Dataset search in biodiversity research: Do metadata in data repositories reflect scholarly information needs?
pmc-PMC7990268.pdf · Phiên bản 1 · 36 trang
4. Khalsa S, Cotroneo P, Wu M. A survey of current practices in data search services. Research Data Alli- ance Data (RDA) Discovery Paradigms Interest Group; 2018. 5. Kacprzak E, Koesten L, Iba´ ñez LD, Blount T, Tennison J, Simperl E. Characterising dataset search— An analysis of search logs and data requests. Journal of Web Semantics. 2018; https://doi.org/10.1016/ j.websem.2018.11.003. 6. Parker TH, Forstmeier W, Koricheva J, Fidler F, Hadfield JD, Chee YE, et al. Transparency in Ecology and Evolution: Real Problems, Real Solutions. Trends in Ecology & Evolution. 2016; 31(9):711—719. https://doi.org/10.1016/j.tree.2016.07.002 PMID: 27461041 7. Ramakers J, Culina A, Visser M, Gienapp P. Environmental coupling of heritability and selection is rare and of minor evolutionary significance in wild populations. Nature Ecology & Evolution. 2018;. https:// doi.org/10.1038/s41559-018-0577-4 PMID: 29915341 8. Gregory K, Groth P, Scharnhorst A, Wyatt S. Lost or Found? Discovering Data Needed for Research. Harvard Data Science Review. 2020;. https://doi.org/10.1162/99608f92.30a5e938 9. Kilicoglu H, Ben Abacha A, Mrabet Y, Shooshan SE, Rodriguez L, Masterton K, et al. Semantic annota- tion of consumer health questions. BMC Bioinformatics. 2018; 19(1):34. https://doi.org/10.1186/ s12859-018-2045-1 PMID: 29409442 10. Nentidis A, Bougiatiotis K, Krithara A, Paliouras G, Kakadiaris I. Results of the fifth edition of the BioASQ Challenge. In: BioNLP 2017. Vancouver, Canada,: Association for Computational Linguistics;
2017. p. 48–57. Available from: http://www.aclweb.org/anthology/W17-2306. 11. Wilkinson M, Dumontier M, Aalbersberg Iea. The FAIR Guiding Principles for scientific data manage- ment and stewardship. Scientific Data. 2016; 3(1):160018. https://doi.org/10.1038/sdata.2016.18 PMID: 26978244 12. Manning CD, Raghavan P, Schu¨tze H. Introduction to Information Retrieval. New York, NY, USA: Cambridge University Press; 2008. 13. Croft B, Metzler D, Strohman T. Search Engines: Information Retrieval in Practice. 1st ed. USA: Addi- son-Wesley Publishing Company; 2009. 14. AquaDiva. CRC AquaDiva; 2020. http://www.aquadiva.uni-jena.de/, accessed on 12.01.2020. 15. GFBio. The German Federation for Biological Data; 2020. https://www.gfbio.org, accessed on 12.01.2020. 16. Nature. Scientific Data, Recommended Data Repositories; 2018. https://www.nature.com/sdata/ policies/repositories, accessed on 18.12.2018. 17. Dryad; 2019. https://datadryad.org/, accessed on 16.05.2019. 18. Zenodo; 2019. https://zenodo.org/, accessed on 16.05.2019. 19. Figshare; 2019. https://figshare.com/, accessed on 16.05.2019. 20. Pangaea. Data Publisher for Earth & Environmental Science; 2019. https://www.pangaea.de/, accessed on 30.11.2019. 21. GBIF. Global Biodiversity Information Facility; 2020. https://www.gbif.org/, accessed on 12.01.2020. 22. Chapman A, Simperl E, Koesten L, Konstantinidis G, Iba´ ñez LD, Kacprzak E, et al. Dataset search: a survey. The VLDB Journal. 2019;. https://doi.org/10.1007/s00778-019-00564-x
23. Unger C, Freitas A, Cimiano P. In: Koubarakis M, Stamou G, Stoilos G, Horrocks I, Kolaitis P, Lausen G, et al., editors. An Introduction to Question Answering over Linked Data. Springer International Pub- lishing; 2014. p. 100–140. 24. Jurafsky D, Martin JH. Speech and Language Processing: An Introduction to Natural Language Pro- cessing, Computational Linguistics, and Speech Recognition. 1st ed. Upper Saddle River, NJ, USA: Prentice Hall PTR; 2008. 25. Roberts K, Gururaj AE, Chen X, Pournejati S, Hersh WR, Demner-Fushman D, et al. Information retrieval for biomedical datasets: the 2016 bioCADDIE dataset retrieval challenge. Database. 2017;. https://doi.org/10.1093/database/bax068 26. Chamanara J, Ko¨nig-Ries B, Jagadish HV. QUIS: In-situ Heterogeneous Data Source Querying. Proc VLDB Endow. 2017; 10(12):1877–1880. https://doi.org/10.14778/3137765.3137798 27. Faith D, Collen B, Arturo A, Koleff P, Guinotte J, Kerr J, et al. Bridging the biodiversity data gaps: Rec- ommendations to meet users’ data needs. Biodiversity Informatics. 2013; 8(2). https://doi.org/10. 17161/bi.v8i2.4126 28. Ariño AH, Chavan V, Faith DP. Assessment of user needs of primary biodiversity data: Analysis, con- cerns, and challenges. Biodiversity Informatics. 2013; 8(2). 29. Hersh W, Voorhees E. TREC genomics special issue overview. Information Retrieval. 2009; 12(1):1– 15. https://doi.org/10.1007/s10791-008-9076-6 PLOS ONE Dataset search in biodiversity research PLOS ONE | https://doi.org/10.1371/journal.pone.0246099 March 24, 2021 33 / 36