BioPatML Pattern sharing for the Genomic Sciences - PowerPoint PPT Presentation

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BioPatML Pattern sharing for the Genomic Sciences

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  1. BioPatMLPattern sharing for the Genomic Sciences Stefan Maetschke, Michael Towsey and James M. Hogan MQUTeR Microsoft QUT eResearch Centre 2008 Microsoft eScience Workshop7-9 December Indianapolis Queensland University of Technology,Australia

  2. A comprehensive pattern description language • Web services for pattern storage and searching • Integration with the semantic web The BioPatML project includes:

  3. Unifying the Description of Patterns in Biological Sequences BioPatML supports: • DNA, RNA, AA sequences • Principled aggregation of different pattern types e.g.motifs, gaps, loops • Hierarchical patterns • Pattern libraries • Integratedscoring of pattern matches • Some existing pattern databases e.g. Prosite BioPatML exploits the advantages of XML and RDF.

  4. C A G A T A T A A T T C C A G A T A Simple Patterns <Motif alphabet=“DNA” motif=“TA[AT]AAW” /> <Motif alphabet=“DNA” motif=“TA[AT]AAW” name=“Pribnow-box”threshold=“0.5” />

  5. Series Patterns Series <Series ... > <Motif ... /> <Gap .../> <Motif .../> </Series> Motif Gap Motif TTGACA TATAAT -35 element gap -10 element bacterial promoter

  6. Libraries of Patterns (BioPatML resource: uri=biopatml/promoter.bpl) <Definition name=“sigma70” > <Definitions> < Definition name=“-35element” /> <Motif motif=“TTGACA” alphabet=“DNA” /> </Definition> < Definition name=“-10element” /> <Motif motif=“TATAAT” alphabet=“DNA” /> </Definition> </Definitions> <Void /> </Definition> <Definition name=“Promoter” > <Definitions> <Import uri=“biopatml/promoter.bpl” </Definitions> <Series ... > <Use definition=“sigma70.-35element” /> <Gap min=“13” max=’21” /> <Use definition=“sigma70.-10element” /> </Series> </Definition>

  7. BioPatML Web serviceshttp://bio.mquter.qut.edu.au/biopatml Pattern creation Semantic tagging Annotation XML

  8. SilverGene: Genome browser Gene CT323 Pattern matches

  9. BioPatML in the Semantic Web • BioPatML is part of the Bio2RDF project • Bio2RDF is an initiative of Quebec Genomics Centre and Université Laval • Described as "a new integrated way to surf genomic knowledge"

  10. The world according to Bio2RDF

  11. BioPatML in the Semantic Web • BioPatML in Bio2RDF • created a name space and terms • http://bio2rdf.org/ns/biopatml • Created an RDF database of BioPatML patterns • encapsulate BioPatML patterns as RDF literals • RDF tagging and search

  12. BioPatML: Semantic Tagging

  13. BioPatML Resources http://bio.mquter.qut.edu.au/biopatml (web demo) http://www.mquter.qut.edu.au/bio (BioPatML manual) http://bio2rdf.org/ns/biopatml (namespace & terms) http://bio2rdf.org (Bio2RDF home page)

  14. Bioinformatics team at MQUTER Peter Ansell Michael Towsey Jiro Sumitomo Lawrence Buckingham ChrisBowles Scott Mann Xin-Yi Chua Jim Hogan