HCLSIG BioRDF Subgroup/Nuts and bolts

Nuts and Bolts

Links, initially collected from the mailing list, to resources that concern working with/converting to RDF. Feel free to organize this better.

• Mapping RDBMS schemas onto RDF
• Navigate data with the Mapper framework
• Ontology Definition Metamodel - This lengthy and dense, but generally very well written, document goes into extreme detail as to the similarities and differences between UML and "RDF" (which I take to be a blanket term encompassing other Semantic Web specs). I'm not by any means an expert, but it looked to me like there are very significant overlaps in both detail and general philosophy of approach and implementation. I got the impression, but this is by no means spelled out, that this document is an artifact of the process of the UML folk getting "on board" the SW train. It certainly represents a very impressive amount of effort in preparation. - Roger Cutler
• An Efficient SQL-based RDF Querying Scheme - via Susie Stephens
• BRAHMS: A WorkBench RDF Store And High Performance Memory System for Semantic Association - A high performance RDF storage system. Discussion of Three of its applications - via Amit Sheth
• UniProt RDF Data - work of Eric Jain
• Data for benchmarks - various sized chunks of the UniProt set - Thanks Eric Jain!
• Tripletest is a testing framework for RDF triplestores - via Ian Wilson
• Simile Shootout, Simile Shootout Core. Similar efforts underway at the SIMILE project - via Ian Wilson
• LifeSciencesQueries
• Bridging the Gap between RDF and XML via Peter Mork
• Comparing XSLT and XQuery via Duncan Hull
• Integrating XML data sources using RDF/S Schemas: The ICS-FORTH Semantic Web Integration Middleware (SWIM) via Chris Mungall
• A Comparison of RDF Query Languages via Duncan Hull
• Entrez Programming Utilities Entrez Programming Utilities are tools that provide access to Entrez data outside of the regular web query interface and may be helpful for retrieving search results for future use in another environment.
• D2RQ A language that maps relational schemas to RDF.
• GENIA Natural language processing for biomedical text via Brian Gilman.
• GATE "the Eclipse of Natural Language Engineering, the Lucene of Information Extraction, the leading toolkit for Text Mining"
• Media:HCLSIG_BioRDF_Subgroup$$Nuts_and_bolts$gene-summary-human-mouse-rat-2005-10-20.txt.gz A tab delimited version of some of the data in Entrez gene, generated by AlanRuttenberg
• Newt: An interface to species taxonomy
• uBio uses names and taxonomic intelligence to manage information about organisms

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