A cell-cycle knowledge integration framework research paper

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4075 LNBI, Issue , 2006, Pages 19-34

  Antezana, Erick ^a   Tsiporkova, Elena ^a   Mironov, Vladimir ^a   Kuiper, Martin ^a  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; CELL CULTURE; COMPUTATIONAL METHODS; DATA STRUCTURES; KNOWLEDGE BASED SYSTEMS; PROBLEM SOLVING;

ANNOTATION; AUTOMATIC FORMAT MAPPINGS; CELL CYCLE REGULATION PROCESS; HYPOTHESES EVALUATION;

KNOWLEDGE ENGINEERING;

EID: 33746748757     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11799511_4     Document Type: Conference Paper

References (32)

1. Baader, F., Calvanese, D., McGuinness, D., Nardi, D., Patel-Schneider, P.(eds.): The Description Logic Handbook. Theory, Implementation and Applications. Cambridge University Press (2003)
2. Bader, G.D., Betel, D., Hogue, C.W.V.: BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res, (2003) 31 1 248-250
3. Bard, J., Rhee, S.Y., Ashburner, M.: An ontology for cell types. Genome Biology, (2005) 6 R21
4. Berners-Lee, T., Hendler, J., Lassila, O.: The Semantic Web. Scientific American (May 2001)
5. Blake, J.: Bio-ontologies-fast and furious. Nature Biotechnology, (2004) 22 773-774
6. Bairoch, A., Apweiler, R., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Natale, D.A., ODonovan, C., Redaschi, N., Yeh, L.S.: The universal protein resource (Uniprot). Nucleic Acids Res., (2005) 33 Database issue D154D159
7. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Wheeler, D.L.: Genbank. Nucleic Acids Res., (2005) 33 Database issue D34D38
8. Covitz, P.A., Hartel, F., Schaefer, C., De Coronado, S., Fragoso, G., Sahni, H., Gustafson, S., Buetow, K.H. caCORE: A common infrastructure for cancer informatics. Bioinformatics, (2003) 19 18 2404-2412
9. Gene Ontology Consortium.: The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res., (2004) 32 Database issue D258-D261
10. Gomez-Perez, A., Corcho, O., Fernandez-Lopez, M.: Ontological Engineering: with examples from the areas of Knowledge Management, e-Commerce and the Semantic Web. Springer (2004)
11. Gruninger, M., Fox M.S.: Methodology for the Design and Evaluation of Ontologies. Workshop on Basic Ontological Issues in Knowledge Sharing, IJCAI-95 (Montreal) (1995)
12. Guarino, N.: Formal Ontology In Information Systems. In Proceedings of FOIS '98, Trento, Italy 6-8 June. IOS Press (1998)
13. Hermjakob, H., Montecchi-Palazzi, L., Lewington, C., Mudali, S., Kerrien, S., Orchard, S., Vingron, M., Roechert, B., Roepstorff, P., Valencia, A., Margalit, H., Armstrong, J., Bairoch, A., Cesareni, G., Sherman, D., Apweiler, R.: IntAct: an open source molecular interaction database. Nucleic Acids Res., (2004) 32 Database issue D452-D455
14. Inze, D.: Why should we study the plant cell cycle? J. Exp. Bot., (2003) 54 385 11251126
15. Joshi-Tope, G., Gillespie, M., Vastrik, I., DEustachio, P., Schmidt, E., de Bono, B., Jassal, B., Gopinath, G.R., Wu, G.R., Matthews, L., Lewis, S., Birney, E., Stein, L.: Reactome: a knowledgebase of biological pathways. Nucleic Acids Res., (2005) 33 Database issue D428D432
16. Knublauch, H., Dameron, O., Mussen, M.A.: Weaving the biomedical semantic web with the Protege OWL plugin (2004)
17. Maedche, A.: Ontology Learning For The Semantic Web. Norwell, Massachusetts, Kluwer Academic Publishers (2003)
18. Maedche, A., Volz R.: The Ontology Extraction & Maintenance Framework Text-To-Onto. In Proceedings of the ICDM-2001 Workshop on the integration of Data Mining and Knowledge Management, San Jose, USA, November, 31 (2001)
19. Noy, N.F., McGuiness, D.L.: Ontology development 101: A guide to creating your first ontology. Technical Report SMI-2001-0880, Stanford University, SMI technical report (2001)
20. Ogden, C., Richards, I.: The Meaning of Meaning: A Study of the Influence of Language upon Thought and of the Science of Symbolism. Routledge & Kegan Paul Ltd., London, 1.0 edition (1923)
21. McGuinness, D.L., van Harmelen, F.(eds.): OWL Web Ontology Language Overview. http://www.w3.org/TR/2004/REC-owl-features-20040210/
22. Lopez, M.F., Perez, A.G., Juristo, N.: METHONTOLOGY: From Ontological Art Towards Ontological Engineering. Workshop on Ontological Engineering. Spring Symposium Series: Stanford, USA (1997)
23. Smith, B., Kohler, J., Kumar, A.: On the application of formal principles to life science data: A case study in the Gene Ontology. Database Integration in the Life Sciences (DILS), Berlin: Springer (2004)
24. Smith, B., Ceusters, W., Klagges, B., Kohler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, P., Rector, A.L., Rosse, C.: Relations in biomedical ontologies. Genome Biology, (2005) 6 R46
25. Stevens, R., Baker, P., Bechhofer, S., Ng, G., Jacoby, A., Paton, NW., Goble, CA., Brass, A. TAMBIS: transparent access to multiple bioinformatics information sources. Bioinformatics, (2000) 16 2 184-185
26. Thompson, J.D., Holbrook, S.R., Katoh, K., Koehl, K., Moras, D., Westhof, E., Poch, O.: MAO: a multiple alignment ontology for nucleic acid and protein sequences. Nucleic Acids Res., (2005) 33 13 4164-4171
27. Uschold, M., King, M. Towards Methodology for Building Ontologies. Workshop on Basic Ontological Issues in Knowledge Sharing, held in conjunction with IJCAI-95 (1995)
28. Uschold, M., Gruninger, M. Ontologies: Principles, methods and applications. Knowledge Engineering Review, (1996) 11 2 93-136
29. Vermeulen, K., Van Bockstaele, D.R., Berneman, Z.N.: The cell cycle: a review of regulation, deregulation and therapeutic targets in cancer. Cell Prolif., (2003) 36 3 131149
30. Yeh, I., Karp, P.D., Noy, N.F., Altman, R.B.: Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics, (2003) 19 2 241-248
31. Yu, A.C.: Methods in biomedical ontology. Journal of Biomedical Informatics, (2005) 78 315-333
32. Zhang, Z., Miller, J.A.: Ontology query languages for the semantic web. A performance evaluation (2004)