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BioPatML Pattern sharing for the Genomic Sciences

BioPatML Pattern sharing for the Genomic Sciences. Stefan Maetschke, Michael Towsey and James M. Hogan. MQUTeR Microsoft QUT eResearch Centre. 2008 Microsoft eScience Workshop 7-9 December Indianapolis. Queensland University of Technology , Australia.

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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

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