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Section 0. Contact and confidentiality

Contact e-mail:

Do you mind your use case being made public on the working group website and documents?
I agree that you can make it public.

Section 1. Application

  1.1. What is the title of the application?

bio-zen Semantic Web Framework.

  1.2. What is the general purpose of the application?
       What services does it provide to the end-user?

The bio-zen framework will not consist of a single application, but will make use of several applications, especially Semantic Wikis like OntoWiki. 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.
Development of bio-zen has so far concentrated on the creation of ontologies; the integration into applications is still rudimentary.

  1.7. Any additional information, references and/or hyperlinks.

SKOS/SKOSX are tightly integrated into the main bio-zen ontology as a single OWL file. It 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). 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.

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)

Section 2. Vocabulary(ies)

  2.1. What is the title of the vocabulary? If you're describing multiple vocabularies, please provide as many titles as you can.

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. 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).

  2.2. Briefly describe the general characteristics of the vocabulary, e.g. scope, size...

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.

  2.3. In which language(s) is the vocabulary provided?
       In the case of partial translations, how complete are these?

The taxonomies of OBO are primarily available in the OBO format, which is a generic text-based format. There is also an inoffical XML version (in the 'OBO_XML' format) for each taxonomy. The OBO_XML taxonomies are converted to SKOS with XQuery.

 *2.4. Please provide below some extracts from the vocabulary. Use the layout or presentation format that you would normally provide for the users of the vocabulary. Please ensure that the extracts you provide illustrate all of the features of the vocabulary.

  2.5. Describe the structure of the vocabulary.
       What are the main building blocks?
       What types of relationship are used? If you can, provide examples by referring to the extracts given in paragraph 2.4.

  2.6. Is a machine-readable representation of the vocabulary already available (e.g. as an XML document)? If so, we would be grateful if you could provide some example data or point us to a hyperlink.