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Haystack, BioDash and the Semantic Web

Haystack, BioDash and the Semantic Web. David Gallardo. Some background on RDF and the Semantic Web. RDF uses XML syntax, but encodes semantics, using subject-verb-object triples, that encode “facts”.

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Haystack, BioDash and the Semantic Web

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  1. Haystack, BioDash and the Semantic Web David Gallardo

  2. Some background on RDF and the Semantic Web • RDF uses XML syntax, but encodes semantics, using subject-verb-object triples, that encode “facts”. • Information on the web now is just that—information, with no association or organization based on meaning. • Searches, for example, miss synonyms and related terms, and catch similar but unrelated terms. • The idea of the Semantic Web was invented by Tim Berners-Lee and is now a project of the W3C that intends to extend the existing web to support information with well-defined meaning

  3. A Haystack built on Eclipse • Haystack--an Eclipse plug-in--is a “universal information client”: • A Personal Information Manager • A Semantic Web browser • A platform for building RDF—Resource Description Framework--applications • Removes the arbitrary barriers to using information that are created by applications • A project at the MIT Computer Science and Artificial Intelligence Lab • All data behind the scenes is RDF—Resource Description Framework

  4. Very cool but… • Still under development • Slow, clunky and hard to use—crashes my system • No documentation • See more at: http://haystack.csail.mit.edu/index.html

  5. The BioDash demo • An application built on top of Haystack • Combines RDF data from different sources: • Drug targets and compounds • Biological entities such as genes, proteins and pathways • Discover new relationships! • More info: http://www.w3.org/2005/04/swls/BioDash/Demo/

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