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A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases SeaLife Simon Jupp 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 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 Qu ic kTi me™ a nd a de co mpre ss or are n ee de d to s ee th is pi ctu re . 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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) 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 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…. 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. 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 – • Navigation is still an important aspect of information gathering on the Web – • Serendipitous information retrieval Problem – – – – – – – • A collection of linked nodes 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 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 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 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 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.. A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious -Mosquito gross anatomy Diseases -Protein covalent bond -Protein domain -UniProt taxonomy -Sequence types and features -Genetic Context -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 -Pathway ontology -Event (INOH pathway ontology) -Systems Biology -Protein-protein interaction BRENDA tissue / enzyme source Proteins Sequence Pathways Phenotype Anatomy Phenotype Gene products Transcript - Molecule role - Molecular Function - Biological process - Cellular component eVOC (Expressed Sequence Annotation for Humans) Cell type Development -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 Plasmodium life cycle -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 A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases Knowledge representation Infectious Disease TB Bacteria abbreviation Caused by BCG vaccine Tuberculosis vaccine Chest X-ray Is a Diagnosis/ detection Symptom Isoniazid drug Affects Similar to Coughing Lung Mycobacterium bovis Can’t make these close links with strict semantics! A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases SKOS conversions Infectious Disease TB Bacteria skos:altLabel skos:broader BCG vaccine skos:narrower Chest X-ray skos:broader Tuberculosis Isoniazid skos:related 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 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…. 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