Making data more meaningful with BioMOBY and my Grid services

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The document summarizes the use of semantic web standards and ontologies to add meaning and enable discovery of bioinformatics web services. It provides examples using the InterProScan protein domain identifier service, described through standards like XML, RDF and OWL. Registries like BioMOBY and myGrid are discussed that annotate services with ontologies to enable more powerful searches beyond just name or description. Reasoners can also check annotations for consistency and infer new facts to further enhance discovery.

Tecnología Educación

Making your data more meaningful Using BioMOBY and my Grid Taverna services as examples Duncan Hull University of Manchester BioSapiens Network of Excellence 2007-12-04

Outline ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

The semantic web “knows what you mean” thanks to added meaning ,[object Object],[object Object],[object Object],[object Object]

Semantic Web “stack” ,[object Object],[object Object]

… But first, InterProScan… ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

URI, Unicode, XML and Namespaces ,[object Object],[object Object],[object Object],[object Object],[object Object]

URI: Uniform Resource IDENTIFIER ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Unicode: Boring but important ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

XML: eXtensible Markup Language, boring but incredibly useful ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Namespaces ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Are different because they belong in different namespaces, “ xsi:fred ” is shorthand for http://www.w3.org/2001/XMLSchema-instance:fred Allows us to have lots of different things called “fred”

Describing Web Services ,[object Object],[object Object],[object Object],[object Object],[object Object]

WSDL, WuzzDuLL, MiserabuL… ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

RDF and OWL: Adding metadata and semantics ,[object Object],[object Object],[object Object]

RDF and RDF schema ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

BioMOBY.org ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

myGrid Taverna ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Web Ontology Language (OWL) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

What can a reasoner do? ,[object Object],[object Object],[object Object],[object Object],[object Object]

Semantic Web Services in a nutshell User driven Bit of an afterthought Lots of user generated metadata Metadata yes Kind of Yes Yes Yes! Community participation possibly? A bit No no no! Reasoning / semantics Maybe? no yes API? Taverna 2 / myExperiment myGrid BioMOBY

www.myExperiment.org ,[object Object],[object Object],[object Object],[object Object],[object Object]

Conclusions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Acknowledgements and References ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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