SADI, SHARE, and the in silico scientific method

BMC Bioinformatics

Volumn 11, Issue SUPPL. 12, 2010, Pages

  Wilkinson, Mark D ^a   McCarthy, Luke ^a   Vandervalk, Benjamin ^a   Withers, David ^a   Kawas, Edward ^a   Samadian, Soroush ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CLIENT LIBRARIES; CLINICAL RESEARCH; DESCRIPTION LOGIC; HYPOTHESIS GENERATION; LOGICAL REASONING; REFERENCE IMPLEMENTATION; SCIENTIFIC METHOD; SEMANTIC WEB TECHNOLOGY;

WEB SERVICES;

DATA DESCRIPTION;

ARTICLE; BIOLOGY; BIOMEDICINE; COMPUTER PROGRAM; FACTUAL DATABASE; INFORMATION RETRIEVAL; INTERNET; METHODOLOGY; SEMANTICS; WORKFLOW;

BIOLOGICAL SCIENCE DISCIPLINES; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; INFORMATION STORAGE AND RETRIEVAL; INTERNET; SEMANTICS; SOFTWARE; WORKFLOW;

EID: 78650823775     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S12-S7     Document Type: Article

References (18)

1. Goble CA, Bhagat J, Aleksejevs S, Cruickshank D, Michaelides D, Newman D, Borkum M, Bechhofer S, Roos M, Li P, De Roure D. myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucleic Acids Research 2010, 38(Web Server issue):W677-W682. 10.1093/nar/gkq429, 2896080, 20501605.
2. Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs A, Stevens R, Pettifer S, Lopez R, Goble CA. BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Research 2010, 38(Web Server issue):W689-W694. 10.1093/nar/gkq394, 2896129, 20484378.
3. OWL Web Ontology Language Overview. , http://www.w3.org/TR/owl-features/
4. Semantic Web Health Care and Life Sciences (HCLS) Interest Group. , http://www.w3.org/2001/sw/hcls/
5. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007, 25:1251-1255. 10.1038/nbt1346, 2814061, 17989687.
6. Wilkinson MD, Vandervalk B, McCarthy L. SADI Semantic Web Services - 'cause you can't always GET what you want!. Proceedings of the IEEE APSCC 2009 2009, Singapore.
7. Vandervalk B, McCarthy L, Wilkinson MD. SHARE: A Semantic Web Query Engine for Bioinformatics. The Semantic Web, Lecture Notes in Computer Science proceedings of the ASWC 2009, 5926:367-369.
8. RDF Semantic Web Standards. , http://www.w3.org/RDF/
9. Prud'hommeaux E, Seaborne A. SPARQL Query Language for RDF. Technical report, W3C 2006,
10. The SADI Semantic Web Service project. , http://code.google.eom/p/sadi/
11. Kawas E, Wilkinson M. OWL2Perl: Creating Perl modules from OWL class definitions. Bioinformatics 2010, Epub ahead of print, 2935399, 20628074.
12. The SADI Protégé Plugin. , http://code.google.eom/p/sacli/source/browse/trunk/sadi.protege
13. Gennari JH, Musen MA, Fergerson RW, Grosso WE, Crubezy M, Eriksson H, Noy NF, Tu SF. The evolution of Protege: an environment for knowledge-based systems development. International Journal of Human-Computer Studies 2003, 58(1):89-123.
14. Knublauch H, Musen MA, Rector AL. Editing Description Logic Ontologies with the Protégé - OWL Plugin. International Workshop on Description Logics - DL2004 2004, Whistler, BC, Canada.
15. The SADI Taverna Plugin. , http://code.google.com/p/taverna-plugins/source/browse/#svn/trunk/sadi
16. Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, Carver T, Glover K, Pocock MR, Wipat A, Li P. Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 2004, 20(17):3045-3054. 10.1093/bioinformatics/bth361, 15201187.
17. Sirin E, Parsia B, Grau BC, Kalyanpur A, Katz Y. Pellet: A practical OWL-DL reasoner. Web Semantics: Science, Services and Agents on the World Wide Web 2007, 5(2):51-53.
18. Clay Shirky on Institutions vs. Collaboration. , http://www.ted.com/talks/clay_shirky_on_institutions_versus_collaboration.html