Bio-zen ontology framework for representing scientific discourse in life science
Contact e-mail: Matthias.samwald # meduniwien.ac.at
General purpose and services to the end user
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.
The bio-zen framework will consist of several applications, especially Semantic Wikis like OntoWiki. In the current version, it is focused on the description of molecular interaction pathways, but can also be used to many other biological phenomena in a more generic fashion. bio-zen also incorporates ontological constructs to make statements about digital information resources.
A Biozen ontology is used to annotate OWL individuals ("concept tags"). Concept-tagging with SKOS concepts is an important feature of bio-zen, because it eases the integration of information from different sources (i.e. the SKOS concepts act as a bridge between graphs). Bio-zen is based on the DOLCE foundational ontology, the Simple Knowledge Organisation System (SKOS) and Dublin Core.
Integration between vocabulary-linked functions and other application functions
The developments of the bio-zen project might soon be integrated into the projects of the W3C Semantic Web Health Care and Life Science Interest Group.
In bio-zen, SKOS is used for the representation of many existing vocabularies, taxonomies and ontologies from the life sciences. Many datasets from the "Open Biomedical Ontologies" (OBO) collection have already been converted in order to be used in Biozen. Examples are the Gene Ontology or Medical Subject Headings (MeSH). It is also planned to convert taxonomies/ontologies from the "Unified Medical Language System" (UMLS).
General characteristics (size, coverage) of the vocabulary
The vocabularies describe widely different information domains from the life sciences and health care. The size of all converted taxonomies taken together is in the order of millions of concepts.
Machine-readable representation of the vocabulary
The taxonomies of OBO are primarily available in the OBO format, which is a generic text-based format.
[Term] 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
There is also an unoffical XML version (in the 'OBO_XML' format) for each taxonomy. The OBO_XML taxonomies are converted to SKOS with XQuery.
SKOS is tightly integrated into the main bio-zen ontology as a single OWL file.
The integrated version of SKOS has been slightly modified:
- It is now valid OWL DL. This is very important for our application. It would be very appreciated if SKOS would be officially available as OWL DL.
- Some constructs have been removed (e.g. skos:hasTopConcept)
- Subclasses of skos:concept have been defined (e.g. biozen:sequence-concept)