1. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases SeaLife Simon Jupp

2. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases SeaLife Conception and realisation of a Semantic Grid Browser, which links the current Web to the emerging eScience infrastructure Partners: Manchester, Dresden, Edinburgh, London, Inria Sophia-Antipolis, Scionics Objectives: –Many grids, few users: make Web servers and services accessible to end users –Semantic Hyperlinks: use ontologies and background knowledge to map web contents to services –Shopping cart: Service composition and enactment module Application: from cells, via tissue to patients –Evidence-based medicine –Patent and literature mining –Molecular biology Implementations: –COHSE –GoPubMed –CORESE

3. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases Objective We have a World Wide Web of data We have e-science and a grid of bioinformatics services We have text-mining tools, ontologies, web services and W3C standards

4. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases Evidence based medicine "Ribavirin with or without alpha interferon for chronic hepatitis C" Background Knowledge: MeSH, Disease Ontology, SNOMED… UK based Resources: –National Institute for Health and Clinical Excellence (NICE) –National Electronic Library of Infection (NeLI) –Health protection Agency (HPA)

5. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases Molecular Biology ‘’Rabaptin-5 interacts with the small GTPase Rab5 and is an essential component of the fusion machinery for targeting endocytic vesicles to early endosomes’’ Background Knowledge: –Rabaptin-5 and Rab5 are proteins –endocytosis as GO biological process –early endosome as GO cellular component. Resources : –Get sequences, execute alignment service –Add proteins to “shopping cart” Rab5 –PubMed query for relevant abstracts

6. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases A Sealife browser Definition: A SeaLife browser is any web browser that can identify domain concepts in web documents via text-mining or use of background knowledge, and provides context based links to related services/resources on the web/grid. Several exists: COHSE, GoPubMed, Magpie, PiggyBank, KIM, Concept Web Linker….

7. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases Implementations COHSE - Conceptual Open Hypermedia Service –Dynamic linking system for WWW documents –Uses background knowledge (ontologies) to identify domain concepts –Service module for navigating to relevant documents on the Web GoPubMed –Ontology based search engine: Query expansion and results filtering –Supports What, Who, Where, When.

8. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases Web Navigation The Semantic Web is still a Web to be used by humans –A collection of linked nodes Navigation is still an important aspect of information gathering on the Web –Serendipitous information retrieval Problem –Links are typically embedded –Hard coded –Difficult to author –Ownership –Unary –Legacy resources –Offer little in the way of semantics Approach –Exploit Semantic Web components to add links dynamically to documents –Exploit knowledge structure to drive Navigation

9. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases Web Navigation with COHSE Knowledge Service –Text processor and background knowledge identify concepts in a page Resource Manager –Finds links targets for concepts found in the page DLS –Dynamically adds the links to the page and manages requests to the resource manager Can be run as browser plugin or through a proxy

10. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases NeLI use case National Electronic Library of Infection, London, UK. –Evidence based, quality tagged resource for public and clinical health records –Diverse set of users GPs, Clinicians, Molecular biologists, General Public –Many documents, few hyperlinks Can COHSE provide useful links to relevant external documents? –Evaluation is underway Searching for guidelines on the use of "Ribavirin with or without alpha interferon for chronic hepatitis C" –Clinicians need up to date, authoritative information

11. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases COHSE-NeLI Demo http://www.cs.man.ac.uk/~sjupp/downloads/COHSE-NELI-2009-demo.mov

12. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases Background knowledge What semantics do we need for the background knowledge to drive navigation? Richer and more granular knowledge is better for navigation. The type of background knowledge varies between types users and the task at hand. –E.g. Nurses, doctors, public, medic etc..

13. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases Phenotype Sequence Proteins Gene products Transcript Pathways Cell type BRENDA tissue / enzyme source Development Anatomy Phenotype Plasmodium life cycle -Sequence types and features -Genetic Context - Molecule role - Molecular Function - Biological process - Cellular component -Protein covalent bond -Protein domain -UniProt taxonomy -Pathway ontology -Event (INOH pathway ontology) -Systems Biology -Protein-protein interaction -Arabidopsis development -Cereal plant development -Plant growth and developmental stage -C. elegans development -Drosophila development FBdv fly development.obo OBO yes yes -Human developmental anatomy, abstract version -Human developmental anatomy, timed version -Mosquito gross anatomy -Mouse adult gross anatomy -Mouse gross anatomy and development -C. elegans gross anatomy -Arabidopsis gross anatomy -Cereal plant gross anatomy -Drosophila gross anatomy -Dictyostelium discoideum anatomy -Fungal gross anatomy FAO -Plant structure -Maize gross anatomy -Medaka fish anatomy and development -Zebrafish anatomy and development -NCI Thesaurus -Mouse pathology -Human disease -Cereal plant trait -PATO PATO attribute and value.obo -Mammalian phenotype -Habronattus courtship -Loggerhead nesting -Animal natural history and life history eVOC (Expressed Sequence Annotation for Humans)

14. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases Knowledge representation Tuberculosis TB Infectious Disease Bacteria Lung Mycobacterium bovis Coughing Chest X-ray BCG vaccine Isoniazid abbreviationIs a vaccine Caused by drug Affects Similar to Symptom Diagnosis/ detection Can’t make these close links with strict semantics!

15. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases SKOS conversions Tuberculosis TB Infectious Disease Bacteria Lung Mycobacterium bovis Coughing Chest X-ray BCG vaccine Isoniazid skos:altLabel skos:broader skos:narrower skos:broader skos:related skos:narrower skos:related skos:narrower We need “something to do with” semantics for Navigation SKOS provides standard for common representation with “enough” semantics

16. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases COHSE and e-science Enhancements to COHSE, working prototype available –Addition of text-mining component Identifies Genes, Proteins, Chemicals in text Query service repositories –E.g. myExperiment, BioCatalogue, Bio-moby –Execute services and workflows within the browser Edinburgh developed shopping cart and argumentation services –Shop online for your genes, proteins, sequences etc… –Shop online for services and workflows –All from within your web browser! –But that’s the future….

17. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases Summary Range of Semantic Web browsers under development Semi-automated addition of semantic content to existing resources is the only viable option in many cases What are we waiting for? –More background knowledge –Semantic web services description