Building models using reactome pathways as templates

Methods in Molecular Biology

Volumn 1021, Issue , 2013, Pages 273-283

  Croft, David ^a  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

Data; Model; Pathway; Reaction; Reactome; SBML

Indexed keywords

ARTICLE; CHEMICAL REACTION KINETICS; COMPUTER PROGRAM; DATA BASE; HUMAN; INFORMATION PROCESSING; PRIORITY JOURNAL; PROTEIN ANALYSIS; REACTOME; SIMULATION;

HOMO SAPIENS;

EID: 84883258242     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-450-0_14     Document Type: Article

References (25)

1. Matthews L, Gopinath G, Gillespie M et al (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 37:D619-D622
2. Matthews L, D'Eustachio P, Gillespie M et al (2007) An Introduction to the Reactome Knowledgebase of Human Biological Pathways and Processes. Bioinformatics Primer, NCI/Nature Pathway Interaction Database. doi:10.1038/pid.2007.3
3. Croft D, O'Kelly G, Wu G et al (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39 (Database Issue):D691-D697
4. Hucka M, Finney A, Sauro HM et al (2003) The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 9(4):524-531
5. Funahashi A, Tanimura N, Morohashi M et al (2003) Cell Designer: a process diagram editor for gene-regulatory and biochemical networks. BIOSILICO 1:159-162
6. Kanehisa M, Goto S, Kawashima S et al (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32(Suppl 1): D277-D280
7. Bolton E, Wang Y, Thiessen PA et al (2008) PubChem: integrated platform of small molecules and biological activities (Chapter 12). In: Wheeler RA, Spellmeyer DC (eds) Annual reports in computational chemistry, American Chemical Society, Washington, DC
8. de Matos P, Alcántara R, Dekker A et al (2009) Chemical entities of biological interest: an update. Nucleic Acids Res 38(Database Issue):D249-D254
9. Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25-29
10. The UniProt Consortium (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40: D71-D75
11. Pruitt KD, Tatusova T, Maglott DR (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35(Database Issue):D61-D65
12. Paul Flicek M, Amode R, Barrell D et al (2011) Ensembl 2012. Nucleic Acids Res 40(Database Issue):D84-D90
13. Lockhart DJ et al (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14 (13):1675-1680
14. Maglott D, Ostell J, Pruitt KD et al (2005) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 33(Database Issue): D54-D58
15. Kersey PJ, Duarte J, Williams A et al (2004) The International Protein Index: an integrated database for proteomics experiments. Proteomics 4(7):1985-1988
16. Wang C, Krishnakumar S, Wilhelmy J et al (2012) High-throughput, high-fidelity HLA genotyping with deep sequencing. Proc Natl Acad Sci 109(22):8676-8681
17. Hamosh A, Scott A, Amberger J et al (2004) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33(Database Issue): D514-D517. doi:10.1093/nar/gki033
18. Webb EC (1992) Enzyme nomenclature 1992: recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes. Published for the International Union of Biochemistry and Molecular Biology by Academic Press, San Diego. ISBN 0-12-227164-5
19. Eppig JT, Blake JA, Bult CJ et al (2012) The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. Nucleic Acids Res 40(1): D881-D886
20. Berman HM, Henrick K, Nakamura H (2003) Announcing the worldwide Protein Data Bank. Nat Struct Biol 10:980
21. Cochrane G, Akhtar R, Bonfield J et al (2008) Petabyte-scale innovations at the European Nucleotide Archive. Nucleic Acids Res 37 (Database Issue):D19-D25. doi:10.1093/nar/gkn765
22. Griffiths-Jones S (2004) The microRNA Registry. Nucleic Acids Res 32(Suppl 1): D109-D111
23. Smedley D, Haider S, Ballester B et al (2009) BioMart-biological queries made easy. BMC Genomics 10:22
24. Zhang J, Haider S, Baran J et al (2011) Bio-Mart: a data federation framework for large collaborative projects. Database (Oxford) 2011:bar038. doi:10.1093/database/bar038
25. Haw RA, Croft D, Yung CK et al (2011) The Reactome BioMart. Database (Oxford) 2011: bar031