Ontology-driven workflow management for biosequence processing systems

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

Volumn 3180, Issue , 2004, Pages 781-790

  Lemos, Melissa ^a   Casanova, Marco Antonio ^a   Seibel, Luiz Fernando Bessa ^a   De Macedo, José Antonio Fernandes ^a   De Miranda, Antonio Basílio ^b  

^a PONTIFICAL CATHOLIC UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^b INSTITUTO OSWALDO CRUZ   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; EXPERT SYSTEMS;

BIOSEQUENCE PROCESSING; COMPLEX TASK; COMPLEX WORKFLOWS; WORK-FLOWS; WORKFLOW MANAGEMENT SYSTEMS; WORKFLOW MANAGEMENTS; WORKFLOW TOOLS;

WORK SIMPLIFICATION;

EID: 35048821109     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-30075-5_75     Document Type: Article

References (22)

1. D.K. Casey, Human Genome Program, U.S. Department of Energy, Genomics and its Impact on Science and Society: A 2003 Primer, (2003), http://www.oml.gov/sci/techresources/Human_Genome/publicat/primer/index.shtml.
2. J. Kim, Computers are from Mars, Organisms are from Venus, Computer, 35(7) (2002), 25-32.
3. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D. J. Lipman, A basic local alignment search tool, Journal of Molecular Biology, 215 (1990), 403-410.
4. Workflow Management Coalition (WfMC), Workflow Management Coalition Terminology and Glossar, Technical Report WFMC-TC-1011 3.0. Brussels, (1999).
5. N. Guarino, Formal Ontology and Information Systems, Formal Ontology in Information Systems, Ed. Amsterdam, Netherlands: IOS Press, (1998).
6. M. Lemos, L.F.B. Seibel, M.A. Casanova, BioNotes: A System for Biosequence Annotation, DEXA Workshops, (2003), 16-20.
7. Department of Biochemistry and Molecular Biology, Oswaldo Cruz Institute, (2004), http://www.dbbm.fiocruz.br.
8. Department of Medical Biochemistry, Federal University of Rio de Janeiro, (2004), http://www.bioqmed.ufrj.br/.
9. OWL Web Ontology Language Overview. W3C Proposed Recommendation 15 Dec 2003. D. L. McGuinness and F. v. Harmelen eds. http://mww.w3.org/TR/owl-features/.
10. P. Green, Documentation for Phrap, March 2003, http://bozeman.mbt.washington.edu/phraps.docs/phrap.html.
11. X. Huang and A. Madan, CAP3: A DNA sequence assembly program, Genome Research, 9 (1999), 868-877.
12. B. Boeckmann, et al., The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003, Nucleic Acids Research, 31 (2003), 365-370.
13. B. Ewing, et al., Base-Calling of Automated Sequencer Traces using Phred. I. Accuracy Assessment, Genome Research, 8 (1998), 175-185.
14. National Center of Biotechnology Information, The BLAST Databases, (2004), ftp://ftp.ncbi.nih.gov/blast/db/.
15. L.F.B. Seibel, S. Lifschitz, A Genome Database Framework, DEXA (2001), 319-329.
16. Gene Ontology, (2004), http://www.geneontology.org/.
17. Encyclopedia of Escherichia coli K12 Genes and Metabolism, (2004), http://ecocyc.org/.
18. R.D. Stevens, A.J. Robinson and C.A. Goble, myGrid: personalised bioinformatics on the information grid, Bioinformatics, 19 Suppl. 1, (2003),
19. (Eleventh International Conference on Intelligent Systems for Molecular Biology).
20. T. Kulikova, et al, The EMBL Nucleotide Sequence Database, Nucl. Acids. Res., (2004) 32, D27-D30.
21. S. Rudd, Expressed sequence tags: Alternative or complement to whole genome sequences?, Trends in Plant Science (2003), 8 (7), 321-329.
22. W. R. Pearson and D. J. Lipman, Improved Tools for Biological Sequence Comparison, (1988), PNAS 85, 2444-2448.