Hello Stanbol Developers, We're bioinformatics group <http://bioputer.mimuw.edu.pl/> at the University of Warsaw, and we deployed Apache Stanbol technologies at the Institute of Mother and Child, Cytogenetics Labs<http://www.imid.med.pl/klient1/view-content/218/Pracownia-Cytogenetyki-Molekularnej--oferta-diagnostyczna.html>, Warsaw,PL.
You can try the *demo* of what we've achieved so far here: http://bioputer.mimuw.edu.pl:9442/welcome/ This is a realization of the http://wiki.iks-project.eu/index.php/Cytogenetic_Proposal , a part of IKS Early Adopters. The demo presents integration of Apache Stanbol with software used at IMID Cytogenetics Labs. The purpose of the integration is to allow geneticists to annotate experiment data with relevant content: information about genes, genetic diseases, scientific publications, and more, and later allow for searching through, and summarized reports of the annotated content. The demo features: 1. annotation of biological content (in this case it's a result of aCGH<http://en.wikipedia.org/wiki/aCGH> experiment) with relevant Linked Data: user may add enhancements found with engines, and create his own tree of enhanced content. 2. a set of semi-automated enhancers which communicate with Apache Stanbol and search Linked Data for relevant entries 3. faceted search<http://bioputer.mimuw.edu.pl:9442/welcome/stanbol_search/search/> through content annotations provided by Apache Stanbol Contenthub. - For the purpose of this demo UNIPROT linked data was indexed using Apache Stanbol tools (the resulting index is 10GB in size) - UNIPROT RDF release<ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/README> - http://incubator.apache.org/stanbol/docs/trunk/customvocabulary.html - This UNIPROT relase also contains following Linked Data: *Gene Ontology* terms, *PubMed* abstracts - the site was built on web2py <http://web2py.com/> What you may find useful in your projects: - A Stanbol connection module in Python<http://bioputer.mimuw.edu.pl:33000/projects/ikscyt/repository/entry/applications/welcome/modules/stanbol.py> was created for the puprose of this integration. - and a set of content enhancers in Python for web2py<http://bioputer.mimuw.edu.pl:33000/projects/ikscyt/repository/entry/applications/welcome/controllers/stanbol_enhancers.py> were created for the purpose of this integration. If you don't use web2py, you'll find there examples of how to use stanbol.py module. You can try these enhancers at the demo site. What we didn't quite succeed yet: - we wanted to integrate VIE <http://viejs.org/> in our presentation side, however, as far as i know, VIE does not support getting content from Stanbol Contenthub. We tried to modify VIE to allow for that http://bioputer.mimuw.edu.pl:33000/projects/ikscyt/repository/diff/applications/welcome/static/vie/vie-2.0.0.debug.js?utf8=%E2%9C%93&rev=4175&rev_to=4164 however some more modifications would be needed since the resulting json from contenthub is parsed in unexpected way. - the resulting content/enhacements graph is not yet stored in a triple store, our Stanbol does not allow for SPARQL queries for content ("There is no registered TripleCollection." I'll make another post about it). The demo site: http://bioputer.mimuw.edu.pl:9442/welcome/ Home page for this Early Adopters project: http://bioputer.mimuw.edu.pl/iks/ Don't hesitate to ask questions or issue any comments. Best, Maciek Sykulski
