Dataset search in biodiversity research: Do metadata in data repositories reflect scholarly information needs?

30. Polychronopoulos D, Almirantis Y, Krithara A, Paliouras G. Expert Team; 2013. D3.1. Available from: http://www.bioasq.org/sites/default/files/PublicDocuments/BioASQ_D3.1-ExpertTeam_final_0.pdf. 31. Thessen AE, Cui H, Mozzherin D. Applications of Natural Language Processing in Biodiversity Science. Advances in Bioinformatics. 2012; 2012(Article ID 391574):17 pages. https://doi.org/10.1155/2012/ 391574 PMID: 22685456 32. Ananiadou S, Friedman C, Tsujii J. Introduction: named entity recognition in biomedicine. Journal of Biomedical Informatics. 2004; 37(6):393—395. https://doi.org/10.1016/j.jbi.2004.08.011 33. White RW, Roth RA. Exploratory Search: Beyond the Query-Response Paradigm, Synthesis Lectures on Information Concepts, Retrieval, and Services. Marchionini G, editor. Morgan & Claypool; 2009. 34. Hearst MA. Clustering versus faceted categories for information exploration. Communications of the ACM. 2006; 49(4):59–61. https://doi.org/10.1145/1121949.1121983 35. Hildebrand M, van Ossenbruggen J, Hardman L. /facet: A Browser for Heterogeneous Semantic Web Repositories. In: Cruz I, Decker S, Allemang D, Preist C, Schwabe D, Mika P, et al., editors. The Semantic Web—ISWC 2006. Berlin, Heidelberg: Springer Berlin Heidelberg; 2006. p. 272–285. 36. Dakka W, Ipeirotis PG. Automatic Extraction of Useful Facet Hierarchies from Text Databases. In: 2008 IEEE 24th International Conference on Data Engineering; 2008. p. 466–475. 37. Xu B, Zhuge H. Automatic faceted navigation. Future Generation Computer Systems. 2014; 32:187— 197. https://doi.org/10.1016/j.future.2012.12.003

38. Moreno-Vega J, Hogan A. GraFa: Scalable Faceted Browsing for RDF Graphs. In: Vrandečić D, Bontcheva K, Sua´ rez-Figueroa MC, Presutti V, Celino I, Sabou M, et al., editors. The Semantic Web— ISWC 2018. Cham: Springer International Publishing; 2018. p. 301–317. 39. Feddoul L, Schindler S, Lo¨ffler F. Automatic Facet Generation and Selection over Knowledge Graphs. In: Acosta M, Cudre´ -Mauroux P, Maleshkova M, Pellegrini T, Sack H, Sure-Vetter Y, editors. Semantic Systems. The Power of AI and Knowledge Graphs. Cham: Springer International Publishing; 2019. p. 310–325. 40. Google; 2019. https://developers.google.com/search/docs/guides/intro-structured-data, accessed on: 20.02.2019. 41. RDA Data Discovery Paradigm Interest Group; 2019. https://www.rd-alliance.org/groups/data- discovery-paradigms-ig, accessed on: 20.2.2019. 42. Michel F, Community TB. Bioschemas & Schema.org: a Lightweight Semantic Layer for Life Sciences Websites. Biodiversity Information Science and Standards. 2018; 2:e25836. https://doi.org/10.3897/ biss.2.25836 43. Pfaff CT, Eichenberg D, Liebergesell M, Ko¨ nig-Ries B, Wirth C. Essential Annotation Schema for Ecol- ogy (EASE)—A framework supporting the efficient data annotation and faceted navigation in ecology. PLOS ONE. 2017; 12(10):1–13. https://doi.org/10.1371/journal.pone.0186170 PMID: 29023519 44. Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnol-

ogy. 2008; 889. https://doi.org/10.1038/nbt.1411 PMID: 18688244 45. Sansone SA, McQuilton P, Rocca-Serra P, Gonzalez-Beltran A, Izzo M, Lister AL, et al. FAIRsharing as a community approach to standards, repositories and policies. Nature Biotechnology. 2019; 37(4):358– 367. https://doi.org/10.1038/s41587-019-0080-8 PMID: 30940948 46. Cook B, Michener W, Vieglais D, Budden A, Koskela R. DataONE: A Distributed Environmental and Earth Science Data Network Supporting the Full Data Life Cycle. In: EGU General Assembly 2012, held 22-27 April, 2012 in Vienna, Austria., p.11863; 2012. 47. DataONE. Indexer Documentation; 2019. https://github.com/DataONEorg/indexer_documentation, accessed on 20.11.2019. 48. DataONE. Quantifying FAIR: metadata improvement and guidance in the DataONE repository network; 2019. https://www.dataone.org/webinars/quantifying-fair-metadata-improvement-and-guidance- dataone-repository-network. 49. Diepenbroek M, Glo¨ ckner F, Grobe P, Gu¨ ntsch A, Huber R, Ko¨ nig-Ries B, et al. Towards an Integrated Biodiversity and Ecological Research Data Management and Archiving Platform: GFBio. In: Informatik 2014; 2014. 50. Krallinger M, Rabal O, Leitner F, Vazquez M, Salgado D, Lu Z, et al. The CHEMDNER corpus of chemi- cals and drugs and its annotation principles. Journal of Cheminformatics. 2015; 7(1):S2. https://doi.org/ 10.1186/1758-2946-7-S1-S2 PMID: 25810773 51. Lo¨ ffler F, Pfaff CT, Karam N, Fichtmu¨ ller D, Klan F. What do Biodiversity Scholars Search for? Identify-

ing High-Level Entities for Biological Metadata. In: Algergawy A, Karam N, Klan F, Jonquet C, editors. Proceedings of the 2nd Semantics for Biodiversity Workshop held in conjunction with ISWC2017. PLOS ONE Dataset search in biodiversity research PLOS ONE | https://doi.org/10.1371/journal.pone.0246099 March 24, 2021 34 / 36