{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,2]],"date-time":"2022-04-02T11:21:54Z","timestamp":1648898514236},"reference-count":46,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Ontologies such as the Gene Ontology can enable the construction of complex queries over biological information in a conceptual way, however existing systems to do this are too technical. Within the biological domain there is an increasing need for software that facilitates the flexible retrieval of information. OntoDas aims to fulfil this need by allowing the definition of queries by selecting valid ontology terms.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>OntoDas is a web-based tool that uses information visualisation techniques to provide an intuitive, interactive environment for constructing ontology-based queries against the Gene Ontology Database. Both a comprehensive use case and the interface itself were designed in a participatory manner by working with biologists to ensure that the interface matches the way biologists work. OntoDas was further tested with a separate group of biologists and refined based on their suggestions.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>OntoDas provides a visual and intuitive means for constructing complex queries against the Gene Ontology. It was designed with the participation of biologists and compares favourably with similar tools. It is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/ontodas.nbn.ac.za\" ext-link-type=\"uri\">http:\/\/ontodas.nbn.ac.za<\/jats:ext-link>\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-437","type":"journal-article","created":{"date-parts":[[2008,10,16]],"date-time":"2008-10-16T18:13:43Z","timestamp":1224180823000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["OntoDas \u2013 a tool for facilitating the construction of complex queries to the Gene Ontology"],"prefix":"10.1186","volume":"9","author":[{"given":"Kieran","family":"O'Neill","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander","family":"Garcia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anita","family":"Schwegmann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rafael C","family":"Jimenez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dan","family":"Jacobson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henning","family":"Hermjakob","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,10,16]]},"reference":[{"issue":"4","key":"2422_CR1","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1093\/bib\/3.4.389","volume":"3","author":"L Wong","year":"2002","unstructured":"Wong L: Technologies for integrating biological data. Briefings in Bioinformatics 2002, 3(4):389\u2013404.","journal-title":"Briefings in Bioinformatics"},{"issue":"1","key":"2422_CR2","first-page":"49","volume":"9","author":"T Etzold","year":"1993","unstructured":"Etzold T, Argos P: SRS-an indexing and retrieval tool for flat file data libraries. Comput Appl Biosci 1993, 9(1):49\u201357.","journal-title":"Comput Appl Biosci"},{"key":"2422_CR3","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1016\/S0076-6879(96)66012-1","volume":"266","author":"G Schuler","year":"1996","unstructured":"Schuler G, Epstein J, Ohkawa H, Kans J: Entrez: molecular biology database and retrieval system. Methods in Enzymology 1996, 266: 141\u201362.","journal-title":"Methods in Enzymology"},{"key":"2422_CR4","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/1471-2105-2-7","volume":"2","author":"R Dowell","year":"2001","unstructured":"Dowell R, Jokerst RM, Day A, Eddy SR, Stein L: The Distributed Annotation System. BMC Bioinformatics 2001, 2: 7.","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"2422_CR5","doi-asserted-by":"publisher","first-page":"157","DOI":"10.2165\/00822942-200504030-00001","volume":"4","author":"A Garcia","year":"2005","unstructured":"Garcia A, Chen Y, Ragan M: Information Integration in Molecular Bioscience. Applied Bioinformatics 2005, 4(3):157\u2013173.","journal-title":"Applied Bioinformatics"},{"key":"2422_CR6","volume-title":"Readings in Information Visualization: Using Vision to Think. Morgan Kaufmann","author":"S Card","year":"1999","unstructured":"Card S, Mackinlay J, Shneiderman B: Readings in Information Visualization: Using Vision to Think. Morgan Kaufmann. 1999."},{"key":"2422_CR7","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1016\/S1741-8364(04)02423-0","volume":"2","author":"Y Tao","year":"2004","unstructured":"Tao Y, Liu Y, Friedman C, Lussier Y: Information visualization techniques in bioinformatics during the postgenomic era. Drug Discovery Today BIOSILICO 2004, 2: 237\u2013245.","journal-title":"Drug Discovery Today BIOSILICO"},{"issue":"4","key":"2422_CR8","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1109\/TVCG.2005.53","volume":"11","author":"P Saraiya","year":"2005","unstructured":"Saraiya P, North C, Duca K: An Insight-Based Methodology for Evaluating Bioinformatics Visualizations. IEEE Trans Vis Comput Graph 2005, 11(4):443\u2013456.","journal-title":"IEEE Trans Vis Comput Graph"},{"key":"2422_CR9","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1186\/1471-2105-5-84","volume":"5","author":"E Baehrecke","year":"2004","unstructured":"Baehrecke E, Dang N, Babaria K, Shneiderman B: Visualization and analysis of microarray and gene ontology data with treemaps. BMC Bioinformatics 2004, 5: 84.","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"2422_CR10","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1038\/nrd1608","volume":"4","author":"D Searls","year":"2005","unstructured":"Searls D: Data integration: challenges for drug discovery. Nat Rev Drug Discov 2005, 4(1):45\u201358.","journal-title":"Nat Rev Drug Discov"},{"issue":"8","key":"2422_CR11","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1002\/cfg.442","volume":"5","author":"C Goble","year":"2004","unstructured":"Goble C, Wroe C: The Montagues and the Capulets. Comp Funct Genomics 2004, 5(8):623\u2013632.","journal-title":"Comp Funct Genomics"},{"issue":"1","key":"2422_CR12","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J, Davis A, Dolinski K, Dwight S, Eppig J, Harris M, Hill D, Issel-Tarver L, Kasarskis A, Lewis S, Matese J, Richardson J, Ringwald M, Rubin G, Sherlock G: Gene Ontology: Tool for the unification of biology. Nature Genetics 2000, 25(1):25\u201329.","journal-title":"Nature Genetics"},{"issue":"3","key":"2422_CR13","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1145\/314516.314522","volume":"17","author":"C Plaisant","year":"1999","unstructured":"Plaisant C, Shneiderman B, Doan K, Bruns T: Interface and data architecture for query preview in networked information systems. ACM Transactions on Information Systems 1999, 17(3):320\u2013341.","journal-title":"ACM Transactions on Information Systems"},{"issue":"3","key":"2422_CR14","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1093\/bib\/bbl027","volume":"7","author":"O Bodenreider","year":"2006","unstructured":"Bodenreider O, Stevens R: Bio-ontologies: current trends and future directions. Briefings in Bioinformatics 2006, 7(3):256\u2013274.","journal-title":"Briefings in Bioinformatics"},{"key":"2422_CR15","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1145\/642611.642681","volume-title":"Proceedings of the conference on Human factors in computing systems","author":"K Yee","year":"2003","unstructured":"Yee K, Swearingen K, Li K, Hearst M: Faceted metadata for image search and browsing. Proceedings of the conference on Human factors in computing systems 2003, 401\u2013408."},{"key":"2422_CR16","volume-title":"Proceedings of the WWW'04 workshop on Application Design, Development and Implementation Issues in the Semantic Web, New York","author":"J Broekstra","year":"2004","unstructured":"Broekstra J, Fluit C, Kampman A, van Harmelen F, Stuckenschmidt H, Bhogal R, Scerri A, de Waard A, van Mulligen E: The Drug Ontology Project for Elsevier. Proceedings of the WWW'04 workshop on Application Design, Development and Implementation Issues in the Semantic Web, New York 2004."},{"key":"2422_CR17","unstructured":"The Gene Ontology Consortium: AmiGO! Your friend in the gene ontology.[http:\/\/amigo.geneontology.org\/]"},{"key":"2422_CR18","unstructured":"European Bioinformatics Institute: QuickQO GO Browser.[http:\/\/www.ebi.ac.uk\/ego\/]"},{"issue":"7","key":"2422_CR19","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1186\/1471-2105-7-97","volume":"2006","author":"R C\u00f4t\u00e9","year":"2006","unstructured":"C\u00f4t\u00e9 R, Jones P, Apweiler R, Hermjakob H: The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics 2006, 2006(7):97.","journal-title":"BMC Bioinformatics"},{"key":"2422_CR20","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1101\/gr.1645104","volume":"14","author":"A Kasprzyk","year":"2004","unstructured":"Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P, Cox T, Birney E: EnsMart: a generic system for fast and flexible access to biological data. Genome Research 2004, 14: 160\u2013169.","journal-title":"Genome Research"},{"key":"2422_CR21","volume-title":"MartView, a web interface to BioMart","author":"S Haider","year":"2007","unstructured":"Haider S, Holland R, Smedley D, Kaspryzk A: MartView, a web interface to BioMart.2007. [http:\/\/www.biomart.org\/biomart\/martview\/]"},{"issue":"7\u20138","key":"2422_CR22","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1002\/cfg.498","volume":"6","author":"M Shimoyama","year":"2005","unstructured":"Shimoyama M, Petri V, Pasko D, Bromberg S, Wu W, Chen J, Nenasheva N, Kwitek A, Twigger S, Jacob H: Using Multiple Ontologies to Integrate Complex Biological Data. Comp Funct Genomics 2005, 6(7\u20138):373\u2013378.","journal-title":"Comp Funct Genomics"},{"key":"2422_CR23","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1093\/nar\/30.1.125","volume":"30","author":"S Twigger","year":"2002","unstructured":"Twigger S, Lu J, Shimoyama M, Chen D, Pasko D, Long H, Ginster J, Chen C, Nigam R, Kwitek A, et al.: Rat Genome Database (RGD): mapping disease onto the genome. Nucleic Acids Research 2002, 30: 125\u2013128.","journal-title":"Nucleic Acids Research"},{"key":"2422_CR24","doi-asserted-by":"crossref","unstructured":"Fluit C, Sabou M, van Harmelen F: Visualising the Semantic Web, Springer Verlag 2002 chap. Ontology-based Information Visualisation. Chapter 3:","DOI":"10.1007\/978-1-4471-3737-5_3"},{"issue":"2","key":"2422_CR25","doi-asserted-by":"publisher","first-page":"532","DOI":"10.1147\/sj.402.0532","volume":"40","author":"C Goble","year":"2001","unstructured":"Goble C, Stevens R, Ng G, Bechhofer S, Paton N, Baker P, Peim M, Brass A: Transparent access to multiple bioinformatics information sources. IBM Systems Journal 2001, 40(2):532\u2013551.","journal-title":"IBM Systems Journal"},{"key":"2422_CR26","volume-title":"Poster, Joint AFP Biosapiens meeting, ISMB 2007","author":"RC Jimenez","year":"2007","unstructured":"Jimenez RC, Quinn AF, Labarga A, O'Neill K, Garcia A, Hermjakob H: Dasty2, a web client for visualizing protein sequence features. Poster, Joint AFP Biosapiens meeting, ISMB 2007 2007."},{"key":"2422_CR27","volume-title":"Ajax: A New Approach to Web Applications","author":"J Garrett","year":"2005","unstructured":"Garrett J: Ajax: A New Approach to Web Applications.2005. [http:\/\/www.adaptivepath.com\/publications\/essays\/archives\/000385.php]"},{"key":"2422_CR28","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1145\/108844.108896","volume-title":"CHI '91: Proceedings of the SIGCHI conference on Human factors in computing systems","author":"M Muller","year":"1991","unstructured":"Muller M: PICTIVE: an exploration in participatory design. In CHI '91: Proceedings of the SIGCHI conference on Human factors in computing systems. New York, NY, USA: ACM Press; 1991:225\u2013231."},{"key":"2422_CR29","first-page":"22","volume-title":"Proceedings of NordiCHI 2000","author":"S B\u00f8dker","year":"2000","unstructured":"B\u00f8dker S, Ehn P, Sj\u00f6gren D, Sundblad Y: Co-operative Design \u2013 perspectives on 20 years with the Scandinavian IT Design Model. Proceedings of NordiCHI 2000 2000, 22\u201324."},{"issue":"3","key":"2422_CR30","doi-asserted-by":"publisher","first-page":"770","DOI":"10.1086\/314008","volume":"31","author":"W Schlech III","year":"2000","unstructured":"Schlech W III: Foodborne Listeriosis. Clinical Infectious Diseases 2000, 31(3):770\u2013775.","journal-title":"Clinical Infectious Diseases"},{"issue":"2","key":"2422_CR31","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1093\/clinids\/17.2.224","volume":"17","author":"R Jurado","year":"1993","unstructured":"Jurado R, Farley M, Pereira E, Harvey R, Schuchat A, Wenger J, Stephens D: Increased risk of meningitis and bacteremia due to Listeria monocytogenes in patients with human immunodeficiency virus infection. Clinical Infectious Diseases 1993, 17(2):224\u20137.","journal-title":"Clinical Infectious Diseases"},{"issue":"Part 3","key":"2422_CR32","doi-asserted-by":"publisher","first-page":"689","DOI":"10.1042\/bj20020691","volume":"366","author":"O Vieira","year":"2002","unstructured":"Vieira O, Botelho R, Grinstein S: Phagosome maturation: aging gracefully. Biochem J 2002, 366(Part 3):689\u2013704.","journal-title":"Biochem J"},{"issue":"4","key":"2422_CR33","doi-asserted-by":"publisher","first-page":"280","DOI":"10.1038\/nri1053","volume":"3","author":"M Desjardins","year":"2003","unstructured":"Desjardins M: ER-mediated phagocytosis: a new membrane for new functions. Nature Reviews Immunology 2003, 3(4):280\u2013291.","journal-title":"Nature Reviews Immunology"},{"issue":"5","key":"2422_CR34","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1016\/S0962-8924(00)88989-8","volume":"5","author":"M Desjardins","year":"1995","unstructured":"Desjardins M: Biogenesis of phagolysosomes: the'kiss and run'hypothesis. Trends Cell Biol 1995, 5(5):183\u20136.","journal-title":"Trends Cell Biol"},{"issue":"17","key":"2422_CR35","doi-asserted-by":"publisher","first-page":"11459","DOI":"10.1074\/jbc.274.17.11459","volume":"274","author":"C Alvarez-Dominguez","year":"1999","unstructured":"Alvarez-Dominguez C, Stahl P: Increased Expression of Rab5a Correlates Directly with Accelerated Maturation of Listeria monocytogenes Phagosomes. Journal of Biological Chemistry 1999, 274(17):11459\u201311462.","journal-title":"Journal of Biological Chemistry"},{"issue":"22","key":"2422_CR36","doi-asserted-by":"publisher","first-page":"19059","DOI":"10.1074\/jbc.M101639200","volume":"276","author":"A Prada-Delgado","year":"2001","unstructured":"Prada-Delgado A, Carrasco-Marin E, Bokoch G, Alvarez-Dominguez C: Interferon- \u03b3 Listericidal Action Is Mediated by Novel Rab5a Functions at the Phagosomal Environment. Journal of Biological Chemistry 2001, 276(22):19059\u201319065.","journal-title":"Journal of Biological Chemistry"},{"issue":"3","key":"2422_CR37","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1083\/jcb.200205009","volume":"158","author":"D Portnoy","year":"2002","unstructured":"Portnoy D, Auerbuch V, Glomski I: The cell biology of Listeria monocytogenes infection the intersection of bacterial pathogenesis and cell-mediated immunity. The Journal of Cell Biology 2002, 158(3):409\u2013414.","journal-title":"The Journal of Cell Biology"},{"issue":"3","key":"2422_CR38","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1111\/j.1600-0854.2005.00265.x","volume":"6","author":"A Prada-Delgado","year":"2005","unstructured":"Prada-Delgado A, Carrasco-Marin E, Pena-Macarro C, del Cerro-Vadillo E, Fresno-Escudero M, Leyva-Cobian F, Alvarez-Dominguez C: Inhibition of Rab 5 a exchange activity is a key step for Listeria monocytogenes survival. Traffic 2005, 6(3):252\u2013265.","journal-title":"Traffic"},{"key":"2422_CR39","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1016\/S1534-5807(01)00008-9","volume":"1","author":"H Horiuchi","year":"2001","unstructured":"Horiuchi H, Lipp\u00e9 R, McBride H, Rubino M, Woodman P, Stenmark H, Rybin V, Wilm M, Ashman K, Mann M, et al.: A Novel Rab5 GDP\/GTP Exchange Factor Complexed to Rabaptin-5 Links Nucleotide Exchange to Effector Recruitment and Function. Developmental Cell 2001, 1: 73\u201382.","journal-title":"Developmental Cell"},{"issue":"41","key":"2422_CR40","doi-asserted-by":"publisher","first-page":"16251","DOI":"10.1073\/pnas.0703496104","volume":"104","author":"A Schwegmann","year":"2007","unstructured":"Schwegmann A, Guler R, Cutler A, Arendse B, Horsnell W, Flemming A, Kottmann A, Ryan G, Hide W, Leitges M, et al.: Protein kinase C {delta} is essential for optimal macrophage-mediated phagosomal containment of Listeria monocytogenes. Proc Natl Acad Sci U S A 2007, 104(41):16251\u201316256.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2422_CR41","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 A, Rosse C: Relations in biomedical ontologies. Genome Biology 2005, 6: R46.","journal-title":"Genome Biology"},{"issue":"4","key":"2422_CR42","doi-asserted-by":"publisher","first-page":"643","DOI":"10.1037\/0033-295X.106.4.643","volume":"106","author":"P Pirolli","year":"1999","unstructured":"Pirolli P, Card S: Information foraging. Psychological Review 1999, 106(4):643\u2013675.","journal-title":"Psychological Review"},{"issue":"3","key":"2422_CR43","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1109\/MIS.2004.9","volume":"19","author":"H Stuckenschmidt","year":"2004","unstructured":"Stuckenschmidt H, van Harmelen F, de Waard A, Scerri T, Bhogal R, van Buel J, Crowlesmith I, Fluit C, Kampman A, Broekstra J, van Mulligen E: Exploring Large Document Repositories with RDF Technology: The DOPE Project. IEEE Intelligent Systems 2004, 19(3):34\u201340.","journal-title":"IEEE Intelligent Systems"},{"key":"2422_CR44","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1186\/1471-2105-8-401","volume":"8","author":"RG Cote","year":"2007","unstructured":"Cote RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H: The Protein Identifier Cross-Reference (PICR) service: reconciling protein identifiers across multiple source databases. BMC Bioinformatics 2007, 8: 401.","journal-title":"BMC Bioinformatics"},{"issue":"Database issue","key":"2422_CR45","doi-asserted-by":"publisher","first-page":"D562","DOI":"10.1093\/nar\/gkj085","volume":"34","author":"J Blake","year":"2006","unstructured":"Blake J, Eppig J, Bult C, Kadin J, Richardson J, et al.: The Mouse Genome Database (MGD): updates and enhancements. Nucleic Acids Res 2006, 34(Database issue):D562-D567.","journal-title":"Nucleic Acids Res"},{"key":"2422_CR46","volume-title":"Nucleic Acids Research","author":"S Twigger","year":"2007","unstructured":"Twigger S, Shimoyama M, Bromberg S, Kwitek A, Jacob H: The Rat Genome Database, update 2007-Easing the path from disease to data and back again. Nucleic Acids Research 2007, (35 Database):D658."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-437.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T03:33:57Z","timestamp":1630467237000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-437"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,10,16]]},"references-count":46,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2422"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-437","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,10,16]]},"assertion":[{"value":"7 January 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 October 2008","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 October 2008","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"437"}}