Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases

Taylor CF, Paton NW, Garwood KL, Kirby PD, Stead DA, Yin Z, Deutsch EW, Selway L, Walker J, Riba-Garcia I, Mohammed S, Deery MJ, Howard JA, Dunkley T, Aebersold R, Kell DB, Lilley KS, Roepstorff P, Yates JR, Brass A, Brown AJ, Cash P, Gaskell SJ, Hubbard SJ, Oliver SG: A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol 2003, 21: 247–254. 10.1038/nbt0303-247

Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M: The Ensembl genome database project. Nucleic Acids Res 2002, 30: 38–41. 10.1093/nar/30.1.38

Oliver DE, Rubin DL, Stuart JM, Hewett M, Klein TE, Altman RB: Ontology development for a pharmacogenetics knowledge base. Pac Symp Biocomput 2002, 65–76.

Rubin DL, Hewett M, Oliver DE, Klein TE, Altman RB: Automating data acquisition into ontologies from pharmacogenetics relational data sources using declarative object definitions and XML. Pac Symp Biocomput 2002, 88–99.

Horn F, Bettler E, Oliveira L, Campagne F, Cohen FE, Vriend G: GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res 2003, 31: 294–297. 10.1093/nar/gkg103

Horn F, Weare J, Beukers MW, Horsch S, Bairoch A, Chen W, Edvardsen O, Campagne F, Vriend G: GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res 1998, 26: 275–279. 10.1093/nar/26.1.275

Horn F, Vriend G, Cohen FE: Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems. Nucleic Acids Res 2001, 29: 346–349. 10.1093/nar/29.1.346

Karp PD, Riley M, Paley SM, Pelligrini-Toole A: EcoCyc: an encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res 1996, 24: 32–39. 10.1093/nar/24.1.32

Karp PD, Riley M, Saier M, Paulsen IT, Collado-Vides J, Paley SM, Pellegrini-Toole A, Bonavides C, Gama-Castro S: The EcoCyc Database. Nucleic Acids Res 2002, 30: 56–58. 10.1093/nar/30.1.56

Karp PD, Riley M, Saier M, Paulsen IT, Paley SM, Pellegrini-Toole A: The EcoCyc and MetaCyc databases. Nucleic Acids Res 2000, 28: 56–59. 10.1093/nar/28.1.56

Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW: BIND--The Biomolecular Interaction Network Database. Nucleic Acids Res 2001, 29: 242–245. 10.1093/nar/29.1.242

ISO: Specification of abstraction syntax notation one (asn.1). Information Processing Systems 1987., Standard 8824:

Nentwich C, Emmerich W: Valid versus Meaningful: Raising the Level of Semantic Validation: ; Budapest, Hungary. ACM; 2003.

Konvicka K, Campagne F, Weinstein H: Interactive construction of residue-based diagrams of proteins: the RbDe web service. Protein Eng 2000, 13: 395–396. 10.1093/protein/13.6.395

Skrabanek L, Campagne F: TissueInfo: high-throughput identification of tissue expression profiles and specificity. Nucleic Acids Res 2001, 29: E102–2. 10.1093/nar/29.21.e102

Nelson MR, Reisinger SJ, SG. H: Designing databases to store biological information. BIOSILICO 2003, 1: 134–142. 10.1016/S1478-5382(03)02357-6

Bancilhon F, Delobel C, Kanellakis P: Building an object-oriented database-the story of O2. , Morgan Kaufmann; 1992.

Java Data Objects (JDO) Java Specification Request.[http://www.jcp.org/en/jsr/detail?id=12]

Cattell RGG, Barry DK, Catell R, Berler M, Eastman J, Jordan D, Russell C, Schadow O, Stanienda T, Velez F: The Object Data Standard: ODMG 3.0. Edited by: R.G.G. Cattell DKBRCMBJE. , Morgan Kaufmann Publishers;; 2000.

FastObjects JDO implementation[http://www.fastobjects.com/us]

Solarmetric Kodo JDO implementation[http://www.solarmetric.com]

Campagne F, Neves S, Chang CW, Skrabanek L, Ram PT, Iyengar R, Weinstein H: SigPath Project Pages.[http://www.sigpath.org]

Campagne F, Neves S, Chang CW, Skrabanek L, Ram PT, Iyengar R, Weinstein H: Quantitative information management for the biochemical computation of cellular networks. Sci STKE 2004, 2004: pl11. 10.1126/stke.2482004pl11

Jordan D, Russell C: Java Data Objects. 1st edition edition. , O'Reilly & Associates; 2003.

JUnit, Unit Test Framework[http://www.junit.org]

Fleischmann W, Hermjakob HAG: SwissKnife.1999. [http://swissknife.sourceforge.net/]

Witten IH, Moffat A, TC B: Managing Gigabytes: Compressing and Indexing Documents and Images. 2nd edition edition. , Morgan Kaumann Publishers; 1999.