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Overview of the interactive task in BioCreative V

Wang, Qinghua and Wang, Xiaodong and Van Auken, Kimberly (2016) Overview of the interactive task in BioCreative V. Database: The Journal of Biological Databases and Curation, 2016 . Art. No. baw119. ISSN 1758-0463. PMCID PMC5009325. http://resolver.caltech.edu/CaltechAUTHORS:20161018-094110037

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1093/database/baw119DOIArticle
http://database.oxfordjournals.org/content/2016/baw119PublisherArticle
http://database.oxfordjournals.org/content/2016/baw119/suppl/DC1PublisherSupplementary Data
http://www.biocreative.orgOrganizationDatabase URL
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009325/PubMed CentralArticle
ORCID:
AuthorORCID
Van Auken, Kimberly0000-0002-1706-4196
Additional Information:Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US. Received April 4, 2016. Revision received July 27, 2016. Accepted July 28, 2016. We would like to acknowledge all the users and team members who have participated in this activity throughout BioCreative. Funding: National Institutes of Health [R13GM109648 to C.N.A., P41HG003751 and U54GM114833 to K.R. and M.M.]; Intramural Research Program at National Library of Medicine to Z.L.]; National Institutes of Health Office of Director [R24OD011883 to N.V.]; the US Department of Energy [DE-SC0010838 to C.H.W. and L.H.]; National Science Foundation [#1340112 to L.C., DBI#1356374 for B.F.]; Ontario Research Fund; the European Molecular Biology Laboratory; Facultad de Ciencias, UNAM; the post-doctoral program fellowship from DGAPA-UNAM to Y.I.B.-M. Conflict of interest. None declared.
Funders:
Funding AgencyGrant Number
NIHR13GM109648
NIHP41HG003751
NIHU54GM114833
National Library of MedicineUNSPECIFIED
NIHR24OD011883
Department of Energy (DOE)DE-SC0010838
NSFIOS-1340112
NSFDBI-1356374
Ontario Research FundUNSPECIFIED
European Molecular Biology Laboratory (EMBL)UNSPECIFIED
Universidad Nacional Autónoma de México (UNAM)UNSPECIFIED
PubMed Central ID:PMC5009325
Record Number:CaltechAUTHORS:20161018-094110037
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20161018-094110037
Official Citation:Qinghua Wang, Shabbir S. Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai, Barbra Ferrell, Juliane Fluck, Socorro Gama-Castro, Nancy George, Georgios Gkoutos, Afroza K. Irin, Lars J. Jensen, Silvia Jimenez, Toni R. Jue, Ingrid Keseler, Sumit Madan, Sérgio Matos, Peter McQuilton, Marija Milacic, Matthew Mort, Jeyakumar Natarajan, Evangelos Pafilis, Emiliano Pereira, Shruti Rao, Fabio Rinaldi, Karen Rothfels, David Salgado, Raquel M. Silva, Onkar Singh, Raymund Stefancsik, Chu-Hsien Su, Suresh Subramani, Hamsa D. Tadepally, Loukia Tsaprouni, Nicole Vasilevsky, Xiaodong Wang, Andrew Chatr-Aryamontri, Stanley J. F. Laulederkind, Sherri Matis-Mitchell, Johanna McEntyre, Sandra Orchard, Sangya Pundir, Raul Rodriguez-Esteban, Kimberly Van Auken, Zhiyong Lu, Mary Schaeffer, Cathy H. Wu, Lynette Hirschman, and Cecilia N. Arighi Overview of the interactive task in BioCreative V Database 2016: baw119 doi:10.1093/database/baw119 published online September 1, 2016
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:71210
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:18 Oct 2016 17:33
Last Modified:18 Oct 2016 17:33

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