BioPatML Pattern sharing for the Genomic Sciences

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BioPatMLPattern sharing for the Genomic Sciences
Stefan Maetschke, Michael Towsey and James M.
Hogan
MQUTeR Microsoft QUT eResearch Centre
Queensland University of Technology,Australia

• 2008 Microsoft eScience Workshop7-9 December
• Indianapolis

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The BioPatML project includes

• A comprehensive pattern description language
• Web services for pattern storage and searching
• Integration with the semantic web

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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
• Integrated scoring of pattern matches
• Some existing pattern databases e.g. Prosite
• BioPatML exploits the advantages of XML and RDF.

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Simple Patterns
ltMotif alphabetDNA motifTAATAAW /gt
ltMotif alphabetDNA motifTAATAAW
namePribnow-box threshold0.5 /gt
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Series Patterns
Series
ltSeries ... gt ltMotif ... /gt ltGap .../gt
ltMotif .../gt lt/Seriesgt
Motif
Gap
Motif
TTGACA
TATAAT
-10 element
-35 element
gap
bacterial promoter
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Libraries of Patterns
(BioPatML resource uribiopatml/promoter.bpl) ltD
efinition namesigma70 gt ltDefinitionsgt lt
Definition name-35element /gt ltMotif
motifTTGACA alphabetDNA /gt
lt/Definitiongt lt Definition name-10element
/gt ltMotif motifTATAAT alphabetDNA /gt
lt/Definitiongt lt/Definitionsgt ltVoid
/gt lt/Definitiongt
ltDefinition namePromoter gt ltDefinitionsgt
ltImport uribiopatml/promoter.bpl
lt/Definitionsgt ltSeries ... gt ltUse
definitionsigma70.-35element /gt ltGap
min13 max21 /gt ltUse definitionsigma70.
-10element /gt lt/Seriesgt lt/Definitiongt
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BioPatML Web serviceshttp//bio.mquter.qut.edu.au
/biopatml
Pattern creation
Semantic tagging
Annotation
XML
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SilverGene Genome browser
Gene CT323
Pattern matches
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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"

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The world according to Bio2RDF
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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

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BioPatML Semantic Tagging
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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)
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Bioinformatics team at MQUTER
Peter Ansell
Michael Towsey
Jiro Sumitomo
Lawrence Buckingham
ChrisBowles
Scott Mann
Jim Hogan
Xin-Yi Chua