BioPatML Pattern sharing for the Genomic Sciences Stefan

BioPatML Pattern sharing for the Genomic Sciences Stefan

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 2008 Microsoft eScience Workshop 7-9 December Indianapolis The BioPatML project includes:

A comprehensive pattern description language Web services for pattern storage and searching Integration with the semantic web 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. Simple Patterns C A G A T A T A

A T T C C A G A T A Series Patterns

Series Motif Gap TTGACA -35 element Motif TATAAT gap

-10 element bacterial promoter Libraries of Patterns (BioPatML (BioPatML resource: resource: uri=biopatml/promoter.bpl) uri=biopatml/promoter.bpl) > << Definition Definition name=-35element name=-35element /> />

/> << Definition Definition name=-10element name=-10element /> /> />

> /> >

/> /> BioPatML Web services

http://bio.mquter.qut.edu.au/biopatml Pattern creation Annotation XML Semantic tagging 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 Universit 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 http://bio2rdf.org/ns/biopatml

Created an RDF database of BioPatML patterns encapsulate BioPatML patterns as RDF literals RDF tagging and search BioPatML: Semantic Tagging BioPatML Resources http://bio.mquter.qut.edu.au/biopatml http://www.mquter.qut.edu.au/bio http://bio2rdf.org/ns/biopatml http://bio2rdf.org (web demo) (BioPatML manual)

(namespace & terms) (Bio2RDF home page) Bioinformatics team at MQUTER Michael Towsey Jiro Sumitomo Lawrence Buckingham Chris Bowles Xin-Yi Chua

Peter Ansell Jim Hogan Scott Mann

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