{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T00:47:25Z","timestamp":1775263645908,"version":"3.50.1"},"reference-count":87,"publisher":"Springer Science and Business Media LLC","issue":"S10","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2009,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Life scientists need help in coping with the plethora of fast growing and scattered knowledge resources. Ideally, this knowledge should be integrated in a form that allows them to pose complex questions that address the properties of biological systems, independently from the origin of the knowledge. Semantic Web technologies prove to be well suited for knowledge integration, knowledge production (hypothesis formulation), knowledge querying and knowledge maintenance.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We implemented a semantically integrated resource named BioGateway, comprising the entire set of the OBO foundry candidate ontologies, the GO annotation files, the SWISS-PROT protein set, the NCBI taxonomy and several in-house ontologies. BioGateway provides a single entry point to query these resources through SPARQL. It constitutes a key component for a Semantic Systems Biology approach to generate new hypotheses concerning systems properties. In the course of developing BioGateway, we faced challenges that are common to other projects that involve large datasets in diverse representations. We present a detailed analysis of the obstacles that had to be overcome in creating BioGateway. We demonstrate the potential of a comprehensive application of Semantic Web technologies to global biomedical data.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>The time is ripe for launching a community effort aimed at a wider acceptance and application of Semantic Web technologies in the life sciences. We call for the creation of a forum that strives to implement a truly semantic life science foundation for Semantic Systems Biology.<\/jats:p>\n            <jats:p>Access to the system and supplementary information (such as a listing of the data sources in RDF, and sample queries) can be found at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.semantic-systems-biology.org\/biogateway\" ext-link-type=\"uri\">http:\/\/www.semantic-systems-biology.org\/biogateway<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-10-s10-s11","type":"journal-article","created":{"date-parts":[[2009,10,1]],"date-time":"2009-10-01T18:14:53Z","timestamp":1254420893000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":46,"title":["BioGateway: a semantic systems biology tool for the life sciences"],"prefix":"10.1186","volume":"10","author":[{"given":"Erick","family":"Antezana","sequence":"first","affiliation":[]},{"given":"Ward","family":"Blond\u00e9","sequence":"additional","affiliation":[]},{"given":"Mikel","family":"Ega\u00f1a","sequence":"additional","affiliation":[]},{"given":"Alistair","family":"Rutherford","sequence":"additional","affiliation":[]},{"given":"Robert","family":"Stevens","sequence":"additional","affiliation":[]},{"given":"Bernard","family":"De Baets","sequence":"additional","affiliation":[]},{"given":"Vladimir","family":"Mironov","sequence":"additional","affiliation":[]},{"given":"Martin","family":"Kuiper","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,10,1]]},"reference":[{"key":"3379_CR1","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1038\/nrg1922","volume":"7","author":"A Brazma","year":"2006","unstructured":"Brazma A, Krestyaninova M, Sarkans U: Standards for systems biology. Nat Rev Genet 2006, 7: 593\u2013605.","journal-title":"Nat Rev Genet"},{"key":"3379_CR2","doi-asserted-by":"publisher","first-page":"e76","DOI":"10.1371\/journal.pcbi.0010076","volume":"1","author":"N Cannata","year":"2005","unstructured":"Cannata N, Merelli E, Altman RB: Time to organize the bioinformatics resourceome. PLoS Comput Biol 2005, 1: e76.","journal-title":"PLoS Comput Biol"},{"key":"3379_CR3","doi-asserted-by":"publisher","first-page":"1099","DOI":"10.1038\/nbt1139","volume":"23","author":"X Wang","year":"2005","unstructured":"Wang X, Gorlitsky R, Almeida JS: From XML to RDF: how semantic web technologies will change the design of 'omic' standards. Nat Biotechnol 2005, 23: 1099\u20131103.","journal-title":"Nat Biotechnol"},{"key":"3379_CR4","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1093\/bib\/bbm016","volume":"8","author":"D Quan","year":"2007","unstructured":"Quan D: Improving life sciences information retrieval using semantic web technology. Brief Bioinform 2007, 8: 172\u2013182.","journal-title":"Brief Bioinform"},{"key":"3379_CR5","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1038\/nrg2414","volume":"9","author":"LD Stein","year":"2008","unstructured":"Stein LD: Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges. Nat Rev Genet 2008, 9: 678\u2013688.","journal-title":"Nat Rev Genet"},{"key":"3379_CR6","unstructured":"Semantic Web Health Care and Life Sciences (HCLS) Interest Group2009. [http:\/\/www.w3.org\/2001\/sw\/hcls\/]"},{"key":"3379_CR7","unstructured":"Resource Description Framework (RDF)2008. [http:\/\/www.w3.org\/RDF\/]"},{"key":"3379_CR8","unstructured":"OWL Web Ontology Language (OWL) Reference2009. [http:\/\/www.w3.org\/TR\/owl-ref\/]"},{"key":"3379_CR9","unstructured":"SPARQL Query Language for RDF2008. [http:\/\/www.w3.org\/TR\/rdf-sparql-query\/]"},{"issue":"Suppl 3","key":"3379_CR10","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1186\/1471-2105-8-S3-S2","volume":"8","author":"A Ruttenberg","year":"2007","unstructured":"Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Ogbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH: Advancing translational research with the Semantic Web. BMC Bioinformatics 2007, 8(Suppl 3):S2.","journal-title":"BMC Bioinformatics"},{"key":"3379_CR11","unstructured":"Semantic Systems Biology2009. [http:\/\/www.semantic-systems-biology.org\/biogateway]"},{"key":"3379_CR12","unstructured":"OBO ontologies2009. [http:\/\/www.berkeleybop.org\/ontologies\/]"},{"key":"3379_CR13","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1093\/bioinformatics\/btn042","volume":"24","author":"E Antezana","year":"2008","unstructured":"Antezana E, Ega\u00f1a M, De Baets B, Kuiper M, Mironov V: ONTO-PERL: an API for supporting the development and analysis of bio-ontologies. Bioinformatics 2008, 24: 885\u2013887.","journal-title":"Bioinformatics"},{"key":"3379_CR14","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1186\/1471-2105-8-57","volume":"8","author":"M Ega\u00f1a","year":"2007","unstructured":"Ega\u00f1a M, Bechhofer S, Lord P, Sattler U, Stevens R: Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL. BMC Bioinformatics 2007, 8: 57.","journal-title":"BMC Bioinformatics"},{"key":"3379_CR15","volume-title":"OWLED","author":"C Golbreich","year":"2007","unstructured":"Golbreich C, Horrocks I: The OBO to OWL Mapping, GO to OWL 1.1! OWLED 2007."},{"key":"3379_CR16","unstructured":"OBO specification 1.22009. [http:\/\/www.geneontology.org\/GO.format.obo-1_2.shtml]"},{"key":"3379_CR17","unstructured":"ONTO-PERL distribution2009. [http:\/\/search.cpan.org\/dist\/ONTO-PERL\/]"},{"key":"3379_CR18","unstructured":"BioGateway resources2009. [http:\/\/www.semantic-systems-biology.org\/biogateway\/resources]"},{"key":"3379_CR19","doi-asserted-by":"publisher","first-page":"1251","DOI":"10.1038\/nbt1346","volume":"25","author":"B Smith","year":"2007","unstructured":"Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007, 25: 1251\u20131255.","journal-title":"Nat Biotechnol"},{"key":"3379_CR20","doi-asserted-by":"publisher","first-page":"D262","DOI":"10.1093\/nar\/gkh021","volume":"32","author":"E Camon","year":"2004","unstructured":"Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R: The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res 2004, 32: D262-D266.","journal-title":"Nucleic Acids Res"},{"key":"3379_CR21","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1093\/nar\/29.1.11","volume":"29","author":"DL Wheeler","year":"2001","unstructured":"Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM, Tatusova TA, Wagner L, Rapp BA: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2001, 29: 11\u201316.","journal-title":"Nucleic Acids Res"},{"key":"3379_CR22","doi-asserted-by":"publisher","first-page":"D190","DOI":"10.1093\/nar\/gkm895","volume":"36","author":"UniProt_Consortium","year":"2008","unstructured":"UniProt_Consortium: The universal protein resource (UniProt). Nucleic Acids Res 2008, 36: D190-D195.","journal-title":"Nucleic Acids Res"},{"key":"3379_CR23","unstructured":"The Cell Cycle Ontology2009. [http:\/\/www.semantic-systems-biology.org\/cco]"},{"key":"3379_CR24","unstructured":"Gene Ontology Annotations for A. Thaliana2009. [ftp:\/\/ftp.ebi.ac.uk\/pub\/databases\/GO\/goa\/proteomes\/3.A_thaliana.goa]"},{"key":"3379_CR25","unstructured":"Biometarel2009. [http:\/\/www.bioontology.org\/files\/38667\/biometarel.obo]"},{"key":"3379_CR26","unstructured":"Metarel2009. [http:\/\/www.semantic-systems-biology.org\/about\/resources]"},{"key":"3379_CR27","doi-asserted-by":"publisher","first-page":"R46","DOI":"10.1186\/gb-2005-6-5-r46","volume":"6","author":"B Smith","year":"2005","unstructured":"Smith B, Ceusters W, Klagges B, K\u00f6hler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C: Relations in biomedical ontologies. Genome Biol 2005, 6: R46.","journal-title":"Genome Biol"},{"key":"3379_CR28","unstructured":"Best Practice Recipes for Publishing RDF Vocabularies2009. [http:\/\/www.w3.org\/TR\/2008\/WD-swbp-vocab-pub-20080123\/]"},{"key":"3379_CR29","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1016\/j.jbi.2005.11.003","volume":"39","author":"S Schulz","year":"2006","unstructured":"Schulz S, Kumar A, Bittner T: Biomedical ontologies: what part-of is and isn't. J Biomed Inform 2006, 39: 350\u2013361.","journal-title":"J Biomed Inform"},{"issue":"Suppl 5","key":"3379_CR30","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1186\/1471-2105-9-S5-S2","volume":"9","author":"DP Hill","year":"2008","unstructured":"Hill DP, Smith B, McAndrews-Hill MS, Blake JA: Gene Ontology annotations: what they mean and where they come from. BMC Bioinformatics 2008, 9(Suppl 5):S2.","journal-title":"BMC Bioinformatics"},{"key":"3379_CR31","unstructured":"Gene Ontology Annotation files2009. [http:\/\/www.ebi.ac.uk\/GOA\/proteomes.html]"},{"key":"3379_CR32","unstructured":"Open Virtuoso2009. [http:\/\/virtuoso.openlinksw.com\/]"},{"key":"3379_CR33","unstructured":"Semantic Systems Biology Endpoint2009. [http:\/\/www.semantic-systems-biology.org\/biogateway\/endpoint]"},{"key":"3379_CR34","unstructured":"Spatial Ontology2009. [http:\/\/obofoundry.org\/cgi-bin\/detail.cgi?id=spatial]"},{"key":"3379_CR35","unstructured":"Worm Anatomy Ontology2009. [http:\/\/www.obofoundry.org\/cgi-bin\/detail.cgi?id=worm_anatomy]"},{"key":"3379_CR36","unstructured":"Open Biomedical Ontologies: Current Principles2009. [http:\/\/www.obofoundry.org\/crit.shtml]"},{"key":"3379_CR37","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1038\/nbt.1411","volume":"26","author":"CF Taylor","year":"2008","unstructured":"Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Nov\u00e8re N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S: Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 2008, 26: 889\u2013896.","journal-title":"Nat Biotechnol"},{"key":"3379_CR38","volume-title":"Mol Syst Biol","author":"J Quackenbush","year":"2006","unstructured":"Quackenbush J: Standardizing the standards. Mol Syst Biol 2006., 2: 2006.0010 2006.0010"},{"issue":"Suppl 3","key":"3379_CR39","doi-asserted-by":"publisher","first-page":"S4","DOI":"10.1186\/1471-2105-8-S3-S4","volume":"8","author":"HYK Lam","year":"2007","unstructured":"Lam HYK, Marenco L, Clark T, Gao Y, Kinoshita J, Shepherd G, Miller P, Wu E, Wong GT, Liu N, Crasto C, Morse T, Stephens S, Cheung KH: AlzPharm: integration of neurodegeneration data using RDF. BMC Bioinformatics 2007, 8(Suppl 3):S4.","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"3379_CR40","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1016\/j.websem.2006.05.006","volume":"4","author":"Y Gao","year":"2006","unstructured":"Gao Y, Kinoshita J, Wu E, Miller E, Lee R, Seaborne A, Cayzer S, Clark T: SWAN: A distributed knowledge infrastructure for Alzheimer disease research. J Web Sem 2006, 4(3):222\u2013228. [http:\/\/dblp.uni-trier.de\/db\/journals\/ws\/ws4.html#GaoKWMLSCC06]","journal-title":"J Web Sem"},{"issue":"Suppl 1","key":"3379_CR41","doi-asserted-by":"publisher","first-page":"i85","DOI":"10.1093\/bioinformatics\/bti1026","volume":"21","author":"KH Cheung","year":"2005","unstructured":"Cheung KH, Yip KY, Smith A, Deknikker R, Masiar A, Gerstein M: YeastHub: a semantic web use case for integrating data in the life sciences domain. Bioinformatics 2005, 21(Suppl 1):i85-i96.","journal-title":"Bioinformatics"},{"key":"3379_CR42","first-page":"176","volume-title":"Pacific Symposium on Biocomputing","author":"EK Neumann","year":"2006","unstructured":"Neumann EK, Quan D: Biodash: A Semantic Web Dashboard for Drug Development. In Pacific Symposium on Biocomputing. Edited by: Altman RB, Murray T, Klein TE, Dunker AK, Hunter L. World Scientific; 2006:176\u2013187."},{"issue":"Suppl 3","key":"3379_CR43","doi-asserted-by":"publisher","first-page":"S5","DOI":"10.1186\/1471-2105-8-S3-S5","volume":"8","author":"AK Smith","year":"2007","unstructured":"Smith AK, Cheung KH, Yip KY, Schultz M, Gerstein MK: LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics. BMC Bioinformatics 2007, 8(Suppl 3):S5.","journal-title":"BMC Bioinformatics"},{"key":"3379_CR44","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1016\/j.biochi.2008.02.007","volume":"90","author":"C Pasquier","year":"2008","unstructured":"Pasquier C: Biological data integration using Semantic Web technologies. Biochimie 2008, 90: 584\u2013594.","journal-title":"Biochimie"},{"key":"3379_CR45","doi-asserted-by":"publisher","first-page":"i322","DOI":"10.1093\/bioinformatics\/btn159","volume":"24","author":"F Lemoine","year":"2008","unstructured":"Lemoine F, Labedan B, Froidevaux C: GenoQuery: a new querying module for functional annotation in a genomic warehouse. Bioinformatics 2008, 24: i322-i329.","journal-title":"Bioinformatics"},{"key":"3379_CR46","doi-asserted-by":"publisher","first-page":"706","DOI":"10.1016\/j.jbi.2008.03.004","volume":"41","author":"F Belleau","year":"2008","unstructured":"Belleau F, Nolin MA, Tourigny N, Rigault P, Morissette J: Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J Biomed Inform 2008, 41: 706\u2013716.","journal-title":"J Biomed Inform"},{"key":"3379_CR47","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1093\/bib\/bbl025","volume":"7","author":"BM Good","year":"2006","unstructured":"Good BM, Wilkinson MD: The Life Sciences Semantic Web is full of creeps! Brief Bioinform 2006, 7: 275\u2013286.","journal-title":"Brief Bioinform"},{"key":"3379_CR48","first-page":"254","volume-title":"IPAW, Volume 4145 of Lecture Notes in Computer Science","author":"J Zhao","year":"2006","unstructured":"Zhao J, Goble CA, Stevens R: An Identity Crisis in the Life Sciences. In IPAW, Volume 4145 of Lecture Notes in Computer Science. Edited by: Moreau L, Foster IT. Springer; 2006:254\u2013269."},{"key":"3379_CR49","unstructured":"bio2rdf: Banff Manifesto2009. [http:\/\/bio2rdf.wiki.sourceforge.net\/Banff+Manifesto]"},{"key":"3379_CR50","unstructured":"Life Science Record Name (LSRN)2009. [http:\/\/lsrn.org]"},{"key":"3379_CR51","unstructured":"OKKAM Large-Scale Integrating Project2009. [http:\/\/www.okkam.org\/]"},{"key":"3379_CR52","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1186\/1752-0509-1-58","volume":"1","author":"C Laibe","year":"2007","unstructured":"Laibe C, Le Nov\u00e8re N: MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. BMC Syst Biol 2007, 1: 58.","journal-title":"BMC Syst Biol"},{"key":"3379_CR53","unstructured":"Shared Names2009. [http:\/\/neurocommons.org\/page\/Sharednames]"},{"key":"3379_CR54","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1016\/j.datak.2008.02.002","volume":"66","author":"M Ega\u00f1a","year":"2008","unstructured":"Ega\u00f1a M, Wroe C, Goble C, Stevens R: In situ migration of handcrafted ontologies to reason-able forms. Data and Knowledge Engineering 2008, 66: 147\u2013162.","journal-title":"Data and Knowledge Engineering"},{"issue":"Suppl 5","key":"3379_CR55","doi-asserted-by":"publisher","first-page":"S1","DOI":"10.1186\/1471-2105-9-S5-S1","volume":"9","author":"M Ega\u00f1a","year":"2008","unstructured":"Ega\u00f1a M, Antezana E, Kuiper M, Stevens R: Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology. BMC Bioinformatics 2008, 9(Suppl 5):S1.","journal-title":"BMC Bioinformatics"},{"key":"3379_CR56","unstructured":"Microformats2009. [http:\/\/microformats.org]"},{"key":"3379_CR57","unstructured":"Gleaning Resource Descriptions from Dialects of Languages (GRDDL)2009. [http:\/\/www.w3.org\/TR\/grddl\/]"},{"key":"3379_CR58","unstructured":"RDFa primer2009. [http:\/\/www.w3.org\/TR\/xhtml-rdfa-primer\/]"},{"key":"3379_CR59","unstructured":"Prot\u00e9g\u00e92008. [http:\/\/protege.stanford.edu\/]"},{"issue":"16","key":"3379_CR60","doi-asserted-by":"publisher","first-page":"2198","DOI":"10.1093\/bioinformatics\/btm112","volume":"23","author":"J Day-Richter","year":"2007","unstructured":"Day-Richter J, Harris MAA, Haendel M, Lewis S: OBO-Edit \u2013 an ontology editor for biologists. Bioinformatics 2007, 23(16):2198\u20132200.","journal-title":"Bioinformatics"},{"key":"3379_CR61","first-page":"292","volume":"4130 LNAI","author":"D Tsarkov","year":"2006","unstructured":"Tsarkov D, Horrocks I: FaCT++ description logic reasoner: System description. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2006, 4130 LNAI: 292\u2013297.","journal-title":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)"},{"key":"3379_CR62","volume-title":"OWLED, Volume 258 of CEUR Workshop Proceedings","author":"M Horridge","year":"2007","unstructured":"Horridge M, Bechhofer S, Noppens O: Igniting the OWL 1.1 Touch Paper: The OWL API. In OWLED, Volume 258 of CEUR Workshop Proceedings. Edited by: Golbreich C, Kalyanpur A, Parsia B. CEUR-WS.org; 2007."},{"key":"3379_CR63","unstructured":"OWL 2 Web Ontology Language Document Overview2009. [http:\/\/www.w3.org\/News\/2009#item39]"},{"key":"3379_CR64","unstructured":"Towards LarKC: a Platform for Web-scale Reasoning. IEEE Computer Society Press Los Alamitos, CA, USA; 2008. [http:\/\/www.larkc.eu\/wp-content\/uploads\/2008\/05\/larkc-icsc08.pdf]"},{"key":"3379_CR65","volume-title":"Semantic Web Applications and Tools for Life Sciences 2008. Proc. of 1st Workshop SWAT4LS08, Edinburgh, United Kingdom, November 28, Volume 435 of CEUR Workshop Proceedings, CEUR-WS.org","year":"2008","unstructured":"Burger A, Paschke A, Romano P, Splendiani A, Eds: Semantic Web Applications and Tools for Life Sciences 2008. Proc. of 1st Workshop SWAT4LS08, Edinburgh, United Kingdom, November 28, Volume 435 of CEUR Workshop Proceedings, CEUR-WS.org. 2008."},{"key":"3379_CR66","unstructured":"Wolfram Alpha2009. [http:\/\/www.wolframalpha.com\/]"},{"key":"3379_CR67","unstructured":"Semantic Systems Biology Wiki2009. [http:\/\/www.bio.ntnu.no\/systemsbiology\/ssbwiki]"},{"key":"3379_CR68","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1093\/bib\/bbp004","volume":"10","author":"A Ruttenberg","year":"2009","unstructured":"Ruttenberg A, Rees JA, Samwald M, Marshall MS: Life sciences on the Semantic Web: the Neurocommons and beyond. Brief Bioinform 2009, 10: 193\u2013204.","journal-title":"Brief Bioinform"},{"key":"3379_CR69","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1016\/j.drudis.2008.01.008","volume":"13","author":"T Slater","year":"2008","unstructured":"Slater T, Bouton C, Huang ES: Beyond data integration. Drug Discov Today 2008, 13: 584\u2013589.","journal-title":"Drug Discov Today"},{"key":"3379_CR70","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1038\/msb.2008.39","volume":"4","author":"JA Sagotsky","year":"2008","unstructured":"Sagotsky JA, Zhang L, Wang Z, Martin S, Deisboeck TS: Life Sciences and the web: a new era for collaboration. Mol Syst Biol 2008, 4: 201.","journal-title":"Mol Syst Biol"},{"key":"3379_CR71","volume-title":"Brief Bioinform","author":"E Antezana","year":"2009","unstructured":"Antezana E, Kuiper M, Mironov V: Biological knowledge management: the emerging role of the Semantic Web technologies. Brief Bioinform 2009. doi:10.1093\/bib\/bbp024 doi:10.1093\/bib\/bbp024"},{"key":"3379_CR72","unstructured":"OBO Foundry CVS repository2009. [http:\/\/obo.cvs.sourceforge.net\/viewvc\/obo\/obo\/ontology\/]"},{"key":"3379_CR73","unstructured":"UniProt-SwissProt FTP repository2009. [ftp:\/\/ftp.uniprot.org\/pub\/databases\/uniprot\/current_release\/knowledgebase\/complete\/uniprot_sprot.dat.gz]"},{"key":"3379_CR74","unstructured":"NCBI taxonomy2009. [ftp:\/\/ftp.ncbi.nih.gov\/pub\/taxonomy\/taxdump.tar.gz]"},{"key":"3379_CR75","unstructured":"Gene Ontology Annotation FTP repository2009. [ftp:\/\/ftp.ebi.ac.uk\/pub\/databases\/GO\/goa\/proteomes\/]"},{"key":"3379_CR76","unstructured":"The Cell Cycle Ontology \u2013 Ontologies repository2009. [http:\/\/www.semantic-systems-biology.org\/cco\/downloadcco\/ontologies]"},{"key":"3379_CR77","volume-title":"Proc of the 1st International Conference on Biomedical Ontologies (ICBO)","author":"W Blond\u00e9","year":"2009","unstructured":"Blond\u00e9 W, Antezana E, Baets BD, Mironov V, Kuiper M: Metarel: an Ontology to support the inferencing of Semantic Web relations within Biomedical Ontologies. Proc of the 1st International Conference on Biomedical Ontologies (ICBO) 2009, in press."},{"key":"3379_CR78","unstructured":"SPARQL Query Language for RDF2009. [http:\/\/jena.hpl.hp.com\/~afs\/SPARQL-Update.html]"},{"key":"3379_CR79","unstructured":"Transitive closure subroutine in ONTO-PERL2009. [http:\/\/search.cpan.org\/dist\/ONTO-PERL\/OBO\/Util\/Ontolome.pm#transitiveclosure]"},{"key":"3379_CR80","volume-title":"Introduction to Algorithms","author":"TH Cormen","year":"2001","unstructured":"Cormen TH, Leiserson CE, Rivest RL, Stein C: Introduction to Algorithms. Second edition. McGraw-Hill Science\/Engineering\/Math; 2001.","edition":"Second"},{"key":"3379_CR81","unstructured":"Perl DBI2009. [http:\/\/dbi.perl.org\/]"},{"key":"3379_CR82","unstructured":"DBD ODBC2009. [http:\/\/search.cpan.org\/dist\/DBD-ODBC\/]"},{"key":"3379_CR83","unstructured":"Perl ODBC2009. [http:\/\/www.iodbc.org\/index.php?page=languages\/perl\/odbc-perlHOWTO]"},{"key":"3379_CR84","unstructured":"Semantic Systems Biology Query Interface2009. [http:\/\/www.semantic-systems-biology.org\/biogateway\/querying]"},{"key":"3379_CR85","unstructured":"Joomla2009. [http:\/\/www.joomla.org\/]"},{"key":"3379_CR86","unstructured":"Semantic Systems Biology SPARQL viewer2009. [http:\/\/www.semantic-systems-biology.org\/sparql-viewer]"},{"key":"3379_CR87","unstructured":"Adobe Flex 32009. [http:\/\/www.adobe.com\/products\/flex\/]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-S10-S11.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,31]],"date-time":"2021-08-31T21:47:30Z","timestamp":1630446450000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-S10-S11"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,10]]},"references-count":87,"journal-issue":{"issue":"S10","published-print":{"date-parts":[[2009,10]]}},"alternative-id":["3379"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-s10-s11","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,10]]},"assertion":[{"value":"1 October 2009","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S11"}}