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Bio-zen ontology framework for representing scientific discourse in life science

Bio-zen ( is intended to be used by researchers and developers in the life sciences. It allows the description of biological systems and the representation of scientific discourse on the web in a highly distributed manner.

SKOS is used in bio-zen for the representation of many existing life sciences vocabularies, taxonomies and ontologies coming from the "Open Biomedical Ontologies" (OBO) collection ( The size of all converted taxonomies taken together is in the order of millions of concepts. Typical examples are the Gene Ontology or Medical Subject Headings (MeSH), an entry of which is displayed here:

id: MESH:A.01.047.025
name: abdominal_cavity
def: "The region in the abdomen extending from the thoracic DIAPHRAGM to the plane of the superior pelvic aperture (pelvic inlet). The abdominal cavity contains the PERITONEUM and abdominal VISCERA\, as well as the extraperitoneal space which includes the RETROPERITONEAL SPACE." [MESH:A.01.047.025]
synonym: "abdominal_cavity" 
synonym: "cavitas_abdominis" 
is_a: MESH:A.01.047 ! abdomen

To represent such vocabulary elements as well as other type of information, the existing SKOS model has been integrated into a single OWL ontology, together with the DOLCE fundational ontology and the Dublin core metadata model. In the process, the SKOS model has been extended with special types of concepts, e.g. biozen:sequence-concept. To enable efficient reasoning with the available dataset, it is important to notice that existing constructs have been made compatible with the OWL-DL language.

The bio-zen framework will consist of several applications, especially Semantic Wikis. A Bio-zen ontology incorporates constructs to make statements about digital information resources, that is creating "concept tags". This concept-tagging is an important feature of bio-zen, because it eases the integration of information from different sources.