Cross reference for [Ontology Name] classes, properties and dataproperties back to ToC

This section provides details for each class and property defined by [Ontology Name].

Classes

Accessionc back to ToC or Class ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/Accession

[description] An accession is a string value, assigned with dcterms:identifier and at least one data source in which the accession value is usually unique. Set bk:isAccessionAmbiguous to false to specify the accession is not necessarily unique. bk:Concept instances are associated to bk:Accession instances via dc:identifier (NOT dcterms:identifier).
has super-classes
data source op some Data Source c
is in domain of
is ambiguous accession dp

Conceptc back to ToC or Class ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/Concept

[editorial note] Those used to the ONDEX model should note that we are mapping the 'concept type' relations straight to rdf:type and the ONDEX Concept Classes to rdfs:subClassOf, with this class on the top. We see this as a natural mapping of the ONDEX model to the RDF/RDF-S/OWL standards. [description] A Concept is the a basic unit of information in the Bio Knowledge Network Ontology. The main type of knowledge in BioKNet consists of relations (either RDF triples based on bk:relationType, or bk:Relation instances) between bk:Concept instances. The recommended way to use bk:Concept is: - subclass bk:Concept with specific classes (eg, Protein, Gene) - instance those specific classes - optionally, but recommended in production environments like triple stores backing SPARQL, declare your new instance an instance of bk:Concept too. While this can be inferred, having explicit instances make things easier for applications.
has super-classes
Describeable Entity c
Relation Element c
is in domain of
concept relation op
is in range of
concept relation op, rel from op, rel to op, related to concept op
has members
test concept0 1 ni, test concept0 2 ni

Data Sourcec back to ToC or Class ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/DataSource

[editorial note] Due to possible clashes with other identifiers, you should use the namespace bkds: <http://knetminer.org/data/rdf/terms/biokno/dataSources/> to define new data source.
has super-classes
Describeable Entity c
is in range of
data source op

Describeable Entityc back to ToC or Class ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/Describeable

[description] This is an abstract container to factorise those individuals for which a minimum of description attributes can be defined. These are: - dcterms:identifier, to provide a resource identifier. Note that this is possibly valid only within a given context. it is also recommended that it is unique/unambiguous under that context, however, that is not strictly prescribed. - rdfs:label, to provide a resource human-readable label - dcterms:description, to provide a longer resource description. [editorial note] [kNetMiner] these properties correspond to id, fullName, description in the ONDEX model.
has sub-classes
Concept c, Data Source c, Evidence Type c, Unit c

Evidence Typec back to ToC or Class ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/EvidenceType

[editorial note] Due to possible clashes with other identifiers, you should use the namespace bkev: <http://knetminer.org/data/rdf/terms/biokno/evidences/> to define new evidence types.
has super-classes
Describeable Entity c
is in range of
evidence op

Graphc back to ToC or Class ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/Graph

[editorial note] [TODO] to be completed, using VoID, pav, etc. [description] A biological knowledge network can be grouped together into a graph. This is typically a named graph as well and used in triple stores like Virtuoso to identify networks/subsets.
is in domain of
graph summary figure dp

Relationc back to ToC or Class ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/Relation

[description] Relations in BioKNet are created in two ways: - as straight RDF statements between instances of Concept, and using subclasses of the relatedConcept property. - as instances of Relation, with links from the Relation instance to the relation source (relFrom property), target (relTo property) and predicate (relTypeRef property). This way to define relations is well-known as reification and it is necessary when further properties/links need to be associated to a statement. A reified relation can have attributes attached (bk:attribute property). WARNING: We strongly recommend that, if an instance of Relation (i.e., a reified relation) exists in a data set, then the corresponding plain triple exists too. For instance, if this is defined: <code> ex:r0 a bk:Relation; bk:relTypeRef ex:encodes; bk:relFrom ex:gene0; bk:relTo ex:prot0. </code> we recommend to also define the triple ex:gene0 ex:encodes ex:prot0. This is to ease queries and start them from a base representation that is compliant with RDF principles. The opposite (i.e., to create a bk:Relation for each bk:Concept triple based on subproperties of bk:relatedConcept, even when there aren't further properties to attach to the triple) is less important, however, we recommend to introduce this redundancy, for the same sake of easy-to-write queries and performance. We suggest to base the identifiers of reified relations on the IDs (or URIs) of its three parts, e.g., MD5 ( gene0 + encodes + prot0 ). This makes it easier to find the reified version of a relation once you have the components of its identifiers. WARNING: this should be considered an application facility and never be assumed as a reliable rule.
has super-classes
Relation Element c
rel from op exactly 1 Relation Element c
rel to op exactly 1 Concept c
is in domain of
is instance of relation type op, rel from op, rel to op
has members
test stmt0 ni

Relation Elementc back to ToC or Class ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/RelationElement

[description] A bk:Relation, or the corresponding BioKNet triple, is composed mainly of two bk:Concept instances and a relation type. The bk:RelationElement is a convenience common container for such components.
has sub-classes
Concept c, Relation c
is in domain of
attribute dp, evidence op, related to concept op

Unitc back to ToC or Class ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/Unit

has super-classes
Describeable Entity c
is in range of
attribute unit op
has members
test unit ni

Object Properties

attribute unitop back to ToC or Object Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/attributeUnit

[description] When a bk:attribute property is associated to a unit by means of this property, literal values of that property are measure values expressed in the associated unit. [editorial note] Note that the domain of this property is a subclass of bk:attribute. This is specified by means of schema:domainIncludes, in order to keep OWL correctness.
has range
Unit c

concept relationop back to ToC or Object Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/conceptsRelation

[editorial note] All ONDEX/kNetMiner relations should go under this property. [description] This is a top-level container, which is used to define specific relations of interest between between bk:Concept instances. See bk:Relation for a detailed description of how concept relations are model in BioKNet. This property should never be used directly, a concept/concept relation of interest should always be instance of some specific subproperty of this one (TODO: closure axiom).
has super-properties
related to concept op
has sub-properties
test prop op
has domain
Concept c
has range
Concept c

data sourceop back to ToC or Object Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/dataSource

[editorial note] [TODO] Align to PAV and alike. [description] The source from which an entity comes from, or was imported or alike.
has domain
Accession c or Relation Element c
has range
Data Source c

evidenceop back to ToC or Object Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/evidence

[description] Links an entity, such as a concept or a relation, to the type of evidence that prove it exists, such as 'imported from database', evidence codes, 'inferred from literature'.
has domain
Relation Element c
has range
Evidence Type c

is instance of relation typeop back to ToC or Object Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/relTypeRef

[editorial note] The fact that the values of this should be subclasses of bk:relationType is documented by means of schema:rangeIncludes. We don't use rdfs:range bk:relationType, because this tends to confuse ontology editors and libraries (i.e., Protege and OWL-API), which infer bk:relationType is also a clsass. It shouldn't be a big deal to link to bk:relationType using an owl:objectProperty like this, since OWL-2 should deal with this through punning (TODO: check).
has domain
Relation c

rel fromop back to ToC or Object Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/relFrom

has domain
Relation c
has range
Concept c

rel toop back to ToC or Object Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/relTo

has domain
Relation c
has range
Concept c

related to conceptop back to ToC or Object Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/relatedConcept

[description] A generic reference to a concept This is used to attach a cross-reference of type bk:Concept to another concept or a bk:Relation. This is used to relate a relation element with a non better-specified relation (which might mean things like 'see also', 'cross reference'). [editorial note] In the ONDEX/kNetMiner software, this corresponds to the concept and relation's property 'tags'.
has sub-properties
concept relation op
has domain
Relation Element c
has range
Concept c

test propop back to ToC or Object Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/testProp

has super-properties
concept relation op
is also defined as
named individual

Data Properties

attributedp back to ToC or Data Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/attribute

[editorial note] Note that the way units are modelled is different than other structured value models (e.g., schema.org, good relations), where units can be specified for each value. Here, units are linked to an attribute property, to specify once for all the unit to which all that property values refer to. [description] An attribute is a literal property associated to a concept or a relation. Specific attribute types (e.g., pValue, geneBegin) should be defined as subproperty of this one and proper annotations (rdfs:label, dcterms:description) attached. The new properties should also specify their range via rdfs:range and preferrably using an XSD type. Hierarchical attribute type relations should be defined via rdfs:subPropertyOf. Note that attributes can refer to measure values, in which case you should associate a unit to the corresponding bk:attribute subproperty. Note that bk:attribute is considered an abstract property container: rather than using it directly, you should always define a specific attribute subproperty to represent attributes properly. [editorial note] Due to possible clashes with other identifiers, you should use the namespace bka: <http://knetminer.org/data/rdf/terms/biokno/attributes/> to define new attributes. [editorial note] This property is conceptually equivalent to AttributeName in ONDEX. It doesn't look correct to call it name.
has sub-properties
test attribute dp
has domain
Relation Element c

graph concepts countdp back to ToC or Data Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/graphConceptsCount

has super-properties
graph summary figure dp
has range
long

graph relations countdp back to ToC or Data Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/graphRelationsCount

has super-properties
graph summary figure dp
has range
long

graph summary figuredp back to ToC or Data Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/graphSummaryFigure

[description] a property of this type provides summary figures for the contents of a graph, such as the number of concepts or relations.
has sub-properties
graph concepts count dp, graph relations count dp
has domain
Graph c

has alternative namedp back to ToC or Data Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/altName

has super-properties
name dp

has preferred namedp back to ToC or Data Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/prefName

has super-properties
name dp

is ambiguous accessiondp back to ToC or Data Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/isAmbiguousAccession

[editorial note] TODO: we need to clarify what this is exactly. How can an accession be ambiguous? Examples?
has domain
Accession c
has range
boolean

namedp back to ToC or Data Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/name

[editorial note] Compared to the ONDEX model, we use bk:prefName to represent a name that has the preferred flag set to true, bk:altName to represent all the other names, bk:name for generic names. This is simpler than having a class just to store an additional flag. [description] In bio-databases a name is often meant as something more specific than a title or a label (being more official and often shorter) and not as unique as accessions.
has sub-properties
has alternative name dp, has preferred name dp
has range
string

test attributedp back to ToC or Data Property ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/attributes/testAttribute

has super-properties
attribute dp
has range
double
is also defined as
named individual

Named Individuals

test attributeni back to ToC or Named Individual ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/attributes/testAttribute

has facts
attribute unit op test unit
is also defined as
data property

test concept0 1ni back to ToC or Named Individual ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/testConcept0_1

belongs to
Concept c
has facts
test attribute dp "1.2"^^double

test concept0 2ni back to ToC or Named Individual ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/testConcept0_2

belongs to
Concept c

test stmt0ni back to ToC or Named Individual ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/testStmt0

belongs to
Relation c
has facts
rel from op test concept0 1
rel to op test concept0 2
is instance of relation type op test prop
test attribute dp "2.5"^^double

test unitni back to ToC or Named Individual ToC

IRI: http://knetminer.org/data/rdf/terms/biokno/testUnit

[description] This is a test unit, which shows how attributes and their units are modelled in BioKNet.
belongs to
Unit c

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties
ni: Named Individuals