What the semantic web could do for the life sciences

Abstract Scientific research is predicated on the effective exchange of knowledge. The effective exchange of data and accompanying interpretation underpin new hypotheses and experimental designs, typically followed by a community-based process of debate and rebuttal. This community-driven process clarifies and strengthens the elements of facts and hypothesis. Within the life sciences, the result of this process is a collective understanding of emerging biological viewpoints. The methodologies for community debate and knowledge transfer have changed little over the past twenty years, although both scientific instrumentation and publishing technologies have undergone revolutionary change. It is proposed that newly published recommendations from the World Wide Web Consortium (W3C), which handle the domain and process-specific semantics of life sciences, would better support the application of peer-reviewed knowledge in discovery research. W3C semantic web technologies support flexible, extensible and evolvable knowledge transfer and reuse, enabling scientists and their organizations to increase efficiency across the scientific process.

[1]  Carole A. Goble,et al.  myGrid: personalised bioinformatics on the information grid , 2003, ISMB.

[2]  P D Karp,et al.  Pathway Databases: A Case Study in Computational Symbolic Theories , 2001, Science.

[3]  D. Botstein,et al.  Singular value decomposition for genome-wide expression data processing and modeling. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Carole A. Goble,et al.  Transparent access to multiple bioinformatics information sources , 2001, IBM Syst. J..

[5]  Gene Ontology Consortium The Gene Ontology (GO) database and informatics resource , 2003 .

[6]  Ian Horrocks,et al.  OIL in a Nutshell , 2000, EKAW.

[7]  Béla Bollobás,et al.  Modern Graph Theory , 2002, Graduate Texts in Mathematics.

[8]  Robert D. Finn,et al.  The Distributed Annotation System for Integration of Biological Data , 2006, DILS.

[9]  Richard Fikes,et al.  The Ontolingua Server: a tool for collaborative ontology construction , 1997, Int. J. Hum. Comput. Stud..

[10]  P. Heinrich,et al.  Principles of interleukin (IL)-6-type cytokine signalling and its regulation. , 2003, The Biochemical journal.

[11]  E Birney,et al.  The Genome Knowledgebase: a resource for biologists and bioinformaticists. , 2003, Cold Spring Harbor symposia on quantitative biology.

[12]  Carole A. Goble,et al.  TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources , 1998, ISMB.

[13]  Carol Ezzell The $13-Billion Man , 2001 .

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

[15]  R N Re,et al.  On the sequencing of the human genome. , 2000, Hypertension.

[16]  Robert M. MacGregor,et al.  Inside the LOOM description classifier , 1991, SGAR.

[17]  E. Neumann,et al.  Knowledge assembly for the life sciences. , 2002, Drug discovery today.

[18]  Peter D. Karp,et al.  An Evaluation of Ontology Exchange Languages for Bioinformatics , 2000, ISMB.