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

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

Unifying the Description of Patterns in Biological Sequences BioPatML supports: 1.DNA, RNA, AA sequences 2.Principled aggregation of different pattern types e.g. motifs, gaps, loops 3.Hierarchical patterns 4.Pattern libraries 5.Integrated scoring of pattern matches 6.Some existing pattern databases e.g. Prosite BioPatML exploits the advantages of XML and RDF.

TAATTCCAGATATAGACA Simple Patterns

Series MotifGapMotif -10 element-35 elementgap TTGACA bacterial promoter Series Patterns TATAAT

Libraries of Patterns (BioPatML resource: uri=biopatml/promoter.bpl) (BioPatML resource: uri=biopatml/promoter.bpl) <Import uri=“biopatml/promoter.bpl” <Import uri=“biopatml/promoter.bpl”

Pattern creation Annotation XML Semantic tagging BioPatML Web services

SilverGene: Genome browser Gene CT323 Pattern matches

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"

The world according to Bio2RDF

BioPatML in the Semantic Web  BioPatML in Bio2RDF –created a name space and terms –  Created an RDF database of BioPatML patterns –encapsulate BioPatML patterns as RDF literals –RDF tagging and search

BioPatML: Semantic Tagging

BioPatML Resources (web demo) (BioPatML manual) (namespace & terms) (Bio2RDF home page)

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