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Introduction

The Resource Description Framework (RDF) and the Open Biomedical Ontolgy Format (OBOF) share a common basis in their representation models. Both models connect resources or terms trough predicates or labeled relations. Their common basis model has the advantage of simplicity, 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 certain semantical meaning. 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 predicates that connect class resources and predicates that connect instance resources. This distinction allows to make definitions for class level predicate types by reusing definitions of instance level predicate types.


Metarel

Metarel is a meta-ontology for predicates or relation types. It allows to add existing predicates in its hierarchy and to make appropriate meta-relations between them. Metarel assumes the labeled directed graph model that is common for RDF and OBOF: the nodes in the graph are resources or terms and the directed relation arrows are RDF triples. The nodes have a Unique Resource Identifier (URI) and they can be both instances or classes. A formal classification of predicates follows from this graph model. Metarel is developed as an OBOF formatted ontology. It is exported to a representation in RDF.

BioGateway uses Metarel for Knowledge Management (KM). The relation types in BioGateway are contained in Biorel, which is an of extension OBO's Relationship Ontology (RO). Biorel is integrated in Metarel, forming BioMetarel. The integrated ontology BioMetarel can be readily used for KM tasks in an RDF triple store. 

 
Last Updated on Thursday, 26 February 2009 17:29
 

Newsflash

Doctoral Degree for Erick Antezana  On Sep 28, 2009, Erick Antezana successfully defended his Ph.D. thesis "Towards semantic systems biology: biological knowledge management using semantic web technologies" and was awarded the title of Doctor in Sciences: Biotechnology. 
 

CCO 1.03 CCO has recently been expanded to include in addition to the 'cell cycle' branch of GO the three additional branches: 'cell proliferation', 'cell division' and 'DNA replication'. (Monday, 25 May 2009 13:19)

Important message

From 14/04/09 till 28/10/09 the CCO contained some superfluous  terms. If you downloaded it diriing this time span you are advised to download anew.
 
Biogateway: A Semantic Systems Biology Tool for the Life Sciences" paper will appear in 'BMC Bioinformatics' Journal.(20.05.09)