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

[2]  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..

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

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

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

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

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

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

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

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

[11]  Carole A. Goble,et al.  e-Science and the Semantic Web: A Symbiotic Relationship , 2006, ALT.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[36]  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.

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

[38]  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..

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

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

[41]  Daniel Lewis,et al.  What is web 2.0? , 2006, CROS.

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