TY - STD TI - Hoehndorf R, Schofield PN, Gkoutos GV. The role of ontologies in biological and biomedical research: a functional perspective. Brief Bioinform. 2015; 16(6):1069–80. https://doi.org/10.1093/bib/bbv011. UR - https://doi.org/10.1093/bib/bbv011 ID - ref1 ER - TY - JOUR AU - Ashburner, M. PY - 2000 DA - 2000// TI - Gene ontology: Tool for the unification of biology JO - Nat Genet VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Ashburner2000 ER - TY - STD TI - Poolparty: Selected Customer References. http://www.poolparty.biz/customers/. Accessed 13 March 2017. UR - http://www.poolparty.biz/customers/ ID - ref3 ER - TY - BOOK AU - Baader, F. AU - Calvanese, D. AU - McGuinness, D. AU - Nardi, D. AU - Patel-Schneider, P. F. PY - 2007 DA - 2007// TI - The Description Logic Handbook: Theory, Implementation and Applications (Second Edition) PB - Cambridge University Press CY - Cambridge UR - https://doi.org/10.1017/CBO9780511711787 DO - 10.1017/CBO9780511711787 ID - Baader2007 ER - TY - JOUR AU - Grau, B. C. AU - Horrocks, I. AU - Motik, B. AU - Parsia, B. AU - Patel-Schneider, P. F. AU - Sattler, U. PY - 2008 DA - 2008// TI - OWL 2: The Next Step for OWL JO - J Web Semant VL - 6 UR - https://doi.org/10.1016/j.websem.2008.05.001 DO - 10.1016/j.websem.2008.05.001 ID - Grau2008 ER - TY - STD TI - Bourne PE, Clark TW, Dale R, de Waard A, Herman I, Hovy EH, Shotton D. Improving the future research communications and e-scholarship (Dagstuhl Perspectives Workshop 11331). Dagstuhl Manifestos. Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik. 2012;1(1). ID - ref6 ER - TY - STD TI - Zhao J, Alexander K, Hausenblas M, Cyganiak R. Describing linked datasets with the VoID vocabulary. 2011. http://www.w3.org/TR/2011/NOTE-void-20110303/. Accessed 29 Dec 2018. UR - http://www.w3.org/TR/2011/NOTE-void-20110303/ ID - ref7 ER - TY - STD TI - Knublauch H, Fergerson RW, Noy NF, Musen MA. The Protégé OWL Plugin: An Open Development Environment for Semantic Web Applications. In: The Semantic Web - ISWC 2004: Third International Semantic Web Conference,Hiroshima, Japan, November 7-11, 2004. Proceedings: 2004. p. 229–243. https://doi.org/10.1007/978-3-540-30475-3_17. UR - https://doi.org/10.1007/978-3-540-30475-3_17 ID - ref8 ER - TY - STD TI - DC Dublin Core Metadata Element Set, Version 1.1. http://dublincore.org/documents/dces/. Accessed 13 March 2017. UR - http://dublincore.org/documents/dces/ ID - ref9 ER - TY - STD TI - Hartmann J, Sure Y, Haase P, Palma R, Suárez-Figueroa MDC. OMV - Ontology Metadata Vocabulary In: Welty C, editor. ISWC 2005 - In Ontology Patterns for the Semantic Web: 2005. ID - ref10 ER - TY - STD TI - Dutta B, Nandini D, Shahi GK. MOD: Metadata for Ontology Description and Publication. In: Proceedings of the 2015 International Conference on Dublin Core and Metadata Applications, DC 2015, September 1-4. São Paulo: 2015. p. 1–9. http://dcpapers.dublincore.org/pubs/article/view/3758. UR - http://dcpapers.dublincore.org/pubs/article/view/3758 ID - ref11 ER - TY - STD TI - Alexander K, Cyganiak R, Hausenblas M, Zhao J. Describing Linked Datasets. In: Proceedings of the WWW2009 Workshop on Linked Data on the Web, LDOW 2009, April 20. Madrid: 2009. http://ceur-ws.org/Vol-538/ldow2009_paper20.pdf. UR - http://ceur-ws.org/Vol-538/ldow2009_paper20.pdf ID - ref12 ER - TY - STD TI - 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 S, Scheuermann RH, Shah N, Whetzel PL, Lewis S. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007; 25(11):1251–5. https://doi.org/10.1038/nbt1346. UR - https://doi.org/10.1038/nbt1346 ID - ref13 ER - TY - STD TI - OBO Principles: Overview. http://www.obofoundry.org/principles/fp-000-summary.html. Accessed 13 March 2017. UR - http://www.obofoundry.org/principles/fp-000-summary.html ID - ref14 ER - TY - STD TI - Ontology Summit. 2013. http://ontologforum.org/OntologySummit/2013/. Accessed 13 March 2017. UR - http://ontologforum.org/OntologySummit/2013/ ID - ref15 ER - TY - STD TI - UKON UK Ontology Network. 2016. http://www.ukontology.org/. Accessed 13 March 2017. UR - http://www.ukontology.org/ ID - ref16 ER - TY - STD TI - MIRO Public Survey. 2015. https://jamesmalone.typeform.com/to/uJIhzR. Accessed 15 Aug 2017. UR - https://jamesmalone.typeform.com/to/uJIhzR ID - ref17 ER - TY - STD TI - Kitchenham B, Charters S. Guidelines for performing Systematic Literature Reviews in Software Engineering. 2007. http://www.dur.ac.uk/ebse/resources/Systematic-reviews-5-8.pdf. Accessed 27 Jan 2009. UR - http://www.dur.ac.uk/ebse/resources/Systematic-reviews-5-8.pdf ID - ref18 ER - TY - STD TI - Bradner S. Key words for use in rfcs to indicate requirement levels. 1997. https://tools.ietf.org/html/rfc2119. Accessed 29 Dec 2018. UR - https://tools.ietf.org/html/rfc2119 ID - ref19 ER - TY - STD TI - MIRO Minimum information for the reporting of an ontology guidelines (GitHub). https://github.com/owlcs/miro/. Accessed 13 March 2017. UR - https://github.com/owlcs/miro/ ID - ref20 ER - TY - STD TI - MIRO Minimum information for the reporting of an ontology guidelines (RPubs). http://rpubs.com/matentzn/miro. Accessed 13 March 2017. UR - http://rpubs.com/matentzn/miro ID - ref21 ER - TY - STD TI - Malone J, Stevens R, Jupp S, Hancocks T, Parkinson H, Brooksbank C. Ten simple rules for selecting a bio-ontology. PLoS Comput Biol. 2016; 12(2):1004743. https://doi.org/10.1371/journal.pcbi.1004743. UR - https://doi.org/10.1371/journal.pcbi.1004743 ID - ref22 ER - TY - STD TI - DC Dublin Core Metadata Element Set, Version 1.1. https://jena.apache.org/. Accessed 13 March 2017. UR - https://jena.apache.org/ ID - ref23 ER - TY - JOUR AU - Horridge, M. AU - Bechhofer, S. PY - 2011 DA - 2011// TI - The OWL API: A Java API for OWL Ontologies JO - Semant Web VL - 2 ID - Horridge2011 ER - TY - STD TI - Furnham A. Response bias, social desirability and dissimulation. Personal Individ Differ. 1986; 7(3):385–400. https://doi.org/10.1016/0191-8869(86)90014-0. UR - https://doi.org/10.1016/0191-8869(86)90014-0 ID - ref25 ER - TY - STD TI - Mikroyannidi E, Iannone L, Stevens R, Rector AL. Inspecting regularities in ontology design using clustering. In: The Semantic Web - ISWC 2011 - 10th International Semantic Web Conference, October 23-27, 2011, Proceedings, Part I. Bonn: 2011. p. 438–53. https://doi.org/10.1007/978-3-642-25073-6_28. UR - https://doi.org/10.1007/978-3-642-25073-6_28 ID - ref26 ER - TY - STD TI - Distinto I, d’Aquin M, Motta E. LOTED2: An ontology of European public procurement notices. Semant Web. 2016; 7(3):267–93. https://doi.org/10.3233/SW-140151. UR - https://doi.org/10.3233/SW-140151 ID - ref27 ER - TY - STD TI - Muñoz-Soro JF, Esteban G, Corcho O, Serón FJ. PPROC, an ontology for transparency in public procurement. Semant Web. 2016; 7(3):295–309. https://doi.org/10.3233/SW-150195. UR - https://doi.org/10.3233/SW-150195 ID - ref28 ER - TY - STD TI - Rodríguez-Doncel V, Delgado J, Llorente S, Rodríguez E, Boch L. Overview of the MPEG-21 media contract ontology. Semant Web. 2016; 7(3):311–32. https://doi.org/10.3233/SW-160215. UR - https://doi.org/10.3233/SW-160215 ID - ref29 ER - TY - STD TI - Constantin A, Peroni S, Pettifer S, Shotton D, Vitali F. The Document Components Ontology (DoCO). Semant Web. 2016; 7(2):167–81. https://doi.org/10.3233/SW-150177. UR - https://doi.org/10.3233/SW-150177 ID - ref30 ER - TY - STD TI - Keet CM, Lawrynowicz A, d’Amato C, Kalousis A, Nguyen P, Palma R, Stevens R, Hilario M. The Data Mining OPtimization Ontology. J Web Sem. 2015; 32:43–53. https://doi.org/10.1016/j.websem.2015.01.001. UR - https://doi.org/10.1016/j.websem.2015.01.001 ID - ref31 ER - TY - STD TI - Rabattu PY, Massé B, Ulliana F, Rousset MC, Rohmer D, Léon JC, Palombi O. My Corporis Fabrica Embryo: An ontology-based 3d spatio-temporal modeling of human embryo development. J Biomed Semant. 2015; 6:36. https://doi.org/10.1186/s13326-015-0034-0. UR - https://doi.org/10.1186/s13326-015-0034-0 ID - ref32 ER - TY - STD TI - Suzuki A, Takai-Igarashi T, Nakaya J, Tanaka H. Development of an Ontology for Periodontitis. J Biomed Semant. 2015; 6:30. https://doi.org/10.1186/s13326-015-0028-y. UR - https://doi.org/10.1186/s13326-015-0028-y ID - ref33 ER - TY - STD TI - Amith M, Gong Y, Cunningham R, Boom J, Tao C. Developing VISO: vaccine information statement ontology for patient education. J Biomed Semant. 2015; 6:23. https://doi.org/10.1186/s13326-015-0016-2. UR - https://doi.org/10.1186/s13326-015-0016-2 ID - ref34 ER - TY - STD TI - Hur J, Özgür A, Xiang Z, He Y. Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. J Biomed Semant. 2015; 6:2. https://doi.org/10.1186/2041-1480-6-2. UR - https://doi.org/10.1186/2041-1480-6-2 ID - ref35 ER - TY - STD TI - Jupp S, Malone J, Burdett T, Hériché J-K, Williams E, Ellenberg J, Parkinson HE, Rustici G. The cellular microscopy phenotype ontology. J Biomed Semant. 2016; 7:28. https://doi.org/10.1186/s13326-016-0074-0. UR - https://doi.org/10.1186/s13326-016-0074-0 ID - ref36 ER - TY - STD TI - Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M. The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. J Biomed Semant. 2016; 7:24. https://doi.org/10.1186/s13326-016-0066-0. UR - https://doi.org/10.1186/s13326-016-0066-0 ID - ref37 ER - TY - STD TI - Lin Y, Zheng J, He Y. VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms. J Biomed Semant. 2016; 7:20. https://doi.org/10.1186/s13326-016-0062-4. UR - https://doi.org/10.1186/s13326-016-0062-4 ID - ref38 ER - TY - STD TI - Blank CE, Cui H, Moore LR, Walls RL. MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. J Biomed Semant. 2016; 7:18. https://doi.org/10.1186/s13326-016-0060-6. UR - https://doi.org/10.1186/s13326-016-0060-6 ID - ref39 ER - TY - STD TI - Bamparopoulos G, Konstantinidis EI, Bratsas C, Bamidis PD. Towards exergaming commons: composing the exergame ontology for publishing open game data. J Biomed Semant. 2016; 7:4. https://doi.org/10.1186/s13326-016-0046-4. UR - https://doi.org/10.1186/s13326-016-0046-4 ID - ref40 ER - TY - STD TI - Vita R, Overton JA, Seymour E, Sidney J, Kaufman J, Tallmadge RL, Ellis S, Hammond J, Butcher GW, Sette A, Peters B. An ontology for major histocompatibility restriction. J Biomed Semant. 2016; 7:1. https://doi.org/10.1186/s13326-016-0045-5. UR - https://doi.org/10.1186/s13326-016-0045-5 ID - ref41 ER -