1 / 17

SeaLife Simon Jupp

SeaLife Simon Jupp. 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 :

kiana
Download Presentation

SeaLife Simon Jupp

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. SeaLifeSimon Jupp

  2. 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. 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. 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. 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 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. 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. 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. 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. 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 alphainterferon for chronic hepatitis C" • Clinicians need up to date, authoritative information

  11. COHSE-NeLI Demo http://www.cs.man.ac.uk/~sjupp/downloads/COHSE-NELI-2009-demo.mov

  12. 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. -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 • Protein covalent bond • Protein domain • UniProt taxonomy -Pathway ontology -Event (INOH pathway ontology) -Systems Biology -Protein-protein interaction • Sequence types and features • Genetic Context BRENDA tissue / enzyme source Phenotype Proteins Sequence Pathways Anatomy Phenotype Development Plasmodium life cycle Transcript Gene products Cell type -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 -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 - Molecule role - Molecular Function - Biological process - Cellular component eVOC (Expressed Sequence Annotation for Humans)

  14. Knowledge representation Infectious Disease TB Bacteria abbreviation Is a BCG vaccine Caused by Isoniazid Tuberculosis vaccine drug Chest X-ray Diagnosis/detection Symptom Affects Lung Similar to Coughing Mycobacterium bovis Can’t make these close links with strict semantics!

  15. SKOS conversions Infectious Disease TB Bacteria skos:altLabel skos:broader BCG vaccine skos:broader Isoniazid Tuberculosis skos:narrower skos:related Chest X-ray skos:narrower skos:related skos:related Lung skos:narrower Coughing Mycobacterium bovis • We need “something to do with” semantics for Navigation • SKOS provides standard for common representation with “enough” semantics

  16. 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. 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

More Related