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@article{Li_2017, title={InterVar: Clinical Interpretation of Genetic Variants by the 2015 ACMG-AMP Guidelines}, volume={100}, ISSN={0002-9297}, url={http://dx.doi.org/10.1016/j.ajhg.2017.01.004}, DOI={10.1016/j.ajhg.2017.01.004}, number={2}, journal={The American Journal of Human Genetics}, publisher={Elsevier BV}, author={Li, Quan and Wang, Kai}, year={2017}, month={Feb}, pages={267–280}}
@article{Paila_2013, title={GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations}, volume={9}, ISSN={1553-7358}, url={http://dx.doi.org/10.1371/journal.pcbi.1003153}, DOI={10.1371/journal.pcbi.1003153}, number={7}, journal={PLoS Computational Biology}, publisher={Public Library of Science (PLoS)}, author={Paila, Umadevi and Chapman, Brad A. and Kirchner, Rory and Quinlan, Aaron R.}, editor={Gardner, Paul P.Editor}, year={2013}, month={Jul}, pages={e1003153}}
@article{J_ger_2014, title={Jannovar: A Java Library for Exome Annotation}, volume={35}, ISSN={1059-7794}, url={http://dx.doi.org/10.1002/humu.22531}, DOI={10.1002/humu.22531}, number={5}, journal={Human Mutation}, publisher={Wiley-Blackwell}, author={Jäger, Marten and Wang, Kai and Bauer, Sebastian and Smedley, Damian and Krawitz, Peter and Robinson, Peter N.}, year={2014}, month={Apr}, pages={548–555}}
@article{Cheng_2012, title={VarioWatch: providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era}, volume={40}, ISSN={1362-4962}, url={http://dx.doi.org/10.1093/nar/gks397}, DOI={10.1093/nar/gks397}, number={W1}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Cheng, Y.-C. and Hsiao, F.-C. and Yeh, E.-C. and Lin, W.-J. and Tang, C.-Y. L. and Tseng, H.-C. and Wu, H.-T. and Liu, C.-K. and Chen, C.-C. and Chen, Y.-T. and et al.}, year={2012}, month={May}, pages={W76–W81}}
@article{Miller_2015, title={A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases}, volume={7}, ISSN={1756-994X}, url={http://dx.doi.org/10.1186/s13073-015-0221-8}, DOI={10.1186/s13073-015-0221-8}, number={1}, journal={Genome Medicine}, publisher={Springer Nature}, author={Miller, Neil A. and Farrow, Emily G. and Gibson, Margaret and Willig, Laurel K. and Twist, Greyson and Yoo, Byunggil and Marrs, Tyler and Corder, Shane and Krivohlavek, Lisa and Walter, Adam and et al.}, year={2015}, month={Sep}}
@article{Kennedy_2014, title={Using VAAST to Identify Disease-Associated Variants in Next-Generation Sequencing Data}, ISBN={http://id.crossref.org/isbn/9780471142904}, url={http://dx.doi.org/10.1002/0471142905.hg0614s81}, DOI={10.1002/0471142905.hg0614s81}, journal={Current Protocols in Human Genetics}, publisher={Wiley-Blackwell}, author={Kennedy, Brett and Kronenberg, Zev and Hu, Hao and Moore, Barry and Flygare, Steven and Reese, Martin G. and Jorde, Lynn B. and Yandell, Mark and Huff, Chad}, year={2014}, month={Apr}, pages={6.14.1–6.14.25}}
@article{Brownstein_2014, title={An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge}, volume={15}, ISSN={1465-6906}, url={http://dx.doi.org/10.1186/gb-2014-15-3-r53}, DOI={10.1186/gb-2014-15-3-r53}, number={3}, journal={Genome Biology}, publisher={Springer Nature}, author={Brownstein, Catherine A and Beggs, Alan H and Homer, Nils and Merriman, Barry and Yu, Timothy W and Flannery, Katherine C and DeChene, Elizabeth T and Towne, Meghan C and Savage, Sarah K and Price, Emily N and et al.}, year={2014}, pages={R53}}
@article{van_der_Velde_2013a, title={WormQTLHD—a web database for linking human disease to natural variation data in C. elegans}, volume={42}, ISSN={1362-4962}, url={http://dx.doi.org/10.1093/nar/gkt1044}, DOI={10.1093/nar/gkt1044}, number={D1}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={van der Velde, K. Joeri and de Haan, Mark and Zych, Konrad and Arends, Danny and Snoek, L. Basten and Kammenga, Jan E. and Jansen, Ritsert C. and Swertz, Morris A. and Li, Yang}, year={2013}, month={Nov}, pages={D794–D801}}
@article{Pang_2015, title={SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data}, volume={2015}, ISSN={1758-0463}, url={http://dx.doi.org/10.1093/database/bav089}, DOI={10.1093/database/bav089}, journal={Database}, publisher={Oxford University Press (OUP)}, author={Pang, Chao and Sollie, Annet and Sijtsma, Anna and Hendriksen, Dennis and Charbon, Bart and de Haan, Mark and de Boer, Tommy and Kelpin, Fleur and Jetten, Jonathan and van der Velde, Joeri K. and et al.}, year={2015}, pages={bav089}}
@article{Ziemann_2016, title={Gene name errors are widespread in the scientific literature}, volume={17}, ISSN={1474-760X}, url={http://dx.doi.org/10.1186/s13059-016-1044-7}, DOI={10.1186/s13059-016-1044-7}, number={1}, journal={Genome Biology}, publisher={Springer Nature}, author={Ziemann, Mark and Eren, Yotam and El-Osta, Assam}, year={2016}, month={Aug}}
@article{Lappalainen_2015, title={The European Genome-phenome Archive of human data consented for biomedical research}, volume={47}, ISSN={1546-1718}, url={http://dx.doi.org/10.1038/ng.3312}, DOI={10.1038/ng.3312}, number={7}, journal={Nature Genetics}, publisher={Springer Nature}, author={Lappalainen, Ilkka and Almeida-King, Jeff and Kumanduri, Vasudev and Senf, Alexander and Spalding, John Dylan and ur-Rehman, Saif and Saunders, Gary and Kandasamy, Jag and Caccamo, Mario and Leinonen, Rasko and et al.}, year={2015}, month={Jun}, pages={692–695}}
@article{Byron_2016, title={Translating RNA sequencing into clinical diagnostics: opportunities and challenges}, volume={17}, ISSN={1471-0064}, url={http://dx.doi.org/10.1038/nrg.2016.10}, DOI={10.1038/nrg.2016.10}, number={5}, journal={Nature Reviews Genetics}, publisher={Springer Nature}, author={Byron, Sara A. and Van Keuren-Jensen, Kendall R. and Engelthaler, David M. and Carpten, John D. and Craig, David W.}, year={2016}, month={Mar}, pages={257–271}}
@article{Heyn_2012, title={DNA methylation profiling in the clinic: applications and challenges}, volume={13}, ISSN={1471-0064}, url={http://dx.doi.org/10.1038/nrg3270}, DOI={10.1038/nrg3270}, number={10}, journal={Nature Reviews Genetics}, publisher={Springer Nature}, author={Heyn, Holger and Esteller, Manel}, year={2012}, month={Sep}, pages={679–692}}
@article{Gargalionis_2012, title={Histone modifications as a pathogenic mechanism of colorectal tumorigenesis}, volume={44}, ISSN={1357-2725}, url={http://dx.doi.org/10.1016/j.biocel.2012.05.002}, DOI={10.1016/j.biocel.2012.05.002}, number={8}, journal={The International Journal of Biochemistry \& Cell Biology}, publisher={Elsevier BV}, author={Gargalionis, Antonios N. and Piperi, Christina and Adamopoulos, Christos and Papavassiliou, Athanasios G.}, year={2012}, month={Aug}, pages={1276–1289}}
@article{Raes_2016, title={Microbiome-based companion diagnostics: no longer science fiction?}, volume={65}, ISSN={1468-3288}, url={http://dx.doi.org/10.1136/gutjnl-2015-311015}, DOI={10.1136/gutjnl-2015-311015}, number={6}, journal={Gut}, publisher={BMJ}, author={Raes, J}, year={2016}, month={Jan}, pages={896–897}}
@article{Bonder_2016, title={The effect of host genetics on the gut microbiome}, volume={48}, ISSN={1546-1718}, url={http://dx.doi.org/10.1038/ng.3663}, DOI={10.1038/ng.3663}, number={11}, journal={Nature Genetics}, publisher={Springer Nature}, author={Bonder, Marc Jan and Kurilshikov, Alexander and Tigchelaar, Ettje F and Mujagic, Zlatan and Imhann, Floris and Vila, Arnau Vich and Deelen, Patrick and Vatanen, Tommi and Schirmer, Melanie and Smeekens, Sanne P and et al.}, year={2016}, month={Oct}, pages={1407–1412}}
@article{Heiner_Fokkema_2016, title={Reliable Diagnosis of Carnitine Palmitoyltransferase Type IA Deficiency by Analysis of Plasma Acylcarnitine Profiles}, ISSN={2192-8312}, url={http://dx.doi.org/10.1007/8904_2016_564}, DOI={10.1007/8904_2016_564}, journal={JIMD Reports}, publisher={Springer Nature}, author={Heiner-Fokkema, M. Rebecca and Vaz, Frédéric M. and Maatman, Ronald and Kluijtmans, Leo A. J. and van Spronsen, Francjan J. and Reijngoud, Dirk-Jan}, year={2016}}
@article{Miller_2015b, title={Untargeted metabolomic analysis for the clinical screening of inborn errors of metabolism}, volume={38}, ISSN={1573-2665}, url={http://dx.doi.org/10.1007/s10545-015-9843-7}, DOI={10.1007/s10545-015-9843-7}, number={6}, journal={Journal of Inherited Metabolic Disease}, publisher={Springer Nature}, author={Miller, Marcus J. and Kennedy, Adam D. and Eckhart, Andrea D. and Burrage, Lindsay C. and Wulff, Jacob E. and Miller, Luke A.D. and Milburn, Michael V. and Ryals, John A. and Beaudet, Arthur L. and Sun, Qin and et al.}, year={2015}, month={Apr}, pages={1029–1039}}
@article{Gowda_2008, title={Metabolomics-based methods for early disease diagnostics}, volume={8}, ISSN={1744-8352}, url={http://dx.doi.org/10.1586/14737159.8.5.617}, DOI={10.1586/14737159.8.5.617}, number={5}, journal={Expert Review of Molecular Diagnostics}, publisher={Informa Healthcare}, author={Gowda, GA Nagana and Zhang, Shucha and Gu, Haiwei and Asiago, Vincent and Shanaiah, Narasimhamurthy and Raftery, Daniel}, year={2008}, month={Sep}, pages={617–633}}
@article{Hanash_2003, title={Disease proteomics}, volume={422}, ISSN={0028-0836}, url={http://dx.doi.org/10.1038/nature01514}, DOI={10.1038/nature01514}, number={6928}, journal={Nature}, publisher={Springer Nature}, author={Hanash, Sam}, year={2003}, month={Mar}, pages={226–232}}
@article{F_z_ry_2013, title={Translation of proteomic biomarkers into FDA approved cancer diagnostics: issues and challenges}, volume={10}, ISSN={1559-0275}, url={http://dx.doi.org/10.1186/1559-0275-10-13}, DOI={10.1186/1559-0275-10-13}, number={1}, journal={Clinical Proteomics}, publisher={Springer Nature}, author={Füzéry, Anna K and Levin, Joshua and Chan, Maria M and Chan, Daniel W}, year={2013}, pages={13}}
@article{Gstaiger_2009, title={Applying mass spectrometry-based proteomics to genetics, genomics and network biology}, volume={10}, ISSN={1471-0064}, url={http://dx.doi.org/10.1038/nrg2633}, DOI={10.1038/nrg2633}, number={9}, journal={Nature Reviews Genetics}, publisher={Springer Nature}, author={Gstaiger, Matthias and Aebersold, Ruedi}, year={2009}, month={Sep}, pages={617–627}}
@inproceedings{Resnik:1995:UIC:1625855.1625914, author = {Resnik, Philip}, title = {Using Information Content to Evaluate Semantic Similarity in a Taxonomy}, booktitle = {Proceedings of the 14th International Joint Conference on Artificial Intelligence - Volume 1}, series = {IJCAI'95}, year = {1995}, isbn = {1-55860-363-8, 978-1-558-60363-9}, location = {Montreal, Quebec, Canada}, pages = {448--453}, numpages = {6}, url = {http://dl.acm.org/citation.cfm?id=1625855.1625914}, acmid = {1625914}, publisher = {Morgan Kaufmann Publishers Inc.}, address = {San Francisco, CA, USA}}
@article{Mina2015, author="Mina, Eleni and Thompson, Mark and Kaliyaperumal, Rajaram and Zhao, Jun and der Horst, van Eelke and Tatum, Zuotian and Hettne, Kristina M. and Schultes, Erik A. and Mons, Barend and Roos, Marco", title="Nanopublications for exposing experimental data in the life-sciences: a Huntington's Disease case study", journal="Journal of Biomedical Semantics", year="2015", volume="6", number="1", pages="5", abstract="Data from high throughput experiments often produce far more results than can ever appear in the main text or tables of a single research article. In these cases, the majority of new associations are often archived either as supplemental information in an arbitrary format or in publisher-independent databases that can be difficult to find. These data are not only lost from scientific discourse, but are also elusive to automated search, retrieval and processing. Here, we use the nanopublication model to make scientific assertions that were concluded from a workflow analysis of Huntington's Disease data machine-readable, interoperable, and citable. We followed the nanopublication guidelines to semantically model our assertions as well as their provenance metadata and authorship. We demonstrate interoperability by linking nanopublication provenance to the Research Object model. These results indicate that nanopublications can provide an incentive for researchers to expose data that is interoperable and machine-readable for future use and preservation for which they can get credits for their effort. Nanopublications can have a leading role into hypotheses generation offering opportunities to produce large-scale data integration.", issn="2041-1480", doi="10.1186/2041-1480-6-5", url="http://dx.doi.org/10.1186/2041-1480-6-5" }
@article{Walter_2015, title={The UK10K project identifies rare variants in health and disease}, volume={526}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/nature14962}, DOI={10.1038/nature14962}, number={7571}, journal={Nature}, publisher={Springer Nature}, author={Walter, Klaudia and Min, Josine L. and Huang, Jie and Crooks, Lucy and Memari, Yasin and McCarthy, Shane and Perry, John R. B. and Xu, ChangJiang and Futema, Marta and Lawson, Daniel and et al.}, year={2015}, month={Sep}, pages={82–90}}
@article{van_der_Velde_2017, title={GAVIN: Gene-Aware Variant INterpretation for medical sequencing}, volume={18}, ISSN={1474-760X}, url={http://dx.doi.org/10.1186/s13059-016-1141-7}, DOI={10.1186/s13059-016-1141-7}, number={1}, journal={Genome Biology}, publisher={Springer Nature}, author={van der Velde, K. Joeri and de Boer, Eddy N. and van Diemen, Cleo C. and Sikkema-Raddatz, Birgit and Abbott, Kristin M. and Knopperts, Alain and Franke, Lude and Sijmons, Rolf H. and de Koning, Tom J. and Wijmenga, Cisca and et al.}, year={2017}, month={Jan}}
@article{Brookes_2015, title={Human genotype–phenotype databases: aims, challenges and opportunities}, volume={16}, ISSN={1471-0064}, url={http://dx.doi.org/10.1038/nrg3932}, DOI={10.1038/nrg3932}, number={12}, journal={Nature Reviews Genetics}, publisher={Springer Nature}, author={Brookes, Anthony J. and Robinson, Peter N.}, year={2015}, month={Nov}, pages={702–715}}
@article{Jupp_2014, title={The EBI RDF platform: linked open data for the life sciences}, volume={30}, ISSN={1460-2059}, url={http://dx.doi.org/10.1093/bioinformatics/btt765}, DOI={10.1093/bioinformatics/btt765}, number={9}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Jupp, S. and Malone, J. and Bolleman, J. and Brandizi, M. and Davies, M. and Garcia, L. and Gaulton, A. and Gehant, S. and Laibe, C. and Redaschi, N. and et al.}, year={2014}, month={Jan}, pages={1338–1339}}
@article{Anguita_2013, title={NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases}, volume={2013}, ISSN={2314-6141}, url={http://dx.doi.org/10.1155/2013/983805}, DOI={10.1155/2013/983805}, journal={BioMed Research International}, publisher={Hindawi Publishing Corporation}, author={Anguita, Alberto and García-Remesal, Miguel and de la Iglesia, Diana and Maojo, Victor}, year={2013}, pages={1–9}}
@article{Pang_2014, title={BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing}, ISSN={1527-974X}, url={http://dx.doi.org/10.1136/amiajnl-2013-002577}, DOI={10.1136/amiajnl-2013-002577}, journal={Journal of the American Medical Informatics Association}, publisher={Oxford University Press (OUP)}, author={Pang, C. and Hendriksen, D. and Dijkstra, M. and van der Velde, K. J. and Kuiper, J. and Hillege, H. and Swertz, M.}, year={2014}, month={Oct}}
@article{Callahan_2011, title={HyQue: evaluating hypotheses using Semantic Web technologies}, volume={2}, ISSN={2041-1480}, url={http://dx.doi.org/10.1186/2041-1480-2-S2-S3}, DOI={10.1186/2041-1480-2-s2-s3}, number={Suppl 2}, journal={Journal of Biomedical Semantics}, publisher={Springer Nature}, author={Callahan, Alison and Dumontier, Michel and Shah, Nigam H}, year={2011}, pages={S3}}
@article{Wolstencroft_2013, title={The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud}, volume={41}, ISSN={1362-4962}, url={http://dx.doi.org/10.1093/nar/gkt328}, DOI={10.1093/nar/gkt328}, number={W1}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Wolstencroft, K. and Haines, R. and Fellows, D. and Williams, A. and Withers, D. and Owen, S. and Soiland-Reyes, S. and Dunlop, I. and Nenadic, A. and Fisher, P. and et al.}, year={2013}, month={May}, pages={W557–W561}}
@article{Amstutz2016, author={Peter Amstutz and Michael R. Crusoe and Nebojša Tijanić and Brad Chapman and John Chilton and Michael Heuer and Andrey Kartashov and Dan Leehr and Hervé Ménager and Maya Nedeljkovich and Matt Scales and Stian Soiland-Reyes and Luka Stojanovic}, title={Common Workflow Language, v1.0}, year={2016} ,month={7}, url={https://figshare.com/articles/Common_Workflow_Language_draft_3/3115156}, doi={10.6084/m9.figshare.3115156.v2}, journal={Figshare}}
@article{Wilkinson_2010, title={SADI, SHARE, and the in silico scientific method}, volume={11}, ISSN={1471-2105}, url={http://dx.doi.org/10.1186/1471-2105-11-S12-S7}, DOI={10.1186/1471-2105-11-s12-s7}, number={Suppl 12}, journal={BMC Bioinformatics}, publisher={Springer Nature}, author={Wilkinson, Mark D and McCarthy, Luke and Vandervalk, Benjamin and Withers, David and Kawas, Edward and Samadian, Soroush}, year={2010}, pages={S7}}
@article{Withers_2010, title={Semantically-Guided Workflow Construction in Taverna: The SADI and BioMoby Plug-Ins}, ISBN={http://id.crossref.org/isbn/978-3-642-16558-0}, ISSN={1611-3349}, url={http://dx.doi.org/10.1007/978-3-642-16558-0_26}, DOI={10.1007/978-3-642-16558-0_26}, journal={Leveraging Applications of Formal Methods, Verification, and Validation}, publisher={Springer Nature}, author={Withers, David and Kawas, Edward and McCarthy, Luke and Vandervalk, Benjamin and Wilkinson, Mark}, year={2010}, pages={301–312}}
@article{Goble_2010, title={myExperiment: a repository and social network for the sharing of bioinformatics workflows}, volume={38}, ISSN={1362-4962}, url={http://dx.doi.org/10.1093/nar/gkq429}, DOI={10.1093/nar/gkq429}, number={Web Server}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Goble, C. A. and Bhagat, J. and Aleksejevs, S. and Cruickshank, D. and Michaelides, D. and Newman, D. and Borkum, M. and Bechhofer, S. and Roos, M. and Li, P. and et al.}, year={2010}, month={May}, pages={W677–W682}}
@article{Wallis_2013, title={Practice guidelines for the evaluation of pathogenicity and the reporting of sequence variants in clinical molecular genetics}, author={Wallis, Yvonne and Payne, Stewart and McAnulty, Ciaron and Bodmer, Danielle and Sistermans, Erik and Robertson, Kathryn and Moore, David and Abbs, Stephen and Deans, Zandra and Devereau, Andrew}, journal={Association for Clinical Genetic Science and the Dutch Society of Clinical Genetic Laboratory Specialists}, year={2013}}
@article{Ritchie_2015, title={Methods of integrating data to uncover genotype–phenotype interactions}, volume={16}, ISSN={1471-0064}, url={http://dx.doi.org/10.1038/nrg3868}, DOI={10.1038/nrg3868}, number={2}, journal={Nature Reviews Genetics}, publisher={Springer Nature}, author={Ritchie, Marylyn D. and Holzinger, Emily R. and Li, Ruowang and Pendergrass, Sarah A. and Kim, Dokyoon}, year={2015}, month={Jan}, pages={85–97}}
@article{Eriksson_2003, title={Recurrent de novo point mutations in lamin A cause Hutchinson–Gilford progeria syndrome}, volume={423}, ISSN={0028-0836}, url={http://dx.doi.org/10.1038/nature01629}, DOI={10.1038/nature01629}, number={6937}, journal={Nature}, publisher={Springer Nature}, author={Eriksson, Maria and Brown, W. Ted and Gordon, Leslie B. and Glynn, Michael W. and Singer, Joel and Scott, Laura and Erdos, Michael R. and Robbins, Christiane M. and Moses, Tracy Y. and Berglund, Peter and et al.}, year={2003}, month={Apr}, pages={293–298}}
@article{Shawky_2014, title={Reduced penetrance in human inherited disease}, volume={15}, ISSN={1110-8630}, url={http://dx.doi.org/10.1016/j.ejmhg.2014.01.003}, DOI={10.1016/j.ejmhg.2014.01.003}, number={2}, journal={Egyptian Journal of Medical Human Genetics}, publisher={Elsevier BV}, author={Shawky, Rabah M.}, year={2014}, month={Apr}, pages={103–111}}
@article{Sanger_1977, title={DNA sequencing with chain-terminating inhibitors}, volume={74}, url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC431765/}, number={12}, journal={Proc Natl Acad Sci U S A.}, publisher={}, author={Sanger, F. and Nicklen, S. and Coulson, A.R.}, year={1977}, month={December}, pages={5463–5467}}
@book{RDF-PRIMER, citeulike-article-id = {498572}, citeulike-linkout-0 = {http://www.w3.org/TR/rdf-primer/}, day = {10}, editor = {Manola, Frank and Miller, Eric}, institution = {W3C}, keywords = {dt, dt-n7, rdf, w3c}, month = feb, posted-at = {2007-08-13 07:57:25}, priority = {2}, publisher = {World Wide Web Consortium}, series = {W3C Recommendation}, title = {{RDF Primer}}, url = {http://www.w3.org/TR/rdf-primer/}, year = {2004}}
@techreport{Prudhommeaux08, citeulike-article-id = {2620569}, day = {15}, editor = {Prud'hommeaux, Eric and Seaborne, Andy}, howpublished = {W3C Recommendation}, institution = {World Wide Web Consortium}, keywords = {dea, semantic}, month = jan, posted-at = {2008-04-01 17:47:43}, priority = {2}, title = {{SPARQL} Query Language for {RDF}}, year = {2008}}
@article{Sansone_2012, title={Toward interoperable bioscience data}, volume={44}, ISSN={1546-1718}, url={http://dx.doi.org/10.1038/ng.1054}, DOI={10.1038/ng.1054}, number={2}, journal={Nature Genetics}, publisher={Springer Nature}, author={Sansone, Susanna-Assunta and Rocca-Serra, Philippe and Field, Dawn and Maguire, Eamonn and Taylor, Chris and Hofmann, Oliver and Fang, Hong and Neumann, Steffen and Tong, Weida and Amaral-Zettler, Linda and et al.}, year={2012}, month={Jan}, pages={121–126}}
@article{Wolstencroft_2016, title={FAIRDOMHub: a repository and collaboration environment for sharing systems biology research}, volume={45}, ISSN={1362-4962}, url={http://dx.doi.org/10.1093/nar/gkw1032}, DOI={10.1093/nar/gkw1032}, number={D1}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Wolstencroft, Katherine and Krebs, Olga and Snoep, Jacky L. and Stanford, Natalie J. and Bacall, Finn and Golebiewski, Martin and Kuzyakiv, Rostyk and Nguyen, Quyen and Owen, Stuart and Soiland-Reyes, Stian and et al.}, year={2016}, month={Nov}, pages={D404–D407}}
@article{Crosas_2016, title={The Rise of Data Publishing (and how Dataverse 4 can help)}, journal={Journal of Technology Science}, year={Working Paper}, abstract={\ The research community needs reliable, standard ways to make the data produced by scientific research available to the community, while getting credit\ as data authors. As a result, a new form of scholarly publication is emerging: data publishing. Data pubishing - or making data long-term accessible, reusable\ and citable - is more involved than simply providing\ a link to a data file or posting the data to the researchers web site. In this paper, we define what is\ needed for proper data publishing and describe how the\ open-source Dataverse software helps define, enable and\ enhance data publishing for all.}, url={http://scholar.harvard.edu/mercecrosas/publications/dataverse-4-defining-data-publishing}, author={Merc{\`e} Crosas}}
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