{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:10:53Z","timestamp":1772165453494,"version":"3.50.1"},"reference-count":45,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,9,6]],"date-time":"2019-09-06T00:00:00Z","timestamp":1567728000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,9,6]],"date-time":"2019-09-06T00:00:00Z","timestamp":1567728000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Medical Technologies Centre of Research Excellence's Doctoral Scholarship","award":["N\/A"],"award-info":[{"award-number":["N\/A"]}]},{"name":"Aotearoa Foundation Fellowship","award":["N\/A"],"award-info":[{"award-number":["N\/A"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health grant","doi-asserted-by":"crossref","award":["R01LM011969"],"award-info":[{"award-number":["R01LM011969"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health grant","doi-asserted-by":"crossref","award":["R01LM011969"],"award-info":[{"award-number":["R01LM011969"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health grant","doi-asserted-by":"crossref","award":["R01LM011969"],"award-info":[{"award-number":["R01LM011969"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,12]]},"DOI":"10.1186\/s12859-019-2987-y","type":"journal-article","created":{"date-parts":[[2019,9,6]],"date-time":"2019-09-06T09:05:24Z","timestamp":1567760724000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Model annotation and discovery with the Physiome Model Repository"],"prefix":"10.1186","volume":"20","author":[{"given":"Dewan M.","family":"Sarwar","sequence":"first","affiliation":[]},{"given":"Reza","family":"Kalbasi","sequence":"additional","affiliation":[]},{"given":"John H.","family":"Gennari","sequence":"additional","affiliation":[]},{"given":"Brian E.","family":"Carlson","sequence":"additional","affiliation":[]},{"given":"Maxwell L.","family":"Neal","sequence":"additional","affiliation":[]},{"given":"Bernard de","family":"Bono","sequence":"additional","affiliation":[]},{"given":"Koray","family":"Atalag","sequence":"additional","affiliation":[]},{"given":"Peter J.","family":"Hunter","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4667-9779","authenticated-orcid":false,"given":"David P.","family":"Nickerson","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,9,6]]},"reference":[{"key":"2987_CR1","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1038\/nrm1054","volume":"4","author":"PJ Hunter","year":"2003","unstructured":"Hunter PJ, Borg TK. Integration from proteins to organs: the Physiome Project. Nat Rev Mol Cell Biol. 2003; 4:237\u201343. \n                    https:\/\/doi.org\/10.1038\/nrm1054\n                    \n                  .","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2987_CR2","doi-asserted-by":"publisher","first-page":"2595","DOI":"10.1098\/rsta.2010.0048","volume":"368","author":"P Hunter","year":"2010","unstructured":"Hunter P, Coveney PV, de Bono B, Diaz V, Fenner J, Frangi AF, Harris P, Hose R, Kohl P, Lawford P, McCormack K, Mendes M, Omholt S, Quarteroni A, Sk\u00e5r J, Tegner J, Thomas SR, Tollis I, Tsamardinos I, van Beek JHGM, Viceconti M. A vision and strategy for the virtual physiological human in 2010 and beyond. Philos Trans A Math Phys Eng Sci. 2010; 368:2595\u2013614. \n                    https:\/\/doi.org\/10.1098\/rsta.2010.0048\n                    \n                  .","journal-title":"Philos Trans A Math Phys Eng Sci"},{"key":"2987_CR3","unstructured":"Nielsen PF, Nickerson DP. VPHi Webinar: Reproducibility and reuse in the Virtual Physiological Human. 2017. http:\/\/www.vph-institute.org\/webinar\/reproducibility-and-reuse-in-the-virtual-physiological-human.html. Accessed 24 Oct https:\/\/doi.org\/10.17608\/k6.auckland.5552746.v1."},{"key":"2987_CR4","doi-asserted-by":"publisher","first-page":"1003849","DOI":"10.1371\/journal.pcbi.1003849","volume":"10","author":"ML Neal","year":"2014","unstructured":"Neal ML, Cooling MT, Smith LP, Thompson CT, Sauro HM, Carlson BE, Cook DL, Gennari JH. A reappraisal of how to build modular, reusable models of biological systems. PLOS Comp Biol. 2014; 10:1003849. \n                    https:\/\/doi.org\/10.1371\/journal.pcbi.1003849\n                    \n                  .","journal-title":"PLOS Comp Biol"},{"key":"2987_CR5","doi-asserted-by":"publisher","first-page":"3026","DOI":"10.1093\/bioinformatics\/btp523","volume":"25","author":"AL Lister","year":"2009","unstructured":"Lister AL, Pocock M, Taschuk M, Wipat A. Saint: a lightweight integration environment for model annotation. Oxf Bioinforma. 2009; 25:3026\u20137.","journal-title":"Oxf Bioinforma"},{"key":"2987_CR6","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1016\/j.jbi.2010.06.007","volume":"44","author":"JH Gennari","year":"2011","unstructured":"Gennari JH, Neal ML, Galdzicki M, Cook DL. Multiple ontologies in action: Composite annotations for biosimulation models. J Biomed Informa. 2011; 44:146\u201354. \n                    https:\/\/doi.org\/10.1016\/j.jbi.2010.06.007\n                    \n                  .","journal-title":"J Biomed Informa"},{"issue":"9","key":"2987_CR7","doi-asserted-by":"publisher","first-page":"1600","DOI":"10.1093\/bioinformatics\/bty829","volume":"35","author":"Maxwell L Neal","year":"2018","unstructured":"Neal ML, Thompson CT, Kim KG, James RC, Cook DL, Carlson BE, Gennari JH. Semgen: a tool for semantics-based annotation and composition of biosimulation models. Bioinformatics. 2018; 829. https:\/\/doi.org\/10.1093\/bioinformatics\/bty829.","journal-title":"Bioinformatics"},{"key":"2987_CR8","unstructured":"Neal ML. Modular, semantics-based composition of biosimulation models. Ph.D. Dissertation: University of Washington; 2010. https:\/\/search.proquest.com\/docview\/753931061. Accessed 21 Jan 2019."},{"issue":"5","key":"2987_CR9","doi-asserted-by":"publisher","first-page":"743","DOI":"10.1093\/bioinformatics\/btq723","volume":"27","author":"T. Yu","year":"2011","unstructured":"Yu T, Lloyd CM, Nickerson1 DP, Cooling MT, Miller AK, Garny A, Terkildsen JR, Lawson J, Britten1 RD, Hunter PJ, Nielsen PMF. The Physiome Model Repository 2. Bioinformatics. 2011; 27:743\u20134. https:\/\/doi.org\/10.1093\/bioinformatics\/btq723.","journal-title":"Bioinformatics"},{"key":"2987_CR10","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1016\/j.drudis.2012.05.016","volume":"17","author":"A J.Williams","year":"2012","unstructured":"J.Williams A, Groth LHP, Pettifer S, Chichester C, Willighagen EL, Evelo CT, Blomberg N, Ecker G, Goble C, Mons B. Open PHACTS: semantic interoperability for drug discovery. Drug Discov Today. 2012; 17:1188\u201398. \n                    https:\/\/doi.org\/10.1016\/j.drudis.2012.05.016\n                    \n                  .","journal-title":"Drug Discov Today"},{"issue":"2","key":"2987_CR11","doi-asserted-by":"publisher","first-page":"101","DOI":"10.3233\/SW-2012-0088","volume":"5","author":"AJG Gray","year":"2014","unstructured":"Gray AJG, Groth P, Loizou A, Askjaer S, Brenninkmeijer C, Burger K, Chichester C, Evelo CT, Goble C, Harland L, Pettifer S, Thompson M, Waagmeester A, Williams AJ. Applying linked data approaches to pharmacology: Architectural decisions and implementation. Semant Web. 2014; 5(2):101\u201313. \n                    https:\/\/doi.org\/10.3233\/SW-2012-0088\n                    \n                  .","journal-title":"Semant Web"},{"key":"2987_CR12","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1093\/nar\/gkw943","volume":"45","author":"J Pi\u00f1ero","year":"2017","unstructured":"Pi\u00f1ero J, \u00c0lex Bravo, Queralt-Rosinach N, Guti\u00e9rrez-Sacrist\u00e1n A, Deu-Pons J, Centeno E, Garc\u00eda-Garc\u00eda J, Sanz F, Furlong LI. DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. Nucleic Acids Res. 2017; 45:833\u20139. \n                    https:\/\/doi.org\/10.1093\/nar\/gkw943\n                    \n                  .","journal-title":"Nucleic Acids Res"},{"key":"2987_CR13","doi-asserted-by":"publisher","first-page":"028","DOI":"10.1093\/database\/bav028","volume":"2015","author":"J Pi\u00f1ero","year":"2015","unstructured":"Pi\u00f1ero J, Queralt-Rosinach N, \u00c0lex Bravo, Deu-Pons J, Bauer-Mehren A, Baron M, Sanz F, Furlong LI. DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. Database (Oxf). 2015; 2015:028. \n                    https:\/\/doi.org\/10.1093\/database\/bav028\n                    \n                  .","journal-title":"Database (Oxf)"},{"issue":"2","key":"2987_CR14","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1093\/bib\/bbn056","volume":"10","author":"M Dumontier","year":"2009","unstructured":"Dumontier M, Villanueva-Rosales N. Towards pharmacogenomics knowledge discovery with the semantic web. Brief Bioinform. 2009; 10(2):153\u201363. \n                    https:\/\/doi.org\/10.1093\/bib\/bbn056\n                    \n                  .","journal-title":"Brief Bioinform"},{"key":"2987_CR15","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-48438-9_17","volume-title":"Knowledge Discovery for Biology with Taverna","author":"C Goble","year":"2007","unstructured":"Goble C, Wolstencroft K, Goderis A, Hull D, Zhao J, Alper P, Lord P, Wroe C, Belhajjame K, Turi D, Stevens R, Oinn T, Roure DD. Knowledge Discovery for Biology with Taverna. Boston: Springer; 2007, pp. 355\u201395. \n                    https:\/\/doi.org\/10.1007\/978-0-387-48438-9\/_17\n                    \n                  ."},{"key":"2987_CR16","doi-asserted-by":"publisher","first-page":"740","DOI":"10.1177\/0037549703040939","volume":"79","author":"AA Cuellar","year":"2003","unstructured":"Cuellar AA, C.M. L, P.F. N, D.P. B, Nickerson DP, P.J. H. An overview of CellML 1.1, a biological model description language. SIMULATION. 2003; 79:740\u20137. \n                    https:\/\/doi.org\/10.1177\/0037549703040939\n                    \n                  .","journal-title":"SIMULATION"},{"issue":"2","key":"2987_CR17","doi-asserted-by":"publisher","first-page":"20150103","DOI":"10.1098\/rsfs.2015.0103","volume":"6","author":"David Nickerson","year":"2016","unstructured":"Nickerson D, Atalag K, de Bono B, Geiger J, Goble C, Hollmann S, Lonien J, M\u00fcller W, Regierer B, Stanford NJ, Golebiewski M, Hunter P. The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. Interface Focus. 2016; 6. https:\/\/doi.org\/10.1098\/rsfs.2015.0103.","journal-title":"Interface Focus"},{"key":"2987_CR18","doi-asserted-by":"publisher","DOI":"10.1002\/9781118952788.ch9","volume-title":"The Physiome Project, openEHR Archetypes, and the Digital Patient","author":"DP Nickerson","year":"2016","unstructured":"Nickerson DP, Atalag K, de Bono B, Hunter PJ. The Physiome Project, openEHR Archetypes, and the Digital Patient. Hoboken: Wiley; 2016, pp. 101\u201325. \n                    https:\/\/doi.org\/10.1002\/9781118952788.ch9\n                    \n                  ."},{"key":"2987_CR19","unstructured":"Klyne G, Carroll JJ, McBride B. RDF 1.1 Concepts and Abstract Syntax. W3C Recomm. 2019. \n                    http:\/\/www.w3.org\/TR\/2014\/REC-rdf11-concepts-20140225\/\n                    \n                  . Accessed 21 Jan."},{"key":"2987_CR20","unstructured":"COMBINE. The COmputational Modeling in Biology NEtwork (combine). 2019. http:\/\/co.mbine.org\/. Accessed 21 Jan."},{"issue":"2","key":"2987_CR21","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1093\/bib\/bby087","volume":"20","author":"Maxwell Lewis Neal","year":"2018","unstructured":"Neal ML, K\u00f6nig M, Nickerson D, M \u2223s\u2223rl\u2223 G, Kalbasi R, Dr\u00e4ger A, et al.Harmonizing semantic annotations for computational models in biology. Brief Bioinforma. 2018; 087. https:\/\/doi.org\/10.1093\/bib\/bby087.","journal-title":"Briefings in Bioinformatics"},{"key":"2987_CR22","unstructured":"Prud\u2019hommeaux E, Seaborne A. SPARQL Query Language for RDF. W3C Recomm. 2019. https:\/\/www.w3.org\/TR\/rdf-sparql-query\/. Accessed 21 Jan."},{"key":"2987_CR23","unstructured":"Cooling MT, Hunter P. The CellML Metadata Framework 2.0 Specification. J Integr Bioinforma JIB. 2015; 12(2). https:\/\/doi.org\/10.2390\/biecoll-jib-2015-260."},{"issue":"D1","key":"2987_CR24","doi-asserted-by":"publisher","first-page":"1214","DOI":"10.1093\/nar\/gkv1031","volume":"44","author":"J Hastings","year":"2015","unstructured":"Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res. 2015; 44(D1):1214\u20139. \n                    https:\/\/doi.org\/10.1093\/nar\/gkv1031\n                    \n                  .","journal-title":"Nucleic Acids Res"},{"key":"2987_CR25","doi-asserted-by":"publisher","first-page":"28708","DOI":"10.1371\/journal.pone.0028708","volume":"6","author":"DL Cook","year":"2011","unstructured":"Cook DL, Bookstein FL, Gennari JH. Physical Properties of Biological Entities: An Introduction to the Ontology of Physics for Biology. PLoS ONE. 2011; 6:28708. \n                    https:\/\/doi.org\/10.1371\/journal.pone.0028708\n                    \n                  .","journal-title":"PLoS ONE"},{"issue":"6","key":"2987_CR26","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1016\/j.jbi.2003.11.007","volume":"36","author":"C Rosse","year":"2003","unstructured":"Rosse C, Mejino JLV. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform. 2003; 36(6):478\u2013500. \n                    https:\/\/doi.org\/10.1016\/j.jbi.2003.11.007\n                    \n                  .","journal-title":"J Biomed Inform"},{"key":"2987_CR27","unstructured":"OLS. EBI Ontology Lookup Service. 2019. https:\/\/www.ebi.ac.uk\/ols\/index. Accessed 21 Jan."},{"key":"2987_CR28","doi-asserted-by":"crossref","unstructured":"Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, the rest of the SBML Forum: Arkin AP, Bornstein BJ, Bray7 D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr J-H, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Nov\u2018ere NL, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J. The systems biology markup language (sbml): a medium for representation and exchange of biochemical network models. Bioinforma Oxf J. 2003; 19:524\u201331.","DOI":"10.1093\/bioinformatics\/btg015"},{"issue":"1","key":"2987_CR29","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1085\/jgp.105.5.617","volume":"105","author":"AM Weinstein","year":"1995","unstructured":"Weinstein AM. A kinetically defined Na+\/H+ antiporter within a mathematical model of the rat proximal tubule. J Gen Physiol. 1995; 105(1):617\u201341. http:\/\/arxiv.org\/abs\/https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2216949\/.","journal-title":"J Gen Physiol"},{"key":"2987_CR30","doi-asserted-by":"crossref","unstructured":"Garny A, Hunter PJ. Opencor: a modular and interoperable approach to computational biology. Front Physiol. 2015; 6(26). https:\/\/doi.org\/10.3389\/fphys.2015.00026.","DOI":"10.3389\/fphys.2015.00026"},{"key":"2987_CR31","unstructured":"Yu T. Webservice for the Physiome Model Repository. 2019. http:\/\/aucklandphysiomerepository.readthedocs.io\/en\/latest\/webservice.html. Accessed 21 Jan."},{"key":"2987_CR32","doi-asserted-by":"publisher","first-page":"32678","DOI":"10.1074\/jbc.271.51.32678","volume":"271","author":"M Mackenzie","year":"1996","unstructured":"Mackenzie M, Loo DDF, Panayotova-Heiermann M, Wright EM. Biophysical characteristics of the pig kidney na\/glucose cotransporter sglt2 reveal a common mechanism for sglt1 and sglt2. J Biol Chem. 1996; 271:32678\u201383. \n                    https:\/\/doi.org\/10.1074\/jbc.271.51.32678\n                    \n                  .","journal-title":"J Biol Chem"},{"issue":"6","key":"2987_CR33","first-page":"931","volume":"276","author":"H Chang","year":"1999","unstructured":"Chang H, Fujita T. Am J Physiol. 1999; 276(6):931\u201351. http:\/\/arxiv.org\/abs\/https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/10362782.","journal-title":"Am J Physiol"},{"key":"2987_CR34","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/j.knosys.2013.03.012","volume":"46","author":"J Bobadilla","year":"2013","unstructured":"Bobadilla J, Ortega F, Hernando A, Guti\u00e9rrez A. Recommender systems survey. Knowl Based Syst. 2013; 46:109\u201332. \n                    https:\/\/doi.org\/10.1016\/j.knosys.2013.03.012\n                    \n                  .","journal-title":"Knowl Based Syst"},{"key":"2987_CR35","unstructured":"Almazro D, Shahatah G, Albdulkarim L, Kherees M, Martinez R, Nzoukou W. A survey paper on recommender systems. Cornell Univ Libr. 2010. https:\/\/doi.org\/arXiv:1006.5278 [cs.IR]."},{"key":"2987_CR36","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-35386-4_31","volume-title":"A Survey of Recommender Systems in Twitter","author":"SM Kywe","year":"2012","unstructured":"Kywe SM, Lim E. -P., Zhu F. A Survey of Recommender Systems in Twitter. Berlin, Heidelberg: Springer; 2012, pp. 420\u201333. \n                    https:\/\/doi.org\/10.1007\/978-3-642-35386-4\/_31\n                    \n                  ."},{"key":"2987_CR37","doi-asserted-by":"publisher","first-page":"10990","DOI":"10.1016\/j.eswa.2012.03.025","volume":"39","author":"W Carrer-Neto","year":"2012","unstructured":"Carrer-Neto W, Hern\u00e1ndez-Alcaraz ML, Valencia-Garc\u00eda R, Garc\u00eda-S\u00e1nchez F. Social knowledge-based recommender system. Application to the movies domain. Expert Syst Appl. 2012; 39:10990\u20131000. \n                    https:\/\/doi.org\/10.1016\/j.eswa.2012.03.025\n                    \n                  .","journal-title":"Expert Syst Appl"},{"key":"2987_CR38","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-85820-3\/_1","volume-title":"Introduction to Recommender Systems Handbook","author":"F Ricci","year":"1990","unstructured":"Ricci F, Rokach L, Shapira B. Introduction to Recommender Systems Handbook. Boston, MA: Springer; 1990, pp. 1\u201335. \n                    https:\/\/doi.org\/10.1007\/978-0-387-85820-3\/_1\n                    \n                  ."},{"issue":"3","key":"2987_CR39","doi-asserted-by":"publisher","first-page":"2580","DOI":"10.3390\/ijerph110302580","volume":"11","author":"M Wiesner","year":"2014","unstructured":"Wiesner M, Pfeifer D. Health Recommender Systems: Concepts, Requirements, Technical Basics and Challenges. Int J Environ Res Public Health. 2014; 11(3):2580\u2013607. \n                    https:\/\/doi.org\/10.3390\/ijerph110302580\n                    \n                  .","journal-title":"Int J Environ Res Public Health"},{"key":"2987_CR40","doi-asserted-by":"crossref","unstructured":"L\u00e9mdani R, Polaillon G, Bennacer N, Bourda Y. A semantic similarity measure for recommender systems. In: I-Semantics \u201911 Proceedings of the 7th International Conference on Semantic Systems: 2011. p. 183\u201386. https:\/\/doi.org\/10.1145\/2063518.2063545.","DOI":"10.1145\/2063518.2063545"},{"key":"2987_CR41","unstructured":"WSDbfetch. EBI webservice to get entries from various biological databases. 2019. https:\/\/www.ebi.ac.uk\/seqdb\/confluence\/pages\/viewpage.action?pageId=48923608. Accessed 21 Jan."},{"key":"2987_CR42","unstructured":"Clustal. EBI webservice to get multiple sequence alignment. 2019. https:\/\/www.ebi.ac.uk\/seqdb\/confluence\/display\/WEBSERVICES\/clustalo_rest. Accessed 21 Jan."},{"issue":"1","key":"2987_CR43","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1038\/msb.2011.75","volume":"7","author":"Fabian Sievers","year":"2011","unstructured":"Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, S\u00f6ding J, Thompson JD, Higgins DG. Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega. Mol Syst Biol. 2011; 7(1). https:\/\/doi.org\/10.1038\/msb.2011.75.","journal-title":"Molecular Systems Biology"},{"key":"2987_CR44","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-06695-0\/_12","volume-title":"Natural Language Processing for Biomedical Tools Discovery: A Feasibility Study and Preliminary Results","author":"P Sfakianaki","year":"2014","unstructured":"Sfakianaki P, Koumakis L, fakianakis S, Tsiknakis M. Natural Language Processing for Biomedical Tools Discovery: A Feasibility Study and Preliminary Results. Cham: Springer; 2014, pp. 134\u2013145. \n                    https:\/\/doi.org\/10.1007\/978-3-319-06695-0\/_12\n                    \n                  ."},{"issue":"1","key":"2987_CR45","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1186\/s12911-015-0200-4","volume":"15","author":"P Sfakianaki","year":"2015","unstructured":"Sfakianaki P, Koumakis L, Sfakianakis S, Iatraki G, Zacharioudakis G, Graf N, Marias K, Tsiknakis M. Semantic biomedical resource discovery: a Natural Language Processing framework. BMC Med Inf Decis Mak. 2015; 15(1):77. \n                    https:\/\/doi.org\/10.1186\/s12911-015-0200-4\n                    \n                  .","journal-title":"BMC Med Inf Decis Mak"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2987-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-2987-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2987-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,4]],"date-time":"2020-09-04T19:09:32Z","timestamp":1599246572000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-2987-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,9,6]]},"references-count":45,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["2987"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-2987-y","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/498501","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,9,6]]},"assertion":[{"value":"24 March 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 July 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 September 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"457"}}