inverse of ubiquiotously expressed in" ;
               oboInOwl:inSubset obo:RO_0002259 ;
               rdfs:label "ubiquitously expresses"@en .


###  http://purl.obolibrary.org/obo/RO_0002330
obo:RO_0002330 rdf:type owl:ObjectProperty ;
               rdfs:domain obo:BFO_0000002 ;
               rdfs:range obo:BFO_0000002 ;
               obo:IAO_0000115 "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." ;
               obo:IAO_0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" ;
               rdfs:label "genomically related to"@en .


###  http://purl.org/genex#hasAnatomicalEntity
genex:hasAnatomicalEntity rdf:type owl:ObjectProperty ,
                                   owl:FunctionalProperty ;
                          rdfs:domain genex:ExpressionCondition ;
                          rdfs:range genex:AnatomicalEntity ;
                          rdfs:label "has anatomical entity"@en .


###  http://purl.org/genex#hasConfidenceLevel
genex:hasConfidenceLevel rdf:type owl:ObjectProperty ,
                                  owl:FunctionalProperty ;
                         rdfs:domain [ rdf:type owl:Class ;
                                       owl:unionOf ( genex:AbsenceExpression
                                                     genex:Expression
                                                   )
                                     ] ;
                         rdfs:range [ rdf:type owl:Class ;
                                      owl:oneOf ( obo:CIO_0000029
                                                  obo:CIO_0000030
                                                  obo:CIO_0000031
                                                )
                                    ] ;
                         rdfs:label "has expression or absence confidence level"@en .


###  http://purl.org/genex#hasDevelopmentalStage
genex:hasDevelopmentalStage rdf:type owl:ObjectProperty ,
                                     owl:FunctionalProperty ;
                            rdfs:domain genex:ExpressionCondition ;
                            rdfs:range efo:EFO_0000399 ;
                            rdfs:label "has a developmental stage"@en .


###  http://purl.org/genex#hasExpressionCharacteristic
genex:hasExpressionCharacteristic rdf:type owl:ObjectProperty ,
                                           owl:FunctionalProperty ;
                                  rdfs:domain genex:Expression ;
                                  rdfs:range [ rdf:type owl:Class ;
                                               owl:oneOf ( genex:AVERAGE_EXPRESSED
                                                           genex:HIGHLY_EXPRESSED
                                                           genex:HIGH_EXPRESSED
                                                           genex:LOWLY_EXPRESSED
                                                           genex:LOW_EXPRESSED
                                                           genex:UBIQUITOUSLY_EXPRESSED
                                                         )
                                             ] ;
                                  rdfs:label "has expression level characteristic"@en .


###  http://purl.org/genex#hasExpressionCondition
genex:hasExpressionCondition rdf:type owl:ObjectProperty ;
                             rdfs:domain [ rdf:type owl:Class ;
                                           owl:unionOf ( genex:AbsenceExpression
                                                         genex:Expression
                                                       )
                                         ] ;
                             rdfs:range genex:ExpressionCondition ;
                             rdfs:label "has an expression condition"@en ;
                             skos:altLabel "has an experimental condition"@en .


###  http://purl.org/genex#hasSequenceUnit
genex:hasSequenceUnit rdf:type owl:ObjectProperty ;
                      rdfs:domain [ rdf:type owl:Class ;
                                    owl:unionOf ( genex:AbsenceExpression
                                                  genex:Expression
                                                  obo:CHEBI_59163
                                                  :CancerDifferentialExpression
                                                  :DiseaseMutation
                                                )
                                  ] ;
                      rdfs:range orth:SequenceUnit ;
                      rdfs:label "has sequence unit"@en .


###  http://purl.org/genex#hasStrain
genex:hasStrain rdf:type owl:ObjectProperty ,
                         owl:FunctionalProperty ;
                rdfs:domain genex:ExpressionCondition ;
                rdfs:range efo:EFO_0005135 ;
                rdfs:label "has strain"@en .


###  http://purl.org/genex#isAbsentIn
genex:isAbsentIn rdf:type owl:ObjectProperty ;
                 rdfs:subPropertyOf obo:RO_0002330 ;
                 rdfs:domain orth:SequenceUnit ;
                 rdfs:range [ rdf:type owl:Class ;
                              owl:unionOf ( genex:AnatomicalEntity
                                            genex:ExpressionCondition
                                            efo:EFO_0000399
                                            efo:EFO_0005135
                                          )
                            ] ;
                 rdfs:comment "A sequence unit is absent (not expressed) in some expression condition (e.g. anatomical entity and/or developmental stage). Examples how to assign this property (at a high level of abstraction): GeneA \"is absent in\" Brain; GeneA \"is abent in\" adult stage."@en ,
                              """Recommendation: prefer to instatiate 'absence of gene expression' and 'gene expression experiment condition' classes to represent Gene expression data. For example,  rather than materializing this property at the data store level, it shoud be inferred by applying the logical rules:   
rule1- 'expressed gene'(?e),'has an expression condition'(?e, ?cond), 'has sequence unit'(?e, ?seq) -> 'is expressed in'(?seq, ?cond); 
rule2- 'expressed gene'(?e),'has an expression condition'(?e, ?cond), 'has a developmental stage'(?cond, ?stage), 'has sequence unit'(?e, ?seq) -> 'is expressed in'(?seq, ?stage)
rule3-  'expressed gene'(?e),'has an expression condition'(?e, ?cond), 'has strain'(?cond, ?strain), 'has sequence unit'(?e, ?seq) -> 'is expressed in'(?seq, ?strain)
rule4- 'expressed gene'(?e),'has an expression condition'(?e, ?cond), 'has anatomical entity'(?cond, ?anat), 'has sequence unit'(?e, ?seq) -> 'is expressed in'(?seq, ?anat)

These rules are currently defined in Genex ontology as a SWRL (Semantic Web Rule Language) rule. It can be tanslated into another semantic web language such as  RIF."""@en ;
                 rdfs:label "is absent in"@en ;
                 skos:altLabel "is not expressed in"@en .


###  http://purl.org/genex#isExpressedIn
genex:isExpressedIn rdf:type owl:ObjectProperty ;
                    rdfs:subPropertyOf obo:RO_0002206 ;
                    rdfs:domain orth:SequenceUnit ;
                    rdfs:range [ rdf:type owl:Class ;
                                 owl:unionOf ( genex:AnatomicalEntity
                                               genex:ExpressionCondition
                                               efo:EFO_0000399
                                               efo:EFO_0005135
                                             )
                               ] ;
                    rdfs:comment "A sequence unit (e.g. gene) is present (expressed) in some expression condition (e.g. anatomical entity and/or developmental stage). Examples how to assign this property (at a high level of abstraction): GeneA \"is expressed in\" Brain; GeneA \"is expressed in\" adult stage."@en ,
                                 """Recommendation: prefer to instatiate 'expressed gene' and 'gene expression experiment condition' classes to represent Gene expression data. For example,  rather than materializing this property at the data store level, it shoud be inferred by applying the logical rules:   
- 'absence of gene expression'(?e),'has an expression condition'(?e, ?cond), 'has sequence unit'(?e, ?seq) -> 'is absent in'(?seq, ?cond); 
- 'absence of gene expression'?e),'has an expression condition'(?e, ?cond), 'has a developmental stage'(?cond, ?stage), 'has sequence unit'(?e, ?seq) -> 'is absent in'(?seq, ?stage)
-  'absence of gene expression'(?e),'has an expression condition'(?e, ?cond), 'has strain'(?cond, ?strain), 'has sequence unit'(?e, ?seq) -> 'is absent in'(?seq, ?strain)
- 'absence of gene expression'(?e),'has an expression condition'(?e, ?cond), 'has anatomical entity'(?cond, ?anat), 'has sequence unit'(?e, ?seq) -> 'is absent in'(?seq, ?anat)

These rules are currently defined in Genex ontology as a SWRL (Semantic Web Rule Language) rule. It can be tanslated into another semantic web language such as  RIF."""@en ;
                    rdfs:label "is expressed in"@en .


###  http://purl.org/net/orth#organism
orth:organism rdf:type owl:ObjectProperty ;
              rdfs:domain orth:SequenceUnit ;
              rdfs:range orth:Organism .


###  http://purl.uniprot.org/core/rank
up:rank rdf:type owl:ObjectProperty ,
                 owl:FunctionalProperty ;
        rdfs:domain up:Taxon ;
        rdfs:range up:Rank ;
        rdfs:comment "The rank of a taxon."^^xsd:string .


###  http://purl.uniprot.org/core/replaces
up:replaces rdf:type owl:ObjectProperty ;
            rdfs:domain up:Taxon ;
            rdfs:range up:Taxon ;
            rdfs:comment "A resource that is replaced by this resource."^^xsd:string .



###  http://semanticscience.org/resource/SIO_010078
sio:SIO_010078 rdf:type owl:ObjectProperty ;
               owl:inverseOf sio:SIO_010079 ;
               dc:identifier "SIO_010078" ;
               terms:description "A relation between two objects, in which the first object contains information that is used to produce the second object."@en ;
               rdfs:isDefinedBy <http://semanticscience.org/ontology/sio.owl> ;
               rdfs:label "encodes"@en .




#################################################################
#    Data properties
#################################################################

###  http://purl.org/dc/elements/1.1/description
dc:description 
			   a rdf:Property ;
               rdfs:range rdfs:Literal ;
               terms:description "Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource."@en ;
               rdfs:comment "An account of the resource."@en ;
               rdfs:isDefinedBy dc: ;
               rdfs:label "Description"@en .


###  http://purl.org/genex#hasExpressionLevel
genex:hasExpressionLevel rdf:type owl:DatatypeProperty ;
                         rdfs:domain [ rdf:type owl:Class ;
                                  owl:unionOf ( genex:AbsenceExpression
                                                genex:Expression
                                              )
                                ]  ;
                         rdfs:range xsd:double ;
                         rdfs:label "has expression level score"@en ;
                         skos:altLabel "expression score"@en .


###  http://purl.org/genex#hasSex
genex:hasSex rdf:type owl:DatatypeProperty ,
                      owl:FunctionalProperty ;
             rdfs:domain genex:ExpressionCondition ;
             rdfs:range [ rdf:type rdfs:Datatype ;
                          owl:oneOf [ rdf:type rdf:List ;
                                      rdf:first "NA"^^xsd:string ;
                                      rdf:rest [ rdf:type rdf:List ;
                                                 rdf:first "female"^^xsd:string ;
                                                 rdf:rest [ rdf:type rdf:List ;
                                                            rdf:first "hermaphrodite"^^xsd:string ;
                                                            rdf:rest [ rdf:type rdf:List ;
                                                                       rdf:first "male"^^xsd:string ;
                                                                       rdf:rest [ rdf:type rdf:List ;
                                                                                  rdf:first "mixed"^^xsd:string ;
                                                                                  rdf:rest [ rdf:type rdf:List ;
                                                                                             rdf:first "not annotated"^^xsd:string ;
                                                                                             rdf:rest rdf:nil
                                                                                           ]
                                                                                ]
                                                                     ]
                                                          ]
                                               ]
                                    ]
                        ] .


###  http://purl.uniprot.org/core/commonName
up:commonName rdf:type owl:DatatypeProperty ,
                       owl:FunctionalProperty ;
              rdfs:range xsd:string ;
              rdfs:isDefinedBy "http://purl.uniprot.org/core/" ;
              rdfs:label "common name"^^xsd:string .


###  http://purl.uniprot.org/core/mnemonic
up:mnemonic rdf:type owl:DatatypeProperty ;
            rdfs:range xsd:string ;
            rdfs:comment "A easy to remember identifier for a UniProtKB entry, but it is not a stable identifier and should not be used by programs to identify entries."@en ,
                         "A rememberable string that can be used to find entries, not a stable identifier!"^^xsd:string ;
            rdfs:label "Mnemonic"^^xsd:string ;
            rdfs:seeAlso "http://www.uniprot.org/manual/entry_name" .


###  http://purl.uniprot.org/core/scientificName
up:scientificName rdf:type owl:DatatypeProperty ,
                           owl:FunctionalProperty ;
                  rdfs:range xsd:string ;
                  rdfs:isDefinedBy "http://purl.uniprot.org/core/" ;
                  rdfs:label "scientific name"^^xsd:string .


#################################################################
#    Classes
#################################################################

###  http://purl.obolibrary.org/obo/BFO_0000001
obo:BFO_0000001 rdf:type owl:Class ;
                obo:IAO_0000116 "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 ,
                                "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 ;
                obo:IAO_0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])"@en ;
                rdfs:isDefinedBy obo:bfo.owl ;
                rdfs:label "entity"@en .


###  http://purl.obolibrary.org/obo/BFO_0000002
obo:BFO_0000002 rdf:type owl:Class ;
                rdfs:subClassOf obo:BFO_0000001 ;
                obo:IAO_0000116 "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 ,
                                "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 ;
                obo:IAO_0000600 "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 ;
                rdfs:isDefinedBy obo:bfo.owl ;
                rdfs:label "continuant"@en .


###  http://purl.obolibrary.org/obo/BFO_0000004
obo:BFO_0000004 rdf:type owl:Class ;
                rdfs:subClassOf obo:BFO_0000002 ;
                obo:IAO_0000112 "a chair"@en ,
                                "a heart"@en ,
                                "a leg"@en ,
                                "a molecule"@en ,
                                "a spatial region"@en ,
                                "an atom"@en ,
                                "an orchestra."@en ,
                                "an organism"@en ,
                                "the bottom right portion of a human torso"@en ,
                                "the interior of your mouth"@en ;
                obo:IAO_0000115 "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 ;
                rdfs:isDefinedBy obo:bfo.owl ;
                rdfs:label "independent continuant"@en .


###  http://purl.obolibrary.org/obo/CARO_0000000
obo:CARO_0000000 rdf:type owl:Class ;
                 owl:equivalentClass genex:AnatomicalEntity ;
                 obo:IAO_0000115 "A part of a multicellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex.  Or, a substance produced by a multicellular organism with granularity above the level of a protein complex."^^xsd:string ;
                 oboInOwl:id "CARO:0000000"^^xsd:string ;
                 rdfs:comment "Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach).  The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure." ;
                 rdfs:label "anatomical entity"^^xsd:string .


###  http://purl.obolibrary.org/obo/CARO_0030000
obo:CARO_0030000 rdf:type owl:Class ;
                 rdfs:subClassOf obo:BFO_0000004 ;
                 obo:IAO_0000115 "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them." ;
                 rdfs:comment "Important for alignment with Darwin Core class \"Organism\"." ;
                 rdfs:label "biological entity" .


###  http://purl.obolibrary.org/obo/CDAO_0000140
obo:CDAO_0000140 rdf:type owl:Class ;
                 rdfs:comment "Basic unit of graphs and trees"@en ;
                 rdfs:label "Node"^^xsd:string .


###  http://purl.obolibrary.org/obo/NCIT_C14250
obo:NCIT_C14250 rdf:type owl:Class ;
                owl:equivalentClass orth:Organism ;
                rdfs:label "Organism" .


###  http://purl.obolibrary.org/obo/OBI_0000181
obo:OBI_0000181 rdf:type owl:Class ;
                obo:IAO_0000115 "A population is a group of material entities consisting of individuals which share a particular characteristic such as inhabiting a particular region or area or ability to interbreed."^^xsd:string ;
                rdfs:label "population"^^xsd:string .


###  http://purl.obolibrary.org/obo/SO_0000104
obo:SO_0000104 rdf:type owl:Class ;
               owl:equivalentClass orth:Protein ;
               rdfs:label "polypeptide"^^xsd:string .


###  http://purl.obolibrary.org/obo/SO_0000704
obo:SO_0000704 rdf:type owl:Class ;
               owl:equivalentClass orth:Gene ;
               rdfs:label "gene"^^xsd:string .


###  http://purl.org/genex#AbsenceExpression
genex:AbsenceExpression rdf:type owl:Class ;
                        rdfs:subClassOf [ owl:intersectionOf ( [ rdf:type owl:Restriction ;
                                                                 owl:onProperty genex:hasExpressionCondition ;
                                                                 owl:someValuesFrom genex:ExpressionCondition
                                                               ]
                                                               [ rdf:type owl:Restriction ;
                                                                 owl:onProperty genex:hasSequenceUnit ;
                                                                 owl:someValuesFrom orth:SequenceUnit
                                                               ]
                                                             ) ;
                                          rdf:type owl:Class
                                        ] ,
                                        [ rdf:type owl:Class ;
                                          owl:complementOf genex:Expression
                                        ] ;
                        rdfs:label "absence of gene expression"@en ;
                        skos:altLabel "Not expressed gene"@en ,
                                      "Not expressed sequence unit"@en .


###  http://purl.org/genex#AnatomicalEntity
genex:AnatomicalEntity rdf:type owl:Class ;
                       rdfs:subClassOf obo:CARO_0030000 ;
                       rdfs:comment "An anatomical entity can be an organism part (e.g. brain, blood, liver and so on) or a material anatomical entity such as a cell." ;
                       rdfs:label "Anatomical entity"@en .


###  http://purl.org/genex#Expression
genex:Expression rdf:type owl:Class ;
                 rdfs:subClassOf [ owl:intersectionOf ( [ rdf:type owl:Restriction ;
                                                          owl:onProperty genex:hasExpressionCondition ;
                                                          owl:someValuesFrom genex:ExpressionCondition
                                                        ]
                                                        [ rdf:type owl:Restriction ;
                                                          owl:onProperty genex:hasSequenceUnit ;
                                                          owl:someValuesFrom orth:SequenceUnit
                                                        ]
                                                      ) ;
                                   rdf:type owl:Class
                                 ] ,
                                 [ rdf:type owl:Restriction ;
                                   owl:onProperty genex:hasExpressionCharacteristic ;
                                   owl:allValuesFrom [ rdf:type owl:Class ;
                                                       owl:oneOf ( genex:AVERAGE_EXPRESSED
                                                                   genex:HIGHLY_EXPRESSED
                                                                   genex:HIGH_EXPRESSED
                                                                   genex:LOWLY_EXPRESSED
                                                                   genex:LOW_EXPRESSED
                                                                   genex:UBIQUITOUSLY_EXPRESSED
                                                                 )
                                                     ]
                                 ] ,
                                 [ rdf:type owl:Restriction ;
                                   owl:onProperty genex:hasExpressionLevel ;
                                   owl:allValuesFrom xsd:double
                                 ] ;
                 rdfs:comment "All sequence units (e.g. Gene) that are expressed in some condition (e.g. organ and/or adult stage)."@en ;
                 rdfs:label "gene expression"@en ;
                 skos:altLabel "expression"@en ,
                               "sequence unit expression"@en .


###  http://purl.org/genex#ExpressionCondition
genex:ExpressionCondition rdf:type owl:Class ;
                          owl:equivalentClass [ rdf:type owl:Class ;
                                                owl:unionOf ( [ rdf:type owl:Restriction ;
                                                                owl:onProperty genex:hasAnatomicalEntity ;
                                                                owl:someValuesFrom genex:AnatomicalEntity
                                                              ]
                                                              [ rdf:type owl:Restriction ;
                                                                owl:onProperty genex:hasDevelopmentalStage ;
                                                                owl:someValuesFrom efo:EFO_0000399
                                                              ]
                                                              [ rdf:type owl:Restriction ;
                                                                owl:onProperty genex:hasStrain ;
                                                                owl:someValuesFrom efo:EFO_0005135
                                                              ]
                                                              [ rdf:type owl:Restriction ;
                                                                owl:onProperty genex:hasSex ;
                                                                owl:someValuesFrom xsd:string
                                                              ]
                                                            )
                                              ] ;
                          rdfs:subClassOf [ rdf:type owl:Restriction ;
                                            owl:onProperty obo:RO_0002162 ;
                                            owl:allValuesFrom up:Taxon
                                          ] ;
                          rdfs:comment "A sequence unit (e.g. Gene) is expressed in some expression condition (e.g. anatomical entity and/or developmental stage)."@en ;
                          rdfs:label "gene expression experiment condition"@en ;
                          skos:altLabel "expression condition"@en ,
                                        "sequence unit expression condition"@en .


###  http://purl.org/net/orth#Gene
orth:Gene rdf:type owl:Class ;
          rdfs:subClassOf orth:SequenceUnit ,
                          [ rdf:type owl:Restriction ;
                            owl:onProperty orth:organism ;
                            owl:someValuesFrom orth:Organism
                          ] ,
                          [ rdf:type owl:Restriction ;
                            owl:onProperty obo:RO_0001018 ;
                            owl:allValuesFrom sio:SIO_000750
                          ] ;
          rdfs:label "Gene"@en .


###  http://purl.org/net/orth#GeneTreeNode
orth:GeneTreeNode rdf:type owl:Class ;
                  rdfs:subClassOf obo:CDAO_0000140 ;
                  rdfs:comment "A node of a tree whose leaf nodes are sequence units and whose internal nodes are clusters of homologs"@en ;
                  rdfs:label "Gene tree node"@en .


###  http://purl.org/net/orth#Organism
orth:Organism rdf:type owl:Class ;
              rdfs:subClassOf [ rdf:type owl:Restriction ;
                                owl:onProperty obo:RO_0002162 ;
                                owl:someValuesFrom up:Taxon
                              ] ;
              rdfs:comment "A living being, such as an animal, a plant, a bacterium, or a fungus., Any individual living (or previously living) being. Example: animal, human being. An organim can be associated to a taxon such as \"Homo Sapiens\", NCBI taxonomy identifier: 9606."@en ;
              rdfs:label "Organism"@en ;
              skos:altLabel "Living being"@en .


###  http://purl.org/net/orth#Protein
orth:Protein rdf:type owl:Class ;
             rdfs:subClassOf orth:SequenceUnit ,
                             [ rdf:type owl:Restriction ;
                               owl:onProperty orth:organism ;
                               owl:someValuesFrom orth:Organism
                             ] ,
                             [ rdf:type owl:Restriction ;
                               owl:onProperty obo:RO_0001018 ;
                               owl:allValuesFrom sio:SIO_000750
                             ] ;
             rdfs:label "Protein"@en .


###  http://purl.org/net/orth#SequenceUnit
orth:SequenceUnit rdf:type owl:Class ;
                  rdfs:subClassOf orth:GeneTreeNode ;
                  rdfs:comment "protein or DNA sequence as a unit of comparison"@en ;
                  rdfs:label "Sequence unit"@en .


###  http://purl.org/net/orth#Subgene
orth:Subgene rdf:type owl:Class ;
             rdfs:subClassOf orth:SequenceUnit ,
                             [ rdf:type owl:Restriction ;
                               owl:onProperty obo:CDAO_0000194 ;
                               owl:someValuesFrom orth:Gene
                             ] ;
             rdfs:comment "A region of the sequence of the gene"@en ;
             rdfs:label "gene region"@en ,
                        "region of a gene"@en ,
                        "subgene"@en .


###  http://purl.uniprot.org/core/Rank
up:Rank rdf:type owl:Class ;
        rdfs:comment "A rank of a taxon."^^xsd:string ;
        rdfs:label "Taxon rank"^^xsd:string .


###  http://purl.uniprot.org/core/Taxon
up:Taxon rdf:type owl:Class ;
         rdfs:subClassOf [ rdf:type owl:Restriction ;
                           owl:onProperty up:replaces ;
                           owl:allValuesFrom up:Taxon
                         ] ,
                         [ rdf:type owl:Restriction ;
                           owl:onProperty up:mnemonic ;
                           owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ;
                           owl:onDataRange xsd:string
                         ] ;
         rdfs:comment "An element of a taxonomy for classifying life forms."^^xsd:string ;
         rdfs:label "Taxon"^^xsd:string ;
         rdfs:seeAlso "http://www.ncbi.nlm.nih.gov/books/NBK54428/" .


###  http://semanticscience.org/resource/SIO_000750
sio:SIO_000750 rdf:type owl:Class ;
               rdfs:comment "A database is a data store such as relational, hierarchical and graph databases."@en ;
               rdfs:label "database"@en .


###  http://www.ebi.ac.uk/efo/EFO_0000001
efo:EFO_0000001 rdf:type owl:Class ;
                owl:disjointWith oboInOwl:ObsoleteClass ;
                obo:IAO_0000115 "An experimental factor in Array Express which are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This upper level class is really used to give a root class from which applications can rely on and not be tied to upper ontology classses which do change."^^xsd:string ;
                efo:alternative_term "ExperimentalFactor"^^xsd:string ;
                rdfs:comment "Concept naming convention is lower case natural naming with spaces, when necessary captials should be used, for example disease factor, HIV, breast carcinoma, Ewing's sarcoma"^^xsd:string ;
                rdfs:label "experimental factor"^^xsd:string .


###  http://www.ebi.ac.uk/efo/EFO_0000399
efo:EFO_0000399 rdf:type owl:Class ;
                rdfs:subClassOf <http://www.ifomis.org/bfo/1.1/span#ProcessualEntity> ;
                obo:IAO_0000115 "A developmental stage is spatiotemporal region encompassing some part of the life cycle of an organism, e.g. blastula stage"^^xsd:string ;
                efo:NCI_Thesaurus_definition_citation "NCIt:C43531"^^xsd:string ;
                efo:alternative_term "development stage" ,
                                     "developmental_stage"^^xsd:string ,
                                     "life cycle stage" ;
                rdfs:comment "This branch will be replaced by, and if necessary merged with an Uberon import in future." ;
                rdfs:label "developmental stage"^^xsd:string .


###  http://www.ebi.ac.uk/efo/EFO_0000635
efo:EFO_0000635 rdf:type owl:Class ;
                rdfs:subClassOf genex:AnatomicalEntity ,
                                <http://www.ifomis.org/bfo/1.1/snap#MaterialEntity> ;
                obo:IAO_0000112 "tissue, organ, system, sperm, blood or body location (arm)."^^xsd:string ;
                obo:IAO_0000115 "The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm)."^^xsd:string ;
                efo:NCI_Thesaurus_definition_citation "NCIt:C103199"^^xsd:string ;
                efo:alternative_term "organism_part"^^xsd:string ;
                rdfs:label "organism part"^^xsd:string .


###  http://www.ebi.ac.uk/efo/EFO_0005135
efo:EFO_0005135 rdf:type owl:Class ;
                rdfs:subClassOf obo:OBI_0000181 ;
                obo:IAO_0000115 "A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics." ;
                efo:NCI_Thesaurus_definition_citation "NCIt:C95501"^^xsd:string ;
                rdfs:label "strain"@en .


###  http://www.geneontology.org/formats/oboInOwl#ObsoleteClass
oboInOwl:ObsoleteClass rdf:type owl:Class .


###  http://www.ifomis.org/bfo/1.1/snap#MaterialEntity
<http://www.ifomis.org/bfo/1.1/snap#MaterialEntity> rdf:type owl:Class ;
													skos:relatedMatch sio:SIO_000004;
                                                    rdfs:subClassOf efo:EFO_0000001 ;
                                                    obo:IAO_0000112 "A heart, a human, a fly, a microarray."^^xsd:string ;
                                                    obo:IAO_0000115 "A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray."^^xsd:string ;
                                                    efo:alternative_term "material type" ;
                                                    efo:source_definition "An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology."^^xsd:string ;
                                                    rdfs:label "material entity"^^xsd:string .


###  http://www.ifomis.org/bfo/1.1/span#ProcessualEntity
<http://www.ifomis.org/bfo/1.1/span#ProcessualEntity> rdf:type owl:Class ;
                                                      rdfs:subClassOf efo:EFO_0000001 ;
                                                      obo:IAO_0000115 "A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs."^^xsd:string ;
                                                      efo:NCI_Thesaurus_definition_citation "NCIt:C29862"^^xsd:string ;
                                                      rdfs:label "process"^^xsd:string .


#################################################################
#    Individuals
#################################################################

###  http://purl.obolibrary.org/obo/CIO_0000029
obo:CIO_0000029 rdf:type owl:NamedIndividual ;
                obo:IAO_0000115 "A confidence level representing a high trust in an evidence."^^xsd:string ;
                oboInOwl:id "CIO:0000029"^^xsd:string ;
                rdfs:isDefinedBy "http://purl.obolibrary.org/obo/cio.owl"^^xsd:anyURI ;
                rdfs:label "high confidence level"^^xsd:string .


###  http://purl.obolibrary.org/obo/CIO_0000030
obo:CIO_0000030 rdf:type owl:NamedIndividual ;
                obo:IAO_0000115 "A confidence level representing a moderate trust in an evidence."^^xsd:string ;
                oboInOwl:id "CIO:0000030"^^xsd:string ;
                rdfs:isDefinedBy "http://purl.obolibrary.org/obo/cio.owl"^^xsd:anyURI ;
                rdfs:label "medium confidence level"^^xsd:string .


###  http://purl.obolibrary.org/obo/CIO_0000031
obo:CIO_0000031 rdf:type owl:NamedIndividual ;
                obo:IAO_0000115 "A confidence level representing an absence of trust in an evidence."^^xsd:string ;
                oboInOwl:id "CIO:0000031"^^xsd:string ;
                rdfs:isDefinedBy "http://purl.obolibrary.org/obo/cio.owl"^^xsd:anyURI ;
                rdfs:label "low confidence level"^^xsd:string .


###  http://purl.org/genex#AVERAGE_EXPRESSED
genex:AVERAGE_EXPRESSED rdf:type owl:NamedIndividual ;
                        rdfs:label "average expressed"@en ;
                        skos:altLabel "medium expressed"@en.


###  http://purl.org/genex#HIGHLY_EXPRESSED
genex:HIGHLY_EXPRESSED rdf:type owl:NamedIndividual ;
                       rdfs:comment "g is highly expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background, e.g. all gene expressions taking into account a given gene expression condition."@en ;
                       rdfs:label "highly expressed"@en ;
                       skos:altLabel "over expressed"@en .


###  http://purl.org/genex#HIGH_EXPRESSED
genex:HIGH_EXPRESSED rdf:type owl:NamedIndividual ;
                     rdfs:label "high expressed"@en .


###  http://purl.org/genex#LOWLY_EXPRESSED
genex:LOWLY_EXPRESSED rdf:type owl:NamedIndividual ;
                      rdfs:comment "g is lowly expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background."@en ;
                      rdfs:label "lowly expressed"@en ;
                      skos:altLabel "under expressed"@en .


###  http://purl.org/genex#LOW_EXPRESSED
genex:LOW_EXPRESSED rdf:type owl:NamedIndividual ;
                    rdfs:label "low expressed"@en .


###  http://purl.org/genex#UBIQUITOUSLY_EXPRESSED
genex:UBIQUITOUSLY_EXPRESSED rdf:type owl:NamedIndividual ;
                             rdfs:comment "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x."@en ;
                             rdfs:label "ubiquitously expressed"@en .


###  http://purl.uniprot.org/core/Species
up:Species rdf:type owl:NamedIndividual ,
                    up:Rank ;
           rdfs:label "Taxonomic rank Species"^^xsd:string .


#################################################################
#    Rules
#################################################################

<urn:swrl#e> rdf:type swrl:Variable .

<urn:swrl#cond> rdf:type swrl:Variable .

<urn:swrl#anat> rdf:type swrl:Variable .

<urn:swrl#seq> rdf:type swrl:Variable .

<urn:swrl#stage> rdf:type swrl:Variable .

<urn:swrl#strain> rdf:type swrl:Variable .

[ rdf:type swrl:Imp ;
   swrl:body [ rdf:type swrl:AtomList ;
               rdf:first [ rdf:type swrl:ClassAtom ;
                           swrl:classPredicate genex:AbsenceExpression ;
                           swrl:argument1 <urn:swrl#e>
                         ] ;
               rdf:rest [ rdf:type swrl:AtomList ;
                          rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                      swrl:propertyPredicate genex:hasExpressionCondition ;
                                      swrl:argument1 <urn:swrl#e> ;
                                      swrl:argument2 <urn:swrl#cond>
                                    ] ;
                          rdf:rest [ rdf:type swrl:AtomList ;
                                     rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                                 swrl:propertyPredicate genex:hasStrain ;
                                                 swrl:argument1 <urn:swrl#cond> ;
                                                 swrl:argument2 <urn:swrl#strain>
                                               ] ;
                                     rdf:rest [ rdf:type swrl:AtomList ;
                                                rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                                            swrl:propertyPredicate genex:hasSequenceUnit ;
                                                            swrl:argument1 <urn:swrl#e> ;
                                                            swrl:argument2 <urn:swrl#seq>
                                                          ] ;
                                                rdf:rest rdf:nil
                                              ]
                                   ]
                        ]
             ] ;
   swrl:head [ rdf:type swrl:AtomList ;
               rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                           swrl:propertyPredicate genex:isAbsentIn ;
                           swrl:argument1 <urn:swrl#seq> ;
                           swrl:argument2 <urn:swrl#strain>
                         ] ;
               rdf:rest rdf:nil
             ]
 ] .

[ rdf:type swrl:Imp ;
   swrl:body [ rdf:type swrl:AtomList ;
               rdf:first [ rdf:type swrl:ClassAtom ;
                           swrl:classPredicate genex:Expression ;
                           swrl:argument1 <urn:swrl#e>
                         ] ;
               rdf:rest [ rdf:type swrl:AtomList ;
                          rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                      swrl:propertyPredicate genex:hasExpressionCondition ;
                                      swrl:argument1 <urn:swrl#e> ;
                                      swrl:argument2 <urn:swrl#cond>
                                    ] ;
                          rdf:rest [ rdf:type swrl:AtomList ;
                                     rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                                 swrl:propertyPredicate genex:hasAnatomicalEntity ;
                                                 swrl:argument1 <urn:swrl#cond> ;
                                                 swrl:argument2 <urn:swrl#anat>
                                               ] ;
                                     rdf:rest [ rdf:type swrl:AtomList ;
                                                rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                                            swrl:propertyPredicate genex:hasSequenceUnit ;
                                                            swrl:argument1 <urn:swrl#e> ;
                                                            swrl:argument2 <urn:swrl#seq>
                                                          ] ;
                                                rdf:rest rdf:nil
                                              ]
                                   ]
                        ]
             ] ;
   swrl:head [ rdf:type swrl:AtomList ;
               rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                           swrl:propertyPredicate genex:isExpressedIn ;
                           swrl:argument1 <urn:swrl#seq> ;
                           swrl:argument2 <urn:swrl#anat>
                         ] ;
               rdf:rest rdf:nil
             ]
 ] .

[ rdf:type swrl:Imp ;
   swrl:body [ rdf:type swrl:AtomList ;
               rdf:first [ rdf:type swrl:ClassAtom ;
                           swrl:classPredicate genex:Expression ;
                           swrl:argument1 <urn:swrl#e>
                         ] ;
               rdf:rest [ rdf:type swrl:AtomList ;
                          rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                      swrl:propertyPredicate genex:hasExpressionCondition ;
                                      swrl:argument1 <urn:swrl#e> ;
                                      swrl:argument2 <urn:swrl#cond>
                                    ] ;
                          rdf:rest [ rdf:type swrl:AtomList ;
                                     rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                                 swrl:propertyPredicate genex:hasDevelopmentalStage ;
                                                 swrl:argument1 <urn:swrl#cond> ;
                                                 swrl:argument2 <urn:swrl#stage>
                                               ] ;
                                     rdf:rest [ rdf:type swrl:AtomList ;
                                                rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                                            swrl:propertyPredicate genex:hasSequenceUnit ;
                                                            swrl:argument1 <urn:swrl#e> ;
                                                            swrl:argument2 <urn:swrl#seq>
                                                          ] ;
                                                rdf:rest rdf:nil
                                              ]
                                   ]
                        ]
             ] ;
   swrl:head [ rdf:type swrl:AtomList ;
               rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                           swrl:propertyPredicate genex:isExpressedIn ;
                           swrl:argument1 <urn:swrl#seq> ;
                           swrl:argument2 <urn:swrl#stage>
                         ] ;
               rdf:rest rdf:nil
             ]
 ] .

[ rdf:type swrl:Imp ;
   swrl:body [ rdf:type swrl:AtomList ;
               rdf:first [ rdf:type swrl:ClassAtom ;
                           swrl:classPredicate genex:Expression ;
                           swrl:argument1 <urn:swrl#e>
                         ] ;
               rdf:rest [ rdf:type swrl:AtomList ;
                          rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                      swrl:propertyPredicate genex:hasExpressionCondition ;
                                      swrl:argument1 <urn:swrl#e> ;
                                      swrl:argument2 <urn:swrl#cond>
                                    ] ;
                          rdf:rest [ rdf:type swrl:AtomList ;
                                     rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                                 swrl:propertyPredicate genex:hasSequenceUnit ;
                                                 swrl:argument1 <urn:swrl#e> ;
                                                 swrl:argument2 <urn:swrl#seq>
                                               ] ;
                                     rdf:rest rdf:nil
                                   ]
                        ]
             ] ;
   swrl:head [ rdf:type swrl:AtomList ;
               rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                           swrl:propertyPredicate genex:isExpressedIn ;
                           swrl:argument1 <urn:swrl#seq> ;
                           swrl:argument2 <urn:swrl#cond>
                         ] ;
               rdf:rest rdf:nil
             ]
 ] .

[ rdf:type swrl:Imp ;
   swrl:body [ rdf:type swrl:AtomList ;
               rdf:first [ rdf:type swrl:ClassAtom ;
                           swrl:classPredicate genex:Expression ;
                           swrl:argument1 <urn:swrl#e>
                         ] ;
               rdf:rest [ rdf:type swrl:AtomList ;
                          rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                      swrl:propertyPredicate genex:hasExpressionCondition ;
                                      swrl:argument1 <urn:swrl#e> ;
                                      swrl:argument2 <urn:swrl#cond>
                                    ] ;
                          rdf:rest [ rdf:type swrl:AtomList ;
                                     rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                                 swrl:propertyPredicate genex:hasStrain ;
                                                 swrl:argument1 <urn:swrl#cond> ;
                                                 swrl:argument2 <urn:swrl#strain>
                                               ] ;
                                     rdf:rest [ rdf:type swrl:AtomList ;
                                                rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                                            swrl:propertyPredicate genex:hasSequenceUnit ;
                                                            swrl:argument1 <urn:swrl#e> ;
                                                            swrl:argument2 <urn:swrl#seq>
                                                          ] ;
                                                rdf:rest rdf:nil
                                              ]
                                   ]
                        ]
             ] ;
   swrl:head [ rdf:type swrl:AtomList ;
               rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                           swrl:propertyPredicate genex:isExpressedIn ;
                           swrl:argument1 <urn:swrl#seq> ;
                           swrl:argument2 <urn:swrl#strain>
                         ] ;
               rdf:rest rdf:nil
             ]
 ] .

[ rdf:type swrl:Imp ;
   swrl:body [ rdf:type swrl:AtomList ;
               rdf:first [ rdf:type swrl:ClassAtom ;
                           swrl:classPredicate genex:AbsenceExpression ;
                           swrl:argument1 <urn:swrl#e>
                         ] ;
               rdf:rest [ rdf:type swrl:AtomList ;
                          rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                      swrl:propertyPredicate genex:hasExpressionCondition ;
                                      swrl:argument1 <urn:swrl#e> ;
                                      swrl:argument2 <urn:swrl#cond>
                                    ] ;
                          rdf:rest [ rdf:type swrl:AtomList ;
                                     rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                                 swrl:propertyPredicate genex:hasAnatomicalEntity ;
                                                 swrl:argument1 <urn:swrl#cond> ;
                                                 swrl:argument2 <urn:swrl#anat>
                                               ] ;
                                     rdf:rest [ rdf:type swrl:AtomList ;
                                                rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                                            swrl:propertyPredicate genex:hasSequenceUnit ;
                                                            swrl:argument1 <urn:swrl#e> ;
                                                            swrl:argument2 <urn:swrl#seq>
                                                          ] ;
                                                rdf:rest rdf:nil
                                              ]
                                   ]
                        ]
             ] ;
   swrl:head [ rdf:type swrl:AtomList ;
               rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                           swrl:propertyPredicate genex:isAbsentIn ;
                           swrl:argument1 <urn:swrl#seq> ;
                           swrl:argument2 <urn:swrl#anat>
                         ] ;
               rdf:rest rdf:nil
             ]
 ] .

[ rdf:type swrl:Imp ;
   swrl:body [ rdf:type swrl:AtomList ;
               rdf:first [ rdf:type swrl:ClassAtom ;
                           swrl:classPredicate genex:AbsenceExpression ;
                           swrl:argument1 <urn:swrl#e>
                         ] ;
               rdf:rest [ rdf:type swrl:AtomList ;
                          rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                      swrl:propertyPredicate genex:hasExpressionCondition ;
                                      swrl:argument1 <urn:swrl#e> ;
                                      swrl:argument2 <urn:swrl#cond>
                                    ] ;
                          rdf:rest [ rdf:type swrl:AtomList ;
                                     rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                                 swrl:propertyPredicate genex:hasDevelopmentalStage ;
                                                 swrl:argument1 <urn:swrl#cond> ;
                                                 swrl:argument2 <urn:swrl#stage>
                                               ] ;
                                     rdf:rest [ rdf:type swrl:AtomList ;
                                                rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                                            swrl:propertyPredicate genex:hasSequenceUnit ;
                                                            swrl:argument1 <urn:swrl#e> ;
                                                            swrl:argument2 <urn:swrl#seq>
                                                          ] ;
                                                rdf:rest rdf:nil
                                              ]
                                   ]
                        ]
             ] ;
   swrl:head [ rdf:type swrl:AtomList ;
               rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                           swrl:propertyPredicate genex:isAbsentIn ;
                           swrl:argument1 <urn:swrl#seq> ;
                           swrl:argument2 <urn:swrl#stage>
                         ] ;
               rdf:rest rdf:nil
             ]
 ] .

[ rdf:type swrl:Imp ;
   swrl:body [ rdf:type swrl:AtomList ;
               rdf:first [ rdf:type swrl:ClassAtom ;
                           swrl:classPredicate genex:AbsenceExpression ;
                           swrl:argument1 <urn:swrl#e>
                         ] ;
               rdf:rest [ rdf:type swrl:AtomList ;
                          rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                      swrl:propertyPredicate genex:hasExpressionCondition ;
                                      swrl:argument1 <urn:swrl#e> ;
                                      swrl:argument2 <urn:swrl#cond>
                                    ] ;
                          rdf:rest [ rdf:type swrl:AtomList ;
                                     rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                                                 swrl:propertyPredicate genex:hasSequenceUnit ;
                                                 swrl:argument1 <urn:swrl#e> ;
                                                 swrl:argument2 <urn:swrl#seq>
                                               ] ;
                                     rdf:rest rdf:nil
                                   ]
                        ]
             ] ;
   swrl:head [ rdf:type swrl:AtomList ;
               rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
                           swrl:propertyPredicate genex:isAbsentIn ;
                           swrl:argument1 <urn:swrl#seq> ;
                           swrl:argument2 <urn:swrl#cond>
                         ] ;
               rdf:rest rdf:nil
             ]
 ] .

###  Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi

##############################
###Added new terms from dcterms and dc element vocabularies
#############################

dc:creator
    terms:description "Examples of a Creator include a person, an organization, or a service. Typically, the name of a Creator should be used to indicate the entity."@en ;
    terms:issued "1999-07-02"^^<http://www.w3.org/2001/XMLSchema#date> ;
    a rdf:Property ;
    rdfs:comment "An entity primarily responsible for making the resource."@en ;
    rdfs:isDefinedBy <http://purl.org/dc/elements/1.1/> ;
    rdfs:label "Creator"@en ;
    skos:note "A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/creator) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/).  See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation."@en .

dc:identifier
    terms:description "Recommended practice is to identify the resource by means of a string conforming to an identification system."@en ;
    terms:issued "1999-07-02"^^<http://www.w3.org/2001/XMLSchema#date> ;
    a rdf:Property ;
    rdfs:comment "An unambiguous reference to the resource within a given context."@en ;
    rdfs:isDefinedBy <http://purl.org/dc/elements/1.1/> ;
    rdfs:label "Identifier"@en ;
    skos:note "A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/identifier) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/).  See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation."@en .

terms:source rdf:type rdf:Property, owl:DatatypeProperty ;
    terms:description "This property is intended to be used with non-literal values. The described resource may be derived from the related resource in whole or in part. Best practice is to identify the related resource by means of a URI or a string conforming to a formal identification system."@en ;
    terms:issued "2008-01-14"^^<http://www.w3.org/2001/XMLSchema#date> ;
    rdfs:comment "A related resource from which the described resource is derived."@en ;
    rdfs:range rdfs:Literal; 
    rdfs:isDefinedBy <http://purl.org/dc/terms/> ;
    rdfs:label "Source"@en .

terms:references
   terms:description "This property is intended to be used with non-literal values. This property is an inverse property of Is Referenced By."@en ;
    terms:issued "2000-07-11"^^<http://www.w3.org/2001/XMLSchema#date> ;
    a rdf:Property ;
    rdfs:comment "A related resource that is referenced, cited, or otherwise pointed to by the described resource."@en ;
    rdfs:isDefinedBy <http://purl.org/dc/terms/> ;
    rdfs:label "References"@en .

terms:isReferencedBy
    terms:description "This property is intended to be used with non-literal values. This property is an inverse property of References."@en ;
    owl:inverseOf terms:references;
    terms:issued "2000-07-11"^^<http://www.w3.org/2001/XMLSchema#date> ;
    a rdf:Property ;
    rdfs:comment "A related resource that references, cites, or otherwise points to the described resource."@en ;
    rdfs:isDefinedBy <http://purl.org/dc/terms/> ;
    rdfs:label "Is Referenced By"@en .

terms:license
    terms:description "Recommended practice is to identify the license document with a URI. If this is not possible or feasible, a literal value that identifies the license may be provided."@en ;
    a rdf:Property ;
    rdfs:comment "A legal document giving official permission to do something with the resource."@en ;
    rdfs:isDefinedBy <http://purl.org/dc/terms/> ;
    rdfs:label "License"@en .

terms:modified
    terms:description "Recommended practice is to describe the date, date/time, or period of time as recommended for the property Date, of which this is a subproperty."@en ;
    terms:issued "2000-07-11"^^<http://www.w3.org/2001/XMLSchema#date> ;
    a rdf:Property ;
    rdfs:comment "Date on which the resource was changed."@en ;
    rdfs:isDefinedBy <http://purl.org/dc/terms/> ;
    rdfs:label "Date Modified"@en  .

terms:provenance
    rdfs:range terms:ProvenanceStatement ;
    terms:description "The statement may include a description of any changes successive custodians made to the resource."@en ;
    terms:issued "2004-09-20"^^<http://www.w3.org/2001/XMLSchema#date> ;
    a owl:AnnotationProperty ;
    rdfs:comment "A statement of any changes in ownership and custody of the resource since its creation that are significant for its authenticity, integrity, and interpretation."@en ;
    rdfs:isDefinedBy <http://purl.org/dc/terms/> ;
    rdfs:label "Provenance"@en .

terms:ProvenanceStatement
    terms:issued "2008-01-14"^^<http://www.w3.org/2001/XMLSchema#date> ;
    a rdfs:Class ;
    rdfs:comment "Any changes in ownership and custody of a resource since its creation that are significant for its authenticity, integrity, and interpretation."@en ;
    rdfs:isDefinedBy <http://purl.org/dc/terms/> ;
    rdfs:label "Provenance Statement"@en .

terms:issued
    terms:description "Recommended practice is to describe the date, date/time, or period of time as recommended for the property Date, of which this is a subproperty."@en ;
    terms:issued "2000-07-11"^^<http://www.w3.org/2001/XMLSchema#date> ;
    a rdf:Property ;
    rdfs:comment "Date of formal issuance of the resource."@en ;
    rdfs:isDefinedBy <http://purl.org/dc/terms/> ;
    rdfs:label "Date Issued"@en  .

terms:created
    terms:description "Recommended practice is to describe the date, date/time, or period of time as recommended for the property Date, of which this is a subproperty."@en ;
    terms:issued "2000-07-11"^^<http://www.w3.org/2001/XMLSchema#date> ;
    a rdf:Property ;
    rdfs:comment "Date of creation of the resource."@en ;
    rdfs:isDefinedBy <http://purl.org/dc/terms/> ;
    rdfs:label "Date Created"@en .

terms:creator
    rdfs:range terms:Agent ;
    terms:description "Recommended practice is to identify the creator with a URI.  If this is not possible or feasible, a literal value that identifies the creator may be provided."@en ;
    terms:issued "2008-01-14"^^<http://www.w3.org/2001/XMLSchema#date> ;
    a rdf:Property ;
    rdfs:comment "An entity responsible for making the resource."@en ;
    rdfs:isDefinedBy <http://purl.org/dc/terms/> ;
    rdfs:label "Creator"@en ;
    owl:equivalentProperty <http://xmlns.com/foaf/0.1/maker> .

:MODIFIED_EFO_TERM_RESTRICTIONS a terms:ProvenanceStatement;
    terms:created "2020-08-03"^^<http://www.w3.org/2001/XMLSchema#date> ;
    dc:description "The term from <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> was adapted for the cancer biomarker data context. This provenance statement is asserted only for the case of modifications that include either deletion or replacement of class restrictions (e.g. quantifiers) and disjunction statements or property domain and ranges. Disjunction assertions are often removed for the sake of simplicity. This is because many of the dinjunctions and domain specificities are out of scope when actually structuring cancer biomarker data.";
    terms:creator  <http://purl.org/query/tarcisiomf> .

<http://purl.org/query/tarcisiomf> a foaf:Person;
    foaf:name "Tarcisio Mendes de Farias";
    foaf:homepage <https://www.researchgate.net/profile/Tarcisio_Mendes_De_Farias>;
    foaf:mbox <mailto:tarcisio.mendesdefarias@unil.ch> .

<https://www.sib.swiss/about-sib/organization> a terms:Agent;
    foaf:member <http://purl.org/query/tarcisiomf>;
    foaf:name "SIB Swiss Institute of Bioinformatics";
    foaf:homepage <http://www.sib.swiss> .

terms:title
    terms:issued "2008-01-14"^^<http://www.w3.org/2001/XMLSchema#date> ;
    a rdf:Property ;
    rdfs:comment "A name given to the resource."@en ;
    rdfs:isDefinedBy <http://purl.org/dc/terms/> ;
    rdfs:label "Title"@en ;
    rdfs:range rdfs:Literal .


###################################################
###Other terms extracted from RO core vocabulary
###################################################

###  http://purl.obolibrary.org/obo/RO_0002351
obo:RO_0002351 rdf:type owl:ObjectProperty ;
               rdfs:subPropertyOf obo:BFO_0000051 ;
               rdf:type owl:IrreflexiveProperty ;
               obo:IAO_0000115 "has member is a mereological relation between a collection and an item." ;
               rdfs:label "has member"@en ;
               rdfs:isDefinedBy <http://purl.obolibrary.org/obo/ro/core.owl>;
               terms:license <https://creativecommons.org/publicdomain/zero/1.0/> .


###  http://purl.obolibrary.org/obo/BFO_0000051
obo:BFO_0000051 rdf:type owl:ObjectProperty ,
                         owl:TransitiveProperty ;
                obo:IAO_0000112 "my body has part my brain (continuant parthood, two material entities)"@en ,
                                "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en ,
                                "this year has part this day (occurrent parthood)"@en ;
                obo:IAO_0000115 "a core relation that holds between a whole and its part"@en ;
                obo:IAO_0000116 "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 ,
                                "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 ,
                                """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 ;
                rdfs:label "has part"@en ;
               rdfs:isDefinedBy <http://purl.obolibrary.org/obo/ro/core.owl>;
               terms:license <https://creativecommons.org/publicdomain/zero/1.0/> .


###################################################
### Added new terms from EFO ontology APACHE LICENSE, VERSION 2.0 http://www.apache.org/licenses/LICENSE-2.0
###################################################

###  http://purl.obolibrary.org/obo/RO_0001025
obo:RO_0001025 rdf:type owl:ObjectProperty ;
               oboInOwl:hasDbXref "RO:0001025"^^xsd:string ;
               rdfs:label "located_in"^^xsd:string ;
               skos:altLabel "located in";
               rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl>;
               terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://purl.obolibrary.org/obo/BFO_0000020
obo:BFO_0000020 rdf:type owl:Class ;
                rdfs:subClassOf efo:EFO_0000001 ;
                obo:IAO_0000115 "An experimental factor which is a property or characteristic of some other entity.  For example, the mouse has the colour white."^^xsd:string ;
                efo:source_definition "A continuant [snap: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."^^xsd:string ;
                rdfs:label "material property"^^xsd:string ;
                rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl>;
                terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://purl.obolibrary.org/obo/BFO_0000023
obo:BFO_0000023 rdf:type owl:Class ;
                rdfs:subClassOf obo:BFO_0000020 ;
                obo:IAO_0000112 "For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease."^^xsd:string ;
                obo:IAO_0000115 "A role is an entity which is borne in a material entity in some kinds of natural, social or institutional contexts, but which is not essential to the fundamental definition of that material entity (i.e. the material entity exists with or without the role).  For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease."^^xsd:string ;
                efo:source_definition "A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts."^^xsd:string ;
                rdfs:label "role"^^xsd:string ;
                rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://purl.obolibrary.org/obo/CHEBI_24432
obo:CHEBI_24432 rdf:type owl:Class ;
                rdfs:subClassOf obo:BFO_0000023 ;
                obo:IAO_0000115 "A role played by the molecular entity or part thereof within a biological context."^^xsd:string ;
                rdfs:label "biological role"^^xsd:string ;
                rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://purl.obolibrary.org/obo/CHEBI_59163
obo:CHEBI_59163 rdf:type owl:Class ;
                rdfs:subClassOf obo:CHEBI_24432 ;
                obo:IAO_0000115 "A substance used as an indicator of a biological state."^^xsd:string ;
                rdfs:label "biomarker"^^xsd:string ;
                skos:exactMatch <http://purl.obolibrary.org/obo/NCIT_C16342> ;
                oboInOwl:hasExactSynonym "biological marker"^^xsd:string ;
                rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://www.ebi.ac.uk/efo/EFO_0000408
efo:EFO_0000408 rdf:type owl:Class ;
                rdfs:subClassOf obo:BFO_0000016 ;
                obo:IAO_0000115 "A disease is a disposition that describes states of disease associated with a particular sample and/or organism."^^xsd:string ,
                                "A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism."^^xsd:string ;
                obo:IAO_0000117 "James Malone"^^xsd:string ;
                skos:exactMatch <http://identifiers.org/mesh/D004194> ,
                                 <http://identifiers.org/snomedct/64572001> ,
                                 <http://linkedlifedata.com/resource/umls/id/C0012634> ,
                                 obo:DOID_4 ,
                                 obo:NCIT_C2991 ,
                                 obo:Orphanet_377788 ;
                oboInOwl:hasDbXref "DOID:4"^^xsd:string ,
                                   "ICD10:N18"^^xsd:string ,
                                   "ICD10:R69"^^xsd:string ,
                                   "ICD9:799.9"^^xsd:string ,
                                   "MESH:D004194"^^xsd:string ,
                                   "MONDO:0000001"^^xsd:string ,
                                   "MSH:D004194"^^xsd:string ,
                                   "NCIT:C2991"^^xsd:string ,
                                   "OGMS:0000031"^^xsd:string ,
                                   "Orphanet:377788"^^xsd:string ,
                                   "SCTID:64572001"^^xsd:string ,
                                   "SNOMEDCT:64572001"^^xsd:string ,
                                   "UMLS:C0012634"^^xsd:string ;
                oboInOwl:hasExactSynonym "Homo sapiens disease"^^xsd:string ,
                                         "condition"^^xsd:string ,
                                         "disease"^^xsd:string ,
                                         "disease or disorder"^^xsd:string ,
                                         "disease or disorder, non-neoplastic"^^xsd:string ,
                                         "diseases"^^xsd:string ,
                                         "diseases and disorders"^^xsd:string ,
                                         "disorder"^^xsd:string ,
                                         "disorders"^^xsd:string ,
                                         "human disease"^^xsd:string ,
                                         "medical condition"^^xsd:string ,
                                         "other disease"^^xsd:string ;
                oboInOwl:id "EFO:0000408"^^xsd:string ;
                rdfs:label "disease"^^xsd:string ;
                terms:modified "2020-08-03" ;
                terms:contributor <http://purl.org/query/tarcisiotmf>;
                terms:provenance :MODIFIED_EFO_TERM_RESTRICTIONS ;
                terms:license <http://www.apache.org/licenses/LICENSE-2.0> . 

###  http://purl.obolibrary.org/obo/BFO_0000016
obo:BFO_0000016 rdf:type owl:Class ;
                rdfs:subClassOf obo:BFO_0000020 ;
                obo:IAO_0000112 "For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease."^^xsd:string ;
                obo:IAO_0000115 "A disposition is an entity that causes a specific process or transformation in an entity in which it inheres, under specific circumstances and in conjunction with the laws of nature. For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease."^^xsd:string ;
                obo:IAO_0000117 "James Malone modified from original"^^xsd:string ;
                efo:ArrayExpress_label "disease property"^^xsd:string ;
                efo:EFO_URI "http://www.ebi.ac.uk/efo/EFO_0001438"^^xsd:string ;
                efo:source_definition "A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C."^^xsd:string ;
                oboInOwl:hasAlternativeId "http://www.ifomis.org/bfo/1.1/snap#Disposition" ;
                oboInOwl:hasDbXref "NCIt:C41205"^^xsd:string ;
                rdfs:label "disposition"^^xsd:string ;                
                rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                terms:license <http://www.apache.org/licenses/LICENSE-2.0> .


###  http://purl.obolibrary.org/obo/MONDO_0045024
obo:MONDO_0045024 rdf:type owl:Class ;
                  owl:equivalentClass [ rdf:type owl:Class ;
                                        owl:unionOf ( obo:MONDO_0021074
                                                      obo:MONDO_0023370
                                                      obo:MONDO_0045054
                                                      efo:EFO_0000536
                                                    )
                                      ] ;
                  rdfs:subClassOf efo:EFO_0000408 ;
                  obo:IAO_0000115 "Any disorder that features disrupted cell proliferation. Includes hyperplasia, neoplastic syndrome and isolated neoplasm diseases as well as precancerous conditions."^^xsd:string ;
                  oboInOwl:id "MONDO:0045024"^^xsd:string ;
                  rdfs:label "cell proliferation disorder"^^xsd:string ;                
                  rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                  terms:license <http://www.apache.org/licenses/LICENSE-2.0> .


###  http://purl.obolibrary.org/obo/MONDO_0021074
obo:MONDO_0021074 rdf:type owl:Class ;
                  rdfs:subClassOf obo:MONDO_0045024 ;
                  obo:IAO_0000115 "A pathological process with signs indicating it may become cancerous. Representative examples include leukoplakia, dysplastic nevus, actinic keratosis, xeroderma pigmentosum, and intraepithelial neoplasia."^^xsd:string ;
                  skos:closeMatch <http://linkedlifedata.com/resource/umls/id/C0032927> ;
                  skos:exactMatch <http://identifiers.org/mesh/D011230> ,
                                   obo:NCIT_C3341 ;
                  oboInOwl:hasDbXref "MESH:D011230"^^xsd:string ,
                                     "NCIT:C3341"^^xsd:string ;
                  oboInOwl:hasExactSynonym "precancerous condition"^^xsd:string ,
                                           "precancerous state"^^xsd:string ,
                                           "premalignant condition"^^xsd:string ,
                                           "premalignant state"^^xsd:string ;
                  oboInOwl:id "MONDO:0021074"^^xsd:string ;
                  rdfs:comment "Editor note: check classification. Also consider changing def, NCIT defines as disease. Also consider a grouping for this and paraneoplastic syndrome"^^xsd:string ;
                  rdfs:label "precancerous condition"^^xsd:string ;                
                  rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                  terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://purl.obolibrary.org/obo/MONDO_0023370
obo:MONDO_0023370 rdf:type owl:Class ;
                  owl:equivalentClass [ rdf:type owl:Class ;
                                        owl:unionOf ( obo:MONDO_0021058
                                                      efo:EFO_0000616
                                                    )
                                      ] ;
                  rdfs:subClassOf obo:MONDO_0045024 ;
                  obo:IAO_0000115 "Either an isolated neoplasm or a syndrome with neoplasm as a major feature."^^xsd:string ;
                  oboInOwl:hasRelatedSynonym "neoplastic disease"^^xsd:string ,
                                             "neoplastic disorder"^^xsd:string ;
                  oboInOwl:id "MONDO:0023370"^^xsd:string ;
                  rdfs:label "neoplastic disease or syndrome"^^xsd:string ;                
                  rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                  terms:license <http://www.apache.org/licenses/LICENSE-2.0> .


###  http://purl.obolibrary.org/obo/MONDO_0045054
obo:MONDO_0045054 rdf:type owl:Class ;
                  rdfs:subClassOf obo:MONDO_0045024 ;
                  obo:IAO_0000115 "A disorder either associated with an increased risk for malignant transformation (e.g., intraepithelial neoplasia, leukoplakia, dysplastic nevus, myelodysplastic syndrome) or that develops as a result of the presence of an existing malignant neoplasm (e.g., paraneoplastic syndrome)."^^xsd:string ;
                  skos:exactMatch <http://linkedlifedata.com/resource/umls/id/C0280950> ,
                                   obo:NCIT_C8278 ;
                  oboInOwl:hasDbXref "NCIT:C8278"^^xsd:string ,
                                     "UMLS:C0280950"^^xsd:string ;
                  oboInOwl:hasExactSynonym "cancer related problem/condition"^^xsd:string ,
                                           "cancer-related condition"^^xsd:string ,
                                           "cancer-related problem or condition"^^xsd:string ,
                                           "oncologic complications"^^xsd:string ,
                                           "problem/condition, cancer related"^^xsd:string ,
                                           "problem/condition, cancer-related"^^xsd:string ;
                  oboInOwl:id "MONDO:0045054"^^xsd:string ;
                  rdfs:label "cancer-related condition"^^xsd:string ;                
                  rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                  terms:license <http://www.apache.org/licenses/LICENSE-2.0> .


###  http://www.ebi.ac.uk/efo/EFO_0000536
efo:EFO_0000536 rdf:type owl:Class ;
                rdfs:subClassOf obo:MONDO_0045024 ;
                obo:IAO_0000115 "An abnormal increase in the number of (otherwise normal) cells in an organ or a tissue with consequent enlargement."^^xsd:string ,
                                "An abnormal increase in the number of cells in an organ or a tissue with consequent enlargement."^^xsd:string ;
                skos:closeMatch <http://identifiers.org/snomedct/76197007> ,
                                 <http://linkedlifedata.com/resource/umls/id/C0020507> ;
                skos:exactMatch <http://identifiers.org/mesh/D006965> ,
                                 obo:NCIT_C3113 ;
                oboInOwl:hasDbXref "MESH:D006965"^^xsd:string ,
                                   "MONDO:0005043"^^xsd:string ,
                                   "MSH:D006965"^^xsd:string ,
                                   "NCIT:C3113"^^xsd:string ,
                                   "NCIt:C3113"^^xsd:string ,
                                   "SNOMEDCT:76197007"^^xsd:string ;
                oboInOwl:hasExactSynonym "Hyperplastic"^^xsd:string ,
                                         "hyperplasia"^^xsd:string ,
                                         "hyperplastic"^^xsd:string ;
                oboInOwl:id "EFO:0000536"^^xsd:string ;
                rdfs:label "hyperplasia"^^xsd:string ;                
                rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                terms:license <http://www.apache.org/licenses/LICENSE-2.0> .


###  http://purl.obolibrary.org/obo/MONDO_0021058
obo:MONDO_0021058 rdf:type owl:Class ;
                  owl:equivalentClass [ owl:intersectionOf ( obo:MONDO_0002254
                                                             [ rdf:type owl:Restriction ;
                                                               owl:onProperty mondo:disease_has_major_feature ;
                                                               owl:someValuesFrom efo:EFO_0000616
                                                             ]
                                                           ) ;
                                        rdf:type owl:Class
                                      ] ;
                  rdfs:subClassOf obo:MONDO_0002254 ,
                                  obo:MONDO_0023370 ,
                                  [ rdf:type owl:Restriction ;
                                    owl:onProperty obo:RO_0002573 ;
                                    owl:someValuesFrom obo:MONDO_0021136
                                  ] ,
                                  [ rdf:type owl:Restriction ;
                                    owl:onProperty mondo:disease_has_major_feature ;
                                    owl:someValuesFrom efo:EFO_0000616
                                  ] ;
                  obo:IAO_0000115 "A broad classification for disorders in which the development of neoplasms typically occur in association with a characteristic set of signs or symptoms. These disorders may be inherited or acquired."^^xsd:string ;
                  skos:closeMatch <http://linkedlifedata.com/resource/umls/id/C1882062> ;
                  skos:exactMatch obo:NCIT_C54705 ;
                  oboInOwl:hasDbXref "NCIT:C54705"^^xsd:string ;
                  oboInOwl:hasExactSynonym "cancer-related syndrome"^^xsd:string ,
                                           "neoplastic syndrome"^^xsd:string ,
                                           "tumor syndrome"^^xsd:string ;
                  oboInOwl:id "MONDO:0021058"^^xsd:string ;
                  rdfs:label "neoplastic syndrome"^^xsd:string ;                
                  rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                  terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://purl.obolibrary.org/obo/MONDO_0002254
obo:MONDO_0002254 rdf:type owl:Class ;
                  owl:equivalentClass [ owl:intersectionOf ( efo:EFO_0000408
                                                             [ rdf:type owl:Restriction ;
                                                               owl:onProperty obo:RO_0002573 ;
                                                               owl:someValuesFrom obo:MONDO_0021127
                                                             ]
                                                           ) ;
                                        rdf:type owl:Class
                                      ] ;
                  rdfs:subClassOf efo:EFO_0000408 ,
                                  [ rdf:type owl:Restriction ;
                                    owl:onProperty obo:RO_0002573 ;
                                    owl:someValuesFrom obo:MONDO_0021127
                                  ] ;
                  obo:IAO_0000115 "A group of signs, symptoms, and clinicopathological characteristics that may or may not have a genetic basis and collectively define an abnormal condition."^^xsd:string ;
                  skos:exactMatch <http://identifiers.org/mesh/D013577> ,
                                   <http://linkedlifedata.com/resource/umls/id/C0039082> ,
                                   obo:DOID_225 ,
                                   obo:NCIT_C28193 ;
                  oboInOwl:hasDbXref "DOID:225"^^xsd:string ,
                                     "MESH:D013577"^^xsd:string ,
                                     "NCIT:C28193"^^xsd:string ,
                                     "OGMS:0000086"^^xsd:string ,
                                     "UMLS:C0039082"^^xsd:string ;
                  oboInOwl:hasExactSynonym "cluster, symptom"^^xsd:string ,
                                           "clusters, symptom"^^xsd:string ,
                                           "symptom cluster"^^xsd:string ,
                                           "symptom clusters"^^xsd:string ,
                                           "syndrome"^^xsd:string ,
                                           "syndrome associated with disease or disorder"^^xsd:string ,
                                           "syndromes"^^xsd:string ,
                                           "syndromic disease"^^xsd:string ,
                                           "syndromic disease or disorder"^^xsd:string ;
                  oboInOwl:hasRelatedSynonym "syndrome associated with disease or disorder"^^xsd:string ;
                  oboInOwl:id "MONDO:0002254"^^xsd:string ;
                  rdfs:label "syndromic disease"^^xsd:string ;                
                rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://purl.obolibrary.org/obo/MONDO_0021127
obo:MONDO_0021127 rdf:type owl:Class ;
                  rdfs:subClassOf obo:MONDO_0021126 ;
                  obo:IAO_0000115 "An characteristic of a disease in which the disease is not manifested as an isolated feature but has multiple distinct features."^^xsd:string ;
                  oboInOwl:id "MONDO:0021127"^^xsd:string ;
                  rdfs:label "has a syndromic presentation"^^xsd:string ;                
                rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://purl.obolibrary.org/obo/MONDO_0021126
obo:MONDO_0021126 rdf:type owl:Class ;
                  rdfs:subClassOf efo:EFO_0009813 ;
                  obo:IAO_0000115 "An characteristic of a disease that varies depending on whether the disease appears as an isolated feature or whether the disease is a syndrome consisting of multiple features."^^xsd:string ;
                  oboInOwl:id "MONDO:0021126"^^xsd:string ;
                  rdfs:label "syndromic or isolated"^^xsd:string ;                
                rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://purl.obolibrary.org/obo/mondo#disease_has_major_feature
mondo:disease_has_major_feature rdf:type owl:ObjectProperty ;
                                rdfs:subPropertyOf obo:RO_0004029 ;
                                oboInOwl:id "disease_has_major_feature"^^xsd:string ;
                                rdfs:label "disease has major feature"^^xsd:string ;                
                  rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                  terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://purl.obolibrary.org/obo/RO_0004029
obo:RO_0004029 rdf:type owl:ObjectProperty ;
               obo:IAO_0000115 "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease."^^xsd:string ;
               oboInOwl:hasDbXref "RO:0004029"^^xsd:string ;
               oboInOwl:id "disease_has_feature"^^xsd:string ;
               oboInOwl:shorthand "disease_has_feature"^^xsd:string ;
               rdfs:label "disease has feature"^^xsd:string ;                
               rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
               terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://purl.obolibrary.org/obo/RO_0002573
obo:RO_0002573 rdf:type owl:ObjectProperty ;
               oboInOwl:hasDbXref "RO:0002573"^^xsd:string ;
               oboInOwl:id "has_modifier"^^xsd:string ;
               oboInOwl:shorthand "has_modifier"^^xsd:string ;
               rdfs:label "has modifier"^^xsd:string ;                
               rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
               terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://purl.obolibrary.org/obo/MONDO_0021136
obo:MONDO_0021136 rdf:type owl:Class ;
                  rdfs:subClassOf obo:MONDO_0021135 ;
                  obo:IAO_0000115 "A disease or disorder is defined as rare in Europe when it affects fewer than 1 in 2000. A disease or disorder is defined as rare in the USA when it affects fewer than 200,000 Americans at any given time. Here we take the European definition to be consistent with Orphanet."^^xsd:string ;
                  oboInOwl:hasExactSynonym "rare (European definition)"^^xsd:string ;
                  oboInOwl:id "MONDO:0021136"^^xsd:string ;
                  rdfs:label "rare"^^xsd:string ;                
               rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
               terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://purl.obolibrary.org/obo/MONDO_0021135
obo:MONDO_0021135 rdf:type owl:Class ;
                  rdfs:subClassOf efo:EFO_0009813 ;
                  oboInOwl:id "MONDO:0021135"^^xsd:string ;
                  oboInOwl:inSubset mondo:obsoletion_candidate ;
                  rdfs:label "rare or common"^^xsd:string ;
                  rdfs:seeAlso "https://github.com/monarch-initiative/mondo/issues/254"^^xsd:anyURI ;                
               rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
               terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://www.ebi.ac.uk/efo/EFO_0009813
efo:EFO_0009813 rdf:type owl:Class ;
                rdfs:subClassOf obo:BFO_0000019 ;
                obo:IAO_0000115 "An attribute of a disease."^^xsd:string ;
                skos:closeMatch <http://linkedlifedata.com/resource/umls/id/C1514623> ;
                skos:exactMatch obo:NCIT_C41009 ;
                oboInOwl:hasDbXref "MONDO:0021125"^^xsd:string ,
                                   "NCIT:C41009"^^xsd:string ;
                oboInOwl:hasExactSynonym "disease characteristic"^^xsd:string ,
                                         "disease qualifier"^^xsd:string ,
                                         "modifier"^^xsd:string ,
                                         "qualifier"^^xsd:string ;
                oboInOwl:id "EFO:0009813"^^xsd:string ;
                rdfs:label "disease characteristic"^^xsd:string ;                
               rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
               terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://purl.obolibrary.org/obo/BFO_0000019
obo:BFO_0000019 rdf:type owl:Class ;
                rdfs:subClassOf obo:BFO_0000020 ;
                obo:IAO_0000115 "A quality is an entity that describes some aspect which is intrinsic to that particular object and is dependent on or more material entities in which it inheres in or is borne by. Example the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee"^^xsd:string ;
                obo:IAO_0000117 "James Malone"^^xsd:string ;
                efo:EFO_URI "http://www.ebi.ac.uk/efo/EFO_0001436"^^xsd:string ;
                efo:organizational_class "true"^^xsd:string ;
                efo:source_definition "A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property)."^^xsd:string ;
                oboInOwl:hasAlternativeId "http://www.ifomis.org/bfo/1.1/snap#Quality" ;
                oboInOwl:hasDbXref "NCIt:C25283"^^xsd:string ,
                                   "SNOMEDCT:263496004"^^xsd:string ;
                rdfs:label "quality"^^xsd:string ;                
               rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
               terms:license <http://www.apache.org/licenses/LICENSE-2.0> .                

###  http://www.ebi.ac.uk/efo/EFO_0000616
efo:EFO_0000616 rdf:type owl:Class ;
                rdfs:subClassOf obo:MONDO_0023370  ;
                obo:IAO_0000115 "A benign or malignant tissue growth resulting from uncontrolled cell proliferation.  Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia.  Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias."^^xsd:string ,
                                "A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias."^^xsd:string ;
                obo:IAO_0000117 "James Malone"^^xsd:string ,
                                "Tomasz Adamusiak"^^xsd:string ;
                skos:closeMatch <http://identifiers.org/snomedct/108369006> ,
                                 <http://linkedlifedata.com/resource/umls/id/C0205394> ,
                                 <http://linkedlifedata.com/resource/umls/id/C0375111> ,
                                 obo:NCIT_C17649 ;
                skos:exactMatch <http://identifiers.org/mesh/D009369> ,
                                 <http://identifiers.org/snomedct/55342001> ,
                                 <http://linkedlifedata.com/resource/umls/id/CN236628> ,
                                 obo:DOID_14566 ,
                                 obo:NCIT_C3262 ;
                oboInOwl:hasBroadSynonym "cell process disease"^^xsd:string ;
                oboInOwl:hasDbXref "COHD:438112"^^xsd:string ,
                                   "DOID:14566"^^xsd:string ,
                                   "HP:0002664"^^xsd:string ,
                                   "ICD10:C00.D48"^^xsd:string ,
                                   "ICD10:D48"^^xsd:string ,
                                   "ICD10:Z85"^^xsd:string ,
                                   "ICD9:140-239.99"^^xsd:string ,
                                   "ICD9:239.8"^^xsd:string ,
                                   "ICD9:239.9"^^xsd:string ,
                                   "MESH:D009369"^^xsd:string ,
                                   "MONDO:0005070"^^xsd:string ,
                                   "MSH:D009369"^^xsd:string ,
                                   "NCIT:C3262"^^xsd:string ,
                                   "NCIt:C3262"^^xsd:string ,
                                   "ONCOTREE:OTHER"^^xsd:string ,
                                   "SCTID:55342001"^^xsd:string ,
                                   "SNOMEDCT:108369006"^^xsd:string ,
                                   "UMLS:CN236628"^^xsd:string ;
                oboInOwl:hasExactSynonym "NEOPL"^^xsd:string ,
                                         "NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS)"^^xsd:string ,
                                         "Neoplasia"^^xsd:string ,
                                         "Neoplasms"^^xsd:string ,
                                         "Neoplastic Growth"^^xsd:string ,
                                         "Tumor"^^xsd:string ,
                                         "Tumors"^^xsd:string ,
                                         "disease of cellular proliferation"^^xsd:string ,
                                         "neoplasia"^^xsd:string ,
                                         "neoplasm"^^xsd:string ,
                                         "neoplasm (disease)"^^xsd:string ,
                                         "neoplastic disease"^^xsd:string ,
                                         "neoplastic growth"^^xsd:string ,
                                         "tumor"^^xsd:string ,
                                         "tumor disease"^^xsd:string ,
                                         "tumour"^^xsd:string ,
                                         "tumours"^^xsd:string ;
                oboInOwl:hasNarrowSynonym "other neoplasm"^^xsd:string ;
                oboInOwl:id "EFO:0000616"^^xsd:string ;
                rdfs:label "neoplasm"^^xsd:string ;
                terms:modified "2020-08-03" ;
                terms:contributor <http://purl.org/query/tarcisiotmf>;
                terms:provenance :MODIFIED_EFO_TERM_RESTRICTIONS ;                
                rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                terms:license <http://www.apache.org/licenses/LICENSE-2.0> . 

###  http://www.ebi.ac.uk/efo/EFO_0000311
efo:EFO_0000311 rdf:type owl:Class ;
                rdfs:subClassOf efo:EFO_0000616 ;
                owl:disjointWith efo:EFO_0002422 ;
                obo:IAO_0000112 "ductal carcinoma in situ"^^xsd:string ;
                obo:IAO_0000115 "A malignant neoplasm in which new abnormal tissue grow by excessive cellular division and proliferation more rapidly than normal and continues to grow after the stimuli that initiated the new growth cease."^^xsd:string ,
                                "A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas."^^xsd:string ;
                obo:IAO_0000117 "James Malone"^^xsd:string ,
                                "Tomasz Adamusiak"^^xsd:string ;
                skos:closeMatch <http://identifiers.org/mesh/D009371> ,
                                 <http://identifiers.org/snomedct/154432008> ,
                                 <http://identifiers.org/snomedct/154433003> ,
                                 <http://identifiers.org/snomedct/154577008> ,
                                 <http://identifiers.org/snomedct/187597000> ,
                                 <http://identifiers.org/snomedct/188475001> ,
                                 <http://identifiers.org/snomedct/188482002> ,
                                 <http://identifiers.org/snomedct/190150006> ,
                                 <http://identifiers.org/snomedct/269513004> ,
                                 <http://identifiers.org/snomedct/269623003> ,
                                 <http://identifiers.org/snomedct/269626006> ,
                                 <http://identifiers.org/snomedct/269634000> ,
                                 <http://identifiers.org/snomedct/38807002> ;
                skos:exactMatch <http://identifiers.org/snomedct/363346000> ,
                                 <http://linkedlifedata.com/resource/umls/id/C0006826> ,
                                 obo:DOID_0050686 ,
                                 obo:DOID_0050687 ,
                                 obo:DOID_162 ,
                                 obo:NCIT_C9305 ;
                oboInOwl:hasDbXref "COHD:443392"^^xsd:string ,
                                   "DOID:0050686"^^xsd:string ,
                                   "DOID:0050687"^^xsd:string ,
                                   "DOID:162"^^xsd:string ,
                                   "GARD:0011960"^^xsd:string ,
                                   "ICD10:C80"^^xsd:string ,
                                   "ICD10:C80.1"^^xsd:string ,
                                   "ICD9:195.8"^^xsd:string ,
                                   "ICD9:199"^^xsd:string ,
                                   "ICD9:199.1"^^xsd:string ,
                                   "ICDO:8000/3"^^xsd:string ,
                                   "MONDO:0004992"^^xsd:string ,
                                   "NCIT:C9305"^^xsd:string ,
                                   "NCIt:C9305"^^xsd:string ,
                                   "NIFSTD:birnlex_406"^^xsd:string ,
                                   "ONCOTREE:MT"^^xsd:string ,
                                   "SCTID:363346000"^^xsd:string ,
                                   "UMLS:C0006826"^^xsd:string ;
                oboInOwl:hasExactSynonym "CA"^^xsd:string ,
                                         "Malignant Neoplasm"^^xsd:string ,
                                         "cancer"^^xsd:string ,
                                         "cell type cancer"^^xsd:string ,
                                         "malignancy"^^xsd:string ,
                                         "malignant Growth"^^xsd:string ,
                                         "malignant neoplasia"^^xsd:string ,
                                         "malignant neoplasm"^^xsd:string ,
                                         "malignant neoplasm (disease)"^^xsd:string ,
                                         "malignant neoplastic disease"^^xsd:string ,
                                         "malignant tumor"^^xsd:string ,
                                         "malignant tumour"^^xsd:string ,
                                         "neoplasm (disease), malignant"^^xsd:string ,
                                         "neoplasm, malignant"^^xsd:string ,
                                         "organ system cancer"^^xsd:string ,
                                         "primary cancer"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "MT"^^xsd:string ;
                oboInOwl:id "EFO:0000311"^^xsd:string ;
                rdfs:label "cancer"^^xsd:string ;
                rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                terms:license <http://www.apache.org/licenses/LICENSE-2.0> . 


###  http://www.ebi.ac.uk/efo/EFO_0002422
efo:EFO_0002422 rdf:type owl:Class ;
                rdfs:subClassOf efo:EFO_0000616 ;
                obo:IAO_0000115 "A neoplasm which is characterized by the absence of morphologic features associated with malignancy (severe cytologic atypia, tumor cell necrosis, and high mitotic rate). Benign neoplasms remain confined to the original site of growth and do not metastasize to other anatomic sites."^^xsd:string ;
                obo:IAO_0000117 "James Malone"^^xsd:string ,
                                "Sirarat Sarntivijai"^^xsd:string ,
                                "Tomasz Adamusiak"^^xsd:string ;
                skos:closeMatch <http://identifiers.org/snomedct/3898006> ,
                                 <http://linkedlifedata.com/resource/umls/id/C0086692> ;
                skos:exactMatch <http://identifiers.org/snomedct/20376005> ,
                                 obo:DOID_0060072 ,
                                 obo:DOID_0060084 ,
                                 obo:DOID_0060085 ,
                                 obo:NCIT_C3677 ;
                oboInOwl:hasDbXref "DOID:0060072"^^xsd:string ,
                                   "DOID:0060084"^^xsd:string ,
                                   "DOID:0060085"^^xsd:string ,
                                   "ICD10:D10.D36"^^xsd:string ,
                                   "ICD10:D36"^^xsd:string ,
                                   "ICD9:210-229.99"^^xsd:string ,
                                   "ICD9:229.8"^^xsd:string ,
                                   "ICD9:229.9"^^xsd:string ,
                                   "ICDO:8000/0"^^xsd:string ,
                                   "MONDO:0005165"^^xsd:string ,
                                   "NCIT:C3677"^^xsd:string ,
                                   "NCIt:C3677"^^xsd:string ,
                                   "SCTID:20376005"^^xsd:string ,
                                   "SNOMEDCT:3898006"^^xsd:string ;
                oboInOwl:hasExactSynonym "BENIGN NEOPL"^^xsd:string ,
                                         "Benign Neoplasm"^^xsd:string ,
                                         "Benign Neoplasms"^^xsd:string ,
                                         "NEOPL BENIGN"^^xsd:string ,
                                         "Neoplasm, Benign"^^xsd:string ,
                                         "Neoplasms, Benign"^^xsd:string ,
                                         "benign neoplasm"^^xsd:string ,
                                         "benign neoplasm (disease)"^^xsd:string ,
                                         "benign tumor"^^xsd:string ,
                                         "neoplasm (disease), benign"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "benign tumor"^^xsd:string ,
                                           "benign unclassifiable tumor"^^xsd:string ,
                                           "cell type benign neoplasm"^^xsd:string ,
                                           "neoplasm, benign"^^xsd:string ,
                                           "organ system benign neoplasm"^^xsd:string ;
                oboInOwl:id "EFO:0002422"^^xsd:string ;
                rdfs:comment "Editor note: see https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues/14"^^xsd:string ;
                rdfs:label "benign neoplasm"^^xsd:string ;
                rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                terms:license <http://www.apache.org/licenses/LICENSE-2.0> . 

###  http://www.ebi.ac.uk/efo/EFO_0000548
efo:EFO_0000548 rdf:type owl:Class ;
                rdfs:subClassOf obo:BFO_0000040 ;
                obo:IAO_0000115 "An instrument is a device which provides a mechanical or electronic function."^^xsd:string ;
                obo:IAO_0000117 "James Malone"^^xsd:string ,
                                "Jie Zheng"^^xsd:string ,
                                "Tomasz Adamusiak"^^xsd:string ;
                efo:definition_citation "OBI_0400003"^^xsd:string ;
                oboInOwl:hasDbXref "MO:113"^^xsd:string ,
                                   "MO:134"^^xsd:string ,
                                   "SNOMEDCT:57134006"^^xsd:string ;
                oboInOwl:hasExactSynonym "HardwareType"^^xsd:string ,
                                         "hardware"^^xsd:string ;
                rdfs:label "instrument"^^xsd:string ;
                rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

###  http://purl.obolibrary.org/obo/BFO_0000040
obo:BFO_0000040 rdf:type owl:Class ;
                rdfs:subClassOf obo:BFO_0000004 ;
                skos:relatedMatch sio:SIO_000004;
                obo:IAO_0000112 "A heart, a human, a fly, a microarray."^^xsd:string ;
                obo:IAO_0000115 "A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray."^^xsd:string ;
                obo:IAO_0000117 "James Malone"^^xsd:string ;
                efo:source_definition "An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology."^^xsd:string ;
                owl:equivalentClass <http://www.ifomis.org/bfo/1.1/snap#MaterialEntity> ;
                oboInOwl:hasExactSynonym "material type"^^xsd:string ;
                rdfs:label "material entity"^^xsd:string ;
                rdfs:isDefinedBy obo:bfo.owl ;
                terms:license <http://creativecommons.org/licenses/by/4.0/> .

###  http://purl.obolibrary.org/obo/BFO_0000015
obo:BFO_0000015 rdf:type owl:Class ;
                rdfs:subClassOf obo:BFO_0000003 ;
                obo:IAO_0000115 "A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs."^^xsd:string ;
                obo:IAO_0000117 "James Malone"^^xsd:string ;
                efo:source_definition "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity."^^xsd:string ;
                owl:equivalentClass <http://www.ifomis.org/bfo/1.1/span#ProcessualEntity> ;
                oboInOwl:hasDbXref "NCIt:C29862"^^xsd:string ,
                                   "SNOMEDCT:415178003"^^xsd:string ;
                rdfs:label "process"^^xsd:string ;
                rdfs:isDefinedBy obo:bfo.owl ;
                terms:license <http://creativecommons.org/licenses/by/4.0/> .

###  http://purl.obolibrary.org/obo/BFO_0000003
obo:BFO_0000003 rdf:type owl:Class ;
                rdfs:subClassOf obo:BFO_0000001 ;
                obo:IAO_0000115 "An entity that has temporal parts and that happens, unfolds or develops through time."@en ;
                obo:IAO_0000116 "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 ,
                                "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 ,
                                "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 ,
                                "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." ;
                obo:IAO_0000600 "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 ;
                rdfs:isDefinedBy obo:bfo.owl ;
                rdfs:label "occurrent"@en .

###  http://purl.obolibrary.org/obo/OBI_0000066
obo:OBI_0000066 rdf:type owl:Class ;
                rdfs:subClassOf efo:EFO_0004542 ;
                obo:IAO_0000112 "Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation"^^xsd:string ;
                obo:IAO_0000115 "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)."^^xsd:string ;
                rdfs:label "investigation"^^xsd:string ;
                rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                terms:license <http://www.apache.org/licenses/LICENSE-2.0> .


 ###  http://www.ebi.ac.uk/efo/EFO_0004542
efo:EFO_0004542 rdf:type owl:Class ;
                rdfs:subClassOf obo:BFO_0000015 ;
                obo:IAO_0000115 "A processual entity that realizes a plan which is the concretization of a plan specification."^^xsd:string ;
                efo:definition_citation "OBI_0000011"^^xsd:string ;
                rdfs:label "planned process"^^xsd:string ;
                rdfs:isDefinedBy <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> ;
                terms:license <http://www.apache.org/licenses/LICENSE-2.0> .

##############
######### Terms extracted from OPMI ontology
##############
###  http://purl.obolibrary.org/obo/OPMI_0004507
obo:OPMI_0004507 rdf:type owl:Class ;
                 rdfs:subClassOf obo:OPMI_0000418 ;
                 obo:IAO_0000115 "a clinical trial is a medical interventional study where participants are assigned prospectively to an intervention or interventions according to a protocol to evaluate the safety and efficacy of the intervention(s) on biomedical or other health related outcomes. The Interventions include but are not restricted to drugs, cells and other biological products, surgical procedures, radiologic procedures, devices, behavioral treatments, process-of-care changes, preventive care, etc." ;
                 obo:IAO_0000117 "Oliver He, Asiyah Yu Lin, Qingliang Li" ;
                 skos:altLabel "interventional trial" ;
                 rdfs:seeAlso "https://clinicaltrials.gov/ct2/search/map" ,
                                 "https://en.wikipedia.org/wiki/Clinical_trial" ,
                                 "https://prsinfo.clinicaltrials.gov/definitions.html" ,
                                 "https://www.who.int/ictrp/en/" ;
                 rdfs:label "clinical trial"@en .

###  http://purl.obolibrary.org/obo/OPMI_0000418
obo:OPMI_0000418 rdf:type owl:Class ;
                 rdfs:subClassOf obo:OBI_0000066 ;
                 obo:IAO_0000115 "A systematic, scientific investigation that can be either interventional or observational and involves human beings as research subjects. Human subject research can be either medical (clinical) research or non-medical (e.g., social science) research." ;
                 obo:IAO_0000117 "Oliver He" ;
                 skos:altLabel "human investigation" ,
                                 "human study" ;
                 rdfs:seeAlso "https://en.wikipedia.org/wiki/Human_subject_research" ;
                 rdfs:label "human subject study"@en .

#######
#### uniprot terms
#######

up:Site_Annotation rdf:type owl:Class ;
rdfs:label  "Site"^^xsd:string;
rdfs:subClassOf up:Sequence_Annotation;
rdfs:comment  "Any interesting single amino-acid site on the sequence, that is not defined by another feature key. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids."^^xsd:string;
rdfs:isDefinedBy  up:;
rdfs:seeAlso  <http://www.uniprot.org/manual/site>.

up:Sequence_Annotation rdf:type owl:Class ;
rdfs:label  "Sequence Annotation"^^xsd:string;
rdfs:subClassOf up:Annotation;
rdfs:comment  "Description of a special region or site in a protein sequence."^^xsd:string;
rdfs:isDefinedBy  up: ;
rdfs:seeAlso  <http://www.uniprot.org/manual/sequence_annotation>.

up:Annotation rdf:type owl:Class ;
rdfs:label  "Annotation"^^xsd:string;
rdfs:comment  "Description of a resource on a specific topic."^^xsd:string;
rdfs:isDefinedBy  up:.

up:annotation rdf:type owl:ObjectProperty ;
                rdfs:domain up:Protein ;
                rdfs:range up:Annotation ;
                rdfs:comment "Attaches an annotation to a resource."^^xsd:string ;
                rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                rdfs:label "annotation"^^xsd:string .


###  http://purl.uniprot.org/core/Metal_Binding_Annotation
up:Metal_Binding_Annotation rdf:type owl:Class ;
                              rdfs:subClassOf up:Site_Annotation ;
                              rdfs:comment "Binding site for a metal ion."^^xsd:string ;
                              rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                              rdfs:label "Metal Ion Binding Site"^^xsd:string ;
                              rdfs:seeAlso <http://www.uniprot.org/manual/metal> .

###  http://purl.uniprot.org/core/Modified_Residue_Annotation
up:Modified_Residue_Annotation rdf:type owl:Class ;
                                 rdfs:subClassOf up:Modification_Annotation ;
                                 rdfs:comment "Posttranslational modification of a residue."^^xsd:string ;
                                 rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                                 rdfs:label "Modified Residue"^^xsd:string ;
                                 rdfs:seeAlso <http://www.uniprot.org/manual/mod_res> .

###  http://purl.uniprot.org/core/Modification_Annotation
up:Modification_Annotation rdf:type owl:Class ;
                             rdfs:subClassOf up:Sequence_Annotation ;
                             rdfs:comment "Describes amino acid modifications, post pre- and post-translational."^^xsd:string ;
                             rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                             rdfs:label "Modification"^^xsd:string .

###  http://purl.uniprot.org/core/Lipidation_Annotation
up:Lipidation_Annotation rdf:type owl:Class ;
                           rdfs:subClassOf up:Modification_Annotation ;
                           rdfs:comment "Covalent binding of a lipid moiety."^^xsd:string ;
                           rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                           rdfs:label "Lipid Binding"^^xsd:string ;
                           rdfs:seeAlso <http://www.uniprot.org/manual/lipid> .


###  http://purl.uniprot.org/core/Glycosylation_Annotation
up:Glycosylation_Annotation rdf:type owl:Class ;
                              rdfs:subClassOf up:Modification_Annotation ;
                              rdfs:comment "Describes the occurrence of the attachment of a glycan (mono- or polysaccharide) to a residue of a protein."^^xsd:string ;
                              rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                              rdfs:label "Glycosylation Site"^^xsd:string ;
                              rdfs:seeAlso <http://www.uniprot.org/manual/carbohyd> .

###  http://purl.uniprot.org/core/Disulfide_Bond_Annotation
up:Disulfide_Bond_Annotation rdf:type owl:Class ;
                               rdfs:subClassOf up:Modification_Annotation ;
                               rdfs:comment "Describes residues which are linked by an intra-chain disulfide bond. If the endpoints are identical, the disulfide bond is an interchain one."^^xsd:string ;
                               rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                               rdfs:label "Disulfide Bond"^^xsd:string ;
                               rdfs:seeAlso <http://www.uniprot.org/manual/disulfid> .

###  http://purl.uniprot.org/core/Cross-link_Annotation
up:Cross-link_Annotation rdf:type owl:Class ;
                           rdfs:subClassOf up:Modification_Annotation ;
                           rdfs:comment "Posttranslationally formed amino acid bonds."^^xsd:string ;
                           rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                           rdfs:label "Crosslink"^^xsd:string ;
                           rdfs:seeAlso <http://www.uniprot.org/manual/crosslnk> .

###  http://purl.uniprot.org/core/Glycosylation_Annotation
up:Glycosylation_Annotation rdf:type owl:Class ;
                              rdfs:subClassOf up:Modification_Annotation ;
                              rdfs:comment "Describes the occurrence of the attachment of a glycan (mono- or polysaccharide) to a residue of a protein."^^xsd:string ;
                              rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                              rdfs:label "Glycosylation Site"^^xsd:string ;
                              rdfs:seeAlso <http://www.uniprot.org/manual/carbohyd> .

###  http://purl.uniprot.org/core/Non-standard_Residue_Annotation
up:Non-standard_Residue_Annotation rdf:type owl:Class ;
                                     rdfs:subClassOf up:Modification_Annotation ;
                                     rdfs:comment "Describes the occurrence of a non standard residue in the sequence record."^^xsd:string ;
                                     rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                                     rdfs:label "Non standard residue"^^xsd:string ;
                                     rdfs:seeAlso <http://www.uniprot.org/manual/non_std> .

###  http://purl.uniprot.org/core/Initiator_Methionine_Annotation
up:Initiator_Methionine_Annotation rdf:type owl:Class ;
                                     rdfs:subClassOf up:Molecule_Processing_Annotation ;
                                     rdfs:comment "Indicates that the initiator methionine has been cleaved off and is not shown in the sequence."^^xsd:string  ;
                                     terms:description "Cleavage of the initiator methionine is one of the most common protein modifications and occurs co-translationally."^^xsd:string ;
                                     rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                                     rdfs:label "Initiator Methionine"^^xsd:string ;
                                     rdfs:seeAlso <http://www.uniprot.org/manual/init_met> .                                     

###  http://purl.uniprot.org/core/Molecule_Processing_Annotation
up:Molecule_Processing_Annotation rdf:type owl:Class ;
                                    rdfs:subClassOf up:Sequence_Annotation ;
                                    rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                                    rdfs:label "Molecule Processing"^^xsd:string .



###  http://purl.uniprot.org/core/Natural_Variant_Annotation
up:Natural_Variant_Annotation rdf:type owl:Class ;
                                rdfs:subClassOf up:Natural_Variation_Annotation ;
                                rdfs:comment "Authors report that sequence variants exist."^^xsd:string ;
                                rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                                rdfs:label "Sequence Variant"^^xsd:string ;
                                rdfs:seeAlso <http://www.uniprot.org/manual/variant> .

###  http://purl.uniprot.org/core/Natural_Variation_Annotation
up:Natural_Variation_Annotation rdf:type owl:Class ;
                                  rdfs:subClassOf up:Sequence_Annotation ;
                                  rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                                  rdfs:label "Natural Variation"^^xsd:string .

###  http://purl.uniprot.org/core/Sequence_Annotation
up:Sequence_Annotation rdf:type owl:Class ;
                         rdfs:subClassOf up:Annotation ;
                         rdfs:comment "Description of a special region or site in a protein sequence."^^xsd:string ;
                         rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                         rdfs:label "Sequence Annotation"^^xsd:string ;
                         rdfs:seeAlso <http://www.uniprot.org/manual/sequence_annotation> .


###  http://purl.uniprot.org/core/Active_Site_Annotation
up:Active_Site_Annotation rdf:type owl:Class ;
                            rdfs:subClassOf up:Site_Annotation ;
                            rdfs:comment "Amino acid(s) involved in the activity of an enzyme."^^xsd:string ;
                            rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                            rdfs:label "Active Site"^^xsd:string ;
                            rdfs:seeAlso <http://www.uniprot.org/manual/act_site> .

###  http://purl.uniprot.org/core/Site_Annotation
up:Site_Annotation rdf:type owl:Class ;
                     rdfs:subClassOf up:Sequence_Annotation ;
                     rdfs:comment "Any interesting single amino-acid site on the sequence, that is not defined by another feature key. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids."^^xsd:string ;
                     rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                     rdfs:label "Site"^^xsd:string ;
                     rdfs:seeAlso <http://www.uniprot.org/manual/site> .                            


###  http://purl.uniprot.org/core/Binding_Site_Annotation
up:Binding_Site_Annotation rdf:type owl:Class ;
                             rdfs:subClassOf up:Site_Annotation ;
                             rdfs:comment "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)."^^xsd:string ;
                             rdfs:isDefinedBy <http://purl.uniprot.org/core/> ;
                             rdfs:label "Binding Site"^^xsd:string ;
                             rdfs:seeAlso <http://www.uniprot.org/manual/binding> .



#########################################
## CBIO created new terms
#########################################

:PTM rdf:type owl:Class ;
     rdfs:subClassOf up:Annotation ;
     rdfs:comment "Although proteins can be modified pre-translationally (on the amino acid component of AMINO ACYL TRNA), co-translationally (during the process of GENETIC TRANSLATION), or after translation is completed (POST-TRANSLATIONAL PROTEIN PROCESSING), all protein modifications are generally referred to as PTMs, because a majority of them are made post-translationally, after the protein is folded. As a result, PTM here means a pre-, co- or post-translationally protein modification."^^xsd:string ;
     skos:narrowMatch up:PTM_Annotation;
     rdfs:label "PTM"^^xsd:string ;
     skos:altLabel "post-translational modification"^^xsd:string ;
     rdfs:seeAlso <http://www.uniprot.org/manual/post-translational_modification> .

:probability a owl:DatatypeProperty;
            rdfs:label "has probability";
            rdfs:range xsd:double;
            rdfs:domain :FunctionalImpactPrediction;
            rdfs:comment "A probability is quantity of how likely it is that some event will occur.";
            skos:relatedMatch sio:SIO_000638.

:FunctionalImpactPrediction a owl:Class;
                  rdfs:comment "Predictions for functional affect of variation on the protein reported by a tool such as PolyPhen-2 (e.g. benign, possibly damaging, or probably damaging) and NetNGlyc2.0, and the prediction probability to occur, if applicable.";
                  rdfs:label "functional impact prediction";
                  rdfs:altLabel "site prediction".

:predict a owl:DatatypeProperty;
                 rdfs:comment "It states the funtional impact prediction due to the fact of a variation in the protein sequence (e.g. caused by a mutation) reported by a tool such as PolyPhen-2 (e.g. benign, possibly damaging, or probably damaging) and NetNGlyc2.0 (e.g. gain, loss, no change).";
                 rdfs:domain :FunctionalImpactPrediction;
                 rdfs:range xsd:string;
                 rdfs:label "predict";
                 rdfs:altLabel "has predicted result".

:hasImpactPrediction a owl:ObjectProperty;
                 rdfs:comment "It states a funtional impact prediction (i.e. a predicted effect of the protein variant, for example, due to mutation).";
                 rdfs:domain :DiseaseMutation;
                 rdfs:range :FunctionalImpactPrediction;
                 rdfs:label "has functional impact prediction";
                 rdfs:altLabel "has functional prediction".


:BiomarkerTest rdf:type owl:Class ;
                 rdfs:subClassOf efo:EFO_0000548 ,
                				 [ rdf:type owl:Restriction ;
                                   owl:onProperty :hasTargetDisease ;
                                   owl:someValuesFrom efo:EFO_0000408 ] ;  
                 rdfs:label "biomarker test"^^xsd:string ;
                 rdfs:comment "A biochemical or other measurement device developed to quantitate a biomarker. These tests can evaluate biomarkers for the detection and treatment of asymptomatic individuals (screening), establishing the presence and precise description of disease (diagnosis), estimating the risk or time to clinical outcomes (prognosis), identifying patient likelihood to benefit from certain therapies (predictive) or to experience therapy-related risks (pharmacogenomics), or treatment and post-treatment monitoring purposes (e.g., early detection and treatment of advancing disease or complications).";
                 rdfs:seeAlso <https://www.ncbi.nlm.nih.gov/books/NBK379335/> .

:usedIn rdf:type owl:ObjectProperty ;
		  rdfs:range :BiomarkerTest ;
		  rdfs:domain obo:CHEBI_59163 ;
		  rdfs:label "is used in" ;
		  rdfs:comment "A relationship between a biomarker and a test by which the biomarker is used.". 


:hasTargetDisease rdf:type owl:ObjectProperty ;
		  rdfs:range efo:EFO_0000408 ;
		  rdfs:domain [ rdf:type owl:Class ;
                           owl:unionOf (:BiomarkerTest
										:CancerDifferentialExpression
										:DiseaseMutation )
                        ] ;   
		  rdfs:label "has the target disease" ;
		  rdfs:comment "It states the disease target of a biomarker test or a differential gene expression analysis. The disease is defined by the controlled vocabulary: the Disease Ontology (DO). DO classes is therefore considered instances of efo:EFO_0000408 (EFO Disease class) by applying OWL 2 punning (see https://www.w3.org/TR/owl2-new-features/#F12:_Punning).".

:isManufacturedBy rdf:type owl:DatatypeProperty;
				  rdfs:domain efo:EFO_0000548;
				  rdfs:range xsd:string;
				  rdfs:label "is manufactured by";
				  rdfs:comment "It relates an instrument to its manufacturer name." ;
				  skos:broadMatch <http://purl.org/cerif/frapo/isManufacturedBy>.

:hasFDASubmissionId a owl:DatatypeProperty;
						rdfs:subPropertyOf terms:identifier;
						rdfs:domain :BiomarkerTest;
				  		rdfs:range xsd:string;
				  		rdfs:label "has FDA submission identifier";
				  		rdfs:comment "It relates a biomarker test to its FDA (US Food and Drug Administration) submission identifier.".

:hasClinicalTrial a owl:ObjectProperty;
			rdfs:domain :BiomarkerTest;
			rdfs:range obo:OPMI_0004507;
			rdfs:label "has clinical trial";
			rdfs:comment "It assings clinical trials for a biomarker test device. If it is a FDA biomarker clinical, trials are represented with the following URI scheme https://clinicaltrials.gov/ct2/show/{trial id}.".

:hasApprovedIndication a owl:ObjectProperty;
			rdfs:domain :BiomarkerTest;
			rdfs:range  [ rdf:type owl:Class ;
                           owl:oneOf ( obo:NCIT_C54156
										obo:NCIT_C15220
										obo:NCIT_C15367
										obo:NCIT_C16209
										obo:NCIT_C17013
										:COMPANION_DIAGNOSIS
                                      )
                        ] ;                                             
			rdfs:label "has approved indication";
			rdfs:comment "The approved indication of a biomarker test.".


:hasActualUse a owl:ObjectProperty;
			rdfs:domain :BiomarkerTest;
			rdfs:range [ rdf:type owl:Class ;
                           owl:oneOf ( obo:NCIT_C54156
										obo:NCIT_C15220
										obo:NCIT_C15367
										obo:NCIT_C16505
                                      )
                        ] ; 
			rdfs:label "has actual use";
			rdfs:comment "The actual use of a biomarker test.".


###  http://purl.org/cbio/biomarkerOrigin
:biomarkerOrigin rdf:type owl:DatatypeProperty ,
                          owl:FunctionalProperty ;
                 rdfs:domain :BiomarkerTest ;
                 rdfs:range [ rdf:type rdfs:Datatype ;
                              owl:oneOf [ rdf:type rdf:List ;
                                          rdf:first "amplification" ;
                                          rdf:rest [ rdf:type rdf:List ;
                                                     rdf:first "multigene prediction" ;
                                                     rdf:rest [ rdf:type rdf:List ;
                                                                rdf:first "somatic mutation" ;
                                                                rdf:rest rdf:nil
                                                              ]
                                                   ]
                                        ]
                            ] ;
                 rdfs:comment "It relates a biomarker test to its biomarker origin: multigene prediction, somatic mutation, or amplification." ;
                 rdfs:label "biomarker origin" .


:histologicalType rdf:type owl:DatatypeProperty  ;
                 rdfs:domain  efo:EFO_0000311;
                 rdfs:range xsd:string ;
                 rdfs:comment "It classifies a cancer by the type of tissue in which the cancer originates (histological type)." ;
                 rdfs:label "has histological type";
                 skos:note "In the future this property might be replaced by an object property that assings, if exist, NCIT controlled vocabulary terms as instance values such as http://purl.obolibrary.org/obo/NCIT_C3224 (melanoma)." .

###  http://purl.org/cbio/specimen
:specimen rdf:type owl:DatatypeProperty ;
          rdfs:domain :BiomarkerTest ;
          rdfs:range [ rdf:type rdfs:Datatype ;
                       owl:oneOf [ rdf:type rdf:List ;
                                   rdf:first "blood" ;
                                   rdf:rest [ rdf:type rdf:List ;
                                              rdf:first "fresh tissue" ;
                                              rdf:rest [ rdf:type rdf:List ;
                                                         rdf:first "human stool" ;
                                                         rdf:rest [ rdf:type rdf:List ;
                                                                    rdf:first "paraffin block" ;
                                                                    rdf:rest [ rdf:type rdf:List ;
                                                                               rdf:first "parrafin block" ;
                                                                               rdf:rest [ rdf:type rdf:List ;
                                                                                          rdf:first "saliva" ;
                                                                                          rdf:rest [ rdf:type rdf:List ;
                                                                                                     rdf:first "urine" ;
                                                                                                     rdf:rest rdf:nil
                                                                                                   ]
                                                                                        ]
                                                                             ]
                                                                  ]
                                                       ]
                                            ]
                                 ]
                     ] ;
          rdfs:comment "The specimen type for the biomarker test." ;
          rdfs:label "specimen" .

###  http://purl.org/cbio/platformMethod
:platformMethod rdf:type owl:DatatypeProperty ;
          rdfs:domain :BiomarkerTest ;
          rdfs:range xsd:string;
          rdfs:comment "The platform method used by the biomarker test." ;
          rdfs:label "platform method" .

:geneNumber rdf:type owl:DatatypeProperty ,
                     owl:FunctionalProperty ;
          rdfs:domain :BiomarkerTest ;
          rdfs:range xsd:nonNegativeInteger;
          rdfs:comment "The number of genes that are members of a biomarker test." ;
          rdfs:label "gene amount" .
 
:adoptionEvidence rdf:type owl:DatatypeProperty ,
                           owl:FunctionalProperty ;
                  rdfs:domain :BiomarkerTest ;
                  rdfs:range [ rdf:type rdfs:Datatype ;
                               owl:oneOf [ rdf:type rdf:List ;
                                           rdf:first "clinical use" ;
                                           rdf:rest [ rdf:type rdf:List ;
                                                      rdf:first "experimental use" ;
                                                      rdf:rest rdf:nil
                                                    ]
                                         ]
                             ] ;
                  rdfs:comment "It denotes the adoption evidence of a biomarker test."^^xsd:string ;
                  rdfs:label "has test adoption evidence"^^xsd:string .


:hasApprovalStatus
      rdf:type owl:DatatypeProperty , owl:FunctionalProperty ;
      rdfs:domain :BiomarkerTest  ;
      rdfs:range xsd:string ;
      rdfs:label "has approval status"^^xsd:string ;
      rdfs:comment
              "It denotes the state of a biomarker test approval."^^xsd:string;
      skos:broadMatch <http://voag.linkedmodel.org/schema/voag#hasApprovalStatus> .



###  http://purl.org/cbio/hasTestStudyDesign
:hasTestStudyDesign rdf:type owl:DatatypeProperty ,
                             owl:FunctionalProperty ;
                    rdfs:domain :BiomarkerTest ;
                    rdfs:range xsd:string ;
                    rdfs:comment "It states a specific study design for a biomarker test. A study design is a plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution." ;
                    rdfs:label "has test study design" ;
                    rdfs:seeAlso <http://purl.obolibrary.org/obo/OBI_0500000>.


:hasClinicalSignificance rdf:type owl:DatatypeProperty ,
                             owl:FunctionalProperty ;
                    rdfs:domain :BiomarkerTest ;
                    rdfs:range xsd:string ;
                    rdfs:comment "A finding that has treatment or management implications for a patient's condition." ;
                    rdfs:label "has clinical significance" ;
                    rdfs:seeAlso <http://purl.obolibrary.org/obo/NCIT_C82562>.

:CancerBiomarker rdf:type owl:Class ;
                 rdfs:subClassOf obo:CHEBI_59163 ,
                				 [ rdf:type owl:Restriction ;
                                   owl:onProperty :indicate ;
                                   owl:someValuesFrom efo:EFO_0000311 ] ; 
                 rdfs:label "cancer biomarker"^^xsd:string ;
                 rdfs:comment "A cancer biomarker refers to a substance or process that is indicative of the presence of cancer in the body. A biomarker may be a molecule secreted by a tumor or a specific response of the body to the presence of cancer.";
                 rdfs:seeAlso <https://en.wikipedia.org/wiki/Cancer_biomarker> .

:GeneticBiomarker rdf:type owl:Class ;
                 rdfs:subClassOf :GenomicBiomarker ;
                 rdfs:label "genetic biomarker"^^xsd:string ;
                 skos:exactMatch <http://purl.obolibrary.org/obo/NCIT_C16622> ;
                 rdfs:comment "A segment of DNA with an identifiable physical location on a chromosome and whose inheritance can be followed. It is indeed an alteration in DNA that may indicate an increased risk of developing a specific disease or disorder.".

:GenomicBiomarker rdf:type owl:Class ;
				rdfs:subClassOf obo:CHEBI_59163 ;
				skos:exactMatch <http://purl.obolibrary.org/obo/NCIT_C68753> ;
				rdfs:comment "A measurable DNA or RNA characteristic that is an indicator of normal biologic processes, pathogenic processes, and/or response to therapeutic or other intervention. The definition for a genomic biomarker is not limited to human samples. A genomic biomarker could, for example, reflect: the expression of a gene; the function of a gene; the regulation of a gene. A genomic biomarker can consist of one or more deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) characteristics. The definition for a genomic biomarker does not include the measurement and characterisation of proteins or low molecular weight metabolites. DNA characteristics include, but are not limited to: single nucleotide polymorphisms (SNPs); variability of short sequence repeats; DNA modification, e.g., methylation; insertions; deletions; copy number variation; cytogenetic rearrangements, e.g., translocations, duplications, deletions or inversions. RNA characteristics include, but are not limited to: RNA sequence; RNA expression levels; RNA processing, e.g., splicing and editing; microRNA levels (ICH Draft Consensus Guideline E15).";
				rdfs:label "genomic biomarker"^^xsd:string ;
				owl:disjointWith [ rdf:type owl:Class ;
                                   owl:unionOf ( :ProteomicBiomarker
                                                 :MetabolomicBiomarker
                                                 :EpigeneticBiomarker  )
                                 ] .

:ProteomicBiomarker rdf:type owl:Class ;
				rdfs:subClassOf obo:CHEBI_59163 ;
				rdfs:label "proteomic biomarker" ;
				skos:relatedMatch <http://purl.obolibrary.org/obo/NCIT_C97139> ;
				rdfs:comment "it provides key information about the dynamic nature of proteins, including functionality, post‐translational modifications, interaction with other biological molecules, and response to environmental factors. Proteomic biomarkers are often referred to those biomarkers discovered using technologies capable of analyzing many proteins simultaneously, such as protein microarray and mass spectrometry (MS). ";
				rdfs:seeAlso <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6635916/> ;
				owl:disjointWith [ rdf:type owl:Class ;
                                   owl:unionOf ( :MetabolomicBiomarker
                                                 :EpigeneticBiomarker  )
                                 ] .
 
:MetabolomicBiomarker rdf:type owl:Class ;
				rdfs:subClassOf obo:CHEBI_59163 ;
				rdfs:label "metabolomic biomarker" ;
				skos:narrowMatch <http://purl.obolibrary.org/obo/NCIT_C18520> ;
				rdfs:comment "Metabolomic biomarker refers to the systematic identification and quantification of the small molecule metabolic products (the metabolome) of a biological system (cell, tissue, organ, biological fluid, or organism) at a specific point in time that acts as a biomarker. Mass spectrometry and NMR spectroscopy are the techniques most often used for metabolome profiling. It can also enable diagnostic and prognostic prediction.";
				rdfs:seeAlso <https://www.nature.com/subjects/metabolomics> ;
				owl:disjointWith :EpigeneticBiomarker  .

 
:MetabolicBiomarker rdf:type owl:Class ;
				rdfs:subClassOf :MetabolomicBiomarker ;
				rdfs:label "metabolic biomarker" ;
				skos:exactMatch <http://purl.obolibrary.org/obo/NCIT_C18520> ;
				rdfs:comment "NCI defines a metabolic marker as follows: specific metabolic changes that characterize an organism's state of health or disease, or response to a particular therapeutic intervention, and helps make diagnosis more accurate or enable physicians to make diagnosis before symptoms appear and to track disease progression."  .

:EpigeneticBiomarker rdf:type owl:Class ;
				rdfs:subClassOf obo:CHEBI_59163 ;
				rdfs:label "epigenetic biomarker" ;
				rdfs:comment "Any epigenetic mark or altered epigenetic mechanism that can be measured in the body fluids or tissues and that defines a disease (detection), predicts the outcome of diseases (prognostic) or response to a therapy (predictive), monitors treatment responses (therapy monitoring), or predicts risk of future disease development (risk). It is a dynamic biomarker which changes based on disease evolution and intra- or extra-environmental cellular conditions. Epigenetics is the study of heritable changes in gene expression that do not involve any alterations in the DNA sequence.";
				rdfs:seeAlso <https://doi.org/10.1016/B978-0-12-801899-6.00001-2> .

:GeneBiomarker rdf:type owl:Class ;
				rdfs:subClassOf :GenomicBiomarker ;
				rdfs:label "gene biomarker" ;
				skos:narrowMatch <http://purl.obolibrary.org/obo/NCIT_C48182> ;
				rdfs:comment "A form of gene expression that is indicative of a biological behavior such as a tumor or cancer.";
				rdfs:seeAlso <https://doi.org/10.1016/B978-0-12-801899-6.00001-2> .

:ProteinBiomarker rdf:type owl:Class ;
				rdfs:subClassOf :ProteomicBiomarker ;
				rdfs:label "protein biomarker" ;
				skos:relatedMatch <http://purl.obolibrary.org/obo/NCIT_C97139> ;
				rdfs:comment "it is a biomarker discovered from a simplified, semiquantitative, unbiased binary comparison between diseased and normal using biological samples for maximal detection of significant protein expression differences.";
				rdfs:seeAlso <https://doi.org/10.1177%2F1849454418777186> .

:indicate rdf:type owl:ObjectProperty ;
		  rdfs:range efo:EFO_0000408 ;
		  rdfs:domain obo:CHEBI_59163 ;
		  rdfs:label "is a measurable indicator of" ;
		  rdfs:comment "It relates a biomarker to the severity or presence of some disease state. The disease is defined with the controlled vocabulary: the Disease Ontology (DO). DO classes is therefore considered instances of efo:EFO_0000408 (EFO Disease class) by applying OWL 2 punning (see https://www.w3.org/TR/owl2-new-features/#F12:_Punning).".

###  http://purl.org/cbio/BiomarkerPanel
:BiomarkerPanel rdf:type owl:Class ;
                rdfs:subClassOf obo:CHEBI_59163 ,
                                [ rdf:type owl:Restriction ;
                                  owl:onProperty :consistOf ;
                                  owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger ;
                                  owl:onClass :SingleBiomarker
                                ] ;
                owl:disjointWith :SingleBiomarker ;
                rdfs:comment "A biomarker composed of 2 or more single biomarkers" ;
                rdfs:label "biomarker panel" .

###  http://purl.org/cbio/SingleBiomarker
:SingleBiomarker rdf:type owl:Class ;
                 rdfs:subClassOf obo:CHEBI_59163 ;
                 obo:IAO_0000112 "ALDH1A2 gene by itself is a specific biomarker for prostate cancer." ;
                 rdfs:comment "A biomarker that is composed of solely one marker (e.g. a unique gene)." ;
                 rdfs:label "single biomarker" .

:consistOf rdf:type owl:ObjectProperty ;
               rdfs:subPropertyOf obo:RO_0002351 ;
               rdfs:range obo:CHEBI_59163 ;
               rdfs:domain :BiomarkerPanel ;
               skos:relatedMatch <http://purl.allotrope.org/ontologies/property#AFX_0000940> ;
               rdfs:comment "It states which biomarkers composes a biomarker panel." ;
               rdfs:label "consist of"@en .

###  http://purl.org/cbio/CancerBiomarkerPanel
:CancerBiomarkerPanel rdf:type owl:Class ;
                      owl:equivalentClass [ owl:intersectionOf ( :BiomarkerPanel
                                                                 :CancerBiomarker
                                                               ) ;
                                            rdf:type owl:Class
                                          ] ;
                      rdfs:comment "A biomarker panel that indicates some cancer disease." ;
                      rdfs:label "cancer biomarker panel" .


###  http://purl.org/cbio/CancerSingleBiomarker
:CancerSingleBiomarker rdf:type owl:Class ;
                       owl:equivalentClass [ owl:intersectionOf ( :CancerBiomarker
                                                                  :SingleBiomarker
                                                                ) ;
                                             rdf:type owl:Class
                                           ] ;
                       rdfs:comment "A single biomarker that indicates some cancer disease." ;
                       rdfs:label "cancer single biomarker" .

:hasBiomarkerStatus a owl:ObjectProperty;
					rdfs:label "has biomarker status";
					rdfs:comment "It denotes whether biomarker has been accepted, curated or is under review.";
					rdfs:range :BiomarkerState ;
					rdfs:domain obo:CHEBI_59163 .

:BiomarkerState owl:equivalentClass [ rdf:type owl:Class ;
                                      owl:oneOf ( :CURATED
                                                  obo:NCIT_C62559
                                                  :UNDER_REVIEW	)
                                           ] ;
                                   a owl:Class ;
                                   rdfs:subClassOf skos:Concept;
                                   rdfs:label "Biomarker quality assessment state" ;
                                   rdfs:commnet "The :BiomarkerState class provides a categorisation of the possible states a biomarker may have as a result of a quality evaluation process. For example, whether it has been  Curated', 'Accepted' or 'Under review'.  This categorisation is implemented as a SKOS vocabulary." ;
                                   skos:relatedMatch npg:ReviewState .

:UNDER_REVIEW   a :BiomarkerState ;
                rdfs:label "Under review" ;
                skos:altLabel "under review" ;
                rdfs:commnet "A state to assign the biomarker status under review (i.e. being evaluated). After the reviewing process, the status can change into curated or accepted, for example." .

:CURATED a :BiomarkerState ;
                rdfs:label "Curated" ;
                skos:altLabel "curated" ;
                skos:narrowMatch obo:OBI_0302840 ;
                rdfs:commnet "It indicates that a curation process was performed by a curator for accuracy checks and compliance with a set of requirements to confirm the veracity of an assertion, i.e. statement. The statement which has been assessed for accuracy by domain experts." .

###  http://purl.org/cbio/EDRNFivePhaseApproach
:EDRNFivePhaseApproach rdf:type owl:Class ;
                       owl:equivalentClass [ rdf:type owl:Class ;
                                             owl:oneOf ( :EDRN_PHASE_1
                                                         :EDRN_PHASE_2
                                                         :EDRN_PHASE_3
                                                         :EDRN_PHASE_4
                                                         :EDRN_PHASE_5
                                                       )
                                           ] ;
                       rdfs:subClassOf skos:Concept ;
                       rdfs:comment "The Early Detection Research Network (EDRN) implemented a nationally recognized research schema designed to bring forward into clinical practice verifiably effective cancer biomarkers. The network established a roadmap and standards for research that minimizes chance, bias and over-fitting, based on a protocol driven, five-phase approach." ;
                       rdfs:label "Five-phase approach" ;
                       rdfs:seeAlso <https://doi.org/10.1007/978-1-60327-281-0_21> .
                       
###  http://purl.org/cbio/EDRN_PHASE_1
:EDRN_PHASE_1 rdf:type :EDRNFivePhaseApproach ;
              terms:identifier 1 ;
              rdfs:comment "Preclinical Exploratory – Exploratory studies to identify potentially useful biomarkers" ;
              rdfs:label "phase one" ;
              rdfs:seeAlso "https://edrn.nci.nih.gov/docs/EDRN5.pdf" ;
              skos:altLabel "preclinical exploratory" .


###  http://purl.org/cbio/EDRN_PHASE_2
:EDRN_PHASE_2 rdf:type :EDRNFivePhaseApproach ;
              terms:identifier 2 ;
              rdfs:comment "Clinical Assay and Validation – Studies to determine the capacity of biomarkers to distinguish between people with cancer and those without." ;
              rdfs:label "phase two" ;
              rdfs:seeAlso "https://edrn.nci.nih.gov/docs/EDRN5.pdf" ;
              skos:altLabel "clinical assay and validation" .


###  http://purl.org/cbio/EDRN_PHASE_3
:EDRN_PHASE_3 rdf:type :EDRNFivePhaseApproach ;
              terms:identifier 3 ;
              rdfs:comment "Retrospective Longitudinal – Determine how well biomarkers detect preclinical disease by testing the markers against specimens collected longitudinally from research cohorts." ;
              rdfs:label "phase three" ;
              rdfs:seeAlso "https://edrn.nci.nih.gov/docs/EDRN5.pdf" ;
              skos:altLabel "retrospective longitudinal" .


###  http://purl.org/cbio/EDRN_PHASE_4
:EDRN_PHASE_4 rdf:type :EDRNFivePhaseApproach ;
              terms:identifier 4 ;
              rdfs:comment "Prospective Screening – Identify the extent and characteristics of disease detected by the test and determine the false referral rate." ;
              rdfs:label "phase four" ;
              rdfs:seeAlso "https://edrn.nci.nih.gov/docs/EDRN5.pdf" ;
              skos:altLabel "prospective screening" .


###  http://purl.org/cbio/EDRN_PHASE_5
:EDRN_PHASE_5 rdf:type :EDRNFivePhaseApproach ;
              terms:identifier 5 ;
              rdfs:comment "Cancer Control – Evaluate both the role of the biomarkers for detection of cancer and the overall impact of screening on the population through large-scale population studies." ;
              rdfs:label "phase five" ;
              rdfs:seeAlso "https://edrn.nci.nih.gov/docs/EDRN5.pdf" ;
              skos:altLabel "cancer control" .

###  http://purl.org/cbio/hasEDRNPhase
:hasEDRNPhase rdf:type owl:ObjectProperty ;
              rdfs:subPropertyOf :hasPhase ;
              rdfs:domain :CancerBiomarker ;
              rdfs:comment "It states one of the 5 phases of a biomarker research as defined by Early Detection Research Network (EDRN)." ;
              rdfs:range :EDRNFivePhaseApproach .


###  http://purl.org/cbio/hasPhase
:hasPhase rdf:type owl:ObjectProperty, owl:FunctionalProperty ;
          rdfs:comment "It states the phase of a research or a trial such as a biomarker research phase." ;
          rdfs:label "at phase" ;
          skos:altLabel "has phase" ;
          skos:narrowMatch obo:ERO_0001518 .

:CancerDifferentialExpression a owl:Class;
							skos:broadMatch <http://edamontology.org/operation_3223> ;
							rdfs:comment "Cancer differential gene expression analysis to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between normal (i.e. healthy) and cancer cells. Identify from molecular sequence analysis (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different or not between two sample groups.";
							rdfs:label "cancer differential expression";
							rdfs:subClassOf  [  rdf:type owl:Restriction ;
                                   				owl:onProperty :hasTargetDisease ;
                                   				owl:someValuesFrom efo:EFO_0000311 ],
                                   			 [  rdf:type owl:Restriction ;
                                   				owl:onProperty genex:hasSequenceUnit ;
                                   				owl:someValuesFrom orth:Gene ] ,
                                   			 [  rdf:type owl:Restriction ;
                                   				owl:onProperty :isStatisticallySignificant ;
                                   				owl:someValuesFrom xsd:boolean ].

:log2fc a owl:DatatypeProperty, owl:FunctionalProperty ;
		skos:relatedMatch <http://purl.obolibrary.org/obo/STATO_0000169>;
		rdfs:comment "The logarithm (to base 2) of the fold change from normal expression to tumor expression. Fold change is equivalent to  the expression level of a gene in cancer divided by the expression level of a gene in the same kind of tissue but a healthy one.";
		rdfs:label "fold change log2";
		rdfs:range xsd:double ;
		rdfs:domain :CancerDifferentialExpression .

:pvalue a owl:DatatypeProperty, owl:FunctionalProperty ;
		skos:relatedMatch <http://purl.obolibrary.org/obo/OBI_0000175>;
		rdfs:comment "P-value for statistical significance of the reported change, computed directly by DESeq2. DESeq2 is a tool to verify the change of expression of genes between two samples.";
		rdfs:label "p-value";
		rdfs:range xsd:double ;
		rdfs:domain :CancerDifferentialExpression .

:adjustedPvalue a owl:DatatypeProperty, owl:FunctionalProperty ;
		skos:relatedMatch <http://purl.obolibrary.org/obo/OBI_0001442>;
		rdfs:comment "P-value adjusted for multiple testing with the Benjamini-Hochberg procedure, which controls false discovery rate (FDR).";
		rdfs:label "FDR adjusted p-value";
		rdfs:range xsd:double ;
		rdfs:domain :CancerDifferentialExpression .

:isStatisticallySignificant a owl:DatatypeProperty, owl:FunctionalProperty ;
		skos:relatedMatch <http://purl.obolibrary.org/obo/NCIT_C61040>;
		rdfs:comment "Trends are considered significant when FDR adjusted p-value < 0.05";
		rdfs:label "is statistically significant";
		rdfs:range xsd:boolean ;
		rdfs:domain :CancerDifferentialExpression .

:hasExpressionChange a owl:ObjectProperty, owl:FunctionalProperty ;
 					  rdfs:range 	[ rdf:type owl:Class ;
                                      owl:oneOf ( sio:SIO_000640
                                                  sio:SIO_000751
                                                  sio:SIO_000554
                                                )
                                    ] ;
                      rdfs:domain :CancerDifferentialExpression ;
                      rdfs:label "has expression change";
                      rdfs:comment "Gene expression trend. Possible values are normal (no change), increased (up) and decreased (down).".

:subjectsUpNumber a owl:DatatypeProperty, owl:FunctionalProperty ;
		rdfs:comment "The amount of patients with increased gene expression.";
		rdfs:label "has subjects up number";
		rdfs:range xsd:nonNegativeInteger ;
		rdfs:domain :CancerDifferentialExpression .

:subjectsDownNumber a owl:DatatypeProperty, owl:FunctionalProperty ;
		rdfs:comment "The amount of patients with decreased gene expression.";
		rdfs:label "has subjects down number";
		rdfs:range xsd:nonNegativeInteger ;
		rdfs:domain :CancerDifferentialExpression .

:subjectsNoChangeNumber a owl:DatatypeProperty, owl:FunctionalProperty ;
		rdfs:comment "The amount of patients with no change in terms of gene expression.";
		rdfs:label "has normal subjects number";
		rdfs:range xsd:nonNegativeInteger ;
		rdfs:domain :CancerDifferentialExpression .

:subjectsNoCoverageNumber a owl:DatatypeProperty, owl:FunctionalProperty ;
		rdfs:comment "The amount of patients with no coverage.";
		rdfs:label "has no coverage subjects number";
		rdfs:range xsd:nonNegativeInteger ;
		rdfs:domain :CancerDifferentialExpression .

:totalSubjects a owl:DatatypeProperty, owl:FunctionalProperty ;
		rdfs:comment "The total number of patients with data for the study.";
		rdfs:label "has subject total number";
		rdfs:range xsd:nonNegativeInteger ;
		rdfs:domain :CancerDifferentialExpression .

			
:isSequenceUnitOf rdf:type owl:ObjectProperty ;
					   rdfs:comment "This property relates a sequence unit such as a gene to a biological concept explicilty defined in its range.";
					   owl:inverseOf genex:hasSequenceUnit ;
                       rdfs:range [ rdf:type owl:Class ;
                                    owl:unionOf ( genex:AbsenceExpression
                                                  genex:Expression
                                                  obo:CHEBI_59163
                                                  :CancerDifferentialExpression
                                                )
                                  ] ;
                       rdfs:domain orth:SequenceUnit ;
                       rdfs:label "is a sequence unit related to"@en .


:DiseaseMutation a owl:Class;
	     	skos:closeMatch obo:NCIT_C93100 ;
	     	rdfs:subClassOf 
			 [ rdf:type owl:Restriction ;
                owl:someValuesFrom efo:EFO_0000408 ;
                owl:onProperty :hasTargetDisease
              ], 
              [ rdf:type owl:Restriction ;
                owl:someValuesFrom obo:SO_0001059 ;
                owl:onProperty :hasSequenceAlteration
              ];
			rdfs:comment "A gene alteration due to mutation that causes or predisposes an individual to a specific disease. It depicts mutation positions and functional annotations.";
			rdfs:label "disease mutation".

:mutationFrequency a owl:DatatypeProperty, owl:FunctionalProperty;
						rdfs:label "has mutation frequency";
						rdfs:comment "The mutation frequency.";
						rdfs:range xsd:nonNegativeInteger ;
						rdfs:domain :DiseaseMutation .

:hasSequenceAlteration rdf:type owl:ObjectProperty;
						rdfs:label "has sequence alteration";
						skos:altLabel "has sequence modification";
						skos:closeMatch obo:ERO_0000573;
						rdfs:comment "A sequence variation that deviates from a canonical or reference sequence.";
						rdfs:range obo:SO_0001059 ;
						rdfs:domain :DiseaseMutation .

:alteredFrom rdf:type owl:ObjectProperty, owl:FunctionalProperty ;
						rdfs:domain obo:SO_0001059;
						rdfs:range [ rdf:type owl:Class ;
                                  	owl:unionOf ( :Nucleotide
                                              	:AminoAcid )
                                    ] ;
                        rdfs:label "altered from";
                        skos:altLabel "modified from";
                        rdfs:comment "The nucleotide or amino acid in a sequence before modification."  .

:alteredTo rdf:type owl:ObjectProperty, owl:FunctionalProperty ;
						rdfs:domain obo:SO_0001059;
						rdfs:range [ rdf:type owl:Class ;
                                  	owl:unionOf ( 	:Nucleotide
                                              		:AminoAcid )
                                    ] ;
                        rdfs:label "altered to";
                        skos:altLabel "modified to";
                        rdfs:comment "The nucleotide or amino acid in a sequence after modification."  .

:HumanChromosome a owl:Class;
			rdfs:subClassOf :Chromosome,
			 [ rdf:type owl:Restriction ;
                owl:hasValue  <http://purl.uniprot.org/taxonomy/9606>;
                owl:onProperty obo:RO_0002162
              ] ;
			skos:broadMatch sio:SIO_000899;
			skos:closeMatch obo:NCIT_C13203;
			rdfs:comment "A structure found in the nucleus of human cells that is comprised of a strand of linearized double-stranded DNA plus proteins that package the DNA in a condensed coil form and regulate chromosomal function. [def-source: NCI]";
			rdfs:label "human chromosome".

<http://purl.uniprot.org/taxonomy/9606> a up:Taxon ;
										rdfs:label "Homo sapiens".

:Chromosome a owl:Class;
			skos:exactMatch sio:SIO_000899;
			skos:narrowMatch obo:NCIT_C13203;
			rdfs:comment "One of the bodies in the cell nucleus that is the bearer of genes, has the form of a delicate chromatin filament during interphase, contracts to form a compact cylinder segmented into two arms by the centromere during metaphase and anaphase stages of cell division, and is capable of reproducing its physical and chemical structure through successive cell divisions. [def-source: NCI]";
			rdfs:label "chromosome".

:Nucleotide a owl:Class;
			owl:equivalentClass	[ rdf:type owl:Class ;
                                  owl:oneOf ( obo:CHEBI_17821
                                              obo:CHEBI_16040
                                              obo:CHEBI_16235
                                              obo:CHEBI_16335
                                              obo:CHEBI_17568 )
                                    ] ;
			skos:closeMatch obo:CHEBI_36976;
			skos:exactMatch obo:CHEBI_18282;
			rdfs:comment "Nucleotides are organic molecules consisting of a nucleoside and a phosphate. Nucleobases are used to represent intances of nucleotides. Nucleobases, also known as nitrogenous bases or often simply bases, are nitrogen-containing biological compounds that form nucleosides, which in turn are components of nucleotides. A set of five nitrogenous bases is used in the construction of nucleotides, which in turn build up nucleic acids like DNA and RNA. These nitrogenous bases are adenine (A), uracil (U), guanine (G), thymine (T), and cytosine (C).";
			rdfs:label "nucleotide".

:AminoAcid a owl:Class;
			owl:equivalentClass	[ rdf:type owl:Class ;
                                  owl:oneOf ( obo:CHEBI_16449
                                              obo:CHEBI_15356
                                              obo:CHEBI_22660
                                              obo:CHEBI_18237
                                              obo:CHEBI_28044
                                              obo:CHEBI_15428
											  obo:CHEBI_15971
											  obo:CHEBI_17191
											  obo:CHEBI_25094
											  obo:CHEBI_25017
											  obo:CHEBI_16811
											  obo:CHEBI_22653
											  obo:CHEBI_17203
											  obo:CHEBI_18050 
											  obo:CHEBI_16467
											  obo:CHEBI_17115
											  obo:CHEBI_16857
											  obo:CHEBI_16414
											  obo:CHEBI_27897
											  obo:CHEBI_18186
											  sio:SIO_010448
                                              :ANY_CODON )
                                    ] ;
			skos:closeMatch obo:CHEBI_33709;
			rdfs:comment "A carboxylic acid containing one or more amino groups.";
			rdfs:label "amino acid".

:ANY_CODON rdf:type :AminoAcid;
			rdfs:label "any codon";
			skos:altLabel "X";
			rdfs:comment "It indicates the presence of an undertermined amino acid";
			oboInOwl:hasRelatedSynonym "X"^^xsd:string , "NNN"^^xsd:string , "Xaa"^^xsd:string .
#####
### Other SO terms added
####
###  http://purl.obolibrary.org/obo/SO_0001059
obo:SO_0001059 rdf:type owl:Class ;
               obo:IAO_0000115 "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence."^^xsd:string ;
               obo:IAO_0000118 "partially characterised change in DNA sequence"^^xsd:string ,
                               "partially_characterised_change_in_DNA_sequence"^^xsd:string ,
                               "sequence alteration"^^xsd:string ;
               obo:IAO_0000412 obo:so.owl ;
               rdfs:isDefinedBy obo:so.owl ;
               rdfs:label "sequence_alteration"^^xsd:string .

#####
### CHEBI terms by OWL2 punning as instances
####

##### AMINO ACIDS as individuals

###  http://purl.obolibrary.org/obo/CHEBI_16449
obo:CHEBI_16449 rdf:type :AminoAcid ;
                obo:IAO_0000115 "An alpha-amino acid that consists of propionic acid bearing an amino substituent at position 2."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C3H7NO2"^^xsd:string ;
                chebi:inchi "InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)"^^xsd:string ;
                chebi:inchikey "QNAYBMKLOCPYGJ-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "89.09322"^^xsd:string ;
                chebi:monoisotopicmass "89.04768"^^xsd:string ;
                chebi:smiles "CC(N)C(O)=O"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:13748"^^xsd:string ,
                                          "CHEBI:22277"^^xsd:string ,
                                          "CHEBI:2539"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:635807"^^xsd:string ,
                                   "CAS:302-72-7"^^xsd:string ,
                                   "Drug_Central:4306"^^xsd:string ,
                                   "Gmelin:2449"^^xsd:string ,
                                   "KEGG:C01401"^^xsd:string ,
                                   "PMID:17439666"^^xsd:string ,
                                   "PMID:22264337"^^xsd:string ,
                                   "Reaxys:635807"^^xsd:string ,
                                   "Wikipedia:Alanine"^^xsd:string ;
                oboInOwl:hasExactSynonym "2-aminopropanoic acid"^^xsd:string ,
                                         "Alanine"^^xsd:string ,
                                         "alanine"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "2-Aminopropanoic acid"^^xsd:string ,
                                           "2-Aminopropionic acid"^^xsd:string ,
                                           "A"^^xsd:string ,
                                           "ALA"^^xsd:string ,
                                           "Alanin"^^xsd:string ,
                                           "alanina"^^xsd:string ;
                oboInOwl:id "CHEBI:16449"^^xsd:string ;
                rdfs:label "alanine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_15356
obo:CHEBI_15356 rdf:type :AminoAcid ;
                 obo:IAO_0000115 "A sulfur-containing amino acid that is propanoic acid with an amino group at position 2 and a sulfanyl group at position 3."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C3H7NO2S"^^xsd:string ;
                chebi:inchi "InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)"^^xsd:string ;
                chebi:inchikey "XUJNEKJLAYXESH-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "121.15922"^^xsd:string ;
                chebi:monoisotopicmass "121.01975"^^xsd:string ;
                chebi:smiles "NC(CS)C(O)=O"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:14061"^^xsd:string ,
                                          "CHEBI:23508"^^xsd:string ,
                                          "CHEBI:4050"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:1721406"^^xsd:string ,
                                   "CAS:3374-22-9"^^xsd:string ,
                                   "Gmelin:2933"^^xsd:string ,
                                   "KEGG:C00736"^^xsd:string ,
                                   "KNApSAcK:C00001351"^^xsd:string ,
                                   "KNApSAcK:C00007323"^^xsd:string ,
                                   "PMID:17439666"^^xsd:string ,
                                   "PMID:25181601"^^xsd:string ,
                                   "Reaxys:1721406"^^xsd:string ,
                                   "Wikipedia:Cysteine"^^xsd:string ;
                oboInOwl:hasExactSynonym "Cysteine"^^xsd:string ,
                                         "cysteine"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "2-Amino-3-mercaptopropionic acid"^^xsd:string ,
                                           "2-amino-3-mercaptopropanoic acid"^^xsd:string ,
                                           "2-amino-3-sulfanylpropanoic acid"^^xsd:string ,
                                           "C"^^xsd:string ,
                                           "Cys"^^xsd:string ,
                                           "Cystein"^^xsd:string ,
                                           "Hcys"^^xsd:string ,
                                           "Zystein"^^xsd:string ,
                                           "cisteina"^^xsd:string ;
                oboInOwl:id "CHEBI:15356"^^xsd:string ;
                rdfs:label "cysteine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_22660
obo:CHEBI_22660 rdf:type :AminoAcid ;
                obo:IAO_0000115 "An alpha-amino acid that consists of succinic acid bearing a single alpha-amino substituent"^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C4H7NO4"^^xsd:string ;
                chebi:inchi "InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)"^^xsd:string ;
                chebi:inchikey "CKLJMWTZIZZHCS-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "133.10272"^^xsd:string ;
                chebi:monoisotopicmass "133.03751"^^xsd:string ;
                chebi:smiles "NC(CC(O)=O)C(O)=O"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:774618"^^xsd:string ,
                                   "CAS:617-45-8"^^xsd:string ,
                                   "Gmelin:185140"^^xsd:string ,
                                   "KEGG:C16433"^^xsd:string ,
                                   "PMID:22264337"^^xsd:string ,
                                   "Reaxys:774618"^^xsd:string ,
                                   "Wikipedia:Aspartic_acid"^^xsd:string ;
                oboInOwl:hasExactSynonym "Aspartic acid"^^xsd:string ,
                                         "aspartic acid"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "(+-)-Aspartic acid"^^xsd:string ,
                                           "(R,S)-Aspartic acid"^^xsd:string ,
                                           "2-aminobutanedioic acid"^^xsd:string ,
                                           "Asp"^^xsd:string ,
                                           "D"^^xsd:string ,
                                           "DL-Aminosuccinic acid"^^xsd:string ,
                                           "DL-Asparagic acid"^^xsd:string ;
                oboInOwl:id "CHEBI:22660"^^xsd:string ;
                rdfs:label "aspartic acid"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .


###  http://purl.obolibrary.org/obo/CHEBI_18237
obo:CHEBI_18237 rdf:type :AminoAcid ;
                obo:IAO_0000115 "An alpha-amino acid that is glutaric acid bearing a single amino substituent at position 2."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C5H9NO4"^^xsd:string ;
                chebi:inchi "InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)"^^xsd:string ;
                chebi:inchikey "WHUUTDBJXJRKMK-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "147.12930"^^xsd:string ;
                chebi:monoisotopicmass "147.05316"^^xsd:string ;
                chebi:smiles "NC(CCC(O)=O)C(O)=O"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:24314"^^xsd:string ,
                                          "CHEBI:5431"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:1723799"^^xsd:string ,
                                   "CAS:617-65-2"^^xsd:string ,
                                   "Gmelin:101971"^^xsd:string ,
                                   "KEGG:C00302"^^xsd:string ,
                                   "KEGG:D04341"^^xsd:string ,
                                   "KNApSAcK:C00001358"^^xsd:string ,
                                   "KNApSAcK:C00019577"^^xsd:string ,
                                   "PMID:15739367"^^xsd:string ,
                                   "PMID:17190852"^^xsd:string ,
                                   "PMID:24616376"^^xsd:string ,
                                   "PMID:24984001"^^xsd:string ,
                                   "Reaxys:1723799"^^xsd:string ,
                                   "Wikipedia:Glutamic_acid"^^xsd:string ;
                oboInOwl:hasExactSynonym "2-aminopentanedioic acid"^^xsd:string ,
                                         "Glutamic acid"^^xsd:string ,
                                         "glutamic acid"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "2-Aminoglutaric acid"^^xsd:string ,
                                           "DL-Glutamic acid"^^xsd:string ,
                                           "DL-Glutaminic acid"^^xsd:string ,
                                           "E"^^xsd:string ,
                                           "Glu"^^xsd:string ,
                                           "Glutamate"^^xsd:string ,
                                           "Glutaminic acid"^^xsd:string ,
                                           "Glutaminsaeure"^^xsd:string ;
                oboInOwl:id "CHEBI:18237"^^xsd:string ;
                rdfs:label "glutamic acid"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .


###  http://purl.obolibrary.org/obo/CHEBI_28044
obo:CHEBI_28044 rdf:type :AminoAcid;
                obo:IAO_0000115 "An aromatic amino acid that is alanine in which one of the methyl hydrogens is substituted by a phenyl group."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C9H11NO2"^^xsd:string ;
                chebi:inchi "InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)"^^xsd:string ;
                chebi:inchikey "COLNVLDHVKWLRT-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "165.18918"^^xsd:string ;
                chebi:monoisotopicmass "165.07898"^^xsd:string ;
                chebi:smiles "NC(Cc1ccccc1)C(O)=O"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:25984"^^xsd:string ,
                                          "CHEBI:8089"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:1910407"^^xsd:string ,
                                   "CAS:150-30-1"^^xsd:string ,
                                   "Gmelin:50836"^^xsd:string ,
                                   "KEGG:C02057"^^xsd:string ,
                                   "PMID:17439666"^^xsd:string ,
                                   "PMID:22264337"^^xsd:string ,
                                   "Reaxys:1910407"^^xsd:string ,
                                   "Wikipedia:Phenylalanine"^^xsd:string ;
                oboInOwl:hasExactSynonym "2-amino-3-phenylpropanoic acid"^^xsd:string ,
                                         "Phenylalanine"^^xsd:string ,
                                         "phenylalanine"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "DL-Phenylalanine"^^xsd:string ,
                                           "F"^^xsd:string ,
                                           "PHE"^^xsd:string ,
                                           "Phenylalanin"^^xsd:string ,
                                           "alpha-Amino-beta-phenylpropionic acid"^^xsd:string ,
                                           "fenilalanina"^^xsd:string ;
                oboInOwl:id "CHEBI:28044"^^xsd:string ;
                rdfs:label "phenylalanine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_15428
obo:CHEBI_15428 rdf:type :AminoAcid ;
                obo:IAO_0000115 "The simplest (and the only achiral) proteinogenic amino acid, with a hydrogen atom as its side chain."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C2H5NO2"^^xsd:string ;
                chebi:inchi "InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)"^^xsd:string ;
                chebi:inchikey "DHMQDGOQFOQNFH-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "75.06664"^^xsd:string ;
                chebi:monoisotopicmass "75.03203"^^xsd:string ;
                chebi:smiles "NCC(O)=O"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:10792"^^xsd:string ,
                                          "CHEBI:14344"^^xsd:string ,
                                          "CHEBI:24368"^^xsd:string ,
                                          "CHEBI:42964"^^xsd:string ,
                                          "CHEBI:5460"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:635782"^^xsd:string ,
                                   "CAS:56-40-6"^^xsd:string ,
                                   "DrugBank:DB00145"^^xsd:string ,
                                   "Drug_Central:1319"^^xsd:string ,
                                   "ECMDB:ECMDB00123"^^xsd:string ,
                                   "Gmelin:1808"^^xsd:string ,
                                   "HMDB:HMDB0000123"^^xsd:string ,
                                   "KEGG:C00037"^^xsd:string ,
                                   "KEGG:D00011"^^xsd:string ,
                                   "KNApSAcK:C00001361"^^xsd:string ,
                                   "MetaCyc:GLY"^^xsd:string ,
                                   "PDBeChem:GLY"^^xsd:string ,
                                   "PMID:10930630"^^xsd:string ,
                                   "PMID:11019925"^^xsd:string ,
                                   "PMID:11174716"^^xsd:string ,
                                   "PMID:11542461"^^xsd:string ,
                                   "PMID:11806864"^^xsd:string ,
                                   "PMID:12631515"^^xsd:string ,
                                   "PMID:12754315"^^xsd:string ,
                                   "PMID:12770151"^^xsd:string ,
                                   "PMID:12921899"^^xsd:string ,
                                   "PMID:15331688"^^xsd:string ,
                                   "PMID:15388434"^^xsd:string ,
                                   "PMID:15710237"^^xsd:string ,
                                   "PMID:16105183"^^xsd:string ,
                                   "PMID:16151895"^^xsd:string ,
                                   "PMID:16214212"^^xsd:string ,
                                   "PMID:16417482"^^xsd:string ,
                                   "PMID:16444815"^^xsd:string ,
                                   "PMID:16664855"^^xsd:string ,
                                   "PMID:16901953"^^xsd:string ,
                                   "PMID:16918424"^^xsd:string ,
                                   "PMID:16986325"^^xsd:string ,
                                   "PMID:16998855"^^xsd:string ,
                                   "PMID:17154252"^^xsd:string ,
                                   "PMID:17383967"^^xsd:string ,
                                   "PMID:17582620"^^xsd:string ,
                                   "PMID:17970719"^^xsd:string ,
                                   "PMID:18079355"^^xsd:string ,
                                   "PMID:18396796"^^xsd:string ,
                                   "PMID:18440992"^^xsd:string ,
                                   "PMID:18593588"^^xsd:string ,
                                   "PMID:18816054"^^xsd:string ,
                                   "PMID:18840508"^^xsd:string ,
                                   "PMID:19028609"^^xsd:string ,
                                   "PMID:19120667"^^xsd:string ,
                                   "PMID:19449910"^^xsd:string ,
                                   "PMID:19526731"^^xsd:string ,
                                   "PMID:19544666"^^xsd:string ,
                                   "PMID:19738917"^^xsd:string ,
                                   "PMID:19916621"^^xsd:string ,
                                   "PMID:19924257"^^xsd:string ,
                                   "PMID:21751272"^^xsd:string ,
                                   "PMID:22044190"^^xsd:string ,
                                   "PMID:22079563"^^xsd:string ,
                                   "PMID:22234938"^^xsd:string ,
                                   "PMID:22264337"^^xsd:string ,
                                   "PMID:22293292"^^xsd:string ,
                                   "PMID:22401276"^^xsd:string ,
                                   "PMID:22434786"^^xsd:string ,
                                   "Reaxys:635782"^^xsd:string ,
                                   "Wikipedia:Glycine"^^xsd:string ,
                                   "YMDB:YMDB00016"^^xsd:string ;
                oboInOwl:hasExactSynonym "GLYCINE"^^xsd:string ,
                                         "Glycine"^^xsd:string ,
                                         "aminoacetic acid"^^xsd:string ,
                                         "glycine"^^xsd:string ;
                oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "Aminoacetic acid"^^xsd:string ,
                                           "Aminoessigsaeure"^^xsd:string ,
                                           "G"^^xsd:string ,
                                           "Gly"^^xsd:string ,
                                           "Glycin"^^xsd:string ,
                                           "Glycocoll"^^xsd:string ,
                                           "Glykokoll"^^xsd:string ,
                                           "Glyzin"^^xsd:string ,
                                           "H2N-CH2-COOH"^^xsd:string ,
                                           "Hgly"^^xsd:string ,
                                           "Leimzucker"^^xsd:string ,
                                           "aminoethanoic acid"^^xsd:string ;
                oboInOwl:id "CHEBI:15428"^^xsd:string ;
                rdfs:label "glycine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_15971
obo:CHEBI_15971 rdf:type :AminoAcid ;
                obo:IAO_0000115 "The L-enantiomer of the amino acid histidine."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C6H9N3O2"^^xsd:string ;
                chebi:inchi "InChI=1S/C6H9N3O2/c7-5(6(10)11)1-4-2-8-3-9-4/h2-3,5H,1,7H2,(H,8,9)(H,10,11)/t5-/m0/s1"^^xsd:string ;
                chebi:inchikey "HNDVDQJCIGZPNO-YFKPBYRVSA-N"^^xsd:string ;
                chebi:mass "155.15468"^^xsd:string ;
                chebi:monoisotopicmass "155.06948"^^xsd:string ;
                chebi:smiles "N[C@@H](Cc1c[nH]cn1)C(O)=O"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:13117"^^xsd:string ,
                                          "CHEBI:21324"^^xsd:string ,
                                          "CHEBI:43048"^^xsd:string ,
                                          "CHEBI:43114"^^xsd:string ,
                                          "CHEBI:43190"^^xsd:string ,
                                          "CHEBI:43239"^^xsd:string ,
                                          "CHEBI:6240"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:84088"^^xsd:string ,
                                   "CAS:71-00-1"^^xsd:string ,
                                   "DrugBank:DB00117"^^xsd:string ,
                                   "ECMDB:ECMDB00177"^^xsd:string ,
                                   "Gmelin:83042"^^xsd:string ,
                                   "HMDB:HMDB0000177"^^xsd:string ,
                                   "KEGG:C00135"^^xsd:string ,
                                   "KEGG:D00032"^^xsd:string ,
                                   "KNApSAcK:C00001363"^^xsd:string ,
                                   "MetaCyc:HIS"^^xsd:string ,
                                   "PDBeChem:HIS"^^xsd:string ,
                                   "PMID:15206581"^^xsd:string ,
                                   "PMID:21608102"^^xsd:string ,
                                   "PMID:21719207"^^xsd:string ,
                                   "PMID:22324399"^^xsd:string ,
                                   "PMID:22415677"^^xsd:string ,
                                   "PMID:22517640"^^xsd:string ,
                                   "Reaxys:84088"^^xsd:string ,
                                   "Wikipedia:L-histidine"^^xsd:string ,
                                   "YMDB:YMDB00369"^^xsd:string ;
                oboInOwl:hasExactSynonym "(2S)-2-amino-3-(1H-imidazol-4-yl)propanoic acid"^^xsd:string ,
                                         "L-Histidine"^^xsd:string ,
                                         "L-histidine"^^xsd:string ;
                oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "(S)-4-(2-Amino-2-carboxyethyl)imidazole"^^xsd:string ,
                                           "(S)-alpha-Amino-1H-imidazole-4-propionic acid"^^xsd:string ,
                                           "(S)-alpha-amino-1H-Imidazole-4-propanoic acid"^^xsd:string ,
                                           "H"^^xsd:string ,
                                           "HISTIDINE"^^xsd:string ,
                                           "His"^^xsd:string ,
                                           "L-(-)-histidine"^^xsd:string ,
                                           "L-Histidin"^^xsd:string ;
                oboInOwl:id "CHEBI:15971"^^xsd:string ;
                rdfs:label "L-histidine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_17191
obo:CHEBI_17191 rdf:type :AminoAcid;
                obo:IAO_0000115 "The L-enantiomer of isoleucine."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C6H13NO2"^^xsd:string ;
                chebi:inchi "InChI=1S/C6H13NO2/c1-3-4(2)5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t4-,5-/m0/s1"^^xsd:string ;
                chebi:inchikey "AGPKZVBTJJNPAG-WHFBIAKZSA-N"^^xsd:string ;
                chebi:mass "131.175"^^xsd:string ;
                chebi:monoisotopicmass "131.09463"^^xsd:string ;
                chebi:smiles "OC([C@H]([C@H](CC)C)N)=O"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:13127"^^xsd:string ,
                                          "CHEBI:21344"^^xsd:string ,
                                          "CHEBI:43290"^^xsd:string ,
                                          "CHEBI:43342"^^xsd:string ,
                                          "CHEBI:43366"^^xsd:string ,
                                          "CHEBI:6255"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:1721792"^^xsd:string ,
                                   "CAS:73-32-5"^^xsd:string ,
                                   "DrugBank:DB00167"^^xsd:string ,
                                   "Drug_Central:4129"^^xsd:string ,
                                   "ECMDB:ECMDB00172"^^xsd:string ,
                                   "Gmelin:486381"^^xsd:string ,
                                   "HMDB:HMDB0000172"^^xsd:string ,
                                   "KEGG:C00407"^^xsd:string ,
                                   "KEGG:D00065"^^xsd:string ,
                                   "KNApSAcK:C00001374"^^xsd:string ,
                                   "MetaCyc:ILE"^^xsd:string ,
                                   "PDBeChem:ILE"^^xsd:string ,
                                   "PMID:14651987"^^xsd:string ,
                                   "PMID:16140883"^^xsd:string ,
                                   "PMID:17299083"^^xsd:string ,
                                   "PMID:17409434"^^xsd:string ,
                                   "PMID:22298573"^^xsd:string ,
                                   "PMID:24284437"^^xsd:string ,
                                   "PMID:24406630"^^xsd:string ,
                                   "PMID:24738868"^^xsd:string ,
                                   "PMID:24831709"^^xsd:string ,
                                   "Reaxys:1721792"^^xsd:string ,
                                   "Wikipedia:Isoleucine"^^xsd:string ,
                                   "YMDB:YMDB00038"^^xsd:string ;
                oboInOwl:hasExactSynonym "L-Isoleucine"^^xsd:string ,
                                         "L-isoleucine"^^xsd:string ;
                oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "(2S,3S)-2-amino-3-methylpentanoic acid"^^xsd:string ,
                                           "2-Amino-3-methylvaleric acid"^^xsd:string ,
                                           "I"^^xsd:string ,
                                           "ISOLEUCINE"^^xsd:string ,
                                           "Ile"^^xsd:string ,
                                           "alpha-amino-beta-methylvaleric acid"^^xsd:string ;
                oboInOwl:id "CHEBI:17191"^^xsd:string ;
                rdfs:label "L-isoleucine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_25094
obo:CHEBI_25094 rdf:type :AminoAcid ;
                obo:IAO_0000115 "A diamino acid that is caproic (hexanoic) acid bearing two amino substituents at positions 2 and 6."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C6H14N2O2"^^xsd:string ;
                chebi:inchi "InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)"^^xsd:string ;
                chebi:inchikey "KDXKERNSBIXSRK-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "146.18764"^^xsd:string ;
                chebi:monoisotopicmass "146.10553"^^xsd:string ;
                chebi:smiles "NCCCCC(N)C(O)=O"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:1616991"^^xsd:string ,
                                   "CAS:70-54-2"^^xsd:string ,
                                   "Gmelin:279284"^^xsd:string ,
                                   "KEGG:C16440"^^xsd:string ,
                                   "PMID:17439666"^^xsd:string ,
                                   "PMID:22264337"^^xsd:string ,
                                   "Reaxys:1616991"^^xsd:string ,
                                   "Wikipedia:Lysine"^^xsd:string ;
                oboInOwl:hasExactSynonym "2,6-diaminohexanoic acid"^^xsd:string ,
                                         "lysine"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "K"^^xsd:string ,
                                           "LYS"^^xsd:string ,
                                           "Lysin"^^xsd:string ,
                                           "alpha,epsilon-diaminocaproic acid"^^xsd:string ;
                oboInOwl:id "CHEBI:25094"^^xsd:string ;
                rdfs:label "lysine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_25017
obo:CHEBI_25017 rdf:type :AminoAcid ;
                obo:IAO_0000115 "A branched-chain amino acid that consists of glycine in which one of the hydrogens attached to the alpha-carbon is substituted by an isobutyl group."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C6H13NO2"^^xsd:string ;
                chebi:inchi "InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)"^^xsd:string ;
                chebi:inchikey "ROHFNLRQFUQHCH-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "131.17296"^^xsd:string ;
                chebi:monoisotopicmass "131.09463"^^xsd:string ;
                chebi:smiles "CC(C)CC(N)C(O)=O"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:636005"^^xsd:string ,
                                   "CAS:328-39-2"^^xsd:string ,
                                   "Gmelin:50203"^^xsd:string ,
                                   "KEGG:C16439"^^xsd:string ,
                                   "LIPID_MAPS_instance:LMFA01100048"^^xsd:string ,
                                   "PMID:17439666"^^xsd:string ,
                                   "Reaxys:636005"^^xsd:string ,
                                   "Wikipedia:Leucine"^^xsd:string ;
                oboInOwl:hasExactSynonym "leucine"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "(+-)-Leucine"^^xsd:string ,
                                           "(RS)-Leucine"^^xsd:string ,
                                           "2-amino-4-methylpentanoic acid"^^xsd:string ,
                                           "DL-Leucine"^^xsd:string ,
                                           "Hleu"^^xsd:string ,
                                           "L"^^xsd:string ,
                                           "Leu"^^xsd:string ,
                                           "Leucin"^^xsd:string ,
                                           "Leuzin"^^xsd:string ;
                oboInOwl:id "CHEBI:25017"^^xsd:string ;
                rdfs:label "leucine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .            

###  http://purl.obolibrary.org/obo/CHEBI_16811
obo:CHEBI_16811 rdf:type :AminoAcid ;
                obo:IAO_0000115 "A sulfur-containing amino acid that is butyric acid bearing an amino substituent at position 2 and a methylthio substituent at position 4."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C5H11NO2S"^^xsd:string ;
                chebi:inchi "InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)"^^xsd:string ;
                chebi:inchikey "FFEARJCKVFRZRR-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "149.21238"^^xsd:string ;
                chebi:monoisotopicmass "149.05105"^^xsd:string ;
                chebi:smiles "CSCCC(N)C(O)=O"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:14590"^^xsd:string ,
                                          "CHEBI:25229"^^xsd:string ,
                                          "CHEBI:6829"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:636185"^^xsd:string ,
                                   "CAS:59-51-8"^^xsd:string ,
                                   "Gmelin:3117"^^xsd:string ,
                                   "KEGG:C01733"^^xsd:string ,
                                   "KEGG:D04983"^^xsd:string ,
                                   "PMID:16702333"^^xsd:string ,
                                   "PMID:22264337"^^xsd:string ,
                                   "PMID:2543976"^^xsd:string ,
                                   "Reaxys:636185"^^xsd:string ,
                                   "UM-BBD_compID:c0094"^^xsd:string ,
                                   "Wikipedia:Methionine"^^xsd:string ;
                oboInOwl:hasExactSynonym "Methionine"^^xsd:string ,
                                         "methionine"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "2-Amino-4-(methylthio)butyric acid"^^xsd:string ,
                                           "2-amino-4-(methylsulfanyl)butanoic acid"^^xsd:string ,
                                           "2-amino-4-(methylthio)butanoic acid"^^xsd:string ,
                                           "DL-Methionine"^^xsd:string ,
                                           "Hmet"^^xsd:string ,
                                           "M"^^xsd:string ,
                                           "Met"^^xsd:string ,
                                           "Methionin"^^xsd:string ,
                                           "Racemethionine"^^xsd:string ,
                                           "alpha-amino-gamma-methylmercaptobutyric acid"^^xsd:string ,
                                           "metionina"^^xsd:string ;
                oboInOwl:id "CHEBI:16811"^^xsd:string ;
                rdfs:label "methionine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .


###  http://purl.obolibrary.org/obo/CHEBI_22653
obo:CHEBI_22653 rdf:type :AminoAcid ;
                obo:IAO_0000115 "An alpha-amino acid in which one of the hydrogens attached to the alpha-carbon of glycine is substituted by a 2-amino-2-oxoethyl group."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C4H8N2O3"^^xsd:string ;
                chebi:inchi "InChI=1S/C4H8N2O3/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H2,6,7)(H,8,9)"^^xsd:string ;
                chebi:inchikey "DCXYFEDJOCDNAF-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "132.11800"^^xsd:string ;
                chebi:monoisotopicmass "132.05349"^^xsd:string ;
                chebi:smiles "NC(CC(N)=O)C(O)=O"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:1723525"^^xsd:string ,
                                   "CAS:3130-87-8"^^xsd:string ,
                                   "Gmelin:279043"^^xsd:string ,
                                   "KEGG:C16438"^^xsd:string ,
                                   "PMID:22264337"^^xsd:string ,
                                   "PMID:22770225"^^xsd:string ,
                                   "Reaxys:1723525"^^xsd:string ,
                                   "Wikipedia:Asparagine"^^xsd:string ;
                oboInOwl:hasExactSynonym "asparagine"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "2,4-diamino-4-oxobutanoic acid"^^xsd:string ,
                                           "2-amino-3-carbamoylpropanoic acid"^^xsd:string ,
                                           "ASN"^^xsd:string ,
                                           "Asn"^^xsd:string ,
                                           "Asparagin"^^xsd:string ,
                                           "DL-Asparagine"^^xsd:string ,
                                           "Hasp"^^xsd:string ,
                                           "N"^^xsd:string ,
                                           "asparagina"^^xsd:string ;
                oboInOwl:id "CHEBI:22653"^^xsd:string ;
                rdfs:label "asparagine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .


###  http://purl.obolibrary.org/obo/CHEBI_17203
obo:CHEBI_17203 rdf:type :AminoAcid ;
                obo:IAO_0000115 "Pyrrolidine in which the pro-S hydrogen at position 2 is substituted by a carboxylic acid group. L-Proline is the only one of the twenty DNA-encoded amino acids which has a secondary amino group alpha to the carboxyl group. It is an essential component of collagen and is important for proper functioning of joints and tendons. It also helps maintain and strengthen heart muscles."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C5H9NO2"^^xsd:string ;
                chebi:inchi "InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1"^^xsd:string ;
                chebi:inchikey "ONIBWKKTOPOVIA-BYPYZUCNSA-N"^^xsd:string ;
                chebi:mass "115.13050"^^xsd:string ;
                chebi:monoisotopicmass "115.06333"^^xsd:string ;
                chebi:smiles "OC(=O)[C@@H]1CCCN1"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:13154"^^xsd:string ,
                                          "CHEBI:184637"^^xsd:string ,
                                          "CHEBI:21373"^^xsd:string ,
                                          "CHEBI:42067"^^xsd:string ,
                                          "CHEBI:45040"^^xsd:string ,
                                          "CHEBI:45100"^^xsd:string ,
                                          "CHEBI:45159"^^xsd:string ,
                                          "CHEBI:6286"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:80810"^^xsd:string ,
                                   "CAS:147-85-3"^^xsd:string ,
                                   "DrugBank:DB00172"^^xsd:string ,
                                   "Drug_Central:4125"^^xsd:string ,
                                   "Gmelin:50152"^^xsd:string ,
                                   "HMDB:HMDB0000162"^^xsd:string ,
                                   "KEGG:C00148"^^xsd:string ,
                                   "KEGG:D00035"^^xsd:string ,
                                   "KNApSAcK:C00001388"^^xsd:string ,
                                   "MetaCyc:PRO"^^xsd:string ,
                                   "PDBeChem:PRO"^^xsd:string ,
                                   "PMID:11076505"^^xsd:string ,
                                   "PMID:12770004"^^xsd:string ,
                                   "PMID:14975886"^^xsd:string ,
                                   "PMID:15576824"^^xsd:string ,
                                   "PMID:15838615"^^xsd:string ,
                                   "PMID:15894682"^^xsd:string ,
                                   "PMID:15973048"^^xsd:string ,
                                   "PMID:16033917"^^xsd:string ,
                                   "PMID:16190672"^^xsd:string ,
                                   "PMID:16501220"^^xsd:string ,
                                   "PMID:16656443"^^xsd:string ,
                                   "PMID:16657874"^^xsd:string ,
                                   "PMID:16668324"^^xsd:string ,
                                   "PMID:17127472"^^xsd:string ,
                                   "PMID:17608428"^^xsd:string ,
                                   "PMID:18551589"^^xsd:string ,
                                   "PMID:18802692"^^xsd:string ,
                                   "PMID:18973300"^^xsd:string ,
                                   "PMID:19215998"^^xsd:string ,
                                   "PMID:19580280"^^xsd:string ,
                                   "PMID:19656302"^^xsd:string ,
                                   "PMID:19688381"^^xsd:string ,
                                   "PMID:19811425"^^xsd:string ,
                                   "PMID:22139509"^^xsd:string ,
                                   "PMID:22201772"^^xsd:string ,
                                   "PMID:22451406"^^xsd:string ,
                                   "PMID:22475019"^^xsd:string ,
                                   "PMID:22482728"^^xsd:string ,
                                   "PMID:22491679"^^xsd:string ,
                                   "PMID:22770225"^^xsd:string ,
                                   "Reaxys:80810"^^xsd:string ,
                                   "Wikipedia:L-proline"^^xsd:string ;
                oboInOwl:hasExactSynonym "L-Proline"^^xsd:string ,
                                         "L-proline"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "(-)-(S)-proline"^^xsd:string ,
                                           "(-)-2-pyrrolidinecarboxylic acid"^^xsd:string ,
                                           "(-)-proline"^^xsd:string ,
                                           "(2S)-pyrrolidine-2-carboxylic acid"^^xsd:string ,
                                           "(S)-2-carboxypyrrolidine"^^xsd:string ,
                                           "(S)-2-pyrrolidinecarboxylic acid"^^xsd:string ,
                                           "(S)-pyrrolidine-2-carboxylic acid"^^xsd:string ,
                                           "2-Pyrrolidinecarboxylic acid"^^xsd:string ,
                                           "L-(-)-proline"^^xsd:string ,
                                           "L-Prolin"^^xsd:string ,
                                           "L-alpha-pyrrolidinecarboxylic acid"^^xsd:string ,
                                           "L-pyrrolidine-2-carboxylic acid"^^xsd:string ,
                                           "P"^^xsd:string ,
                                           "PROLINE"^^xsd:string ,
                                           "prolina"^^xsd:string ,
                                           "proline"^^xsd:string ,
                                           "prolinum"^^xsd:string ;
                oboInOwl:id "CHEBI:17203"^^xsd:string ;
                rdfs:label "L-proline"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_18050
obo:CHEBI_18050 rdf:type :AminoAcid ;
                obo:IAO_0000115 "An optically active form of glutamine having L-configuration."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C5H10N2O3"^^xsd:string ;
                chebi:inchi "InChI=1S/C5H10N2O3/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H2,7,8)(H,9,10)/t3-/m0/s1"^^xsd:string ;
                chebi:inchikey "ZDXPYRJPNDTMRX-VKHMYHEASA-N"^^xsd:string ;
                chebi:mass "146.14458"^^xsd:string ;
                chebi:monoisotopicmass "146.06914"^^xsd:string ;
                chebi:smiles "N[C@@H](CCC(N)=O)C(O)=O"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:13110"^^xsd:string ,
                                          "CHEBI:21308"^^xsd:string ,
                                          "CHEBI:42812"^^xsd:string ,
                                          "CHEBI:42814"^^xsd:string ,
                                          "CHEBI:42899"^^xsd:string ,
                                          "CHEBI:42943"^^xsd:string ,
                                          "CHEBI:6227"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:1723797"^^xsd:string ,
                                   "CAS:56-85-9"^^xsd:string ,
                                   "DrugBank:DB00130"^^xsd:string ,
                                   "Drug_Central:1311"^^xsd:string ,
                                   "ECMDB:ECMDB00641"^^xsd:string ,
                                   "Gmelin:3509"^^xsd:string ,
                                   "HMDB:HMDB0000641"^^xsd:string ,
                                   "KEGG:C00064"^^xsd:string ,
                                   "KEGG:D00015"^^xsd:string ,
                                   "KNApSAcK:C00001359"^^xsd:string ,
                                   "LINCS:LSM-4741"^^xsd:string ,
                                   "MetaCyc:GLN"^^xsd:string ,
                                   "PDBeChem:GLN"^^xsd:string ,
                                   "PMID:11139387"^^xsd:string ,
                                   "PMID:15204730"^^xsd:string ,
                                   "PMID:22055478"^^xsd:string ,
                                   "PMID:22206385"^^xsd:string ,
                                   "PMID:22451274"^^xsd:string ,
                                   "PMID:22453904"^^xsd:string ,
                                   "PMID:22575040"^^xsd:string ,
                                   "PMID:22770225"^^xsd:string ,
                                   "PMID:29438107"^^xsd:string ,
                                   "Reaxys:1723797"^^xsd:string ,
                                   "Wikipedia:Glutamine"^^xsd:string ,
                                   "YMDB:YMDB00002"^^xsd:string ;
                oboInOwl:hasExactSynonym "L-Glutamine"^^xsd:string ,
                                         "L-glutamine"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "(2S)-2,5-diamino-5-oxopentanoic acid"^^xsd:string ,
                                           "(2S)-2-amino-4-carbamoylbutanoic acid"^^xsd:string ,
                                           "(S)-2,5-diamino-5-oxopentanoic acid"^^xsd:string ,
                                           "GLUTAMINE"^^xsd:string ,
                                           "Glutamic acid 5-amide"^^xsd:string ,
                                           "Glutamic acid amide"^^xsd:string ,
                                           "L-(+)-glutamine"^^xsd:string ,
                                           "L-2-Aminoglutaramic acid"^^xsd:string ,
                                           "L-2-aminoglutaramic acid"^^xsd:string ,
                                           "L-Glutamin"^^xsd:string ,
                                           "L-Glutaminsaeure-5-amid"^^xsd:string ,
                                           "L-glutamic acid gamma-amide"^^xsd:string ,
                                           "Levoglutamide"^^xsd:string ,
                                           "Q"^^xsd:string ;
                oboInOwl:id "CHEBI:18050"^^xsd:string ;
                rdfs:label "L-glutamine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_16467
obo:CHEBI_16467 rdf:type :AminoAcid;
                obo:IAO_0000115 "An L-alpha-amino acid that is the L-isomer of arginine."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C6H14N4O2"^^xsd:string ;
                chebi:inchi "InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/t4-/m0/s1"^^xsd:string ;
                chebi:inchikey "ODKSFYDXXFIFQN-BYPYZUCNSA-N"^^xsd:string ;
                chebi:mass "174.20100"^^xsd:string ;
                chebi:monoisotopicmass "174.11168"^^xsd:string ;
                chebi:smiles "N[C@@H](CCCNC(N)=N)C(O)=O"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:13077"^^xsd:string ,
                                          "CHEBI:21235"^^xsd:string ,
                                          "CHEBI:42927"^^xsd:string ,
                                          "CHEBI:6185"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:1725413"^^xsd:string ,
                                   "CAS:74-79-3"^^xsd:string ,
                                   "DrugBank:DB00125"^^xsd:string ,
                                   "Drug_Central:1549"^^xsd:string ,
                                   "ECMDB:ECMDB00517"^^xsd:string ,
                                   "Gmelin:83283"^^xsd:string ,
                                   "HMDB:HMDB0000517"^^xsd:string ,
                                   "KEGG:C00062"^^xsd:string ,
                                   "KEGG:D02982"^^xsd:string ,
                                   "KNApSAcK:C00001340"^^xsd:string ,
                                   "MetaCyc:ARG"^^xsd:string ,
                                   "PDBeChem:ARG"^^xsd:string ,
                                   "PDBeChem:GND"^^xsd:string ,
                                   "PMID:10848923"^^xsd:string ,
                                   "PMID:11139824"^^xsd:string ,
                                   "PMID:11300497"^^xsd:string ,
                                   "PMID:11898853"^^xsd:string ,
                                   "PMID:12812828"^^xsd:string ,
                                   "PMID:15016745"^^xsd:string ,
                                   "PMID:15465805"^^xsd:string ,
                                   "PMID:16056256"^^xsd:string ,
                                   "PMID:16416365"^^xsd:string ,
                                   "PMID:17168727"^^xsd:string ,
                                   "PMID:17439666"^^xsd:string ,
                                   "PMID:19030957"^^xsd:string ,
                                   "PMID:21600268"^^xsd:string ,
                                   "PMID:21814794"^^xsd:string ,
                                   "PMID:22179117"^^xsd:string ,
                                   "PMID:22243793"^^xsd:string ,
                                   "PMID:22251130"^^xsd:string ,
                                   "PMID:22361732"^^xsd:string ,
                                   "PMID:22425811"^^xsd:string ,
                                   "PMID:22428068"^^xsd:string ,
                                   "PMID:22439203"^^xsd:string ,
                                   "PMID:22553931"^^xsd:string ,
                                   "PMID:22619480"^^xsd:string ,
                                   "PMID:22626826"^^xsd:string ,
                                   "PMID:22652429"^^xsd:string ,
                                   "PMID:22667467"^^xsd:string ,
                                   "PMID:22709481"^^xsd:string ,
                                   "PMID:8070089"^^xsd:string ,
                                   "Reaxys:1725413"^^xsd:string ,
                                   "Wikipedia:L-arginine"^^xsd:string ,
                                   "YMDB:YMDB00592"^^xsd:string ;
                oboInOwl:hasExactSynonym "L-Arginine"^^xsd:string ,
                                         "L-arginine"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "(2S)-2-amino-5-(carbamimidamido)pentanoic acid"^^xsd:string ,
                                           "(2S)-2-amino-5-guanidinopentanoic acid"^^xsd:string ,
                                           "(S)-2-Amino-5-guanidinovaleric acid"^^xsd:string ,
                                           "(S)-2-amino-5-guanidinopentanoic acid"^^xsd:string ,
                                           "Arg"^^xsd:string ,
                                           "L-(+)-arginine"^^xsd:string ,
                                           "L-Arg"^^xsd:string ,
                                           "L-Arginin"^^xsd:string ,
                                           "R"^^xsd:string ,
                                           "arginine"^^xsd:string ;
                oboInOwl:id "CHEBI:16467"^^xsd:string ;
                rdfs:label "L-arginine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_17115
obo:CHEBI_17115 rdf:type :AminoAcid ;
                obo:IAO_0000115 "The L-enantiomer of serine."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C3H7NO3"^^xsd:string ;
                chebi:inchi "InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1"^^xsd:string ;
                chebi:inchikey "MTCFGRXMJLQNBG-REOHCLBHSA-N"^^xsd:string ;
                chebi:mass "105.09262"^^xsd:string ;
                chebi:monoisotopicmass "105.04259"^^xsd:string ;
                chebi:smiles "N[C@@H](CO)C(O)=O"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:13167"^^xsd:string ,
                                          "CHEBI:21387"^^xsd:string ,
                                          "CHEBI:45440"^^xsd:string ,
                                          "CHEBI:45451"^^xsd:string ,
                                          "CHEBI:45590"^^xsd:string ,
                                          "CHEBI:45597"^^xsd:string ,
                                          "CHEBI:45677"^^xsd:string ,
                                          "CHEBI:6301"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:1721404"^^xsd:string ,
                                   "CAS:56-45-1"^^xsd:string ,
                                   "DrugBank:DB00133"^^xsd:string ,
                                   "Drug_Central:4127"^^xsd:string ,
                                   "ECMDB:ECMDB00187"^^xsd:string ,
                                   "Gmelin:2570"^^xsd:string ,
                                   "HMDB:HMDB0000187"^^xsd:string ,
                                   "KEGG:C00065"^^xsd:string ,
                                   "KEGG:D00016"^^xsd:string ,
                                   "KNApSAcK:C00001393"^^xsd:string ,
                                   "MetaCyc:SER"^^xsd:string ,
                                   "PDBeChem:SER"^^xsd:string ,
                                   "PMID:1650428"^^xsd:string ,
                                   "PMID:17439666"^^xsd:string ,
                                   "PMID:19062365"^^xsd:string ,
                                   "PMID:21956576"^^xsd:string ,
                                   "PMID:22265470"^^xsd:string ,
                                   "PMID:22393170"^^xsd:string ,
                                   "PMID:22547037"^^xsd:string ,
                                   "PMID:22566084"^^xsd:string ,
                                   "PMID:22566694"^^xsd:string ,
                                   "Reaxys:1721404"^^xsd:string ,
                                   "Wikipedia:L-serine"^^xsd:string ,
                                   "YMDB:YMDB00112"^^xsd:string ;
                oboInOwl:hasExactSynonym "L-Serine"^^xsd:string ,
                                         "L-serine"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "(2S)-2-amino-3-hydroxypropanoic acid"^^xsd:string ,
                                           "(S)-(-)-serine"^^xsd:string ,
                                           "(S)-2-amino-3-hydroxypropanoic acid"^^xsd:string ,
                                           "(S)-alpha-Amino-beta-hydroxypropionic acid"^^xsd:string ,
                                           "(S)-serine"^^xsd:string ,
                                           "L-(-)-serine"^^xsd:string ,
                                           "L-2-Amino-3-hydroxypropionic acid"^^xsd:string ,
                                           "L-3-Hydroxy-2-aminopropionic acid"^^xsd:string ,
                                           "L-3-Hydroxy-alanine"^^xsd:string ,
                                           "L-Ser"^^xsd:string ,
                                           "L-Serin"^^xsd:string ,
                                           "S"^^xsd:string ,
                                           "SERINE"^^xsd:string ,
                                           "Ser"^^xsd:string ,
                                           "Serine"^^xsd:string ,
                                           "beta-Hydroxy-L-alanine"^^xsd:string ,
                                           "beta-Hydroxyalanine"^^xsd:string ;
                oboInOwl:id "CHEBI:17115"^^xsd:string ;
                rdfs:label "L-serine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_16857
obo:CHEBI_16857 rdf:type :AminoAcid ;
                obo:IAO_0000115 "An optically active form of threonine having L-configuration."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C4H9NO3"^^xsd:string ;
                chebi:inchi "InChI=1S/C4H9NO3/c1-2(6)3(5)4(7)8/h2-3,6H,5H2,1H3,(H,7,8)/t2-,3+/m1/s1"^^xsd:string ;
                chebi:inchikey "AYFVYJQAPQTCCC-GBXIJSLDSA-N"^^xsd:string ;
                chebi:mass "119.11920"^^xsd:string ;
                chebi:monoisotopicmass "119.05824"^^xsd:string ;
                chebi:smiles "C[C@@H](O)[C@H](N)C(O)=O"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:13175"^^xsd:string ,
                                          "CHEBI:21403"^^xsd:string ,
                                          "CHEBI:42083"^^xsd:string ,
                                          "CHEBI:45843"^^xsd:string ,
                                          "CHEBI:45983"^^xsd:string ,
                                          "CHEBI:6308"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:1721646"^^xsd:string ,
                                   "CAS:72-19-5"^^xsd:string ,
                                   "DrugBank:DB00156"^^xsd:string ,
                                   "Drug_Central:4254"^^xsd:string ,
                                   "ECMDB:ECMDB00167"^^xsd:string ,
                                   "Gmelin:82510"^^xsd:string ,
                                   "HMDB:HMDB0000167"^^xsd:string ,
                                   "KEGG:C00188"^^xsd:string ,
                                   "KEGG:D00041"^^xsd:string ,
                                   "KNApSAcK:C00001394"^^xsd:string ,
                                   "PDBeChem:THR"^^xsd:string ,
                                   "PMID:11964235"^^xsd:string ,
                                   "PMID:12523390"^^xsd:string ,
                                   "PMID:16659349"^^xsd:string ,
                                   "PMID:17379183"^^xsd:string ,
                                   "PMID:22289691"^^xsd:string ,
                                   "PMID:22342587"^^xsd:string ,
                                   "PMID:22513921"^^xsd:string ,
                                   "PMID:22770225"^^xsd:string ,
                                   "PMID:24671569"^^xsd:string ,
                                   "Reaxys:1721646"^^xsd:string ,
                                   "UM-BBD_compID:c0413"^^xsd:string ,
                                   "Wikipedia:Threonine"^^xsd:string ,
                                   "YMDB:YMDB00214"^^xsd:string ;
                oboInOwl:hasExactSynonym "L-Threonine"^^xsd:string ,
                                         "L-threonine"^^xsd:string ;
                oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "(2S)-threonine"^^xsd:string ,
                                           "(2S,3R)-(-)-Threonine"^^xsd:string ,
                                           "(2S,3R)-2-amino-3-hydroxybutanoic acid"^^xsd:string ,
                                           "2-Amino-3-hydroxybutyric acid"^^xsd:string ,
                                           "L-(-)-Threonine"^^xsd:string ,
                                           "L-2-Amino-3-hydroxybutyric acid"^^xsd:string ,
                                           "L-Threonin"^^xsd:string ,
                                           "L-alpha-amino-beta-hydroxybutyric acid"^^xsd:string ,
                                           "T"^^xsd:string ,
                                           "THREONINE"^^xsd:string ,
                                           "Thr"^^xsd:string ;
                oboInOwl:id "CHEBI:16857"^^xsd:string ;
                rdfs:label "L-threonine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_27897
obo:CHEBI_27897 rdf:type :AminoAcid ;
                obo:IAO_0000115 "An alpha-amino acid that is alanine bearing an indol-3-yl substituent at position 3."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C11H12N2O2"^^xsd:string ;
                chebi:inchi "InChI=1S/C11H12N2O2/c12-9(11(14)15)5-7-6-13-10-4-2-1-3-8(7)10/h1-4,6,9,13H,5,12H2,(H,14,15)"^^xsd:string ;
                chebi:inchikey "QIVBCDIJIAJPQS-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "204.22526"^^xsd:string ;
                chebi:monoisotopicmass "204.08988"^^xsd:string ;
                chebi:smiles "NC(Cc1c[nH]c2ccccc12)C(O)=O"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:27163"^^xsd:string ,
                                          "CHEBI:9769"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:86196"^^xsd:string ,
                                   "CAS:54-12-6"^^xsd:string ,
                                   "Gmelin:4532"^^xsd:string ,
                                   "KEGG:C00806"^^xsd:string ,
                                   "KNApSAcK:C00001396"^^xsd:string ,
                                   "LINCS:LSM-36836"^^xsd:string ,
                                   "PMID:17439666"^^xsd:string ,
                                   "PMID:22264337"^^xsd:string ,
                                   "Reaxys:86196"^^xsd:string ,
                                   "Wikipedia:Tryptophan"^^xsd:string ;
                oboInOwl:hasExactSynonym "Tryptophan"^^xsd:string ,
                                         "tryptophan"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "2-amino-3-(1H-indol-3-yl)propanoic acid"^^xsd:string ,
                                           "Htrp"^^xsd:string ,
                                           "Trp"^^xsd:string ,
                                           "W"^^xsd:string ,
                                           "alpha-Amino-beta-(3-indolyl)-propionic acid"^^xsd:string ,
                                           "alpha-amino-beta-3-indolepropionic acid"^^xsd:string ,
                                           "beta-3-indolylalanine"^^xsd:string ,
                                           "triptofano"^^xsd:string ,
                                           "tryptophane"^^xsd:string ;
                oboInOwl:id "CHEBI:27897"^^xsd:string ;
                rdfs:label "tryptophan"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_18186
obo:CHEBI_18186 rdf:type :AminoAcid ;
                obo:IAO_0000115 "An alpha-amino acid that is phenylalanine bearing a hydroxy substituent at position 4 on the phenyl ring."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C9H11NO3"^^xsd:string ;
                chebi:inchi "InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)"^^xsd:string ;
                chebi:inchikey "OUYCCCASQSFEME-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "181.18858"^^xsd:string ;
                chebi:monoisotopicmass "181.07389"^^xsd:string ;
                chebi:smiles "NC(Cc1ccc(O)cc1)C(O)=O"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:15277"^^xsd:string ,
                                          "CHEBI:27176"^^xsd:string ,
                                          "CHEBI:9800"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:515881"^^xsd:string ,
                                   "CAS:55520-40-6"^^xsd:string ,
                                   "CAS:556-03-6"^^xsd:string ,
                                   "Gmelin:27744"^^xsd:string ,
                                   "KEGG:C01536"^^xsd:string ,
                                   "KNApSAcK:C00001397"^^xsd:string ,
                                   "PMID:17190852"^^xsd:string ,
                                   "Reaxys:515881"^^xsd:string ;
                oboInOwl:hasExactSynonym "Tyrosine"^^xsd:string ,
                                         "tyrosine"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "2-Amino-3-(p-hydroxyphenyl)propionic acid"^^xsd:string ,
                                           "2-amino-3-(4-hydroxyphenyl)propanoic acid"^^xsd:string ,
                                           "3-(p-Hydroxyphenyl)alanine"^^xsd:string ,
                                           "Tyr"^^xsd:string ,
                                           "Tyrosin"^^xsd:string ,
                                           "Y"^^xsd:string ,
                                           "tirosina"^^xsd:string ;
                oboInOwl:id "CHEBI:18186"^^xsd:string ;
                rdfs:label "tyrosine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_16414
obo:CHEBI_16414 rdf:type :AminoAcid ;
                obo:IAO_0000115 "The L-enantiomer of valine."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C5H11NO2"^^xsd:string ;
                chebi:inchi "InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1"^^xsd:string ;
                chebi:inchikey "KZSNJWFQEVHDMF-BYPYZUCNSA-N"^^xsd:string ;
                chebi:mass "117.14638"^^xsd:string ;
                chebi:monoisotopicmass "117.07898"^^xsd:string ;
                chebi:smiles "CC(C)[C@H](N)C(O)=O"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:13186"^^xsd:string ,
                                          "CHEBI:21417"^^xsd:string ,
                                          "CHEBI:46282"^^xsd:string ,
                                          "CHEBI:46376"^^xsd:string ,
                                          "CHEBI:46418"^^xsd:string ,
                                          "CHEBI:46484"^^xsd:string ,
                                          "CHEBI:6321"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:1721136"^^xsd:string ,
                                   "CAS:72-18-4"^^xsd:string ,
                                   "DrugBank:DB00161"^^xsd:string ,
                                   "Drug_Central:4128"^^xsd:string ,
                                   "Gmelin:2827"^^xsd:string ,
                                   "HMDB:HMDB0000883"^^xsd:string ,
                                   "KEGG:C00183"^^xsd:string ,
                                   "KEGG:D00039"^^xsd:string ,
                                   "KNApSAcK:C00001398"^^xsd:string ,
                                   "MetaCyc:VAL"^^xsd:string ,
                                   "PDBeChem:VAL"^^xsd:string ,
                                   "PMID:14608070"^^xsd:string ,
                                   "PMID:17670823"^^xsd:string ,
                                   "PMID:21706252"^^xsd:string ,
                                   "PMID:22138982"^^xsd:string ,
                                   "PMID:22287678"^^xsd:string ,
                                   "PMID:22585822"^^xsd:string ,
                                   "Reaxys:1721136"^^xsd:string ,
                                   "Wikipedia:L-valine"^^xsd:string ;
                oboInOwl:hasExactSynonym "L-Valine"^^xsd:string ,
                                         "L-valine"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "(2S)-2-amino-3-methylbutanoic acid"^^xsd:string ,
                                           "(S)-valine"^^xsd:string ,
                                           "2-Amino-3-methylbutyric acid"^^xsd:string ,
                                           "L-(+)-alpha-Aminoisovaleric acid"^^xsd:string ,
                                           "L-Valin"^^xsd:string ,
                                           "L-alpha-Amino-beta-methylbutyric acid"^^xsd:string ,
                                           "V"^^xsd:string ,
                                           "VALINE"^^xsd:string ,
                                           "Val"^^xsd:string ;
                oboInOwl:id "CHEBI:16414"^^xsd:string ;
                rdfs:label "L-valine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_33709
obo:CHEBI_33709 rdf:type skos:Concept ;
                obo:IAO_0000115 "A carboxylic acid containing one or more amino groups."^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:13815"^^xsd:string ,
                                          "CHEBI:22477"^^xsd:string ;
                oboInOwl:hasDbXref "Wikipedia:Amino_acid"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "Aminocarbonsaeure"^^xsd:string ,
                                           "Aminokarbonsaeure"^^xsd:string ,
                                           "Aminosaeure"^^xsd:string ,
                                           "amino acids"^^xsd:string ;
                oboInOwl:id "CHEBI:33709"^^xsd:string ;
                skos:inScheme <http://purl.obolibrary.org/obo/chebi.owl> ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> ;
                rdfs:label "amino acid"^^xsd:string .


###  http://purl.obolibrary.org/obo/CHEBI_36976
obo:CHEBI_36976 rdf:type skos:Concept ;
                obo:IAO_0000115 "A nucleotide is a nucleoside phosphate resulting from the condensation of the 3 or 5 hydroxy group of a nucleoside with phosphoric acid."^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:13215"^^xsd:string ,
                                          "CHEBI:13663"^^xsd:string ,
                                          "CHEBI:7656"^^xsd:string ;
                oboInOwl:hasDbXref "KEGG:C00215"^^xsd:string ;
                oboInOwl:hasExactSynonym "Nucleotide"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "nucleotides"^^xsd:string ;
                oboInOwl:id "CHEBI:36976"^^xsd:string ;
                skos:inScheme <http://purl.obolibrary.org/obo/chebi.owl> ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> ;
                rdfs:label "nucleotide"^^xsd:string .


###  http://purl.obolibrary.org/obo/CHEBI_18282
obo:CHEBI_18282 rdf:type skos:Concept ;
                obo:IAO_0000115 "That part of DNA or RNA that may be involved in pairing."^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:13873"^^xsd:string ,
                                          "CHEBI:25598"^^xsd:string ,
                                          "CHEBI:2995"^^xsd:string ;
                oboInOwl:hasDbXref "KEGG:C00701"^^xsd:string ,
                                   "Wikipedia:Nucleobase"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "Base"^^xsd:string ,
                                           "nucleobases"^^xsd:string ;
                oboInOwl:id "CHEBI:18282"^^xsd:string ;
                rdfs:label "nucleobase"^^xsd:string ;
                skos:inScheme <http://purl.obolibrary.org/obo/chebi.owl> ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .


###  http://purl.obolibrary.org/obo/CHEBI_17568
obo:CHEBI_17568 rdf:type :Nucleotide ;
                obo:IAO_0000115 "A common and naturally occurring pyrimidine nucleobase in which the pyrimidine ring is substituted with two oxo groups at positions 2 and 4. Found in RNA, it base pairs with adenine and replaces thymine during DNA transcription."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C4H4N2O2"^^xsd:string ;
                chebi:inchi "InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)"^^xsd:string ;
                chebi:inchikey "ISAKRJDGNUQOIC-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "112.08684"^^xsd:string ;
                chebi:monoisotopicmass "112.02728"^^xsd:string ;
                chebi:smiles "O=c1cc[nH]c(=O)[nH]1"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:15288"^^xsd:string ,
                                          "CHEBI:27210"^^xsd:string ,
                                          "CHEBI:46375"^^xsd:string ,
                                          "CHEBI:9882"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:606623"^^xsd:string ,
                                   "CAS:66-22-8"^^xsd:string ,
                                   "DrugBank:DB03419"^^xsd:string ,
                                   "Gmelin:2896"^^xsd:string ,
                                   "HMDB:HMDB0000300"^^xsd:string ,
                                   "KEGG:C00106"^^xsd:string ,
                                   "KEGG:D00027"^^xsd:string ,
                                   "KNApSAcK:C00001513"^^xsd:string ,
                                   "MetaCyc:URACIL"^^xsd:string ,
                                   "PDBeChem:URA"^^xsd:string ,
                                   "PMID:11279060"^^xsd:string ,
                                   "PMID:12855717"^^xsd:string ,
                                   "PMID:15274295"^^xsd:string ,
                                   "PMID:16834123"^^xsd:string ,
                                   "PMID:17439666"^^xsd:string ,
                                   "PMID:18533995"^^xsd:string ,
                                   "PMID:18815805"^^xsd:string ,
                                   "PMID:19175333"^^xsd:string ,
                                   "PMID:22020693"^^xsd:string ,
                                   "PMID:22074393"^^xsd:string ,
                                   "PMID:22120518"^^xsd:string ,
                                   "PMID:22171528"^^xsd:string ,
                                   "PMID:22237209"^^xsd:string ,
                                   "PMID:22299724"^^xsd:string ,
                                   "PMID:22356544"^^xsd:string ,
                                   "PMID:22447672"^^xsd:string ,
                                   "PMID:22483865"^^xsd:string ,
                                   "PMID:22567906"^^xsd:string ,
                                   "PMID:22685418"^^xsd:string ,
                                   "PMID:3654008"^^xsd:string ,
                                   "Reaxys:606623"^^xsd:string ,
                                   "Wikipedia:Uracil"^^xsd:string ;
                oboInOwl:hasExactSynonym "URACIL"^^xsd:string ,
                                         "Uracil"^^xsd:string ,
                                         "pyrimidine-2,4(1H,3H)-dione"^^xsd:string ,
                                         "uracil"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "2,4(1H,3H)-pyrimidinedione"^^xsd:string ,
                                           "2,4-Dioxopyrimidine"^^xsd:string ,
                                           "2,4-Pyrimidinedione"^^xsd:string ,
                                           "U"^^xsd:string ,
                                           "Ura"^^xsd:string ,
                                           "Urazil"^^xsd:string ;
                oboInOwl:id "CHEBI:17568"^^xsd:string ;
                rdfs:label "uracil"^^xsd:string .

###  http://purl.obolibrary.org/obo/CHEBI_16235
obo:CHEBI_16235 rdf:type :Nucleotide ;
                obo:IAO_0000115 "A 2-aminopurine carrying a 6-oxo substituent."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C5H5N5O"^^xsd:string ;
                chebi:inchi "InChI=1S/C5H5N5O/c6-5-9-3-2(4(11)10-5)7-1-8-3/h1H,(H4,6,7,8,9,10,11)"^^xsd:string ;
                chebi:inchikey "UYTPUPDQBNUYGX-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "151.126"^^xsd:string ;
                chebi:monoisotopicmass "151.04941"^^xsd:string ;
                chebi:smiles "C12=C(N=C(NC1=O)N)NC=N2"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:14371"^^xsd:string ,
                                          "CHEBI:14372"^^xsd:string ,
                                          "CHEBI:24443"^^xsd:string ,
                                          "CHEBI:42948"^^xsd:string ,
                                          "CHEBI:5563"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:147911"^^xsd:string ,
                                   "CAS:73-40-5"^^xsd:string ,
                                   "DrugBank:DB02377"^^xsd:string ,
                                   "Gmelin:431879"^^xsd:string ,
                                   "HMDB:HMDB0000132"^^xsd:string ,
                                   "KEGG:C00242"^^xsd:string ,
                                   "KNApSAcK:C00001501"^^xsd:string ,
                                   "MetaCyc:GUANINE"^^xsd:string ,
                                   "PDBeChem:GUN"^^xsd:string ,
                                   "PMID:22770225"^^xsd:string ,
                                   "PMID:8070089"^^xsd:string ,
                                   "Reaxys:147911"^^xsd:string ,
                                   "Wikipedia:Guanine"^^xsd:string ;
                oboInOwl:hasExactSynonym "2-amino-1,9-dihydro-6H-purin-6-one"^^xsd:string ,
                                         "GUANINE"^^xsd:string ,
                                         "Guanine"^^xsd:string ,
                                         "guanine"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "2-Amino-6-hydroxypurine"^^xsd:string ,
                                           "2-amino-6-oxopurine"^^xsd:string ,
                                           "G"^^xsd:string ,
                                           "Gua"^^xsd:string ;
                oboInOwl:id "CHEBI:16235"^^xsd:string ;
                rdfs:label "guanine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_16708
obo:CHEBI_16708 rdf:type :Nucleotide ;
                obo:IAO_0000115 "The parent compound of the 6-aminopurines, composed of a purine having an amino group at C-6."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C5H5N5"^^xsd:string ;
                chebi:inchi "InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10)"^^xsd:string ;
                chebi:inchikey "GFFGJBXGBJISGV-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "135.12690"^^xsd:string ;
                chebi:monoisotopicmass "135.05450"^^xsd:string ;
                chebi:smiles "Nc1ncnc2[nH]cnc12"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:13733"^^xsd:string ,
                                          "CHEBI:22236"^^xsd:string ,
                                          "CHEBI:2470"^^xsd:string ,
                                          "CHEBI:40579"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:608603"^^xsd:string ,
                                   "CAS:73-24-5"^^xsd:string ,
                                   "DrugBank:DB00173"^^xsd:string ,
                                   "Drug_Central:89"^^xsd:string ,
                                   "Gmelin:3903"^^xsd:string ,
                                   "HMDB:HMDB0000034"^^xsd:string ,
                                   "KEGG:C00147"^^xsd:string ,
                                   "KEGG:D00034"^^xsd:string ,
                                   "KNApSAcK:C00001490"^^xsd:string ,
                                   "MetaCyc:ADENINE"^^xsd:string ,
                                   "PDBeChem:ADE"^^xsd:string ,
                                   "PMID:11985597"^^xsd:string ,
                                   "PMID:12829005"^^xsd:string ,
                                   "PMID:12951489"^^xsd:string ,
                                   "PMID:15063338"^^xsd:string ,
                                   "PMID:15715490"^^xsd:string ,
                                   "PMID:17439666"^^xsd:string ,
                                   "PMID:8070089"^^xsd:string ,
                                   "Reaxys:608603"^^xsd:string ,
                                   "Wikipedia:Adenine"^^xsd:string ;
                oboInOwl:hasExactSynonym "9H-purin-6-amine"^^xsd:string ,
                                         "ADENINE"^^xsd:string ,
                                         "Adenine"^^xsd:string ,
                                         "adenine"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "6-Aminopurine"^^xsd:string ,
                                           "A"^^xsd:string ,
                                           "Ade"^^xsd:string ,
                                           "Adenin"^^xsd:string ;
                oboInOwl:id "CHEBI:16708"^^xsd:string ;
                rdfs:label "adenine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .


###  http://purl.obolibrary.org/obo/CHEBI_16040
obo:CHEBI_16040 rdf:type :Nucleotide ;
                obo:IAO_0000115 "An aminopyrimidine that is pyrimidin-2-one having the amino group located at position 4."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C4H5N3O"^^xsd:string ;
                chebi:inchi "InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)"^^xsd:string ;
                chebi:inchikey "OPTASPLRGRRNAP-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "111.10212"^^xsd:string ;
                chebi:monoisotopicmass "111.04326"^^xsd:string ;
                chebi:smiles "Nc1cc[nH]c(=O)n1"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:14066"^^xsd:string ,
                                          "CHEBI:23531"^^xsd:string ,
                                          "CHEBI:4072"^^xsd:string ,
                                          "CHEBI:41732"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:2637"^^xsd:string ,
                                   "CAS:71-30-7"^^xsd:string ,
                                   "Gmelin:82472"^^xsd:string ,
                                   "HMDB:HMDB0000630"^^xsd:string ,
                                   "KEGG:C00380"^^xsd:string ,
                                   "KNApSAcK:C00001498"^^xsd:string ,
                                   "MetaCyc:CYTOSINE"^^xsd:string ,
                                   "PDBeChem:CYT"^^xsd:string ,
                                   "PMID:14253484"^^xsd:string ,
                                   "PMID:22770225"^^xsd:string ,
                                   "PMID:7877593"^^xsd:string ,
                                   "Reaxys:2637"^^xsd:string ,
                                   "Wikipedia:Cytosine"^^xsd:string ;
                oboInOwl:hasExactSynonym "4-aminopyrimidin-2(1H)-one"^^xsd:string ,
                                         "Cytosine"^^xsd:string ,
                                         "cytosine"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "4-amino-2(1H)-pyrimidinone"^^xsd:string ,
                                           "4-amino-2-hydroxypyrimidine"^^xsd:string ,
                                           "C"^^xsd:string ,
                                           "Cyt"^^xsd:string ,
                                           "Cytosin"^^xsd:string ,
                                           "Zytosin"^^xsd:string ;
                oboInOwl:id "CHEBI:16040"^^xsd:string ;
                rdfs:label "cytosine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/CHEBI_17821
obo:CHEBI_17821 rdf:type :Nucleotide;
                obo:IAO_0000115 "A pyrimidine nucleobase that is uracil in which the hydrogen at position 5 is replaced by a methyl group."^^xsd:string ;
                chebi:charge "0"^^xsd:string ;
                chebi:formula "C5H6N2O2"^^xsd:string ;
                chebi:inchi "InChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)"^^xsd:string ;
                chebi:inchikey "RWQNBRDOKXIBIV-UHFFFAOYSA-N"^^xsd:string ;
                chebi:mass "126.11342"^^xsd:string ;
                chebi:monoisotopicmass "126.04293"^^xsd:string ;
                chebi:smiles "Cc1c[nH]c(=O)[nH]c1=O"^^xsd:string ;
                oboInOwl:hasAlternativeId "CHEBI:15247"^^xsd:string ,
                                          "CHEBI:27004"^^xsd:string ,
                                          "CHEBI:46017"^^xsd:string ,
                                          "CHEBI:9580"^^xsd:string ;
                oboInOwl:hasDbXref "Beilstein:607626"^^xsd:string ,
                                   "CAS:65-71-4"^^xsd:string ,
                                   "DrugBank:DB03462"^^xsd:string ,
                                   "Gmelin:278790"^^xsd:string ,
                                   "KEGG:C00178"^^xsd:string ,
                                   "KNApSAcK:C00001511"^^xsd:string ,
                                   "PDBeChem:TDR"^^xsd:string ,
                                   "PMID:23237383"^^xsd:string ,
                                   "Wikipedia:Thymine"^^xsd:string ;
                oboInOwl:hasExactSynonym "THYMINE"^^xsd:string ,
                                         "Thymine"^^xsd:string ,
                                         "thymine"^^xsd:string ;
                oboInOwl:hasRelatedSynonym "2,4-dihydroxy-5-methylpyrimidine"^^xsd:string ,
                                           "5-Methyluracil"^^xsd:string ,
                                           "5-methyl-2,4(1H,3H)-pyrimidinedione"^^xsd:string ,
                                           "5-methylpyrimidine-2,4(1H,3H)-dione"^^xsd:string ,
                                           "5-methyluracil"^^xsd:string ,
                                           "T"^^xsd:string ,
                                           "Thy"^^xsd:string ,
                                           "Thymin"^^xsd:string ;
                oboInOwl:id "CHEBI:17821"^^xsd:string ;
                rdfs:label "thymine"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/chebi/charge
chebi:charge rdf:type owl:AnnotationProperty ;
                skos:inScheme <http://purl.obolibrary.org/obo/chebi.owl> ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .


###  http://purl.obolibrary.org/obo/chebi/formula
chebi:formula rdf:type owl:AnnotationProperty ;
                skos:inScheme <http://purl.obolibrary.org/obo/chebi.owl> ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .

###  http://purl.obolibrary.org/obo/chebi/inchi
chebi:inchi rdf:type owl:AnnotationProperty ;
                skos:inScheme <http://purl.obolibrary.org/obo/chebi.owl> ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .


###  http://purl.obolibrary.org/obo/chebi/inchikey
chebi:inchikey rdf:type owl:AnnotationProperty ;
                skos:inScheme <http://purl.obolibrary.org/obo/chebi.owl> ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .


###  http://purl.obolibrary.org/obo/chebi/mass
chebi:mass rdf:type owl:AnnotationProperty ;
                skos:inScheme <http://purl.obolibrary.org/obo/chebi.owl> ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .


###  http://purl.obolibrary.org/obo/chebi/monoisotopicmass
chebi:monoisotopicmass rdf:type owl:AnnotationProperty ;
                skos:inScheme <http://purl.obolibrary.org/obo/chebi.owl> ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .


###  http://purl.obolibrary.org/obo/chebi/smiles
chebi:smiles rdf:type owl:AnnotationProperty ;
                skos:inScheme <http://purl.obolibrary.org/obo/chebi.owl> ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/chebi.owl> .



#####
### Additional imported SIO terms  
####
###  http://semanticscience.org/resource/SIO_010079
sio:SIO_010079 rdf:type owl:ObjectProperty ;
               dc:identifier "SIO_010079" ;
               terms:description "A relation between two objects, in which the first object is produced from the information contained in the second object."@en ;
               rdfs:isDefinedBy <http://semanticscience.org/ontology/sio.owl> ;
               rdfs:label "is encoded by"@en .

#####
### SIO terms by OWL2 punning as SKOS instances
####

###  http://semanticscience.org/resource/SIO_000638
sio:SIO_000638 rdf:type skos:Concept ;
               skos:inScheme <http://semanticscience.org/ontology/sio.owl> ;
               dc:identifier "SIO_000638" ;
               terms:description "A probability measure is quantity of how likely it is that some event will occur."@en ;
               rdfs:isDefinedBy <http://semanticscience.org/ontology/sio.owl> ;
               rdfs:label "probability measure"@en .

###  http://semanticscience.org/resource/SIO_010448
sio:SIO_010448 rdf:type :AminoAcid;
               dc:identifier "SIO_010448" ;
               terms:description "A stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals a termination of translation."@en ;
               rdfs:isDefinedBy <http://semanticscience.org/ontology/sio.owl> ;
               rdfs:label "stop codon"@en ;
               skos:altLabel "*".



###  http://semanticscience.org/resource/SIO_000640
sio:SIO_000640 rdf:type skos:Concept ;
			   rdfs:subClassOf sio:SIO_000555 ;
               owl:disjointWith sio:SIO_000751 ;
               dc:identifier "SIO_000640" ;
               terms:description "A quality that has a value that is increased compared to normal or average."@en ;
               terms:identifier "SIO:000640" ;
               rdfs:isDefinedBy <http://semanticscience.org/ontology/sio.owl> ;
               rdfs:label "increased"@en ;
   			   skos:inScheme <http://semanticscience.org/ontology/sio.owl> ;
               skos:altLabel "up".

###  http://semanticscience.org/resource/SIO_000751
sio:SIO_000751 rdf:type skos:Concept ;
               rdfs:subClassOf sio:SIO_000555 ;
               dc:identifier "SIO_000751" ;
               terms:description "A quality that has a value that is decreased compared to normal or average."@en ;
               terms:identifier "SIO:000751" ;
               rdfs:isDefinedBy <http://semanticscience.org/ontology/sio.owl> ;
               rdfs:label "decreased"@en ;
   			   skos:inScheme <http://semanticscience.org/ontology/sio.owl> ;
               skos:altLabel "down".

###  http://semanticscience.org/resource/SIO_000554
sio:SIO_000554 rdf:type skos:Concept ;
               owl:disjointWith sio:SIO_000555 ;
               dc:identifier "SIO_000554" ;
               terms:description "A quality that has a value that is normal or average."@en ;
               terms:identifier "SIO:000554" ;
   			   skos:inScheme <http://semanticscience.org/ontology/sio.owl> ;
               rdfs:isDefinedBy <http://semanticscience.org/ontology/sio.owl> ;
               rdfs:label "normal"@en ;
               skos:altLabel "no change".

###  http://semanticscience.org/resource/SIO_000555
sio:SIO_000555  a skos:Concept;
				terms:description "A quality that has a value that is outside normal or average."@en ;
				dc:identifier "SIO_000555" ;
                terms:identifier "SIO:000555" ;
                rdfs:isDefinedBy <http://semanticscience.org/ontology/sio.owl> ;
                skos:inScheme <http://semanticscience.org/ontology/sio.owl> ;
				rdfs:label "abnormal"@en .

###  http://semanticscience.org/resource/SIO_000899
sio:SIO_000899 rdf:type skos:Concept ;
               dc:identifier "SIO_000899" ;
               terms:description "A chromosome is a molecular complex of circular or linear DNA and bound proteins."@en ;
               rdfs:isDefinedBy <http://semanticscience.org/ontology/sio.owl> ;
               skos:inScheme <http://semanticscience.org/ontology/sio.owl> ;
               rdfs:label "chromosome"@en .






##### Extracted from OBI
###  http://purl.obolibrary.org/obo/OBI_0302840
obo:OBI_0302840 a skos:Concept ;
		        obo:IAO_0000111 "curated information"^^xsd:string ;
                obo:IAO_0000112 "PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6."^^xsd:string ;
                obo:IAO_0000115 "A information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts."^^xsd:string ;
                obo:IAO_0000116 "2010-01-31 Philippe Rocca-Serra: restriction now changed to be the output of a digital curation process + reflected in example of usage and reference"^^xsd:string ;
                obo:IAO_0000117 "Person:Bjoern Peters"^^xsd:string ,
                                "Person:Philippe Rocca-Serra"^^xsd:string ;
                rdfs:label "curated information"@en ;
                skos:altLabel "Curated";
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/obi/2020-04-23/obi.owl> ;
                skos:inScheme <http://purl.obolibrary.org/obo/obi.owl> ;
                terms:license <http://creativecommons.org/licenses/by/4.0/> . 


obo:OBI_0001442 rdf:type skos:Concept ;
                obo:IAO_0000111 "q-value"^^xsd:string ;
                obo:IAO_0000112 """PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines.
\"After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)\""""^^xsd:string ;
                obo:IAO_0000115 """A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. 
To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level."""@en ;
                skos:altLabel "FDR adjusted p-value" ;
                obo:IAO_0000118 "FDR adjusted p-value"@en ;
                rdfs:label "q-value"^^xsd:string ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/obi/2020-04-23/obi.owl> ;
                skos:inScheme <http://purl.obolibrary.org/obo/obi.owl> ;
                terms:license <http://creativecommons.org/licenses/by/4.0/> .

###  http://purl.obolibrary.org/obo/OBI_0000175
obo:OBI_0000175 rdf:type owl:Class ;
                obo:IAO_0000111 "p-value"@en ;
                obo:IAO_0000112 """PMID:19696660
in contrast to the in-vivo data AT-III increased significantly from
113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2)."""^^xsd:string ;
                obo:IAO_0000115 "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone."@en ;
                obo:IAO_0000119 "WEB: http://en.wikipedia.org/wiki/P-value"^^xsd:string ;
                rdfs:label "p-value"@en ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/obi/2020-04-23/obi.owl> ;
                skos:inScheme <http://purl.obolibrary.org/obo/obi.owl> ;
                terms:license <http://creativecommons.org/licenses/by/4.0/> .
########
#### STATO terms
########
###  http://purl.obolibrary.org/obo/STATO_0000169
obo:STATO_0000169 rdf:type owl:Class ;
                  obo:IAO_0000115 "Fold change is a number describing how much a quantity changes going from an initial to a final value or one condition to another condition"@en ;
                   obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en ,
                                  "Orlaith Burke" ,
                                  "Philippe Rocca-Serra"@en ;
                  obo:IAO_0000119 "http://en.wikipedia.org/wiki/Fold_change"@en ;
                  rdfs:label "fold change"@en ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/stato.owl> ;
                skos:inScheme <http://purl.obolibrary.org/obo/stato.owl> ;
                terms:license <http://creativecommons.org/licenses/by/3.0/> .

########
#### IAO addtional properties
########
###  http://purl.obolibrary.org/obo/IAO_0000118
obo:IAO_0000118 rdf:type owl:AnnotationProperty ;
                obo:IAO_0000111 "alternative term"@en ;
                obo:IAO_0000115 "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)"@en ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/iao.owl> ;
                rdfs:label "alternative term"@en .
######
## Extracted terms from the VOAG vocabulary

voag:approves
      rdf:type owl:ObjectProperty ;
      rdfs:label "approves"^^xsd:string ;
      rdfs:subPropertyOf voag:governs ;
      rdfs:comment "An object property that specifies that a party governs the approval of a resource."^^xsd:string ;
      owl:inverseOf voag:isApprovedBy ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 


voag:isApprovedBy
      rdf:type owl:ObjectProperty ;
      rdfs:label "is approved by"^^xsd:string ;
      rdfs:subPropertyOf voag:isGovernedBy ;
      rdfs:comment "References to which parties approve an entity." ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 

voag:governs
      rdf:type owl:ObjectProperty ;
      rdfs:label "governs"^^xsd:string ;
      rdfs:comment "A super-property of governance properties: 'approves', 'gives concurrence for', 'reviews' and 'witness to'."^^xsd:string ;
      owl:inverseOf voag:isGovernedBy ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 

voag:isGovernedBy
      rdf:type owl:ObjectProperty ;
      rdfs:label "is governed by"^^xsd:string ;
      rdfs:comment "A pointer to who is responsible for the governance of some entity of interest. This is a two-way reference with the inverse property 'governs'." ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 

voag:Organization
      rdf:type owl:Class ;
      rdfs:label "Organization"^^xsd:string ;
      rdfs:subClassOf voag:Party ;
      rdfs:subClassOf
              [ rdf:type owl:Restriction ;
                owl:allValuesFrom voag:OrganizationLogo ;
                owl:onProperty voag:hasLogo
              ] ;
      rdfs:subClassOf
              [ rdf:type owl:Restriction ;
                owl:minCardinality "0"^^xsd:nonNegativeInteger ;
                owl:onProperty voag:url
              ] ;
      rdfs:subClassOf
              [ rdf:type owl:Restriction ;
                owl:maxCardinality "1"^^xsd:nonNegativeInteger ;
                owl:onProperty voag:hasLogo
              ] ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 

voag:OrganizationLogo
      rdf:type owl:Class ;
      rdfs:label "Organization logo"^^xsd:string ;
      rdfs:subClassOf voag:Logo ;
      rdfs:comment "A logo for an organization"^^xsd:string ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 

voag:url
      rdf:type owl:DatatypeProperty ;
      rdfs:label "url"^^xsd:string ;
      rdfs:range xsd:anyURI ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 

voag:Logo
      rdf:type owl:Class ;
      rdfs:label "Logo"^^xsd:string ;
      rdfs:subClassOf voag:Image ;
      rdfs:comment  "Logo is ..."^^xsd:string ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> .       

voag:Image
      rdf:type owl:Class ;
      rdfs:label "Image"^^xsd:string ;
      rdfs:subClassOf owl:Thing ;
      rdfs:subClassOf
              [ rdf:type owl:Restriction ;
                owl:maxCardinality "1"^^xsd:nonNegativeInteger ;
                owl:onProperty voag:width
              ] ;
      rdfs:subClassOf
              [ rdf:type owl:Restriction ;
                owl:maxCardinality "1"^^xsd:nonNegativeInteger ;
                owl:onProperty voag:caption
              ] ;
      rdfs:subClassOf
              [ rdf:type owl:Restriction ;
                owl:maxCardinality "1"^^xsd:nonNegativeInteger ;
                owl:onProperty voag:height
              ] ;
      rdfs:subClassOf
              [ rdf:type owl:Restriction ;
                owl:cardinality "1"^^xsd:nonNegativeInteger ;
                owl:onProperty voag:image
              ] ;
      rdfs:comment "Image is a class for figures, pictures, logos, and icons  of various kinds"^^xsd:string ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 

voag:image
      rdf:type owl:DatatypeProperty ;
      rdfs:label "image"^^xsd:string ;
      rdfs:range xsd:anyURI ;
      rdfs:comment "The property 'vaem:image' points  to an image using a URL. "^^xsd:string ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 

voag:height
      rdf:type owl:DatatypeProperty ;
      rdfs:label "height"^^xsd:string ;
      rdfs:range xsd:string ;
      rdfs:comment "Height is typically used to specify an image's height attribute."^^xsd:string ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 

voag:hasLogo
      rdf:type owl:ObjectProperty ;
      rdfs:label "has logo"^^xsd:string ;
      rdfs:range voag:Logo ;
      rdfs:comment "A property to reference an image that is used as a logo."^^xsd:string ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 

 voag:caption
      rdf:type owl:DatatypeProperty ;
      rdfs:label "caption"^^xsd:string ;
      rdfs:range xsd:string ;
      rdfs:comment "A short description, typically used on a table or a figure."^^xsd:string ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 

voag:width
      rdf:type owl:DatatypeProperty ;
      rdfs:label "width"^^xsd:string ;
      rdfs:comment "Width is typically used to specify an image's width attribute."^^xsd:string ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 


voag:Party
      rdf:type owl:Class ;
      rdfs:label "Party"^^xsd:string ;
      rdfs:subClassOf
              [ rdf:type owl:Restriction ;
                owl:maxCardinality "1"^^xsd:nonNegativeInteger ;
                owl:onProperty voag:id
              ] ;
      rdfs:subClassOf
              [ rdf:type owl:Restriction ;
                owl:maxCardinality "1"^^xsd:nonNegativeInteger ;
                owl:onProperty voag:shortDescription
              ] ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 

voag:id
	  rdfs:subPropertyOf terms:identifier ;
      rdf:type owl:DatatypeProperty ;
      rdfs:label "id"^^xsd:string ;
      rdfs:range xsd:anySimpleType ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 

voag:shortDescription
      rdf:type owl:DatatypeProperty ;
      rdfs:label "short description"^^xsd:string ;
      rdfs:range xsd:string ;
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 


### VOAG instance metadata for organizations
<http://edrn.nci.nih.gov> a voag:Organization;
							voag:url "https://edrn.nci.nih.gov"^^xsd:anyURI;
							rdfs:label "Early Detection Research Network";
							voag:id "EDRN";
							voag:shortDescription "The Early Detection Research Network (EDRN), an initatve of the National Cancer Institute (NCI), brings together dozens of institutions to help accelerate the translation of biomarker information into clinical applications and to evaluate new ways of testng cancer in its earliest stages and for cancer risk.";
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 

<http://www.fda.gov> a voag:Organization;
							voag:url "https://www.fda.gov"^^xsd:anyURI;
							rdfs:label "Food and Drug Administration";
							voag:id "FDA";
							voag:shortDescription "The Food and Drug Administration (FDA) is an agency within the U.S. Department of Health and Human Services. It consists of the Office of the Commissioner and four directorates overseeing the core functions of the agency: Medical Products and Tobacco, Foods and Veterinary Medicine, Global Regulatory Operations and Policy, and Operations.";
      rdfs:isDefinedBy <http://voag.linkedmodel.org/1.0/schema/OSG_voag-(v1.0).ttl> ;
      terms:license <http://opensource.org/licenses/academic.php> . 


###############
### Extracted NCI thesaurus terms and converted classes into local skos:Concept intances 
###############

###  http://purl.obolibrary.org/obo/NCIT_C93100
obo:NCIT_C93100 rdf:type skos:Concept ;
                rdfs:comment "A gene alteration that causes or predisposes an individual to a specific disease." ;
                oboInOwl:hasExactSynonym "Disease-causing Mutation" ,
                                         "disease-causing mutation" ;
                rdfs:label "Disease-causing Mutation" ;
                owl:isDefinedBy <http://purl.obolibrary.org/obo/ncit/releases/2020-07-17/ncit.owl> ;
                skos:inScheme obo:NCIT_C43816 .

###  http://purl.obolibrary.org/obo/NCIT_C62559
obo:NCIT_C62559 a :BiomarkerState ;
                oboInOwl:hasExactSynonym "Accepted" ,
                                         "Established" ;
                rdfs:label "Accepted" ;
                owl:isDefinedBy <http://purl.obolibrary.org/obo/ncit/releases/2020-07-17/ncit.owl> ;
                skos:inScheme obo:NCIT_C43816 .


###  http://purl.obolibrary.org/obo/NCIT_C17013
obo:NCIT_C17013 rdf:type skos:Concept ;
                obo:IAO_0000115 "Prediction of the probable course and outcome of a disease." ;
                rdfs:comment "The likely outcome or course of a disease; the chance of recovery or recurrence." ;
                oboInOwl:hasExactSynonym "Prediction of Outcome" ,
                                         "Prognosis" ,
                                         "prognosis" ;
                rdfs:label "Prognosis" ;
                terms:identifier "NCIT:C17013" ;
      			rdfs:isDefinedBy <http://purl.obolibrary.org/obo/ncit/releases/2020-07-17/ncit.owl> ;
                skos:inScheme obo:NCIT_C43816 .

###  http://purl.obolibrary.org/obo/NCIT_C54156
obo:NCIT_C54156 rdf:type skos:Concept ;
                obo:IAO_0000115 "An extrapolation of given data into the future." ;
                oboInOwl:hasExactSynonym "Predicted" ,
                                         "Prediction" ;
                terms:identifier "NCIT:C54156" ;                                         
                rdfs:label "Prediction" ;
      			rdfs:isDefinedBy <http://purl.obolibrary.org/obo/ncit/releases/2020-07-17/ncit.owl> ;
                skos:inScheme obo:NCIT_C43816 .


###  http://purl.obolibrary.org/obo/NCIT_C15220
obo:NCIT_C15220 rdf:type skos:Concept ;
                obo:IAO_0000115 "The investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms; also, the scientific determination of any kind; the concise results of such an investigation." ;
                rdfs:comment "The process of identifying a disease, such as cancer, from its signs and symptoms." ;
                oboInOwl:hasExactSynonym "DIAGNOSIS" ,
                                         "Diagnosed" ,
                                         "Diagnosis" ,
                                         "Diagnostic" ,
                                         "Dx" ,
                                         "diagnosis" ;
                rdfs:label "Diagnosis" ;
                terms:identifier "NCIT:C15220" ;             
      			rdfs:isDefinedBy <http://purl.obolibrary.org/obo/ncit/releases/2020-07-17/ncit.owl> ;
                skos:inScheme obo:NCIT_C43816 .

###  http://purl.obolibrary.org/obo/NCIT_C15367
obo:NCIT_C15367 rdf:type skos:Concept ;
                obo:IAO_0000115 "An estimated probability that one or more adverse event(s) will occur as a result of exposure to an actual or potential hazardous situation or chemical." ;
                rdfs:comment "A process used to estimate the risk that a certain event will happen. In medicine, this may include a person's risk of having a child with a certain condition or disease, such as cancer. It may also be used to estimate the risk of carrying a certain gene mutation (change), or of having an adverse event (unexpected medical problem) in response to certain types of drugs or other substances. A risk assessment may be done by collecting information about a person's age, sex, personal and family medical history, ethnic background, lifestyle, and other factors and using statistics tools to calculate risk." ;
                oboInOwl:hasExactSynonym "Risk Assessment" ,
                                         "risk assessment" ;
                rdfs:label "Risk Assessment" ;
                terms:identifier "NCIT:C15367" ; 
      			rdfs:isDefinedBy <http://purl.obolibrary.org/obo/ncit/releases/2020-07-17/ncit.owl> ;
                skos:inScheme obo:NCIT_C43816 .

###  http://purl.obolibrary.org/obo/NCIT_C16209
obo:NCIT_C16209 rdf:type skos:Concept ;
                obo:IAO_0000115 "Use of a device, marker, or other means for the purpose of detecting the presence of a tumor early in its development." ;
                oboInOwl:hasExactSynonym "Early Detection" ;
                rdfs:label "Early Detection" ;
                terms:identifier "NCIT:C16209" ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/ncit.owl>;
                skos:inScheme obo:NCIT_C43816 .

###  http://purl.obolibrary.org/obo/NCIT_C16505
obo:NCIT_C16505 rdf:type skos:Concept ;
                obo:IAO_0000115 "The constitutional or inborn state disposing to a disease, group of diseases, or metabolic or structural anomaly." ;
                oboInOwl:hasExactSynonym "Predisposition" ,
                                         "Susceptibility" ,
                                         "Susceptible" ;
                rdfs:label "Susceptibility";
                terms:identifier "NCIT:C16505" ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/ncit.owl>;
                skos:inScheme obo:NCIT_C43816 .

###  http://purl.obolibrary.org/obo/NCIT_C43816
obo:NCIT_C43816 rdf:type skos:ConceptScheme ;
                obo:IAO_0000115 "The National Cancer Institute (NCI) reference terminology and ontology.  NCI Thesaurus (NCIt) provides controlled terminology for clinical care, translational and basic research, public dissemination of information and associated administrative activities. NCIt is updated monthly to support precise coding of data based on the most recent developments in the cancer and biomedical research community.  NCIt has rich textual and formal logic descriptions of biomedical concepts, including full text definitions, synonyms, a true is_a taxonomic structure, polyhierarchy, inferred partonomy, and other features that make it suitable for supporting accurate human understanding and complex computer processing.  NCIt has been produced by NCI Enterprise Vocabulary Services (EVS) since 1997, and adopted since then for use by numerous federal agencies, standards development and research organizations." ;
                oboInOwl:hasExactSynonym "NCI Thesaurus" ,
                                         "NCIT" ,
                                         "NCIt" ,
                                         "Thesaurus" ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/ncit.owl>;
                rdfs:label "NCI Thesaurus" .

###  http://purl.obolibrary.org/obo/NCIT_C61040
obo:NCIT_C61040 rdf:type skos:Concept ;
                obo:IAO_0000115 "In statistics, a number that expresses the probability that the result of a given experiment or study could have occurred purely by chance. This number can be a margin of error or it can indicate a confidence level." ;
                oboInOwl:hasExactSynonym "Significance" ,
                                         "Statistical Significance" ,
                                         "Statistically Significant" ,
                                         "significant" ,
                                         "statistical significance" ,
                                         "statistically significant" ;
                oboInOwl:inSubset obo:NCIT_C61410 ,
                                  obo:NCIT_C67497 ;
                rdfs:label "Statistical Significance" ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/ncit.owl>;
                skos:inScheme obo:NCIT_C43816 .

###  http://purl.obolibrary.org/obo/NCIT_C13203
obo:NCIT_C13203 rdf:type skos:Concept ;
                obo:IAO_0000115 "A structure found in the nucleus of human cells that is comprised of a strand of linearized double-stranded DNA plus proteins that package the DNA in a condensed coil form and regulate chromosomal function." ;
                obo:NCIT_P98 "Normal human somatic cells have 23 pairs of chromosomes." ;
                oboInOwl:hasExactSynonym "Human Chromosome" ;
                rdfs:label "Human Chromosome" ;
                rdfs:isDefinedBy <http://purl.obolibrary.org/obo/ncit.owl>;
                skos:inScheme obo:NCIT_C43816 .

###  http://purl.obolibrary.org/obo/NCIT_C13204
obo:NCIT_C13204 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the largest human autosomal chromosome pair. Chromosome 1 spans about 247 million nucleotide base pairs and represents about 8% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 1" .                

###  http://purl.obolibrary.org/obo/NCIT_C13215
obo:NCIT_C13215 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the second largest human autosomal chromosome pair. Chromosome 2 spans more than 237 million base pairs and represents almost 8% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 2" .

###  http://purl.obolibrary.org/obo/NCIT_C13219
obo:NCIT_C13219 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the third largest human autosomal chromosome pair. Chromosome 3 spans almost 200 million base pairs and represents about 6.5% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 3" .

###  http://purl.obolibrary.org/obo/NCIT_C13220
obo:NCIT_C13220 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the fourth largest human autosomal chromosome pair. Chromosome 4 spans more than 186 million base pairs and represents between 6 and 6.5% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 4" .

###  http://purl.obolibrary.org/obo/NCIT_C13221
obo:NCIT_C13221 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the fifth largest human autosomal chromosome pair. Chromosome 5 spans about 181 million base pairs and represents almost 6% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 5" .

###  http://purl.obolibrary.org/obo/NCIT_C13222
obo:NCIT_C13222 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the sixth largest human autosomal chromosome pair. Chromosome 6 spans more than 170 million base pairs and represents between 5.5 and 6% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 6" .

###  http://purl.obolibrary.org/obo/NCIT_C13223
obo:NCIT_C13223 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the seventh largest human autosomal chromosome pair. Chromosome 7 spans more than 158 million base pairs and represents between 5 and 5.5% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 7" .

###  http://purl.obolibrary.org/obo/NCIT_C13224
obo:NCIT_C13224 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the eighth largest human autosomal chromosome pair. Chromosome 8 spans about 145 million base pairs and represents between 4.5 and 5.0% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 8" .

###  http://purl.obolibrary.org/obo/NCIT_C13225
obo:NCIT_C13225 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the ninth largest human autosomal chromosome pair. Chromosome 9 spans about 145 million base pairs of nucleic acids and represents between 4 and 4.5% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 9" .

###  http://purl.obolibrary.org/obo/NCIT_P98
obo:NCIT_P98 rdf:type owl:AnnotationProperty ;
             obo:IAO_0000115 "Design notes are notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept." ;
             rdfs:label "DesignNote" ;
             rdfs:range xsd:string ;
             rdfs:isDefinedBy <http://purl.obolibrary.org/obo/ncit.owl>;
             skos:inScheme obo:NCIT_C43816 .

###  http://purl.obolibrary.org/obo/NCIT_C13205
obo:NCIT_C13205 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the tenth largest human autosomal chromosome pair. Chromosome 10 spans about 135 million base pairs and represents between 4 and 4.5% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 10" .

###  http://purl.obolibrary.org/obo/NCIT_C13206
obo:NCIT_C13206 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the eleventh largest human autosomal chromosome pair. Chromosome 11 spans about 134.5 million base pairs and represents between 4 and 4.5% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 11" .

###  http://purl.obolibrary.org/obo/NCIT_C13207
obo:NCIT_C13207 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the twelfth largest human autosomal chromosome pair. Chromosome 12 spans about 143 million base pairs and represents between 4 and 4.5% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 12" .

###  http://purl.obolibrary.org/obo/NCIT_C13208
obo:NCIT_C13208 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the thirteenth largest human autosomal chromosome pair. Chromosome 13 spans about 113 million base pairs and represents between 3.5 and 4% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 13" .

###  http://purl.obolibrary.org/obo/NCIT_C13209
obo:NCIT_C13209 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the fourteenth largest human autosomal chromosome pair. Chromosome 14 spans about 105 million base pairs and represents between 3 and 3.5% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 14" .

###  http://purl.obolibrary.org/obo/NCIT_C13210
obo:NCIT_C13210 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the fifteenth largest human autosomal chromosome pair. Chromosome 15 spans about 106 million base pairs and represents between 3 and 3.5% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 15" .


###  http://purl.obolibrary.org/obo/NCIT_C13211
obo:NCIT_C13211 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the sixteenth largest human autosomal chromosome pair. Chromosome 16 spans about 90 million base pairs and represents just under 3% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 16" .


###  http://purl.obolibrary.org/obo/NCIT_C13212
obo:NCIT_C13212 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the seventeenth largest human autosomal chromosome pair. Chromosome 17 spans more than 81 million base pairs and represents between 2.5 and 3% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 17" .


###  http://purl.obolibrary.org/obo/NCIT_C13213
obo:NCIT_C13213 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the eighteenth largest human autosomal chromosome pair. Chromosome 18 spans about 76 million base pairs and represents about 2.5% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 18" .

###  http://purl.obolibrary.org/obo/NCIT_C13214
obo:NCIT_C13214 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the nineteenth largest human autosomal chromosome pair. Chromosome 19 spans more than 63 million base pairs and represents between 2 and 2.5% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 19" .

###  http://purl.obolibrary.org/obo/NCIT_C13216
obo:NCIT_C13216 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the third smallest human autosomal chromosome pair. Chromosome 20 spans around 63 million base pairs and represents between 2 and 2.5% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 20" .

###  http://purl.obolibrary.org/obo/NCIT_C13217
obo:NCIT_C13217 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the second smallest human autosomal chromosome pair. Chromosome 21 spans around 47 million nucleotides and represents about 1.5% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 21" .

###  http://purl.obolibrary.org/obo/NCIT_C13218
obo:NCIT_C13218 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The designation for each member of the smallest human autosomal chromosome pair. Chromosome 22 spans about 49 million base pairs and represents between 1.5 and 2% of the total DNA in normal diploid cells." ;
                rdfs:label "Chromosome 22" .

###  http://purl.obolibrary.org/obo/NCIT_C13285
obo:NCIT_C13285 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The sex chromosome that is present in both sexes: singly in males and doubly in females." ;
                oboInOwl:hasExactSynonym "Chromosome X" ,
                                         "X Chromosome" ;
                rdfs:label "Chromosome X" .

###  http://purl.obolibrary.org/obo/NCIT_C13286
obo:NCIT_C13286 rdf:type :HumanChromosome ;
                obo:IAO_0000115 "The y-shaped sex chromosome. In mammals, its presence or absence determines male or female sex." ;
                oboInOwl:hasExactSynonym "Chromosome Y" ,
                                         "Y Chromosome" ;
                rdfs:label "Chromosome Y" .


:COMPANION_DIAGNOSIS a skos:Concept;
				obo:IAO_0000115 "A companion diagnosis is a diagnostic test that provides essential information for the safe and effective use of a corresponding drug or biological product. The test helps a health care professional determine whether a particular therapeutic product’s benefits to patients will outweigh any potential serious side effects or risks." ;
				rdfs:comment "This term should be suggested as part of the NCI thesaurus." ;
                oboInOwl:hasExactSynonym "companion diagnostic" ,
                                         "companion diagnosis" ;
                rdfs:label "Companion Diagnosis" ;
                skos:inScheme : ;
                rdfs:seeAlso <https://www.fda.gov/medical-devices/vitro-diagnostics/companion-diagnostics>.




####
#### Other SKOS terms
#########

#################################################################
#    Object Properties
#################################################################

###  http://www.w3.org/2004/02/skos/core#broadMatch
skos:broadMatch rdf:type owl:ObjectProperty ;
                rdfs:subPropertyOf skos:broader ,
                                   skos:mappingRelation ;
                owl:inverseOf skos:narrowMatch ;
                rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
                rdfs:label "has broader match"@en ;
                rdfs:comment "If 'concept A has-broad-match concept B' then the set of resources properly indexed against concept A is a subset of the set of resources properly indexed against concept B." ;
                skos:definition "skos:broadMatch is used to state a hierarchical mapping link between two conceptual resources in different concept schemes."@en .


###  http://www.w3.org/2004/02/skos/core#broader
skos:broader rdf:type owl:ObjectProperty ;
             rdfs:subPropertyOf skos:broaderTransitive ;
             owl:inverseOf skos:narrower ;
             rdfs:comment "Broader concepts are typically rendered as parents in a concept hierarchy (tree)."@en ;
             rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
             rdfs:label "has broader"@en ;
             skos:definition "Relates a concept to a concept that is more general in meaning."@en ;
             skos:scopeNote "By convention, skos:broader is only used to assert an immediate (i.e. direct) hierarchical link between two conceptual resources."@en .


###  http://www.w3.org/2004/02/skos/core#broaderTransitive
skos:broaderTransitive rdf:type owl:ObjectProperty ;
                       rdfs:subPropertyOf skos:semanticRelation ;
                       owl:inverseOf skos:narrowerTransitive ;
                       rdf:type owl:TransitiveProperty ;
                       rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
                       rdfs:label "has broader transitive"@en ;
                       skos:definition "skos:broaderTransitive is a transitive superproperty of skos:broader." ;
                       skos:scopeNote "By convention, skos:broaderTransitive is not used to make assertions. Rather, the properties can be used to draw inferences about the transitive closure of the hierarchical relation, which is useful e.g. when implementing a simple query expansion algorithm in a search application."@en .


###  http://www.w3.org/2004/02/skos/core#closeMatch
skos:closeMatch rdf:type owl:ObjectProperty ;
                rdfs:subPropertyOf skos:mappingRelation ;
                rdf:type owl:SymmetricProperty ;
                rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
                rdfs:label "has close match"@en ;
                skos:definition "skos:closeMatch is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of \"compound errors\" when combining mappings across more than two concept schemes, skos:closeMatch is not declared to be a transitive property."@en .


###  http://www.w3.org/2004/02/skos/core#exactMatch
skos:exactMatch rdf:type owl:ObjectProperty ;
                rdfs:subPropertyOf skos:closeMatch ;
                rdf:type owl:SymmetricProperty ,
                         owl:TransitiveProperty ;
                rdfs:comment "skos:exactMatch is disjoint with each of the properties skos:broadMatch and skos:relatedMatch."@en ;
                rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
                rdfs:label "has exact match"@en ;
                skos:definition "skos:exactMatch is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch."@en .




###  http://www.w3.org/2004/02/skos/core#mappingRelation
skos:mappingRelation rdf:type owl:ObjectProperty ;
                     rdfs:subPropertyOf skos:semanticRelation ;
                     rdfs:comment "These concept mapping relations mirror semantic relations, and the data model defined below is similar (with the exception of skos:exactMatch) to the data model defined for semantic relations. A distinct vocabulary is provided for concept mapping relations, to provide a convenient way to differentiate links within a concept scheme from links between concept schemes. However, this pattern of usage is not a formal requirement of the SKOS data model, and relies on informal definitions of best practice."@en ;
                     rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
                     rdfs:label "is in mapping relation with"@en ;
                     skos:definition "Relates two concepts coming, by convention, from different schemes, and that have comparable meanings"@en .




###  http://www.w3.org/2004/02/skos/core#narrowMatch
skos:narrowMatch rdf:type owl:ObjectProperty ;
                 rdfs:subPropertyOf skos:mappingRelation ,
                                    skos:narrower ;
                 rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
                 rdfs:label "has narrower match"@en ;
                 rdfs:comment "If 'concept A has-narrow-match concept B' then the set of resources properly indexed against concept A is a superset of the set of resources properly indexed against concept B." ;
                 skos:definition "skos:narrowMatch is used to state a hierarchical mapping link between two conceptual resources in different concept schemes."@en .


###  http://www.w3.org/2004/02/skos/core#narrower
skos:narrower rdf:type owl:ObjectProperty ;
              rdfs:subPropertyOf skos:narrowerTransitive ;
              rdfs:comment "Narrower concepts are typically rendered as children in a concept hierarchy (tree)."@en ;
              rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
              rdfs:label "has narrower"@en ;
              skos:definition "Relates a concept to a concept that is more specific in meaning."@en ;
              skos:scopeNote "By convention, skos:broader is only used to assert an immediate (i.e. direct) hierarchical link between two conceptual resources."@en .


###  http://www.w3.org/2004/02/skos/core#narrowerTransitive
skos:narrowerTransitive rdf:type owl:ObjectProperty ;
                        rdfs:subPropertyOf skos:semanticRelation ;
                        rdf:type owl:TransitiveProperty ;
                        rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
                        rdfs:label "has narrower transitive"@en ;
                        skos:definition "skos:narrowerTransitive is a transitive superproperty of skos:narrower." ;
                        skos:scopeNote "By convention, skos:narrowerTransitive is not used to make assertions. Rather, the properties can be used to draw inferences about the transitive closure of the hierarchical relation, which is useful e.g. when implementing a simple query expansion algorithm in a search application."@en .


###  http://www.w3.org/2004/02/skos/core#related
skos:related rdf:type owl:ObjectProperty ;
             rdfs:subPropertyOf skos:semanticRelation ;
             rdf:type owl:SymmetricProperty ;
             rdfs:comment "skos:related is disjoint with skos:broaderTransitive"@en ;
             rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
             rdfs:label "has related"@en ;
             skos:definition "Relates a concept to a concept with which there is an associative semantic relationship."@en .


###  http://www.w3.org/2004/02/skos/core#relatedMatch
skos:relatedMatch rdf:type owl:ObjectProperty ;
                  rdfs:subPropertyOf skos:mappingRelation ,
                                     skos:related ;
                  rdf:type owl:SymmetricProperty ;
                  rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
                  rdfs:label "has related match"@en ;
                  skos:definition "skos:relatedMatch is used to state an associative mapping link between two conceptual resources in different concept schemes."@en .


###  http://www.w3.org/2004/02/skos/core#semanticRelation
skos:semanticRelation rdf:type owl:ObjectProperty ;
                      rdfs:domain skos:Concept ;
                      rdfs:range skos:Concept ;
                      rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
                      rdfs:label "is in semantic relation with"@en ;
                      skos:definition "Links a concept to a concept related by meaning."@en ;
                      skos:scopeNote "This property should not be used directly, but as a super-property for all properties denoting a relationship of meaning between concepts."@en .

###  http://www.w3.org/2004/02/skos/core#ConceptScheme
skos:ConceptScheme rdf:type owl:Class ;
                   rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
                   rdfs:label "Concept Scheme"@en ;
                   skos:definition "A set of concepts, optionally including statements about semantic relationships between those concepts."@en ;
                   skos:example "Thesauri, classification schemes, subject heading lists, taxonomies, 'folksonomies', and other types of controlled vocabulary are all examples of concept schemes. Concept schemes are also embedded in glossaries and terminologies."@en ;
                   skos:scopeNote "A concept scheme may be defined to include concepts from different sources."@en .

###  http://www.w3.org/2004/02/skos/core#inScheme
skos:inScheme rdf:type owl:ObjectProperty ;
              rdfs:range skos:ConceptScheme ;
              rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
              rdfs:label "is in scheme"@en ;
              skos:definition "Relates a resource (for example a concept) to a concept scheme in which it is included."@en ;
              skos:scopeNote "A concept may be a member of more than one concept scheme."@en .

###  http://www.w3.org/2004/02/skos/core#Concept
skos:Concept rdf:type owl:Class ;
             owl:disjointWith skos:ConceptScheme ;
             rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
             rdfs:label "Concept"@en ;
             skos:definition "An idea or notion; a unit of thought."@en .


#####
### NPG ontology is a formal model providing definitions for the key concepts of interest to content publishing
####

npg:Article
    a owl:Class ;
    rdfs:isDefinedBy <http://ns.nature.com/terms/> ;
    rdfs:subClassOf npg:Document ;
    skos:definition "The :Article class represents a scholarly work normally published as an item of a serial publication. In particular, this concept refers to the abstract notion of an article, rather than any of its realisations after it becomes embodied via a physical medium."@en ;
    skos:note "With reference to the FRBR model [http://www.ifla.org/publications/functional-requirements-for-bibliographic-records], an :Article can be mapped directly to the frbr:Expression concept. It is worth noting though that within the NPG core ontology we do not have any notion of a frbr:Work. Hence multiple versions of the same article (e.g. language translations, or revisions) are characterised as such simply by means of some relationship."@en ;
    skos:prefLabel "Article"@en ;
    terms:license <http://creativecommons.org/licenses/by/4.0/> .

npg:Document
    a owl:Class ;
    rdfs:isDefinedBy <http://ns.nature.com/terms/> ;
    rdfs:subClassOf npg:Publication ;
    owl:disjointWith npg:Component, npg:Serial ;
    skos:definition "The :Document class groups together all publications which were created to be distributed and consumed as individual, self-contained entities."@en ;
    skos:prefLabel "Document"@en ;
    terms:license <http://creativecommons.org/licenses/by/4.0/> .

npg:Component
    a owl:Class ;
    rdfs:isDefinedBy <http://ns.nature.com/terms/> ;
    rdfs:subClassOf npg:Publication ;
    owl:disjointWith npg:Dataset, npg:Document, npg:Serial ;
    skos:definition "The :Component class groups together all individuals that normally come into existence as part of a :Document."@en ;
    skos:prefLabel "Component"@en ;
    terms:license <http://creativecommons.org/licenses/by/4.0/> .

npg:Publication
    a owl:Class ;
    rdfs:isDefinedBy <http://ns.nature.com/terms/> ;
    rdfs:subClassOf npg:Concept ;
    skos:definition "The :Publication class groups together all individuals (or part of) created as the result of the publishing process. Note that we are not referring here to the physical artefacts, but just their abstract counterparts."@en ;
    skos:prefLabel "Publication"@en ;
    terms:license <http://creativecommons.org/licenses/by/4.0/> .

npg:Dataset
    a owl:Class ;
    rdfs:isDefinedBy <http://ns.nature.com/terms/> ;
    rdfs:subClassOf npg:Publication ;
    skos:definition "The :Dataset class represents a collection of related sets of information modelled in a known way and stored in a computer system."@en ;
    skos:note "We are currently using this class for RDF datasets."@en ;
    skos:prefLabel "Dataset"@en ;
    terms:license <http://creativecommons.org/licenses/by/4.0/> .

npg:Serial
    a owl:Class ;
    rdfs:isDefinedBy <http://ns.nature.com/terms/> ;
    rdfs:subClassOf npg:Publication ;
    owl:disjointWith npg:Component, npg:Dataset, npg:Document ;
    skos:definition "The :Serial class represents publications which appear in a new edition on a regular schedule. For example, a journal, a magazine or a blog. The :PublishEvent class is used to provide more details about the time, place and other contextual information relevant to when a new edition gets published."@en ;
    skos:prefLabel "Serial"@en ;
    terms:license <http://creativecommons.org/licenses/by/4.0/> .

npg:Concept
    a owl:Class ;
    rdfs:isDefinedBy <http://ns.nature.com/terms/> ;
    rdfs:subClassOf npg:Thing ;
    skos:definition "The :Concept class groups together all individuals which do not exist in the physical world (i.e. have no extension in spacetime)."@en ;
    skos:prefLabel "Concept"@en ;
    terms:license <http://creativecommons.org/licenses/by/4.0/> .

npg:Thing
    a owl:Class ;
    rdfs:isDefinedBy <http://ns.nature.com/terms/> ;
    rdfs:subClassOf owl:Thing ;
    skos:definition "The :Thing class groups together all individuals used by Macmillan Science and Education within the NPG publishing world."@en ;
    skos:prefLabel "Thing"@en ;
    terms:license <http://creativecommons.org/licenses/by/4.0/> .

#####
### Schema.org tool property adapted to cancer research datasets, defined rdfs range and domain
####

<http://schema.org/tool> <http://www.w3.org/2000/01/rdf-schema#comment> "A sub property of instrument. An object used (but not consumed) when performing instructions or a direction." .
<http://schema.org/tool> <http://www.w3.org/2000/01/rdf-schema#subPropertyOf> <http://schema.org/instrument> .
<http://schema.org/tool> <http://www.w3.org/2000/01/rdf-schema#label> "tool" .
<http://schema.org/tool> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/1999/02/22-rdf-syntax-ns#Property> .
<http://schema.org/instrument> <http://www.w3.org/2000/01/rdf-schema#label> "instrument" .
<http://schema.org/instrument> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/1999/02/22-rdf-syntax-ns#Property> .
<http://schema.org/instrument> <http://www.w3.org/2000/01/rdf-schema#comment> "The object that helped the agent perform the action. e.g. John wrote a book with <em>a pen</em>." .

<http://schema.org/tool> rdf:type owl:DatatypeProperty;
                         rdfs:domain :FunctionalImpactPrediction;
                         rdfs:range  xsd:string.


######
### OBOinOWL simplified
########

###  http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
oboInOwl:hasExactSynonym rdf:type owl:AnnotationProperty ;
                         rdfs:comment "An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle"@en;
                         rdfs:label "has_exact_synonym"@en ;
                         rdfs:subPropertyOf oboInOwl:hasSynonym  ;
                rdfs:isDefinedBy oboInOwl: .

###  http://www.geneontology.org/formats/oboInOwl#hasSynonym
oboInOwl:hasSynonym rdf:type owl:AnnotationProperty ;
                    rdfs:comment "A relation between a class and an alias term."@en;
                    rdfs:comment "Note that this should be a super-property of hasRelatedSynonym, hasExactSynonym etc; however, we cannot state this and remain in OWL-DL"^^xsd:string ;
                    rdfs:label "has_synonym"@en  ;
                rdfs:isDefinedBy oboInOwl: .

###  http://www.geneontology.org/formats/oboInOwl#hasAlternativeId
oboInOwl:hasAlternativeId rdf:type owl:AnnotationProperty ;
                          rdfs:label "has_alternative_id"^^xsd:string  ;
                rdfs:isDefinedBy oboInOwl: .


###  http://www.geneontology.org/formats/oboInOwl#hasDbXref
oboInOwl:hasDbXref rdf:type owl:AnnotationProperty ;
                   rdfs:label "has_dbxref"@en ;
                rdfs:isDefinedBy oboInOwl: .

oboInOwl:hasRelatedSynonym rdf:type owl:AnnotationProperty ;
                           rdfs:comment   "An alias in which the alias is related the primary class name, but not necessarily broader or narrower. Example: cytochrome bc1 complex is a related synonym of ubiquinol-cytochrome-c reductase activity; virulence is a related synonym of pathogenesis"@en ;
                           rdfs:label "has_related_synonym"@en ;
                           rdfs:subPropertyOf oboInOwl:hasSynonym ;
                rdfs:isDefinedBy oboInOwl: .



###  http://www.geneontology.org/formats/oboInOwl#hasDbXref
oboInOwl:id rdf:type owl:AnnotationProperty ;
                   rdfs:label "id"^^xsd:string  ;
                rdfs:isDefinedBy oboInOwl: ;
                owl:equivalentProperty dc:identifier.