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A draft for the Bio Knowledge Network, which will power the kNetMiner project.
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README.md

BioKNO, The Biological Knowledge Network Ontology

Ontology Overview

BIOlogical KNowledge Network Ontology (BioKNO, pronounced "bio-know") is a lightweight ontology, aimed at representing biological-related knowledge networks. We use it to power the KnetMiner project.

Further information on the ontology and where it fits in KnetMiner is available from our IB2018 article.

At the most basic level, it provides simple modelling for very general entities, such as concepts, relationships and attributed-attached reified relationships.

In addition to that, entities such as structured accessions, data sources and evidence-tracking predicates are defined.

At a more specific level, the core definitions are extended with common biological entities, such as Protein, Gene, or the 'encodes' relation.

Suitable mappings are also given, in order to map the knowledge networks modelled by means of BioKNO to common linked data standards, both general ones (e.g., SKOS, OWL) and life science-specific (e.g., bioschemas).

We use/are using/plan to use BioKNO in the KnetMiner project to perform various operations, ranging from data import/integration, to graph-based queries and building of APIs.

Web View

You can web-browse the ontology here, and mappings to our KnetMiner/Ondex metadata here. Many thanks to the developers of LODE, which we uses for rendering these pages.

WARNING: sometimes these views might be outdated with respect to the last versions of the original ontology files that they are based on.

The basics

The two main classes in BioKNO are bk:Concept and bk:Relation. The latter is related to the RDF object property bk:relatedConcept, which of main sub-property is bk:conceptsRelation.

Typically, the entities you want to talk about in a BioKNO knowledge network are indirect (i.e., transitive) instances of bk:Concept, while Concepts are linked together by some sub-property of bk:conceptsRelation.

A first instance about a biological pathway, taken from our WikiPathway example:

<http://www.wikipathways.org/id1>
        # A pathway, a predefined class in bk_ondex.owl. This is a subclass of bk:Concept, which subclasses skos:Concept
        a            bk:Path ; 
        bk:evidence  bkev:IMPD ; # Imported from database, a predefined constant on bk_ondex.owl
        # bk:prefName maps to skos-x:prefLabel
        bk:prefName  "Bone Morphogenic Protein (BMP) Signalling and Regulation"^^<xsd:string> .
        
bkr:TOB1  a                 bk:Protein ;
        dc:identifier       bkr:TOB1_acc ;
        # A simplified link, hiding BioPax pathwayComponent -> BioChemicalReaction|Complex -> Protein
        bk:participates_in  <http://www.wikipathways.org/id1> ;
        bk:prefName         "TOB1"^^<xsd:string> .
        
# Structured accession, allow for linking of identifier and context.         
bkr:TOB1_acc  a             bk:Accession ;
        dcterms:identifier  "TOB1"^^<xsd:string> ;
        bk:dataSource       bkds:UNIPROTKB; # instance of bk:DataSource. We havea list of predefined data sources.
        bk:is_annotated_by obo:GO_0030014.

As you can see, we have predefined entities like bk:Path, subclassing core entities like bk:Concept. Moreover, the original link chains between pathways and proteins present in the BioPax data are simplified by means of the bk:participates_in relation.

Another example, about the gene ontology term referred by above:

obo:GO_0030014  a      bk:GeneOntologyTerms ;
        dc:identifier  obo:GO_0030014_acc ;
        bk:is_a        obo:GO_0044424 , obo:GO_0043234 ;
        bk:prefName    "CCR4-NOT complex" .

obo:GO_0044424  a      bk:GeneOntologyTerms ;
        dc:identifier  obo:GO_0044424_acc ;
        bk:is_a        obo:GO_0044464 ;
        bk:prefName    "intracellular part" .
        
obo:GO_0030015  a  bk:GeneOntologyTerms;
        dc:identifier  obo:GO_0030015_acc ;
        bk:is_a        obo:GO_0044424, obo:GO_0043234 ;
        bk:part_of 		obo:GO_0030014;
        bk:prefName    "CCR4-NOT core complex" .

As you can see, original URIs about external RDF data can be reused (in OWL-2, this is possible thanks to punning). Morever, relations like bk:is_a, bk:part_of are more informal than OWL/OBO relations, which might simplify the modelling. For instance, the fact that a CCR4-NOT core complex is part of a CCR4-NOT complex is a simple direct relation, where, in OWL terms must be an axiom like "part of some CCR-NOT complex.

Concept attributes

Under the top-level bk:attribute property, BioKNO provides a number of OWL datatype properties, which can be attached to concepts and relations. For instance:

bkr:20068231  a             bk:Publication ;
        dc:identifier       bkr:20068231_acc ;
        bka:PMID            "20068231" ;
        bka:YEAR            "2010"^^xsd:gYear ;
        bka:abstractHeader  "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis." ;
        bk:evidence         bkev:IMPD , bkev:NAS ;
        bk:prefName         "20068231" .

Attributes can have any suitable range and we made sensible choices for the ranges of our predefine attributes.

Reified relations

Attributes can be associated to relations too. Since RDF structurally supports binary relations/statement only, attributed relations must be modelled through reification:

# For practical reasons, we always expect that the straight triple is asserted, with the reified version optionally added to it.
bkr:TOB1 bk:published_in    bkr:20068231.

bkr:citation_TOB1_15489334
        a              bk:Relation ;
        bk:relTypeRef  bk:published_in;  # the same relations used for straight triples      
        bk:relFrom     bkr:TOB1 ; # This is the protein in the examples above
        bk:relTo       bkr:15489334 ; # And this is the publication above
        bka:Score      0.95 ;
        bk:evidence    bkev:TM. Both attributes and object properties can be linked to a reified relation.

As you can see, a reified relation is an instance of bk:Relation and its main properties are a pointer to the relation type (which is the same object property appearing in the direct relation, and typically a sub-property of bk:conceptsRelation).

We require that a reified relation is asserted by means of both its "straight", common RDF statement version and as an instance of bk:Relation. That ease certain use cases. For instance, if one has to search for the existence of a given relation, independently on the possible attributes it might have, it's easier to search the straight version, without having to deal with both types.

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