Overview of the interactive task in BioCreative V
Por:
Wang, Qinghua, Abdul, Shabbir S., Almeida, Lara, Ananiadou, Sophia, Balderas-Martinez, 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.
Publicada:
1 sep 2016
Categoría:
Medicine (miscellaneous)
Resumen:
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.
Filiaciones:
Wang, Qinghua:
Univ Delaware, Ctr Bioinformat & Computat Biol, Newark, DE 19711 USA
Univ Delaware, Dept Comp & Informat Sci, Newark, DE 19711 USA
Abdul, Shabbir S.:
Taipei Med Univ, Int Ctr Hlth Informat Technol, Taipei, Taiwan
Almeida, Lara:
Univ Aveiro, DETI IEETA, Campus Univ Santiago, P-3810193 Aveiro, Portugal
Ananiadou, Sophia:
Univ Manchester, Natl Ctr Text Min, Manchester, Lancs, England
Balderas-Martinez, Yalbi I.:
Univ Nacl Autonoma Mexico, Fac Ciencias, Mexico City 04510, DF, Mexico
Batista-Navarro, Riza:
Univ Manchester, Natl Ctr Text Min, Manchester, Lancs, England
Campos, David:
BMD Software, Aveiro, Portugal
Chilton, Lucy:
Newcastle Univ, Northern Inst Canc Res, Newcastle Upon Tyne, Tyne & Wear, England
Chou, Hui-Jou:
Rutgers Univ Camden, Camden, NJ 08102 USA
Contreras, Gabriela:
Univ Nacl Autonoma Mexico, Ctr Ciencias Genom, Mexico City 04510, DF, Mexico
Cooper, Laurel:
Oregon State Univ, Dept Bot & Plant Pathol, Corvallis, OR 97331 USA
Dai, Hong-Jie:
Natl Taitung Univ, Dept Comp Sci & Informat Engn, Taitung, Taiwan
Ferrell, Barbra:
Univ Delaware, Coll Agr & Nat Resources, Newark, DE 19711 USA
Fluck, Juliane:
Fraunhofer Inst Algorithms & Sci Comp, D-53754 St Augustin, Germany
Gama-Castro, Socorro:
Univ Nacl Autonoma Mexico, Ctr Ciencias Genom, Mexico City 04510, DF, Mexico
George, Nancy:
EMBO, SourceData, Heidelberg, Germany
Gkoutos, Georgios:
Univ Birmingham, Inst Canc & Genom Sci, Coll Med & Dent Sci, Ctr Computat Biol, Birmingham B15 2TT, W Midlands, England
Univ Hosp Birmingham NHS Fdn Trust, Inst Translat Med, Birmingham B15 2TT, W Midlands, England
Irin, Afroza K.:
Univ Bonn, Life Sci Informat, Bonn, Germany
Jensen, Lars J.:
Univ Copenhagen, Fac Hlth & Med Sci, Novo Nordisk Fdn Ctr Prot Res, Copenhagen, Denmark
Jimenez, Silvia:
EPFL, Blue Brain Project, Biotech Campus, Geneva, Switzerland
Jue, Toni R.:
Univ New South Wales NSW, Prince Wales Clin Sch, Sydney, NSW, Australia
Keseler, Ingrid:
SRI Int, Menlo Pk, CA 94025 USA
Madan, Sumit:
Fraunhofer Inst Algorithms & Sci Comp, D-53754 St Augustin, Germany
Matos, Sergio:
Univ Aveiro, DETI IEETA, Campus Univ Santiago, P-3810193 Aveiro, Portugal
McQuilton, Peter:
Univ Oxford, Oxford E Res Ctr, Oxford, England
Milacic, Marija:
Ontario Inst Canc Res, Dept Informat & Biocomp, Toronto, ON M5G 0A3, Canada
Mort, Matthew:
Cardiff Univ, Inst Med Genet, HGMD, Heath Pk, Cardiff, S Glam, Wales
Natarajan, Jeyakumar:
Bharathiar Univ, Dept Bioinformat, Coimbatore, Tamil Nadu, India
Pafilis, Evangelos:
Hellen Ctr Marine Res, Inst Marine Biol Biotechnol & Aquaculture, Iraklion, Crete, Greece
Pereira, Emiliano:
Max Planck Inst Marine Microbiol, Microbial Genom & Bioinformat Grp, Bremen, Germany
Rao, Shruti:
Georgetown Univ, ICBI, Washington, DC 20007 USA
Rinaldi, Fabio:
Univ Zurich, Inst Computat Linguist, Zurich, Switzerland
Rothfels, Karen:
Ontario Inst Canc Res, Dept Informat & Biocomp, Toronto, ON M5G 0A3, Canada
Salgado, David:
Aix Marseille Univ, GMGF, F-13385 Marseille, France
INSERM, UMR S 910, F-13385 Marseille, France
Silva, Raquel M.:
Univ Aveiro, Dept Med Sci, iBiMED, P-3810193 Aveiro, Portugal
Univ Aveiro, IEETA, P-3810193 Aveiro, Portugal
Singh, Onkar:
Taipei Med Univ, Grad Inst Biomed Informat, Taipei, Taiwan
Stefancsik, Raymund:
Univ Cambridge, Dept Genet, Cambridge, England
Su, Chu-Hsien:
Acad Sinica, Inst Informat Sci, Taipei, Taiwan
Subramani, Suresh:
Bharathiar Univ, Dept Bioinformat, Coimbatore, Tamil Nadu, India
Tsaprouni, Loukia:
Univ Bedfordshire, ISPAR, Bedford, England
Vasilevsky, Nicole:
Oregon Hlth & Sci Univ, Ontol Dev Grp, Portland, OR 97239 USA
Wang, Xiaodong:
CALTECH, WormBase Consortium, Div Biol & Biol Engn, Pasadena, CA 91125 USA
Chatr-Aryamontri, Andrew:
Univ Montreal, Inst Res Immunol & Canc, Montreal, PQ, Canada
Laulederkind, Stanley J. F.:
Med Coll Wisconsin, Milwaukee, WI 53226 USA
Matis-Mitchell, Sherri:
Reed Elsevier, Philadelphia, PA 19103 USA
McEntyre, Johanna:
European Bioinformat Inst EMBL EBI, Hinxton, England
Orchard, Sandra:
European Bioinformat Inst EMBL EBI, Hinxton, England
Pundir, Sangya:
European Bioinformat Inst EMBL EBI, Hinxton, England
Rodriguez-Esteban, Raul:
F Hoffmann La Roche Ltd, Roche Innovat Ctr Basel, Basel, Switzerland
Van Auken, Kimberly:
CALTECH, WormBase Consortium, Div Biol & Biol Engn, Pasadena, CA 91125 USA
Lu, Zhiyong:
NIH, NCBI, Bethesda, MD 20894 USA
Schaeffer, Mary:
ARS, USDA, MaizeGDB, Columbia, MO 65211 USA
Univ Missouri, Columbia, MO 65211 USA
Wu, Cathy H.:
Univ Delaware, Ctr Bioinformat & Computat Biol, Newark, DE 19711 USA
Univ Delaware, Dept Comp & Informat Sci, Newark, DE 19711 USA
Hirschman, Lynette:
Mitre Corp, Bedford, MA 01730 USA
Arighi, Cecilia N.:
Univ Delaware, Ctr Bioinformat & Computat Biol, Newark, DE 19711 USA
Univ Delaware, Dept Comp & Informat Sci, Newark, DE 19711 USA
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