Literature DB >> 33760822

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

Felicitas Löffler1, Valentin Wesp1, Birgitta König-Ries1,2,3, Friederike Klan2,4.   

Abstract

The increasing amount of publicly available research data provides the opportunity to link and integrate data in order to create and prove novel hypotheses, to repeat experiments or to compare recent data to data collected at a different time or place. However, recent studies have shown that retrieving relevant data for data reuse is a time-consuming task in daily research practice. In this study, we explore what hampers dataset retrieval in biodiversity research, a field that produces a large amount of heterogeneous data. In particular, we focus on scholarly search interests and metadata, the primary source of data in a dataset retrieval system. We show that existing metadata currently poorly reflect information needs and therefore are the biggest obstacle in retrieving relevant data. Our findings indicate that for data seekers in the biodiversity domain environments, materials and chemicals, species, biological and chemical processes, locations, data parameters and data types are important information categories. These interests are well covered in metadata elements of domain-specific standards. However, instead of utilizing these standards, large data repositories tend to use metadata standards with domain-independent metadata fields that cover search interests only to some extent. A second problem are arbitrary keywords utilized in descriptive fields such as title, description or subject. Keywords support scholars in a full text search only if the provided terms syntactically match or their semantic relationship to terms used in a user query is known.

Entities:  

Year:  2021        PMID: 33760822      PMCID: PMC7990268          DOI: 10.1371/journal.pone.0246099

Source DB:  PubMed          Journal:  PLoS One        ISSN: 1932-6203            Impact factor:   3.240


  22 in total

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Journal:  Database (Oxford)       Date:  2017-01-01       Impact factor: 3.451

3.  GoPubMed: exploring PubMed with the Gene Ontology.

Authors:  Andreas Doms; Michael Schroeder
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

4.  Identifying gene and protein mentions in text using conditional random fields.

Authors:  Ryan McDonald; Fernando Pereira
Journal:  BMC Bioinformatics       Date:  2005-05-24       Impact factor: 3.169

5.  Ten simple rules for the care and feeding of scientific data.

Authors:  Alyssa Goodman; Alberto Pepe; Alexander W Blocker; Christine L Borgman; Kyle Cranmer; Merce Crosas; Rosanne Di Stefano; Yolanda Gil; Paul Groth; Margaret Hedstrom; David W Hogg; Vinay Kashyap; Ashish Mahabal; Aneta Siemiginowska; Aleksandra Slavkovic
Journal:  PLoS Comput Biol       Date:  2014-04-24       Impact factor: 4.475

6.  The CHEMDNER corpus of chemicals and drugs and its annotation principles.

Authors:  Martin Krallinger; Obdulia Rabal; Florian Leitner; Miguel Vazquez; David Salgado; Zhiyong Lu; Robert Leaman; Yanan Lu; Donghong Ji; Daniel M Lowe; Roger A Sayle; Riza Theresa Batista-Navarro; Rafal Rak; Torsten Huber; Tim Rocktäschel; Sérgio Matos; David Campos; Buzhou Tang; Hua Xu; Tsendsuren Munkhdalai; Keun Ho Ryu; S V Ramanan; Senthil Nathan; Slavko Žitnik; Marko Bajec; Lutz Weber; Matthias Irmer; Saber A Akhondi; Jan A Kors; Shuo Xu; Xin An; Utpal Kumar Sikdar; Asif Ekbal; Masaharu Yoshioka; Thaer M Dieb; Miji Choi; Karin Verspoor; Madian Khabsa; C Lee Giles; Hongfang Liu; Komandur Elayavilli Ravikumar; Andre Lamurias; Francisco M Couto; Hong-Jie Dai; Richard Tzong-Han Tsai; Caglar Ata; Tolga Can; Anabel Usié; Rui Alves; Isabel Segura-Bedmar; Paloma Martínez; Julen Oyarzabal; Alfonso Valencia
Journal:  J Cheminform       Date:  2015-01-19       Impact factor: 5.514

7.  Essential Annotation Schema for Ecology (EASE)-A framework supporting the efficient data annotation and faceted navigation in ecology.

Authors:  Claas-Thido Pfaff; David Eichenberg; Mario Liebergesell; Birgitta König-Ries; Christian Wirth
Journal:  PLoS One       Date:  2017-10-12       Impact factor: 3.240

8.  Semantic annotation of consumer health questions.

Authors:  Halil Kilicoglu; Asma Ben Abacha; Yassine Mrabet; Sonya E Shooshan; Laritza Rodriguez; Kate Masterton; Dina Demner-Fushman
Journal:  BMC Bioinformatics       Date:  2018-02-06       Impact factor: 3.169

9.  Environmental coupling of heritability and selection is rare and of minor evolutionary significance in wild populations.

Authors:  Jip J C Ramakers; Antica Culina; Marcel E Visser; Phillip Gienapp
Journal:  Nat Ecol Evol       Date:  2018-06-18       Impact factor: 15.460

10.  Ten Simple Rules for Creating a Good Data Management Plan.

Authors:  William K Michener
Journal:  PLoS Comput Biol       Date:  2015-10-22       Impact factor: 4.475

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  1 in total

1.  Reference bioimaging to assess the phenotypic trait diversity of bryophytes within the family Scapaniaceae.

Authors:  Kristian Peters; Birgitta König-Ries
Journal:  Sci Data       Date:  2022-10-04       Impact factor: 8.501

  1 in total

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