{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T03:05:38Z","timestamp":1780110338050,"version":"3.54.0"},"reference-count":37,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2007,10,2]],"date-time":"2007-10-02T00:00:00Z","timestamp":1191283200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2007,12]]},"DOI":"10.1186\/1471-2105-8-367","type":"journal-article","created":{"date-parts":[[2007,10,2]],"date-time":"2007-10-02T18:12:56Z","timestamp":1191348776000},"source":"Crossref","is-referenced-by-count":32,"title":["BNDB \u2013 The Biochemical Network Database"],"prefix":"10.1186","volume":"8","author":[{"given":"Jan","family":"K\u00fcntzer","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina","family":"Backes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Torsten","family":"Blum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Gerasch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Kaufmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver","family":"Kohlbacher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hans-Peter","family":"Lenhof","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2007,10,2]]},"reference":[{"issue":"11","key":"1739_CR1","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1016\/j.tibtech.2004.09.010","volume":"22","author":"P Nightingale","year":"2004","unstructured":"Nightingale P, Martin P: The myth of the biotech revolution. Trends Biotechol 2004, 22(11):564\u2013569. 10.1016\/j.tibtech.2004.09.010","journal-title":"Trends Biotechol"},{"key":"1739_CR2","doi-asserted-by":"publisher","first-page":"D3","DOI":"10.1093\/nar\/gkj162","volume":"34","author":"MY Galperin","year":"2006","unstructured":"Galperin MY: The Molecular Biology Database Collection: 2006 update. Nucl Acids Res 2006, 34: D3-D5. 10.1093\/nar\/gkj162","journal-title":"Nucl Acids Res"},{"key":"1739_CR3","volume-title":"Tech rep","author":"M Cassman","year":"2005","unstructured":"Cassman M, Arkin A, Doyle F, Katagiri F, Lauffenburger DA, Stokes C: Assessment of International Research and Development in Systems Biology. In Tech rep. World Technology Evaluation Center (WTEC); 2005."},{"issue":"3","key":"1739_CR4","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1145\/1031570.1031583","volume":"33","author":"T Hernandez","year":"2004","unstructured":"Hernandez T, Kambhampati S: Integration of Biological Sources: Current Systems and Challenges Ahead. SIGMOD Rec 2004, 33(3):51\u201360. 10.1145\/1031570.1031583","journal-title":"SIGMOD Rec"},{"key":"1739_CR5","first-page":"49","volume":"9","author":"T Etzold","year":"1993","unstructured":"Etzold T, Argos P: SRS \u2013 an indexing and retrieval tool for flat file data libraries. Comput Appl Biosci 1993, 9: 49\u201357.","journal-title":"Comput Appl Biosci"},{"key":"1739_CR6","unstructured":"BioNavigator \u2013 BioNode & BioNodeSA: Overview[\n                    http:\/\/www.antigen.com\/library\n                    \n                  ]"},{"key":"1739_CR7","unstructured":"Entrez \u2013 Search and Retrieval System[\n                    http:\/\/www.ncbi.nlm.nih.gov\/sites\/gquery\n                    \n                  ]"},{"issue":"2","key":"1739_CR8","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1147\/sj.402.0489","volume":"40","author":"LM Haas","year":"2001","unstructured":"Haas LM, Schwarz PM, Kodali P, Kotlar E, Rice JE, Swope WC: DiscoveryLink: A system for integrated access to life sciences data sources. IBM Systems J 2001, 40(2):489\u2013511.","journal-title":"IBM Systems J"},{"issue":"2","key":"1739_CR9","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1093\/bioinformatics\/16.2.184","volume":"16","author":"R Stevens","year":"2000","unstructured":"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\u2013185. 10.1093\/bioinformatics\/16.2.184","journal-title":"Bioinformatics"},{"issue":"2","key":"1739_CR10","first-page":"768","volume":"11","author":"L Donelson","year":"2004","unstructured":"Donelson L, Tarczy-Hornoch P, Mork P, Dolan C, Mitchell JA, Barrier M, Mei H: The BioMediator system as a data integration tool to answer diverse biologic queries. Medinfo 2004, 11(2):768\u2013772.","journal-title":"Medinfo"},{"issue":"2","key":"1739_CR11","doi-asserted-by":"publisher","first-page":"512","DOI":"10.1147\/sj.402.0512","volume":"40","author":"SB Davidson","year":"2001","unstructured":"Davidson SB, Crabtree J, Brunk BP, Schug J, Tannen V, Overton GC, Stoeckert CJ: K2\/Kleisli and GUS: Experiments in integrated access to genomic data sources. IBM Systems J 2001, 40(2):512\u2013530.","journal-title":"IBM Systems J"},{"issue":"11","key":"1739_CR12","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1093\/bioinformatics\/btl081","volume":"22","author":"J Koehler","year":"2006","unstructured":"Koehler J, Baumbach J, Taubert J, Specht M, Skusa A, Ruegg A, Rawlings C, Verrier P, Philippi S: Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics 2006, 22(11):1383\u20131390. 10.1093\/bioinformatics\/btl081","journal-title":"Bioinformatics"},{"key":"1739_CR13","volume-title":"BMC Bioinformatics","author":"EG Cerami","year":"2006","unstructured":"Cerami EG, Bader GD, Gross BE, Sander C: cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics 2006., 7(497):"},{"key":"1739_CR14","volume-title":"BMC Bioinformatics","author":"A Birkland","year":"2006","unstructured":"Birkland A, Yona G: BIOZON: a system for unification, management and analysis of heterogeneous biological data. BMC Bioinformatics 2006., 7(70):"},{"issue":"2","key":"1739_CR15","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1093\/bioinformatics\/18.suppl_2.S219","volume":"18","author":"M Sirava","year":"2002","unstructured":"Sirava M, Sch\u00e4fer T, Eigelsperger M, Kohlbacher O, Bornberg-Bauer E, Lenhof HP: BioMiner \u2013 modeling, analyzing, and visualizing biochemical pathways and networks. Bioinformatics 2002, 18(2):219\u2013230. [\n                    http:\/\/www.zbi.uni-saarland.de\/chair\/projects\/BioMiner\n                    \n                  ]","journal-title":"Bioinformatics"},{"issue":"2","key":"1739_CR16","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1515\/jib-2006-34","volume":"3","author":"J K\u00fcntzer","year":"2006","unstructured":"K\u00fcntzer J, Blum T, Gerasch A, Backes C, Hildebrandt A, Kaufmann M, Kohlbacher O, Lenhof HP: BN++ -A Biological Information System. J Integr Bioinformatics 2006, 3(2):34.","journal-title":"J Integr Bioinformatics"},{"key":"1739_CR17","unstructured":"The MySQL Database System[\n                    http:\/\/www.mysql.com\n                    \n                  ]"},{"key":"1739_CR18","volume-title":"Tech rep","author":"JTC1\/SC21 I","year":"1992","unstructured":"JTC1\/SC21 I: Information Technology \u2013 Database Languages \u2013 SQL2. In Tech rep. ANSI; 1992."},{"key":"1739_CR19","doi-asserted-by":"publisher","first-page":"D187","DOI":"10.1093\/nar\/gkj161","volume":"34","author":"CH Wu","year":"2006","unstructured":"Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, Suzek B: The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucl Acids Res 2006, 34: D187-D191. 10.1093\/nar\/gkj161","journal-title":"Nucl Acids Res"},{"key":"1739_CR20","doi-asserted-by":"publisher","first-page":"D501","DOI":"10.1093\/nar\/gki025","volume":"33","author":"KD Pruitt","year":"2005","unstructured":"Pruitt KD, Tatusova T, Maglott DR: NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucl Acids Res 2005, 33: D501-D504. 10.1093\/nar\/gki025","journal-title":"Nucl Acids Res"},{"key":"1739_CR21","doi-asserted-by":"publisher","first-page":"D354","DOI":"10.1093\/nar\/gkj102","volume":"34","author":"M Kanehisa","year":"2006","unstructured":"Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M: From genomics to chemical genomics: new developments in KEGG. Nucl Acids Res 2006, 34: D354-D357. 10.1093\/nar\/gkj102","journal-title":"Nucl Acids Res"},{"key":"1739_CR22","doi-asserted-by":"publisher","first-page":"D438","DOI":"10.1093\/nar\/gkh100","volume":"32","author":"CJ Krieger","year":"2004","unstructured":"Krieger CJ, Zhang P, Mueller LA, Wang A, Paley S, Arnaud M, Pick J, Rhee SY, Karp PD: MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucl Acids Res 2004, 32: D438-D442. 10.1093\/nar\/gkh100","journal-title":"Nucl Acids Res"},{"key":"1739_CR23","doi-asserted-by":"publisher","first-page":"D546","DOI":"10.1093\/nar\/gkj107","volume":"34","author":"M Krull","year":"2006","unstructured":"Krull M, Pistor S, Voss N, Kel A, Reuter I, Kronenberg D, Michael H, Schwarzer K, Potapov A, Choi C, Kel-Margoulis O, Wingender E: TRANSPATH: An Information Resource for Storing and Visualizing Signaling Pathways and their Pathological Aberrations. Nucl Acids Res 2006, 34: D546-D551. 10.1093\/nar\/gkj107","journal-title":"Nucl Acids Res"},{"key":"1739_CR24","doi-asserted-by":"publisher","first-page":"D449","DOI":"10.1093\/nar\/gkh086","volume":"32","author":"L Salwinski","year":"2004","unstructured":"Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The Database of Interacting Proteins: 2004 update. Nucl Acids Res 2004, 32: D449-D451. 10.1093\/nar\/gkh086","journal-title":"Nucl Acids Res"},{"key":"1739_CR25","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1016\/S0014-5793(01)03293-8","volume":"513","author":"A Zanzoni","year":"2002","unstructured":"Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, GC : MINT: a Molecular INTeraction database. FEBS Lett 2002, 513: 135\u2013140. 10.1016\/S0014-5793(01)03293-8","journal-title":"FEBS Lett"},{"key":"1739_CR26","doi-asserted-by":"publisher","first-page":"D452","DOI":"10.1093\/nar\/gkh052","volume":"32","author":"H Hermjakob","year":"2004","unstructured":"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. Nucl Acids Res 2004, 32: D452-D455. 10.1093\/nar\/gkh052","journal-title":"Nucl Acids Res"},{"key":"1739_CR27","doi-asserted-by":"publisher","first-page":"2363","DOI":"10.1101\/gr.1680803","volume":"13","author":"S Peri","year":"2003","unstructured":"Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP, Ramya MA, Zhao Z, Chandrika KN, Padma N, Harsha HC, Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann WP, Constantinescu SN, Huang L, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe GC, Dang CV, Garcia JG, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan AM, Hamosh A, Chakravarti A, Pandey A: Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 2003, 13: 2363\u20132371. 10.1101\/gr.1680803","journal-title":"Genome Res"},{"key":"1739_CR28","doi-asserted-by":"publisher","first-page":"D108","DOI":"10.1093\/nar\/gkj143","volume":"34","author":"V Matys","year":"2006","unstructured":"Matys V, Kel-Margoulis O, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel A, Wingender E: TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucl Acids Res 2006, 34: D108-D110. 10.1093\/nar\/gkj143","journal-title":"Nucl Acids Res"},{"key":"1739_CR29","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1089\/cmb.1995.2.557","volume":"2","author":"S Davidson","year":"1995","unstructured":"Davidson S, Overton GC, Buneman P: Challenges in Integrating Biological Data Sources. J Comput Biol 1995, 2: 557\u2013572.","journal-title":"J Comput Biol"},{"key":"1739_CR30","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1007\/BF01228708","volume":"1","author":"S Spaccapietra","year":"1992","unstructured":"Spaccapietra S, Parent C, Dupont Y: Model Independent Assertions for Integration of Heterogeneous Schemas. VLDB Journal 1992, 1: 81\u2013126. 10.1007\/BF01228708","journal-title":"VLDB Journal"},{"issue":"11","key":"1739_CR31","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 2003, 13(11):2498\u20132504. 10.1101\/gr.1239303","journal-title":"Genome Research"},{"key":"1739_CR32","volume-title":"BMC Bioinformatics","author":"M Baitaluk","year":"2006","unstructured":"Baitaluk M, Qian X, Godbole S, Raval A, Ray A, Gupta A: PathSys: integrating molecular interaction graphs for systems biology. BMC Bioinformatics 2006., 7(55):"},{"key":"1739_CR33","volume-title":"BMC Bioinformatics","author":"Z Hu","year":"2004","unstructured":"Hu Z, Mellor J, Wu J, DeLisi C: VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics 2004., 5(17):"},{"key":"1739_CR34","unstructured":"GeneGo \u2013 System Biology for Drug Discovery[\n                    http:\/\/www.genego.com\n                    \n                  ]"},{"issue":"16","key":"1739_CR35","doi-asserted-by":"publisher","first-page":"2155","DOI":"10.1093\/bioinformatics\/btg290","volume":"19","author":"A Nikitin","year":"2003","unstructured":"Nikitin A, Egorov S, Daraselia N, Mazo I: Pathway studio \u2013 the analysis and navigation of molecular networks. Bioinformatics 2003, 19(16):2155\u20132157. 10.1093\/bioinformatics\/btg290","journal-title":"Bioinformatics"},{"key":"1739_CR36","doi-asserted-by":"publisher","first-page":"W186","DOI":"10.1093\/nar\/gkm323","volume":"35","author":"C Backes","year":"2007","unstructured":"Backes C, Keller A, Kuentzer J, Kneissl B, Comtesse N, Elnakady YA, Muller R, Meese E, Lenhof HP: GeneTrail \u2013 advanced gene set enrichment analysis. Nucl Acids Res 2007, 35: W186-W192. 10.1093\/nar\/gkm323","journal-title":"Nucl Acids Res"},{"issue":"11","key":"1739_CR37","doi-asserted-by":"publisher","first-page":"1261","DOI":"10.1002\/cbic.200700050","volume":"8","author":"YA Elnakady","year":"2007","unstructured":"Elnakady YA, Rohde M, Sasse F, Backes C, Keller A, Lenhof HP, Weissman KJ, M\u00fcller R: Evidence for the mode of action of the highly cytotoxic streptomyces polyketide kendomycin. Chembiochem 2007, 8(11):1261\u20131272. 10.1002\/cbic.200700050","journal-title":"Chembiochem"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-367.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-8-367\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-367.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T10:01:12Z","timestamp":1548237672000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-367"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,10,2]]},"references-count":37,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["1739"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-8-367","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,10,2]]},"article-number":"367"}}