e-Science and the Semantic Web: A Symbiotic Relationship

e-Science is scientific investigation performed through distributed global collaborations between scientists and their resources, and the computing infrastructure that enables this. Scientific progress increasingly depends on pooling know-how and results; making connections between ideas, people, and data; and finding and reusing knowledge and resources generated by others in perhaps unintended ways. It is about harvesting and harnessing the “collective intelligence” of the scientific community. The Semantic Web is an extension of the current Web in which information is given well-defined meaning to facilitate sharing and reuse, better enabling computers and people to work in cooperation. Applying the Semantic Web paradigm to e-Science has the potential to bring significant benefits to scientific discovery. We identify the benefits of lightweight and heavyweight approaches, based on our experiences in the Life Sciences.

[1]  Susie Stephens,et al.  Aggregation of bioinformatics data using Semantic Web technology , 2006, J. Web Semant..

[2]  Carole A. Goble,et al.  Exploring Williams-Beuren syndrome using myGrid , 2004, ISMB/ECCB.

[3]  Olivier Bodenreider,et al.  Experience in Reasoning with the Foundational Model of Anatomy in OWL DL , 2005, Pacific Symposium on Biocomputing.

[4]  Philip E. Bourne,et al.  Will a Biological Database Be Different from a Biological Journal? , 2005, PLoS Comput. Biol..

[5]  G Stix,et al.  The mice that warred. , 2001, Scientific American.

[6]  Ian Horrocks,et al.  A Little Semantic Web Goes a Long Way in Biology , 2005, SEMWEB.

[7]  Nicholas R. Jennings,et al.  The Semantic Grid: Past, Present, and Future , 2005, Proceedings of the IEEE.

[8]  Carole A. Goble,et al.  Using Semantic Web Technologies for Representing E-science Provenance , 2004, SEMWEB.

[9]  Matthew R. Pocock,et al.  Taverna: a tool for the composition and enactment of bioinformatics workflows , 2004, Bioinform..

[10]  Eric K. Neumann,et al.  A Life Science Semantic Web: Are We There Yet? , 2005, Science's STKE.

[11]  Anne E. Trefethen,et al.  Cyberinfrastructure for e-Science , 2005, Science.

[12]  Jonathan W. Essex,et al.  Bringing Chemical Data onto the Semantic Web , 2006, J. Chem. Inf. Model..

[13]  Kei-Hoi Cheung,et al.  Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences , 2006 .

[14]  Xiaoshu Wang,et al.  From XML to RDF: how semantic web technologies will change the design of 'omic' standards , 2005, Nature Biotechnology.

[15]  Carole A. Goble,et al.  Feta: A Light-Weight Architecture for User Oriented Semantic Service Discovery , 2005, ESWC.

[16]  Jane Greenberg,et al.  Metadata and the world wide web , 2002 .

[17]  Kei-Hoi Cheung,et al.  YeastHub: a semantic web use case for integrating data in the life sciences domain , 2005, ISMB.

[18]  James A. Hendler,et al.  The Semantic Web" in Scientific American , 2001 .

[19]  Gregor von Laszewski,et al.  A Collaborative Informatics Infrastructure for Multi-Scale Science , 2004, Proceedings of the Second International Workshop on Challenges of Large Applications in Distributed Environments, 2004. CLADE 2004..

[20]  Enrico Motta,et al.  The Semantic Web - ISWC 2005, 4th International Semantic Web Conference, ISWC 2005, Galway, Ireland, November 6-10, 2005, Proceedings , 2005, SEMWEB.

[21]  Carole A. Goble,et al.  Using the Semantic Web for e-Science: Inspiration, Incubation, Irritation , 2005, SEMWEB.

[22]  Asunción Gómez-Pérez,et al.  Methodologies, tools and languages for building ontologies: Where is their meeting point? , 2003, Data Knowl. Eng..

[23]  Óscar Corcho,et al.  Ontology based document annotation: trends and open research problems , 2006, Int. J. Metadata Semant. Ontologies.

[24]  Les Carr,et al.  Position Paper: Publication at Source: Scientific Communication from a Publication Web to a Data Grid , 2002, EuroWeb.

[25]  Olivier Bodenreider,et al.  Session Introduction , 2005, Pacific Symposium on Biocomputing.

[26]  Andy Seaborne,et al.  SWAN: A distributed knowledge infrastructure for Alzheimer disease research , 2006, J. Web Semant..

[27]  Toni Kazic Putting Semantics into the Semantic Web: How Well Can It Capture Biology? , 2006, Pacific Symposium on Biocomputing.

[28]  Jim Gray,et al.  2020 Computing: Science in an exponential world , 2006, Nature.

[29]  Frank van Harmelen,et al.  A semantic web primer , 2004 .

[30]  C. Bizer,et al.  D2R MAP - A Database to RDF Mapping Language , 2003, WWW.

[31]  J. Blake Bio-ontologies—fast and furious , 2004, Nature Biotechnology.

[32]  Carole Goble,et al.  The semantic web and knowledge grids. , 2005, Drug discovery today. Technologies.

[33]  Gómez-PérezAsunción,et al.  Methodologies, tools and languages for building ontologies , 2003 .

[34]  Eric K. Neumann,et al.  Pacific Symposium on Biocomputing 11:176-187(2006) BIODASH: A SEMANTIC WEB DASHBOARD FOR DRUG DEVELOPMENT , 2022 .

[35]  Anne E. Trefethen,et al.  The Data Deluge: An e-Science Perspective , 2003 .

[36]  Olivier Bodenreider,et al.  Semantic webs for life sciences. , 2006, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[37]  Francine Berman,et al.  Grid Computing: Making the Global Infrastructure a Reality , 2003 .

[38]  Jonathan W. Essex,et al.  CombeChem: A Case Study in Provenance and Annotation Using the Semantic Web , 2006, IPAW.

[39]  Genevieve Bell,et al.  Opening keynote , 2006, Australasian Computer-Human Interaction Conference.

[40]  Carole A. Goble,et al.  A Methodology to Migrate the Gene Ontology to a Description Logic Environment Using DAML+OIL , 2002, Pacific Symposium on Biocomputing.

[41]  Sean Bechhofer,et al.  Ontology Driven Dynamic Linking of Biology Resources , 2005, Pacific Symposium on Biocomputing.

[42]  Luc Moreau,et al.  The semantic smart laboratory: a system for supporting the chemical eScientist. , 2004, Organic & biomolecular chemistry.

[43]  James Hendler,et al.  Science and the Semantic Web , 2003, Science.

[44]  Ian Foster,et al.  The Grid 2 - Blueprint for a New Computing Infrastructure, Second Edition , 1998, The Grid 2, 2nd Edition.

[45]  Carole Goble,et al.  Enhancing Services and Applications with Knowledge and Semantics , 2004, The Grid 2, 2nd Edition.

[46]  Stephen Potter,et al.  Collaborative Tools in the Semantic Grid , 2004 .

[47]  Siegfried Handschuh,et al.  Semantic annotation for knowledge management: Requirements and a survey of the state of the art , 2006, J. Web Semant..

[48]  Carole A. Goble,et al.  The Semantic Grid: Myth Busting and Bridge Building , 2004, ECAI.

[49]  Michael K. Bergman White Paper: The Deep Web: Surfacing Hidden Value , 2001 .

[50]  Jeffrey M. Bradshaw,et al.  Applying KAoS Services to Ensure Policy Compliance for Semantic Web Services Workflow Composition and Enactment , 2004, SEMWEB.

[51]  Jonathan W. Essex,et al.  A semantic datagrid for combinatorial chemistry , 2005, The 6th IEEE/ACM International Workshop on Grid Computing, 2005..

[52]  Simon Miles Electronically Querying for the Provenance of Entities , 2006, IPAW.

[53]  Peishen Qi,et al.  A semantic web approach to biological pathway data reasoning and integration , 2006, J. Web Semant..

[54]  Michael Schroeder,et al.  Editorial - Semantic Web for Life Sciences , 2006, J. Web Semant..

[55]  Carole A. Goble,et al.  Pedro Ontology Services: A Framework for Rapid Ontology Markup , 2005, ESWC.