Overview of the interactive task in BioCreative V

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 JimenezToni R. Jue, Ingrid Keseler, Sumit Madan, Sergio 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, Cecilia N. Arighi

Research output: Contribution to journalArticle

14 Citations (Scopus)

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 predesigned 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.

Original languageEnglish
Article numberbaw119
JournalDatabase
Volume2016
DOIs
Publication statusPublished - 2016

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Data Mining
User interfaces
Feedback
Planning
user interface
planning

ASJC Scopus subject areas

  • Medicine(all)
  • Information Systems
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Wang, Q., Abdul, S. S., Almeida, L., Ananiadou, S., Balderas-Martínez, Y. I., Batista-Navarro, R., ... Arighi, C. N. (2016). Overview of the interactive task in BioCreative V. Database, 2016, [baw119]. https://doi.org/10.1093/database/baw119

Overview of the interactive task in BioCreative V. / Wang, Qinghua; Abdul, Shabbir S.; Almeida, Lara; Ananiadou, Sophia; Balderas-Martínez, Yalbi I.; Batista-Navarro, Riza; Campos, David; Chilton, Lucy; Chou, Hui Jou; Contreras, Gabriela; Cooper, Laurel; Dai, Hong Jie; Ferrell, Barbra; Fluck, Juliane; Gama-Castro, Socorro; George, Nancy; Gkoutos, Georgios; Irin, Afroza K.; Jensen, Lars J.; Jimenez, Silvia; Jue, Toni R.; Keseler, Ingrid; Madan, Sumit; Matos, Sergio; McQuilton, Peter; Milacic, Marija; Mort, Matthew; Natarajan, Jeyakumar; Pafilis, Evangelos; Pereira, Emiliano; Rao, Shruti; Rinaldi, Fabio; Rothfels, Karen; Salgado, David; Silva, Raquel M.; Singh, Onkar; Stefancsik, Raymund; Su, Chu Hsien; Subramani, Suresh; Tadepally, Hamsa D.; Tsaprouni, Loukia; Vasilevsky, Nicole; Wang, Xiaodong; Chatr-Aryamontri, Andrew; Laulederkind, Stanley J F; Matis-Mitchell, Sherri; McEntyre, Johanna; Orchard, Sandra; Pundir, Sangya; Rodriguez-Esteban, Raul; Van Auken, Kimberly; Lu, Zhiyong; Schaeffer, Mary; Wu, Cathy H.; Hirschman, Lynette; Arighi, Cecilia N.

In: Database, Vol. 2016, baw119, 2016.

Research output: Contribution to journalArticle

Wang, Q, Abdul, SS, Almeida, L, Ananiadou, S, Balderas-Martínez, YI, Batista-Navarro, R, Campos, D, Chilton, L, Chou, HJ, Contreras, G, Cooper, L, Dai, HJ, Ferrell, B, Fluck, J, Gama-Castro, S, George, N, Gkoutos, G, Irin, AK, Jensen, LJ, Jimenez, S, Jue, TR, Keseler, I, Madan, S, Matos, S, McQuilton, P, Milacic, M, Mort, M, Natarajan, J, Pafilis, E, Pereira, E, Rao, S, Rinaldi, F, Rothfels, K, Salgado, D, Silva, RM, Singh, O, Stefancsik, R, Su, CH, Subramani, S, Tadepally, HD, Tsaprouni, L, Vasilevsky, N, Wang, X, Chatr-Aryamontri, A, Laulederkind, SJF, Matis-Mitchell, S, McEntyre, J, Orchard, S, Pundir, S, Rodriguez-Esteban, R, Van Auken, K, Lu, Z, Schaeffer, M, Wu, CH, Hirschman, L & Arighi, CN 2016, 'Overview of the interactive task in BioCreative V', Database, vol. 2016, baw119. https://doi.org/10.1093/database/baw119
Wang Q, Abdul SS, Almeida L, Ananiadou S, Balderas-Martínez YI, Batista-Navarro R et al. Overview of the interactive task in BioCreative V. Database. 2016;2016. baw119. https://doi.org/10.1093/database/baw119
Wang, Qinghua ; Abdul, Shabbir S. ; Almeida, Lara ; Ananiadou, Sophia ; Balderas-Martínez, Yalbi I. ; Batista-Navarro, Riza ; Campos, David ; Chilton, Lucy ; Chou, Hui Jou ; Contreras, Gabriela ; Cooper, Laurel ; Dai, Hong Jie ; Ferrell, Barbra ; Fluck, Juliane ; Gama-Castro, Socorro ; George, Nancy ; Gkoutos, Georgios ; Irin, Afroza K. ; Jensen, Lars J. ; Jimenez, Silvia ; Jue, Toni R. ; Keseler, Ingrid ; Madan, Sumit ; Matos, Sergio ; McQuilton, Peter ; Milacic, Marija ; Mort, Matthew ; Natarajan, Jeyakumar ; Pafilis, Evangelos ; Pereira, Emiliano ; Rao, Shruti ; Rinaldi, Fabio ; Rothfels, Karen ; Salgado, David ; Silva, Raquel M. ; Singh, Onkar ; Stefancsik, Raymund ; Su, Chu Hsien ; Subramani, Suresh ; Tadepally, Hamsa D. ; Tsaprouni, Loukia ; Vasilevsky, Nicole ; Wang, Xiaodong ; Chatr-Aryamontri, Andrew ; Laulederkind, Stanley J F ; Matis-Mitchell, Sherri ; McEntyre, Johanna ; Orchard, Sandra ; Pundir, Sangya ; Rodriguez-Esteban, Raul ; Van Auken, Kimberly ; Lu, Zhiyong ; Schaeffer, Mary ; Wu, Cathy H. ; Hirschman, Lynette ; Arighi, Cecilia N. / Overview of the interactive task in BioCreative V. In: Database. 2016 ; Vol. 2016.
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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 predesigned 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.",
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AU - Wang, Qinghua

AU - Abdul, Shabbir S.

AU - Almeida, Lara

AU - Ananiadou, Sophia

AU - Balderas-Martínez, Yalbi I.

AU - Batista-Navarro, Riza

AU - Campos, David

AU - Chilton, Lucy

AU - Chou, Hui Jou

AU - Contreras, Gabriela

AU - Cooper, Laurel

AU - Dai, Hong Jie

AU - Ferrell, Barbra

AU - Fluck, Juliane

AU - Gama-Castro, Socorro

AU - George, Nancy

AU - Gkoutos, Georgios

AU - Irin, Afroza K.

AU - Jensen, Lars J.

AU - Jimenez, Silvia

AU - Jue, Toni R.

AU - Keseler, Ingrid

AU - Madan, Sumit

AU - Matos, Sergio

AU - McQuilton, Peter

AU - Milacic, Marija

AU - Mort, Matthew

AU - Natarajan, Jeyakumar

AU - Pafilis, Evangelos

AU - Pereira, Emiliano

AU - Rao, Shruti

AU - Rinaldi, Fabio

AU - Rothfels, Karen

AU - Salgado, David

AU - Silva, Raquel M.

AU - Singh, Onkar

AU - Stefancsik, Raymund

AU - Su, Chu Hsien

AU - Subramani, Suresh

AU - Tadepally, Hamsa D.

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AU - Vasilevsky, Nicole

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AU - Chatr-Aryamontri, Andrew

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AU - McEntyre, Johanna

AU - Orchard, Sandra

AU - Pundir, Sangya

AU - Rodriguez-Esteban, Raul

AU - Van Auken, Kimberly

AU - Lu, Zhiyong

AU - Schaeffer, Mary

AU - Wu, Cathy H.

AU - Hirschman, Lynette

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