Metarel

Metarel and MDGs

Metarel goes together with a specific paradigm for modelling knowledge and data resources in RDF and Linked Data: MultiDiGraphs (MDGs), which are labelled and directed graphs that allow self-loops and multiple arcs, are better suited for querying in SPARQL compared to the standard syntax in OWL/RDF. The nodes in the MDG are supposed to be either instances or classes. Decidability and reasoning can be achieved by distinguishing more relation types, which is done in Metarel.

The Resource Description Framework (RDF) and the Open Biomedical Ontolgy Format (OBOF) share a common basis in their representation models. Both models create direct links between classes (OBOF) or resources (RDF). Their common basis model has the advantage of easier browsing and querying, but lacks a high expressivity, like the Web Ontology Language (OWL). Still, their are many relational features that can be expressed, apart from only a label with a name. Transitivity, reflexivity, subsumption and compositionality of relations need to be used to exploit this model maximally. On the other hand, a carefull distinction is needed between properties that connect class resources and properties that connect instance resources. This distinction allows to make definitions for class level properties by reusing definitions of instance level properties.

Metarel is a framework that allows to express the semantics of any properties (rdf:Property in OWL parlance, predicate in RDF parlance and relation or relationship type in the bio-ontology parlance of OBO, examples: 'is part of', 'is located'), also properties that stand in between two classes or between an instance and a class. OWL deals only with the semantics of properties between instances (called owl:ObjectProperty). Apart from the different treatment for properties between classes, Metarel is maximally compatible with OWL. Metarel.rdf is the name of the metagraph for the properties. It facilitates the annotation of properties and meta-relations between properties with Metarel terms.

Reasoning on bio-ontologies

Biomedical ontologies are often not formatted in OWL and many of them, especially OBO ontologies, use direct properties between classes (e.g. heart (the class of all hearts) 'is part of' body (the class of all bodies), meaning that all hearts are part of some body). Metarel can be used for semi-automated reasoning with such knowledge statements in large RDF stores.

The preparation of the reasoning process requires that the properties used in the RDF store are merged into metarel.rdf. We did this for BioGateway, an RDF store containing many biomedical ontologies. The properties in BioGateway are contained in Biorel, which is a curated extension of OBO's Relationship Ontology (RO). Biorel is integrated in Metarel, forming BioMetarel. The integrated ontology BioMetarel can be readily used for KM tasks in BioGateway.

The reasoning steps are executed in a semi-automated way in BioGateway through SPARQL/Update queries. They generated about 158 million new knowledge statements of the form class - property - class. The version of BioGateway with the original (explicit) knowledge statements is gathered in the RDF graph SSB, the inferred knowledge is gathered in SSB_tc. Queries can be launched in the query endpoint of BioGateway.

The detailed approach can be followed through the sql files that are used to create BioGateway and the SSB and SSB_tc graphs. The following steps are executed sequentially:
- The creation of BioMetarel: BioMetarel_creation.sql
- The loading of original files in BioGateway (creates SSB): SSB_creation.sql
- The creation of the inferences (creates SSB_tc): SSB_tc_creation.sql
These sql files were executed on a Virtuoso 5.0.8 triple store. The original files can be found in the download section of BioGateway. The files for creating BioMetarel can found in the download section of Metarel, except for the specific file biometarel_merge.rdf.turtle that connects the generic object properties in biorel.owl with the specific all-some relation types used in BioGateway.