{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T04:16:07Z","timestamp":1760242567203,"version":"build-2065373602"},"reference-count":51,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2017,11,16]],"date-time":"2017-11-16T00:00:00Z","timestamp":1510790400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Dutch Province of Limburg"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Algorithms"],"abstract":"<jats:p>Massive amounts of data are currently available and being produced at an unprecedented rate in all domains of life sciences worldwide. However, this data is disparately stored and is in different and unstructured formats making it very hard to integrate. In this review, we examine the state of the art and propose the use of the Linked Data (LD) paradigm, which is a set of best practices for publishing and connecting structured data on the Web in a semantically meaningful format. We argue that utilizing LD in the life sciences will make data sets better Findable, Accessible, Interoperable, and Reusable. We identify three tiers of the research cycle in life sciences, namely (i) systematic review of the existing body of knowledge, (ii) meta-analysis of data, and (iii) knowledge discovery of novel links across different evidence streams to primarily utilize the proposed LD paradigm. Finally, we demonstrate the use of LD in three use case scenarios along the same research question and discuss the future of data\/knowledge integration in life sciences and the challenges ahead.<\/jats:p>","DOI":"10.3390\/a10040126","type":"journal-article","created":{"date-parts":[[2017,11,16]],"date-time":"2017-11-16T11:10:02Z","timestamp":1510830602000},"page":"126","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Linked Data for Life Sciences"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3239-4588","authenticated-orcid":false,"given":"Amrapali","family":"Zaveri","sequence":"first","affiliation":[{"name":"Institute of Data Science, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands"}]},{"given":"G\u00f6khan","family":"Ertaylan","sequence":"additional","affiliation":[{"name":"Maastricht Centre for Systems Biology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands"}]}],"member":"1968","published-online":{"date-parts":[[2017,11,16]]},"reference":[{"key":"ref_1","first-page":"28","article-title":"The semantic web","volume":"284","author":"Hendler","year":"2001","journal-title":"Sci. Am."},{"key":"ref_2","unstructured":"Auer, S., Lehmann, J., Ngomo, A.-C.N., and Zaveri, A. (August, January 30). Introduction to linked data and its lifecycle on the web. Proceedings of the 9th International Conference on Reasoning Web: Semantic Technologies for Intelligent Data Access (RW\u201913), Mannheim, Germany."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"161","DOI":"10.36076\/ppj.2008\/11\/161","article-title":"Evidence based medicine, systematic reviews, and guidelines in interventional pain management, part I: Introduction and general considerations","volume":"11","author":"Manchikanti","year":"2008","journal-title":"Pain Phys."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1136\/bmj.312.7023.71","article-title":"Evidence based medicine: What it is and what it isn\u2019t","volume":"312","author":"Sackett","year":"1996","journal-title":"BMJ"},{"key":"ref_5","first-page":"33","article-title":"What is evidence-based medicine and the role of the systematic review: The revolution coming your way","volume":"56","author":"Manser","year":"2001","journal-title":"Monaldi Arch. Chest Dis."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Heath and Christian Bizer (2011) (2011). Linked Data: Evolving the Web into a Global Data Space, Morgan & Claypool. [1st ed.]. Synthesis Lectures on the Semantic Web: Theory and Technology.","DOI":"10.1007\/978-3-031-79432-2"},{"key":"ref_7","unstructured":"(2017, November 12). W3C: Resource Description Framework (RDF). Available online: http:\/\/www.w3.org\/RDF\/."},{"key":"ref_8","unstructured":"Auer, S., Bizer, C., Muller, C., and Zhdanova, \u2028A.V. (2007, January 26\u201328). RDF support in the virtuoso DBMS. Proceedings of the 1st Conference on Social Semantic Web, Leipzig, Germany."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Broekstra, J., Kampman, A., and van Harmelen, F. (2002). Sesame: A generic architecture for storing and querying RDF \u2028and RDF schema. Lecture Notes in Computer Science, Springer.","DOI":"10.1002\/0470858060.ch5"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3233\/SW-2011-0026","article-title":"OWLIM: A family of scalable semantic repositories","volume":"2","author":"Bishop","year":"2011","journal-title":"Semant. Web"},{"key":"ref_11","unstructured":"Clark, K.G., Feigenbaum, L., and Torres, E. (2017, November 12). SPARQL protocol for RDF. Available online: https:\/\/www.w3.org\/TR\/2008\/REC-rdf-sparql-protocol-20080115\/."},{"key":"ref_12","unstructured":"(2013, March 31). Wikipedia: SPARQL\u2014Wikipedia, the Free Encyclopedia. Available online: https:\/\/en.wikipedia.org\/wiki\/SPARQL."},{"key":"ref_13","unstructured":"Heflin, J. (2017, November 12). Owl Web Ontology Language use Cases and Requirements. Available online: https:\/\/www.w3.org\/TR\/webont-req\/."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR guiding principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1007\/978-3-319-58451-5_11","article-title":"SmartAPI: Towards a more intelligent network of Web APIs","volume":"Volume 10250","author":"Blomqvist","year":"2017","journal-title":"Proceedings of the 14th European Semantic Web Conference"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1093\/nar\/gks1193","article-title":"Ncbi geo: Archive for functional genomics data sets\u2014Update","volume":"41","author":"Barrett","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1093\/nar\/gku1057","article-title":"Arrayexpress update\u2014simplifying data submissions","volume":"43","author":"Kolesnikov","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1093\/nar\/gkw937","article-title":"The string database in 2017: Quality-controlled protein\u2013protein association networks, made broadly accessible","volume":"45","author":"Szklarczyk","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1093\/nar\/gkt1068","article-title":"Drugbank 4.0: Shedding new light on drug metabolism","volume":"42","author":"Law","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1016\/j.jbi.2008.03.004","article-title":"Bio2RDF: Towards a mashup to build bioinformatics knowledge systems","volume":"41","author":"Belleau","year":"2008","journal-title":"J. Biomed. Inform."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/S1574-1400(08)00012-1","article-title":"PubChem: Integrated platform of small molecules and biological activities","volume":"4","author":"Bolton","year":"2008","journal-title":"Annu. Rep. Comput. Chem."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"D344","DOI":"10.1093\/nar\/gkm791","article-title":"ChEBI: A database and ontology for chemical entities of biological interest","volume":"36","author":"Degtyarenko","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_23","unstructured":"Online Mendelian Inheritance in Man, OMIM\u00ae (2017, October 31). McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD, USA). Available online: https:\/\/omim.org\/."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1260419","DOI":"10.1126\/science.1260419","article-title":"Tissue-based map of the human proteome","volume":"347","author":"Fagerberg","year":"2015","journal-title":"Science"},{"key":"ref_25","unstructured":"Dimou, A., Vander Sande, M., Colpaert, P., Verborgh, R., Mannens, E., and Van de Walle, R. (2014, January 8). RML: A generic language for integrated RDF mappings of heterogeneous data. Proceedings of the 7th Workshop on Linked Data on the Web, Seoul, Korea."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.1158\/1055-9965.EPI-17-0230","article-title":"A comparative study on the wcrf international\/university of bristol methodology for systematic reviews of mechanisms underpinning exposure-cancer associations","volume":"26","author":"Ertaylan","year":"2017","journal-title":"Cancer Epidemiol. Prev. Biomark."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"924","DOI":"10.1136\/bmj.39489.470347.AD","article-title":"Grade: An emerging consensus on rating quality of evidence and strength of recommendations","volume":"336","author":"Guyatt","year":"2008","journal-title":"BMJ"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1093\/bioinformatics\/btw431","article-title":"Estimating real cell size distribution from cross-section microscopy imaging","volume":"32","author":"Lenz","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1126\/science.1132939","article-title":"The connectivity map: Using gene-expression signatures to connect small molecules, genes, and disease","volume":"313","author":"Lamb","year":"2006","journal-title":"Science"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1445","DOI":"10.1038\/srep01445","article-title":"Cancerdr: Cancer drug resistance database","volume":"3","author":"Kumar","year":"2013","journal-title":"Sci. Rep."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/nbt.3051","article-title":"Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression","volume":"33","author":"Kuffner","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Ertaylan, G.K., Okawa, S., Schwamborn, J.C., and Del Sol, A. (2014). Gene regulatory network analysis reveals differences in site-specific cell fate determination in mammalian brain. Front. Cell. Neurosci., 8.","DOI":"10.3389\/fncel.2014.00437"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"De Jaime-Soguero, A., Aulicino, F., Ertaylan, G., Griego, A., Cerrato, A., Tallam, A., Del Sol, A., Cosma, M.P., and Lluis, F. (2017). Wnt\/Tcf1 pathway restricts embryonic stem cell cycle through activation of the Ink4\/Arf locus. PLoS Genet., 13.","DOI":"10.1371\/journal.pgen.1006682"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1448","DOI":"10.1046\/j.1365-2168.2000.01610.x","article-title":"Improving the quality of reports of meta-analyses of randomised controlled trials: The QUOROM statement. QUOROM Group","volume":"87","author":"Moher","year":"2000","journal-title":"Br. J. Surg."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2008","DOI":"10.1001\/jama.283.15.2008","article-title":"Meta-analysis of observational studies in epidemiology: A proposal for reporting","volume":"283","author":"Stroup","year":"2000","journal-title":"JAMA"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1016\/S0140-6736(00)04337-3","article-title":"The CONSORT statement: Revised recommendations for improving the quality of reports of parallel-group randomised trials","volume":"357","author":"Moher","year":"2001","journal-title":"Lancet"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1136\/bmj.326.7379.41","article-title":"Towards complete and accurate reporting of studies of diagnostic accuracy: The stard initiative","volume":"326","author":"Bossuyt","year":"2003","journal-title":"BMJ"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1056\/NEJM198708133170706","article-title":"Statistical problems in the reporting of clinical trials","volume":"317","author":"Pocock","year":"1987","journal-title":"N. Engl. J. Med."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1136\/bmj.309.6960.1007","article-title":"Obtaining data from randomised controlled trials: How much do we need for reliable and informative meta-analyses?","volume":"309","author":"Clarke","year":"1994","journal-title":"BMJ"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1487","DOI":"10.1001\/jama.279.18.1487","article-title":"Beyond CONSORT: Need for improved reporting standards for clinical trials","volume":"279","author":"Meinert","year":"1998","journal-title":"JAMA"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"663","DOI":"10.7326\/0003-4819-134-8-200104170-00012","article-title":"The revised consort statement for reporting randomized trials: Explanation and elaboration","volume":"134","author":"Altman","year":"2001","journal-title":"Ann. Intern. Med."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/1745-6215-9-20","article-title":"Endorsement of the consort statement by high impact factor medical journals: A survey of journal editors and journal \u2019instructions to authors\u2019","volume":"9","author":"Hopewell","year":"2008","journal-title":"Trials"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1007\/s12021-010-9079-5","article-title":"Achieving high research reporting quality through the use of computational ontologies","volume":"8","author":"Zaveri","year":"2010","journal-title":"Neuroinformatics"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1038\/nbt0910-897","article-title":"The FEBS Letters\/BioCreative II.5 experiment: Making biological information accessible","volume":"28","author":"Leitner","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/2041-1480-5-14","article-title":"The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery","volume":"5","author":"Dumontier","year":"2014","journal-title":"J. Biomed. Semant."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Zaveri, A., Pietrobon, R., Auer, S., Lehmann, J., Martin, M., and Ermilov, T. (2011, January 22\u201327). Redd-observatory: Using the web of data for evaluating the research-disease disparity. Proceedings of the IEEE\/WIC\/ACM International Conference on Web Intelligence, Lyon, France.","DOI":"10.1109\/WI-IAT.2011.114"},{"key":"ref_47","unstructured":"Zaveri, A., Nowick, K., and Lehmann, J. (2013, January 16\u201317). Towards biomedical data integration for analyzing the evolution of cognition. Proceedings of the Ontology and Data in Life Sciences Workshop (ODLS), Koblenz, Germany."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1016\/j.drudis.2012.05.016","article-title":"Open PHACTS: Semantic interoperability for drug discovery","volume":"17","author":"Williams","year":"2012","journal-title":"Drug Discov. Today"},{"key":"ref_49","unstructured":"Jentzsch, A., Hassanzadeh, O., Bizer, C., Andersson, B., and Stephens, S. (2009, January 20). Enabling tailored therapeutics with linked data. Proceedings of the WWW Workshop on Linked Data on the Web (LDOW), Madrid, Spain."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"315","DOI":"10.3233\/SW-130102","article-title":"Publishing and interlinking the global health observatory dataset","volume":"4","author":"Zaveri","year":"2013","journal-title":"Semant. Web"},{"key":"ref_51","unstructured":"Vissoci, J.R.N., Garcia, C.R., de Andrade, L., Santana, J.E., Zaveri, A., and Pietrobon, R. (arXiv, 2013). A framework for reproducible, interactive research: Application to health and social sciences, arXiv."}],"container-title":["Algorithms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4893\/10\/4\/126\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T18:49:53Z","timestamp":1760208593000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4893\/10\/4\/126"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,11,16]]},"references-count":51,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2017,12]]}},"alternative-id":["a10040126"],"URL":"https:\/\/doi.org\/10.3390\/a10040126","relation":{},"ISSN":["1999-4893"],"issn-type":[{"type":"electronic","value":"1999-4893"}],"subject":[],"published":{"date-parts":[[2017,11,16]]}}}