Brain: biomedical knowledge manipulation by Samuel Croset, John P. Overington and Dietrich Rebholz-Schuhmann. (Bioinformatics (2013) 29 (9): 1238-1239. doi: 10.1093/bioinformatics/btt109)
Abstract:
Summary: Brain is a Java software library facilitating the manipulation and creation of ontologies and knowledge bases represented with the Web Ontology Language (OWL).
Availability and implementation: The Java source code and the library are freely available at https://github.com/loopasam/Brain and on the Maven Central repository (GroupId: uk.ac.ebi.brain). The documentation is available at https://github.com/loopasam/Brain/wiki.
Contact: croset@ebi.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Odd how things like the topic naming constraint show up in unexpected contexts. 😉
This article may be helpful if you are required to create or read OWL based data.
But as I read the article I saw:
The names (short forms) of OWL entities handled by a Brain object have to be unique. It is for instance not possible to add an OWL class, such as http://www.example.org/Cell to the ontology if an OWL entity with the short form ‘Cell’ already exists.
The explanation?
Despite being in contradiction with some Semantic Web principles, this design prevents ambiguous queries and hides as much as possible the cumbersome interaction with prefixes and Internationalized Resource Identifiers (IRI).
I suppose but doesn’t ambiguity exist in the mind of the user? That is they use a term than can have more than one meaning?
Having unique terms simply means inventing odd terms that no user will know.
Rather than unambiguous isn’t that unfound?