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Database (Oxford). 2016 Sep 1;2016. pii: baw119. doi: 10.1093/database/baw119. Print 2016.

Overview of the interactive task in BioCreative V.

Author information

1
Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA.
2
International Centre of Health Information Technology, Taipei Medical University, Taipei, Taiwan.
3
DETI/IEETA, University of Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal.
4
National Centre for Text Mining, University of Manchester, Manchester, UK.
5
Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México.
6
BMD Software, Aveiro, Portugal.
7
Northern Institute for Cancer Research, Newcastle University, New Castle, UK.
8
Rutgers University-Camden, Camden, NJ 08102, USA.
9
Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México.
10
Department of Botany and Plant Pathology, Oregon State University Corvallis, OR 97331, USA.
11
Department of Computer Science and Information Engineering, National Taitung University, Taitung, Taiwan.
12
College of Agriculture and Natural Resources, University of Delaware, Newark, DE 19711, USA.
13
Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, 53754 St. Augustin, Germany.
14
SourceData, EMBO, Heidelberg, Germany.
15
College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham B15 2TT, UK Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK.
16
Life Science Informatics, University of Bonn, Bonn, Germany.
17
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
18
Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL) Biotech Campus, Geneva, Switzerland.
19
Prince of Wales Clinical School, University of New South Wales NSW, Sydney, New South Wales, Australia.
20
SRI International, Menlo Park, CA 94025, USA.
21
Oxford e-Research Centre, University of Oxford, Oxford, UK.
22
Department of Informatics and Bio-Computing, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
23
HGMD, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, UK.
24
Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India.
25
Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece.
26
Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
27
Innovation Center for Biomedical Informatics (ICBI), Georgetown University, Washington, DC 20007, USA.
28
Institute of Computational Linguistics, University of Zurich, Zurich, Switzerland.
29
GMGF, Aix-Marseille Universite, 13385 Marseille, France Inserm, UMR_S 910, 13385 Marseille, France.
30
Department of Medical Sciences, iBiMED & IEETA, University of Aveiro, 3810-193 Aveiro, Portugal.
31
Taipei Medical University Graduate Institute of Biomedical informatics, Taipei, Taiwan.
32
Department of Genetics, University of Cambridge, Cambridge, UK.
33
Institute of Information Science, Academia Sinica, Taipei, Taiwan.
34
Freelance Scientific Curator, Cleveland, OH, USA.
35
Institute of Sport and Physical Activity Research (ISPAR), University of Bedfordshire, Bedford, UK.
36
Ontology Development Group, Oregon Health & Science University, Portland, OR 97239, USA.
37
WormBase Consortium, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
38
Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada.
39
Medical College of Wisconsin, Milwaukee, WI 53226, USA.
40
Reed Elsevier, Philadelphia, PA 19103, USA.
41
European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.
42
Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland.
43
National Center for Biotechnology Information (NCBI), National Institutes of Health, Bethesda, MD 20894, USA.
44
MaizeGDB USDA ARS and University of Missouri, Columbia, MO 65211, USA.
45
The MITRE Corporation, Bedford, MA 01730, USA.
46
Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA arighi@dbi.udel.edu.

Abstract

Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These systems are not meant to replace biocurators, but instead to assist them in one or more literature curation steps. To do so, the user interface is an important aspect that needs to be considered for tool adoption. The BioCreative Interactive task (IAT) is a track designed for exploring user-system interactions, promoting development of useful TM tools, and providing a communication channel between the biocuration and the TM communities. In BioCreative V, the IAT track followed a format similar to previous interactive tracks, where the utility and usability of TM tools, as well as the generation of use cases, have been the focal points. The proposed curation tasks are user-centric and formally evaluated by biocurators. In BioCreative V IAT, seven TM systems and 43 biocurators participated. Two levels of user participation were offered to broaden curator involvement and obtain more feedback on usability aspects. The full level participation involved training on the system, curation of a set of documents with and without TM assistance, tracking of time-on-task, and completion of a user survey. The partial level participation was designed to focus on usability aspects of the interface and not the performance per se In this case, biocurators navigated the system by performing pre-designed tasks and then were asked whether they were able to achieve the task and the level of difficulty in completing the task. In this manuscript, we describe the development of the interactive task, from planning to execution and discuss major findings for the systems tested.Database URL: http://www.biocreative.org.

PMID:
27589961
PMCID:
PMC5009325
DOI:
10.1093/database/baw119
[Indexed for MEDLINE]
Free PMC Article

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