{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T02:56:15Z","timestamp":1780887375054,"version":"3.54.1"},"reference-count":57,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Biomed Semant"],"published-print":{"date-parts":[[2014,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Biomedical ontologists to date have concentrated on ontological descriptions of biomedical entities such as gene products and their attributes, phenotypes and so on. Recently, effort has diversified to descriptions of the laboratory investigations by which these entities were produced. However, much biological insight is gained from the analysis of the data produced from these investigations, and there is a lack of adequate descriptions of the wide range of software that are central to bioinformatics. We need to describe how data are analyzed for discovery, audit trails, provenance and reproducibility.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The Software Ontology (SWO) is a description of software used to store, manage and analyze data. Input to the SWO has come from beyond the life sciences, but its main focus is the life sciences. We used agile techniques to gather input for the SWO and keep engagement with our users. The result is an ontology that meets the needs of a broad range of users by describing software, its information processing tasks, data inputs and outputs, data formats versions and so on. Recently, the SWO has incorporated EDAM, a vocabulary for describing data and related concepts in bioinformatics. The SWO is currently being used to describe software used in multiple biomedical applications.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The SWO is another element of the biomedical ontology landscape that is necessary for the description of biomedical entities and how they were discovered. An ontology of software used to analyze data produced by investigations in the life sciences can be made in such a way that it covers the important features requested and prioritized by its users. The SWO thus fits into the landscape of biomedical ontologies and is produced using techniques designed to keep it in line with user\u2019s needs.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability<\/jats:title><jats:p>The Software Ontology is available under an Apache 2.0 license at<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/theswo.sourceforge.net\/\" ext-link-type=\"uri\">http:\/\/theswo.sourceforge.net\/<\/jats:ext-link>; the Software Ontology blog can be read at<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/softwareontology.wordpress.com\" ext-link-type=\"uri\">http:\/\/softwareontology.wordpress.com<\/jats:ext-link>.<\/jats:p><\/jats:sec>","DOI":"10.1186\/2041-1480-5-25","type":"journal-article","created":{"date-parts":[[2014,6,2]],"date-time":"2014-06-02T15:16:40Z","timestamp":1401722200000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":64,"title":["The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation"],"prefix":"10.1186","volume":"5","author":[{"given":"James","family":"Malone","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andy","family":"Brown","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Allyson L","family":"Lister","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jon","family":"Ison","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Duncan","family":"Hull","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helen","family":"Parkinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Stevens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2014,6,2]]},"reference":[{"key":"176_CR1","volume-title":"International conference on biomedical Ontology (ICBO)","author":"M Copeland","year":"2012","unstructured":"Copeland M, Brown A, Parkinson H, Stevens R, Malone J:The SWO Project: A case study of applying agile ontology engineering methods in community driven ontologies. International conference on biomedical Ontology (ICBO). 2012, Graz, Austrial,"},{"key":"176_CR2","volume-title":"Proc. of Bio-ontologies SIG; Co-located with ISMB","author":"J Malone","year":"2010","unstructured":"Malone J, Badarinarayan N, Ison J, Stevens R, Parkinson H:An ontology of Bioinformatics software. Proc. of Bio-ontologies SIG; Co-located with ISMB. 2010, Boston, MA, USA,"},{"issue":"2","key":"176_CR3","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1038\/ng.295","volume":"41","author":"JPA Ioannidis","year":"2009","unstructured":"Ioannidis JPA, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC, Falchi M, Furlanello C, Game L, Jurman G, Mangion J, Mehta T, Nitzberg M, Page GP, Petretto E, van Noort V:Repeatability of published microarray gene expression analyses. Nat Genet. 2009, 41 (2): 149-155.","journal-title":"Nat Genet"},{"issue":"8","key":"176_CR4","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1016\/j.jclinepi.2011.02.003","volume":"64","author":"ACJ Janssens","year":"2011","unstructured":"Janssens ACJ, Ioannidis JP, Bedrosian S, Boffetta P, Dolan SM, Dowling N, Fortier I, Freedman AN, Grimshaw JM, Gulcher J, Gwinn M, Hlatky MA, Janes H, Kraft P, Melillo S, O\u2019Donnell CJ, Pencina MJ, Ransohoff D, Schully SD, Seminara D, Winn DM, Wright CF, van Duijn CM, Little J, Khoury MJ:Strengthening the reporting of Genetic {RIsk} Prediction Studies (GRIPS): explanation and elaboration. J Clinic Epidemiol. 2011, 64 (8): e1-e22. [http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0895435611000588],","journal-title":"J Clinic Epidemiol"},{"issue":"10","key":"176_CR5","doi-asserted-by":"publisher","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","volume":"5","author":"R Gentleman","year":"2004","unstructured":"Gentleman R, Carey V, Bates D, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini A, Sawitzki G, Smith C, Smyth G, Tierney L, Yang J, Zhang J:Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5 (10): R80-[http:\/\/genomebiology.com\/2004\/5\/10\/R80],","journal-title":"Genome Biol"},{"key":"176_CR6","volume-title":"The scientific method in practice: reproducibility in the computational sciences","author":"V Stodden","year":"2010,","unstructured":"Stodden V:The scientific method in practice: reproducibility in the computational sciences. 2010,, MIT Sloan Research Paper No. 4773-10,"},{"issue":"6060","key":"176_CR7","doi-asserted-by":"publisher","first-page":"1226","DOI":"10.1126\/science.1213847","volume":"334","author":"RD Peng","year":"2011","unstructured":"Peng RD:Reproducible research in computational science. Science. 2011, 334 (6060): 1226-1227. [http:\/\/www.sciencemag.org\/content\/334\/6060\/1226.abstract],","journal-title":"Science"},{"key":"176_CR8","doi-asserted-by":"publisher","first-page":"729","DOI":"10.1093\/nar\/gkl320","volume":"34","author":"D Hull","year":"2006","unstructured":"Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T:Taverna: a tool for building and running workflows of services. Nucleic Acids Res. 2006, 34: 729-732. [http:\/\/www.hubmed.org\/display.cgi?uids=16845108] [Web Server issue],","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"176_CR9","doi-asserted-by":"publisher","first-page":"R86","DOI":"10.1186\/gb-2010-11-8-r86","volume":"11","author":"J Goecks","year":"2010","unstructured":"Goecks J, Nekrutenko A, Taylor J, Team TG:Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010, 11 (8): R86-[http:\/\/genomebiology.com\/2010\/11\/8\/R86],","journal-title":"Genome Biol"},{"issue":"10","key":"176_CR10","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.1002\/cpe.994","volume":"18","author":"B Lud\u00e4scher","year":"2006","unstructured":"Lud\u00e4scher B, Altintas I, Berkley C, Higgins D, Jaeger E, Jones M, Lee EA, Tao J, Zhao Y:Scientific workflow management and the Kepler system. Concurrency Comput: Pract Exp. 2006, 18 (10): 1039-1065. [http:\/\/dx.doi.org\/10.1002\/cpe.994],","journal-title":"Concurrency Comput: Pract Exp"},{"key":"176_CR11","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1016\/j.future.2008.06.010","volume":"25","author":"D De Roure","year":"2009","unstructured":"De Roure D, Goble C, Stevens R:The design and realisation of the myExperiment Virtual Research Environment for social sharing of workflows. Future Generation Comput Syst. 2009, 25: 561-567.","journal-title":"Future Generation Comput Syst"},{"key":"176_CR12","unstructured":"PROV model primer. [http:\/\/www.w3.org\/TR\/prov-primer\/],"},{"issue":"suppl 2","key":"176_CR13","doi-asserted-by":"publisher","first-page":"W689","DOI":"10.1093\/nar\/gkq394","volume":"38","author":"J Bhagat","year":"2010","unstructured":"Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA:BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Res. 2010, 38 (suppl 2): W689-W694. [http:\/\/nar.oxfordjournals.org\/content\/38\/suppl_2\/W689.abstract],","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"176_CR14","doi-asserted-by":"publisher","first-page":"11:1","DOI":"10.1145\/1346337.1346239","volume":"2","author":"K Belhajjame","year":"2008","unstructured":"Belhajjame K, Embury SM, Paton NW, Stevens R, Goble CA:Automatic annotation of Web services based on workflow definitions. ACM Trans Web. 2008, 2 (2): 11:1-11:34. [http:\/\/doi.acm.org\/10.1145\/1346237.1346239],","journal-title":"ACM Trans Web"},{"key":"176_CR15","unstructured":"Description of a Project Wiki Homepage. [https:\/\/github.com\/edumbill\/doap\/wiki],"},{"issue":"3","key":"176_CR16","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1007\/s11280-007-0033-x","volume":"10","author":"D Martin","year":"2007","unstructured":"Martin D, Burstein M, McDermott D, McIlraith S, Paolucci M, Sycara K, McGuinness D, Sirin E, Srinivasan N:Bringing semantics to web services with OWL-S. World Wide Web. 2007, 10 (3): 243-277. [http:\/\/dx.doi.org\/10.1007\/s11280-007-0033-x],","journal-title":"World Wide Web"},{"key":"176_CR17","doi-asserted-by":"crossref","first-page":"77","DOI":"10.3233\/APO-2005-000008","volume":"1","author":"D Roman","year":"2005","unstructured":"Roman D, Keller U, Lausen H, de Bruijn J, Lara R, Stollberg M, Polleres A, Feier C, Bussler C, Fensel D:Web service modeling ontology. Appl Ontol. 2005, 1: 77-106. [http:\/\/portal.acm.org\/citation.cfm?id=1412357],","journal-title":"Appl Ontol"},{"key":"176_CR18","first-page":"76","volume-title":"Proceedings of the ECML\/PKDD09 Workshop on 3rd Generation Data Mining (SoKD-09): 7-11 September 2009","author":"M Hilario","year":"2009","unstructured":"Hilario M, Kalousis A, Nguyen P, Woznica A:A data mining ontology for algorithm selection and meta-mining. Proceedings of the ECML\/PKDD09 Workshop on 3rd Generation Data Mining (SoKD-09): 7-11 September 2009. 2009, Bled, Slovenia, 76-87."},{"issue":"Suppl 1","key":"176_CR19","doi-asserted-by":"publisher","first-page":"S7+","DOI":"10.1186\/2041-1480-1-S1-S7","volume":"1 Suppl 1","author":"RR Brinkman","year":"2010","unstructured":"Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SAA, Soldatova LN, Stoeckert CJ, Turner JA, Zheng J, OBI consortium:Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010, 1 Suppl 1 (Suppl 1): S7+-[http:\/\/dx.doi.org\/10.1186\/2041-1480-1-S1-S7],","journal-title":"J Biomed Semantics"},{"key":"176_CR20","unstructured":"Information artifact ontologyr. [http:\/\/purl.obolibrary.org\/obo\/iao],"},{"key":"176_CR21","volume-title":"Bioinformatics","author":"J Ison","year":"2013","unstructured":"Ison J, Kalas M, Jonassen I, Bolser D, Uludag M, McWilliam H, Malone J, Lopez R, Pettifer S, Rice P:EDAM: An ontology of bioinformatics operations, types of data and identifiers, topics, and formats. Bioinformatics. 2013, [http:\/\/bioinformatics.oxfordjournals.org\/content\/early\/2013\/03\/11\/bioinformatics.btt113.abstract],"},{"key":"176_CR22","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1016\/j.jbi.2010.10.003","volume":"44","author":"JD Tenenbaum","year":"2011","unstructured":"Tenenbaum JD, Whetzel PL, Anderson K, Borromeo CD, Dinov ID, Gabriel D, Kirschner B, Mirel B, Morris T, Noy N, Nyulas C, Rubenson D, Saxman PR, Singh H, Whelan N, Wright Z, Athey BD, Becich MJ, Ginsburg GS, Musen MA, Smith KA, Tarantal AF, Rubin DL, Lyster P:The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research. J Biomed Inform. 2011, 44: 137-145. [http:\/\/www.sciencedirect.com\/science\/article\/pii\/S1532046410001553] [<ce:title>Ontologies for Clinical and Translational Research<\/ce:title>],","journal-title":"J Biomed Inform"},{"issue":"3","key":"176_CR23","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1504\/IJBRA.2007.015005","volume":"3","author":"K Wolstencroft","year":"2007","unstructured":"Wolstencroft K, Alper P, Hull D, Wroe C, Lord P, Stevens R, Goble C:The myGrid Ontology: Bioinformatics Service Discovery. Int J Bioinform Res Appl. 2007, 3 (3): 326-340. [\u201chttp:\/\/www.cs.man.ac.uk\/stevensr\/papers\/IJBRA_3304_Wolstencroft.pdf\u201d],","journal-title":"Int J Bioinform Res Appl"},{"issue":"8","key":"176_CR24","doi-asserted-by":"publisher","first-page":"R88","DOI":"10.1186\/gb-2010-11-8-r88","volume":"11","author":"M Reese","year":"2010","unstructured":"Reese M, Moore B, Batchelor C, Salas F, Cunningham F, Marth G, Stein L, Flicek P, Yandell M, Eilbeck K:A standard variation file format for human genome sequences. Genome Biol. 2010, 11 (8): R88-","journal-title":"Genome Biol"},{"key":"176_CR25","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G:Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet. 2000, 25: 25-29.","journal-title":"Nat Genet"},{"issue":"2","key":"176_CR26","doi-asserted-by":"publisher","first-page":"R21","DOI":"10.1186\/gb-2005-6-2-r21","volume":"6","author":"J Bard","year":"2005","unstructured":"Bard J, Rhee S, Ashburner M:An ontology for cell types. Genome Biol. 2005, 6 (2): R21-","journal-title":"Genome Biol"},{"key":"176_CR27","doi-asserted-by":"publisher","first-page":"R5","DOI":"10.1186\/gb-2012-13-1-r5","volume":"13","author":"C Mungall","year":"2012","unstructured":"Mungall C, Torniai C, Gkoutos G, Lewis S, Haendel M:Uberon, an integrative multi-species anatomy ontology. Genome Biol. 2012, 13: R5-","journal-title":"Genome Biol"},{"key":"176_CR28","doi-asserted-by":"publisher","first-page":"R2","DOI":"10.1186\/gb-2010-11-1-r2","volume":"11","author":"C Mungall","year":"2010","unstructured":"Mungall C, Gkoutos G, Smith C, Haendel M, Lewis S, Ashburner M:Integrating phenotype ontologies across multiple species. Genome Biol. 2010, 11: R2-","journal-title":"Genome Biol"},{"issue":"suppl 1","key":"176_CR29","first-page":"D344","volume":"36","author":"K Degtyarenko","year":"2008","unstructured":"Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alc\u00e1ntara R, Darsow M, Guedj M, Ashburner M:ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 2008, 36 (suppl 1): D344-D350.","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"176_CR30","doi-asserted-by":"publisher","first-page":"1112","DOI":"10.1093\/bioinformatics\/btq099","volume":"26","author":"J Malone","year":"2010","unstructured":"Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H:Modeling sample variables with an experimental factor ontology. Bioinformatics. 2010, 26 (8): 1112-1118. [http:\/\/bioinformatics.oxfordjournals.org\/content\/26\/8\/1112.abstract],","journal-title":"Bioinformatics"},{"key":"176_CR31","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/1471-2105-12-257","volume":"12","author":"U Visser","year":"2011","unstructured":"Visser U, Abeyruwan S, Vempati U, Smith R, Lemmon V, Schurer S:BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results. BMC Bioinformatics. 2011, 12: 257-[http:\/\/www.biomedcentral.com\/1471-2105\/12\/257],","journal-title":"BMC Bioinformatics"},{"key":"176_CR32","volume-title":"User stories applied: for agile software development","author":"M Cohn","year":"2004","unstructured":"Cohn M: User stories applied: for agile software development. 2004, Boston: Addison Wesley"},{"issue":"D1","key":"176_CR33","doi-asserted-by":"publisher","first-page":"D987","DOI":"10.1093\/nar\/gks1174","volume":"41","author":"G Rustici","year":"2013","unstructured":"Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U:ArrayExpress update?trends in database growth and links to data analysis tools. Nucleic Acids Res. 2013, 41 (D1): D987-D990. [http:\/\/nar.oxfordjournals.org\/content\/41\/D1\/D987.abstract],","journal-title":"Nucleic Acids Res"},{"key":"176_CR34","first-page":"2012","volume-title":"Database: J Biol Databases Curation","author":"N Vasilevsky","year":"2012","unstructured":"Vasilevsky N, Johnson T, Corday K, Torniai C, Brush M, Segerdell E, Wilson M, Shaffer C, Robinson D, Haendel M:Research resources: curating the new eagle-i discovery system. Database: J Biol Databases Curation. 2012, 2012-doi:10.1093\/database\/bar067.,"},{"key":"176_CR35","unstructured":"BioMedBridges Consortium. [http:\/\/www.biomedbridges.eu\/l],"},{"key":"176_CR36","unstructured":"BioMedBridges tool registry. [http:\/\/tinyurl.com\/bmbtoolsui],"},{"key":"176_CR37","volume-title":"Succeeding with agile: software development using scrum","author":"M Cohn","year":"2004","unstructured":"Cohn M: Succeeding with agile: software development using scrum. 2004, Boston, MA: Pearson Education"},{"key":"176_CR38","unstructured":"Principles behind the Agile Manifesto. [http:\/\/agilemanifesto.org\/principles.html],"},{"key":"176_CR39","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1007\/978-0-387-34847-6_3","volume-title":"Benchmarking, Theory and Practice","author":"M Gr\u00fcninger","year":"1995","unstructured":"Gr\u00fcninger M, Fox MS:The role of competency questions in enterprise engineering. Benchmarking, Theory and Practice. Edited by: Rolstad\u00e5s A. 1995, Springer, 22-31. doi:10.1007\/978-0-387-34847-6_3.,"},{"key":"176_CR40","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1109\/AGILE.2011.39","volume-title":"AGILE Conference: 7-13 August, 2011","author":"G Kirk","year":"2011","unstructured":"Kirk G:Democracy unleashed: bringing agility to citizen engagement. AGILE Conference: 7-13 August, 2011. 2011, Salt Lake City, Utah: IEEE, 209-215."},{"issue":"Suppl 1","key":"176_CR41","doi-asserted-by":"publisher","first-page":"S5","DOI":"10.1186\/1471-2105-13-S1-S5","volume":"13","author":"S Jupp","year":"2012","unstructured":"Jupp S, Horridge M, Iannone L, Klein J, Owen S, Schanstra J, Wolstencroft K, Stevens R:Populous: a tool for building OWL ontologies from templates. BMC Bioinformatics. 2012, 13 (Suppl 1): S5-[http:\/\/www.biomedcentral.com\/1471-2105\/13\/S1\/S5],","journal-title":"BMC Bioinformatics"},{"key":"176_CR42","unstructured":"Software ontology project. [http:\/\/softwareontology.wordpress.com],"},{"key":"176_CR43","volume-title":"Test driven: practical tdd and acceptance tdd for java developers","author":"L Koskela","year":"2007","unstructured":"Koskela L: Test driven: practical tdd and acceptance tdd for java developers. 2007, Greenwich, CT, USA: Manning Publications Co."},{"key":"176_CR44","unstructured":"User sourced competency questions for software. [http:\/\/softwareontology.wordpress.com\/2011\/04\/01\/user-sourced-competency-questions-for-software\/],"},{"key":"176_CR45","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/j.websem.2003.07.001","volume":"1","author":"I Horrocks","year":"2003","unstructured":"Horrocks I, Patel-Schneider PF, van Harmelen F:From\"Equation missing\"and RDF to OWL: The making of a web ontology language. J Web Semantics. 2003, 1: 7-26.","journal-title":"J Web Semantics"},{"key":"176_CR46","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1186\/1471-2105-14-194","volume":"14","author":"G Duck","year":"2013","unstructured":"Duck G, Nenadic G, Brass A, Robertson D, Stevens R:bioNerDS: exploring bioinformatics\u2019 database and software use through literature mining. BMC Bioinformatics. 2013, 14: 194-[http:\/\/www.biomedcentral.com\/1471-2105\/14\/194],","journal-title":"BMC Bioinformatics"},{"key":"176_CR47","volume-title":"OWL Experiences and Directions OWLEd 2006","author":"N Drummond","year":"2006","unstructured":"Drummond N, Rector A, Stevens R, Moulton G, Horridge M, Wang H, Sedenberg J:Putting OWL in order: Patterns for sequences in OWL. OWL Experiences and Directions OWLEd 2006. 2006, Athens Georgia, USA,"},{"key":"176_CR48","unstructured":"SWO EDAM merge modifying EDAM inOWL. [http:\/\/softwareontology.wordpress.com\/2012\/07\/25\/swo-edam-merge-modifying-edam-in-owl\/],"},{"key":"176_CR49","unstructured":"SWO EDAM merge overview. [http:\/\/softwareontology.wordpress.com\/2012\/07\/25\/swo-edam-merge-overview\/],"},{"key":"176_CR50","unstructured":"SWO refactoring objective. [http:\/\/softwareontology.wordpress.com\/2013\/07\/04\/refactoring-objective-specification-hierarchy\/],"},{"key":"176_CR51","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1145\/945645.945664","volume-title":"K-CAP \u201903: Proceedings of the 2nd international conference on Knowledge capture","author":"AL Rector","year":"2003","unstructured":"Rector AL:Modularisation of domain ontologies implemented in description logics and related formalisms including OWL. K-CAP \u201903: Proceedings of the 2nd international conference on Knowledge capture. 2003, New York, NY, USA: ACM Press, 121-128. [http:\/\/dx.doi.org\/10.1145\/945645.945664],"},{"key":"176_CR52","unstructured":"ELIXIR. [http:\/\/www.elixir-europe.org\/],"},{"issue":"suppl 2","key":"176_CR53","doi-asserted-by":"publisher","first-page":"W689","DOI":"10.1093\/nar\/gkq394","volume":"38","author":"J Bhagat","year":"2010","unstructured":"Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA:BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Res. 2010, 38 (suppl 2): W689-W694.","journal-title":"Nucleic Acids Res"},{"key":"176_CR54","unstructured":"Gene expression atlas RDF project. [http:\/\/www.ebi.ac.uk\/fgpt\/atlasrdf\/index.html],"},{"key":"176_CR55","volume-title":"The EBI RDF platform: linked open data for the life sciences","author":"S Jupp","year":"2014","unstructured":"Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le Nov\u00e8re N, Parkinson H, Birney E, Jenkinson AM: The EBI RDF platform: linked open data for the life sciences. 2014, [http:\/\/bioinformatics.oxfordjournals.org\/content\/early\/2014\/01\/21\/bioinformatics.btt765.abstract]"},{"key":"176_CR56","unstructured":"James Malone\u2019s EBI blog. [http:\/\/drjamesmalone.blogspot.co.uk\/],"},{"key":"176_CR57","unstructured":"CLI-mate. [http:\/\/cli-mate.lumc.nl\/],"}],"container-title":["Journal of Biomedical Semantics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/2041-1480-5-25.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,3]],"date-time":"2025-05-03T06:01:50Z","timestamp":1746252110000},"score":1,"resource":{"primary":{"URL":"https:\/\/jbiomedsem.biomedcentral.com\/articles\/10.1186\/2041-1480-5-25"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,6,2]]},"references-count":57,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["176"],"URL":"https:\/\/doi.org\/10.1186\/2041-1480-5-25","relation":{},"ISSN":["2041-1480"],"issn-type":[{"value":"2041-1480","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,6,2]]},"assertion":[{"value":"20 June 2013","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 April 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 June 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"25"}}