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 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; Cecilia N Arighi

doi:10.1093/database/baw119

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, 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, Cecilia N Arighi

Disease Systems Biology Program

22 Citationer (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.

Originalsprog	Engelsk
Artikelnummer	baw119
Tidsskrift	Database: The Journal of Biological Databases and Curation
Vol/bind	2016
Antal sider	18
ISSN	1758-0463
DOI	https://doi.org/10.1093/database/baw119
Status	Udgivet - 2016

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10.1093/database/baw119Licens: Ikke-specificeret

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Wang, Q., S Abdul, S., Almeida, L., Ananiadou, S., Balderas-Martínez, Y. I., Batista-Navarro, R., Campos, D., Chilton, L., Chou, H.-J., Contreras, G., Cooper, L., Dai, H.-J., Ferrell, B., Fluck, J., Gama-Castro, S., George, N., Gkoutos, G., Irin, A. K., Jensen, L. J., ... Arighi, C. N. (2016). Overview of the interactive task in BioCreative V. Database: The Journal of Biological Databases and Curation, 2016, Artikel baw119. https://doi.org/10.1093/database/baw119

Wang, Q, S Abdul, S, Almeida, L, Ananiadou, S, Balderas-Martínez, YI, Batista-Navarro, R, Campos, D, Chilton, L, Chou, H-J, Contreras, G, Cooper, L, Dai, H-J, 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, C-H, 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: The Journal of Biological Databases and Curation, bind 2016, baw119. https://doi.org/10.1093/database/baw119

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

note = "Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.",

year = "2016",

doi = "10.1093/database/baw119",

language = "English",

volume = "2016",

journal = "Database: The Journal of Biological Databases and Curation",

issn = "1758-0463",

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T1 - Overview of the interactive task in BioCreative V

AU - Wang, Qinghua

AU - S Abdul, Shabbir

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, Sérgio

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

AU - Tsaprouni, Loukia

AU - Vasilevsky, Nicole

AU - Wang, Xiaodong

AU - Chatr-Aryamontri, Andrew

AU - Laulederkind, Stanley J F

AU - Matis-Mitchell, Sherri

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

AU - Arighi, Cecilia N

N1 - Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

KW - Journal Article

U2 - 10.1093/database/baw119

DO - 10.1093/database/baw119

M3 - Journal article

C2 - 27589961

SN - 1758-0463

VL - 2016

JO - Database: The Journal of Biological Databases and Curation

JF - Database: The Journal of Biological Databases and Curation

M1 - baw119

ER -

Overview of the interactive task in BioCreative V

Abstract

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