Tag Archives: BioPAX

BioPAX

Posted on December 5, 2010 by sgtp

I’ve been involved since 2005 with BioPAX, which I first approached in search a suitable knowledge base to develop pathway analysis methods. I have been mostly focused on “consuming” BioPAX, which has meant debugging of the specification and some tools … Continue reading →

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Semantic Web/Linking/CV WorkGroup: next steps ?

Posted on October 7, 2010 by sgtp

Talk @COMBINE meeting, on next step of the BioPAX SemWeb Working Group. Edinburgh, Thursday October 7th, 2010. Info and slides are available here.

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The BioPAX community standard for pathway data sharing

Posted on September 9, 2010 by sgtp

The BioPAX community standard for pathway data sharing Emek Demir, Michael P Cary, Suzanne Paley, Ken Fukuda, Christian Lemer, Imre Vastrik, Guanming Wu, Peter D’Eustachio, Carl Schaefer, Joanne Luciano, Frank Schacherer, Irma Martinez-Flores, Zhenjun Hu, Veronica Jimenez-Jacinto, Geeta Joshi-Tope, Kumaran … Continue reading →

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BioPAX is from Venus, the Semantic Web is from Mars

Posted on November 13, 2009 by sgtp

Talk at BioPAX f2f meeting, NYC, 11-13 November 2009

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Combined CellML SBGN SBO BioPAX MIASE Workshop

Posted on April 9, 2009 by sgtp

“BioPAX for semantic web based data integration”, talk at Combined CellML SBGN SBO BioPAX MIASE Workshop, 5-9 April 2009, Wahieke Island (NZ).

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I-Atlas 2008

Posted on November 14, 2008 by sgtp

Together with Duccio Cavalieri, I have co-organized and co-chaired I-ATLAS, Internatonal Workshop on Gene Signalling Pathway Analysis and Representation for the Dendritic Cell. The workshop was held in Florence, 13-14 November 2008.

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RDFScape: Semantic Web meets Systems Biology

Posted on April 25, 2008 by sgtp

Splendiani A RDFScape: Semantic Web meets Systems Biology (selected In IMIA Yearbook of Medical Informatics) BMC Bioinformatics 2008 Apr 25, 9 (S4):S6 Abstract BACKGROUND The recent availability of high-throughput data in molecular biology has increased the need for a formal … Continue reading →

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Integration of ontologies and high-throughput data in bioinformatics

Posted on July 10, 2006 by sgtp

Integration of ontologies and high-throughput data in bioinformatics (PhD Thesis) Available here

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