Semantic web standards: Legal and social issues and implications

Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences

Volumn 9780387484389, Issue , 2007, Pages 413-433

  Greenbaum, Dov ^a   Gerstein, Mark ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

antitrust; bioinformatics; intellectual property; policy; standards

Indexed keywords

BIOINFORMATICS; INTELLECTUAL PROPERTY; PUBLIC POLICY; STANDARDS;

ACADEMIC SCIENCE; ANTITRUST; BIOLOGICAL DATABASE; PARADIGM SHIFTS; PROPRIETARY STANDARDS; SEMANTIC WEB STANDARDS; SOCIAL PROCESS; STANDARD SETTING;

SEMANTIC WEB;

EID: 41549160084     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-0-387-48438-9_19     Document Type: Chapter

References (48)

1. W3C, "Web Services Activity Statement, " 2006. http://www.w3.org/2002/ws/Activity.
2. Wilkinson M.D. "Bio MOBY - The MOBY-S Platform for Interoperable Data Service Provision, " in Computational Genomics Theory and Application, R. P. Grant, Ed. Wymondham, U.K: Horizon Bio science, 2004.
3. Ludaescher B. and Goble C. "Guest Editors' Introduction to the Special Section on Scientific Workflows, " SIGMOD Record, vol. 34, 2005.
4. Ludascher B., Altintas I., Berkley C, Higgins D., Jaeger-Frank E., Jones M., Lee E., Tao J., and Zhao Y. Scientific Workflow Management and the Kepler System, Concurrency and Computation: Practice & Experience, vol. Special Issue on Scientific Workflows (to appear), 2006.
5. Oinn T., Greenwood M., Addis M., Alpdemir M. N., Ferris J., Glover K., Goble C, Goderis A., Hull D., Marvin D., Li P., Lord P., Pocock M. R., Senger M., Stevens R., Wipat A., and Wroe C. Tavema: Lessons in creating a workflow environment for the life sciences. Concurrency and Computation: Practice and Experience, To appear.
6. Churches D., Gombas G., Harrison A., Maassen J., Robinson C, Shields M., Taylor I., and Wang I. Programming scientific and distributed workflow with Triana services. Concurrency and Computation: Practice & Experience, 2006.
7. Stevens R., Tipney H.J., Wroe C., Oinn T., Senger M., Lord P., Goble C.A., Brass A., and Tassabehji M. Exploring Williams-Beuren Syndrome Using ""Grid, presented at 12th International Conference on Intelligent Systems in Molecular Biology, Glasgow, UK, 2004.
8. Senger M., Rice P., and Oinn T., Soap lab - A unified Sesame door to analysis tools, presented at e-Science Second All Hands Meeting 2003, Nottingham, UK, 2003.
9. Oinn T., Greenwood M., Addis M., Alpdemir M.N., Ferris J., Glover K., Goble C, Goderis A., Hull D., Marvin D., Li P., Lord P., Pocock M.R., Senger M., Stevens R., Wipat A., and Wroe C. Taverna: Lessons in creating a workflow environment for the life sciences. Concurrency and Computation: Practice and Experience, 2006.
10. Oinn T., Addis M., Ferris J., Marvin D., Senger M., Greenwood M, Carver T., Glover K., Pocock M.R., Wipat A., and Li P. Taverna: A tool for the composition and enactment of bioinformatics workflows, Bioinformatics Journal, vol. 20, pp. 3045- 3054, 2004.
11. Li P., Hay ward K., Jennings C, Owen K., Oinn T., Stevens R., Pearce S., and Wipat A. Association of variations on I kappa B-epsilon with Graves' disease using classical and "Grid methodologies, presented at 3rd UK e-Science All Hands Meeting, Nottingham UK, 2004.
12. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSl-BLAST: A new generation of protein database search programs, Nucleic Acids Res., vol. 25, pp. 3389-3402, 1997.
13. Hendler J. Science and the Semantic Web, Science vol. 299, pp. 520-521, 2003.
14. Bairoch A., Apweiler R., Wu C.H., Barker W.C, Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., and Magrane M. The Universal Protein Resource (UniProt), Nucleic Acids Res., vol. 33, pp. D154-D159, 2005.
15. Ashbumer M., Ball C.A., Blake J. A., Botstein D., Butler H., Cherry J. M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C, Richardson J.E., Ringwald M., Rubin G.M., and Sherlock G. Gene Ontology: Tool for the unification of biology, Nat Genet, vol. 25, pp. 25-29, 2000.
16. Wroe C, Goble C, Goderis A., Lord P., Miles S., Papay J., Alper P., and Moreau L. Recycling workflows and services through discovery and reuse. Concurrency and Computation: Practice and Experience, 2006.
17. Bemers-Lee T., Hendler J., and Lassila O. The Semantic Web, Scientific American, vol. 284, pp. 34-43, 2001.
18. Clark T., Martin S., and Liefeld T. Globally Distributed Object Identification for Biological Knowledge bases, Briefings in Bioinformatics, vol. 5, pp. 59-70, 2004.
19. Wikipedia, "Folksomony, " 2006. http://en.wikipedia.org/wiki/Folksonomy.
20. Lord P., Alper P., Wroe C, and Goble C. Feta: A light-weight architecture for user oriented semantic service discovery, presented at 2nd European Semantic Web Conference, Heraklion, Greece, 2005.
21. Wroe C, Goble C. A., Greenwood M., Lord P., Miles S., Papay J., Payne T., and Moreau L. Automating Experiments Using Semantic Data on a Bioinformatics Grid, IEEE Intelligent Systems, vol. 19, pp. 48-55, 2004.
22. Lord P., Bechhofer S., Wilkinson M., Schiltz G., Gessler D., Goble C, Stein L., and Hull D. Applying semantic web services to bioinformatics: Experiences gained, lessons learnt, presented at 3rd International Semantic Web Conference ISWC2004, Hiroshima, Japan, 2004.
23. Goderis A., Li P., and Goble C. Workflow discovery: The problem, a case study from escience and a graph-based solution, presented at 4th IEEE Int. Conference on Web Services (ICWS 2006), Chicago, USA, 2006.
24. Goderis A., Sattler U., and Goble C. Applying descriptions logics for workflow reuse and repurposing, presented at International Description Logics Workshop, Edinburgh, Scotland, 2005.
25. Goderis A., Sattier U., Lord P., and Goble C. Seven bottlenecks to workflow reuse and repurposing, presented at Fourth International Semantic Web Conference (ISWC 2005), Galway, Ireland, 2005.
26. Belhajjame K., Embury S.M., and Paton N.W. On characterising and identifying mismatches in scientific workflows, presented at Data Integration in the Life Sciences (DILS'06), Hinxton, UK 2006.
27. Hull D., Zolin E., Bovykin A., Horrocks I., Satfler U., and Stevens R. Deciding matching of stateless services, presented at Twenty-First National Conference on Artificial Intelligence (AAAr06), Boston, MA, USA, 2006.
28. Szomszor M., Payne T. R., and Moreau L. Using semantic web technology to automate data integration in grid and web service architectures, presented at Semantic Infrastructure for Grid Computing Applications Workshop, Cluster Computing and Grid (CCGrid), Cardiff, UK, 2005.
29. Zhao J., Wroe C, Goble C, Stevens R., Quan D., and Greenwood M. Using Semantic Web Technologies for Representing e-Science Provenance, presented at 3rd International Semantic Web Conference ISWC2004, Hiroshima, Japan, 2004.
30. Zhao J., Goble C, Stevens R., and Bechhofer S. Semantically Linking and Browsing Provenance Logs for e-Science, presented at International Conference on Semantics of a Networked World, Paris, France, 2004.
31. Frey J.G., de Roure D., and Carr L.A. Publication At Source: Scientific Communication from a Publication Web to a Data Grid, presented at Euro web 2002 Conference, The Web and the GRID: from e-science to e-business, Oxford, UK, 2002.
32. Taylor K., Gledhill R., Essex J.W., Frey J.G., Harris S.W., and de Roure D..A Semantic Datagrid for Combinatorial Chemistry, presented at 6th IEEE/ACM International Workshop on Grid Computing, Seattle, 2005.
33. Hughes G., Mills H., de Roure D., Frey J.G., Moreau L., Schraefel M.C., Smith G., and Zaluska E. The Semantic Smart Laboratory: A system for supporting the chemical e- Scientist, Organic & Bio molecular Chemistry., vol. 2, pp. 3284-3293, 2004.
34. Pettifer S., Sinnott J.R., and Attwood T.K. UTOPIA: user friendly tools for operating informatics applications. Comparative and Functional Genomics, vol. 5, pp. 56-60, 2004.
35. Garwood K., Lord P., Parkinson H., Paton N.W., and Goble C, Pedro ontology services: A framework for rapid ontology markup, presented at 2nd European Semantic Web Conference, Heraklion, Greece, 2005.
36. Wong S.C, Tan V., Fang W., Miles S., and Moreau L., Grimoires: Grid Registry with Metadata Oriented Interface: Robustness, Efficiency, Security - Work-in-Progress, presented at Cluster Computing and Grid (CCGrid), Cardiff, UK, 2005.
37. Wroe C, Stevens R., Goble C.A., Roberts A., and Greenwood M. A suite of DAML+OIL Ontologies to Describe Bioinformatics Web Services and Data, International Journal of Cooperative Information Systems, vol. 2, pp. 197-224, 2003.
38. Roman D., Keller U., Lausen H., de Bruijn J., Lara R., Stollberg M., PoUeres A., Feier C, Bussler C, and Fensel D. Web Service Modeling Ontology, Applied Ontology, vol. 1, pp. 77-106, 2005.
39. Martin D., Paolucci M., Mcllraith S., Burstein M., McDermott D., McGuinness D., Parsia B., Payne T., Sabou M., Solanki M., Srinivasan N., and Sycara K. Bringing Semantics to Web Services: The OWL-S Approach, presented at First International Workshop on Semantic Web Services and Web Process Composition (SWSWPC 2004), San Diego, California, USA, 2004.
40. Akkiraju R., Farrell J., Miller J., Nagarajan M., Schmidt M., Sheth A., and Verma K. Web Service Semantics - WSDL-S, Joint UGA-IBM Technical Note, 2005.
41. Broekstra J., Kampman A., and van Harmelen F. Sesame: A generic architecture for storing and querying rdf and rdf schema, presented at International Semantic Web Conference (ISWC 2002), Sardinia, Italy, 2002.
42. Hull D., Stevens R., Lord P., Wroe C, and Goble C. Treating shimantic web syndrome with ontologies, presented at First Advanced Knowledge Technologies workshop on Semantic Web Services (AKT-SWS04), Milton Keynes, UK., 2004.
43. Stevens R., Wroe C, Bechhofer S., Lord P., and Rector A. Building Ontologies in DAML + OIL, Comparative and Functional Genomics, vol. 4, 2003.
44. Szomszor M. and Moreau L. Recording and Reasoning Over Data Provenance in Web and Grid Services, presented at Ontologies, Databases and Applications of Semantics (ODBASE'03), Catania, Sicily, Italy.
45. Zhao J., Goble C, and Stevens R. An Identity Crisis in the Life Sciences, presented at International Provenance and Annotation Workshop (IPAW06), Chicago, 2006.
46. Newscientist.com news service and Translator lets computers "understand" experiments, 2006. http://www.newscientist.com/article/dn9288-translator-letscomputers-understand-experiments-.html.
47. Blake J. Bio-ontologies-fast and furious. Nature Biotechnology vol. 22, pp. 773-774, 2004.
48. Butler D. Mashups mix data into global service, Nature, vol. 439, pp. 6-7, 2006.