BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID

BioC is a simple XML format for text, annotations and relations, and was developed to achieve interoperability for biomedical text processing. Following the success of BioC in BioCreative IV, the BioCreative V BioC track addressed a collaborative task to build an assistant system for BioGRID curatio...

Descripción completa

Detalles Bibliográficos
Autores principales: Kim, Sun, Islamaj Doğan, Rezarta, Chatr-Aryamontri, Andrew, Chang, Christie S., Oughtred, Rose, Rust, Jennifer, Batista-Navarro, Riza, Carter, Jacob, Ananiadou, Sophia, Matos, Sérgio, Santos, André, Campos, David, Oliveira, José Luís, Singh, Onkar, Jonnagaddala, Jitendra, Dai, Hong-Jie, Su, Emily Chia-Yu, Chang, Yung-Chun, Su, Yu-Chen, Chu, Chun-Han, Chen, Chien Chin, Hsu, Wen-Lian, Peng, Yifan, Arighi, Cecilia, Wu, Cathy H., Vijay-Shanker, K., Aydın, Ferhat, Hüsünbeyi, Zehra Melce, Özgür, Arzucan, Shin, Soo-Yong, Kwon, Dongseop, Dolinski, Kara, Tyers, Mike, Wilbur, W. John, Comeau, Donald C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009341/
https://www.ncbi.nlm.nih.gov/pubmed/27589962
http://dx.doi.org/10.1093/database/baw121
_version_ 1782451508159184896
author Kim, Sun
Islamaj Doğan, Rezarta
Chatr-Aryamontri, Andrew
Chang, Christie S.
Oughtred, Rose
Rust, Jennifer
Batista-Navarro, Riza
Carter, Jacob
Ananiadou, Sophia
Matos, Sérgio
Santos, André
Campos, David
Oliveira, José Luís
Singh, Onkar
Jonnagaddala, Jitendra
Dai, Hong-Jie
Su, Emily Chia-Yu
Chang, Yung-Chun
Su, Yu-Chen
Chu, Chun-Han
Chen, Chien Chin
Hsu, Wen-Lian
Peng, Yifan
Arighi, Cecilia
Wu, Cathy H.
Vijay-Shanker, K.
Aydın, Ferhat
Hüsünbeyi, Zehra Melce
Özgür, Arzucan
Shin, Soo-Yong
Kwon, Dongseop
Dolinski, Kara
Tyers, Mike
Wilbur, W. John
Comeau, Donald C.
author_facet Kim, Sun
Islamaj Doğan, Rezarta
Chatr-Aryamontri, Andrew
Chang, Christie S.
Oughtred, Rose
Rust, Jennifer
Batista-Navarro, Riza
Carter, Jacob
Ananiadou, Sophia
Matos, Sérgio
Santos, André
Campos, David
Oliveira, José Luís
Singh, Onkar
Jonnagaddala, Jitendra
Dai, Hong-Jie
Su, Emily Chia-Yu
Chang, Yung-Chun
Su, Yu-Chen
Chu, Chun-Han
Chen, Chien Chin
Hsu, Wen-Lian
Peng, Yifan
Arighi, Cecilia
Wu, Cathy H.
Vijay-Shanker, K.
Aydın, Ferhat
Hüsünbeyi, Zehra Melce
Özgür, Arzucan
Shin, Soo-Yong
Kwon, Dongseop
Dolinski, Kara
Tyers, Mike
Wilbur, W. John
Comeau, Donald C.
author_sort Kim, Sun
collection PubMed
description BioC is a simple XML format for text, annotations and relations, and was developed to achieve interoperability for biomedical text processing. Following the success of BioC in BioCreative IV, the BioCreative V BioC track addressed a collaborative task to build an assistant system for BioGRID curation. In this paper, we describe the framework of the collaborative BioC task and discuss our findings based on the user survey. This track consisted of eight subtasks including gene/protein/organism named entity recognition, protein–protein/genetic interaction passage identification and annotation visualization. Using BioC as their data-sharing and communication medium, nine teams, world-wide, participated and contributed either new methods or improvements of existing tools to address different subtasks of the BioC track. Results from different teams were shared in BioC and made available to other teams as they addressed different subtasks of the track. In the end, all submitted runs were merged using a machine learning classifier to produce an optimized output. The biocurator assistant system was evaluated by four BioGRID curators in terms of practical usability. The curators’ feedback was overall positive and highlighted the user-friendly design and the convenient gene/protein curation tool based on text mining. Database URL: http://www.biocreative.org/tasks/biocreative-v/track-1-bioc/
format Online
Article
Text
id pubmed-5009341
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-50093412016-09-07 BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID Kim, Sun Islamaj Doğan, Rezarta Chatr-Aryamontri, Andrew Chang, Christie S. Oughtred, Rose Rust, Jennifer Batista-Navarro, Riza Carter, Jacob Ananiadou, Sophia Matos, Sérgio Santos, André Campos, David Oliveira, José Luís Singh, Onkar Jonnagaddala, Jitendra Dai, Hong-Jie Su, Emily Chia-Yu Chang, Yung-Chun Su, Yu-Chen Chu, Chun-Han Chen, Chien Chin Hsu, Wen-Lian Peng, Yifan Arighi, Cecilia Wu, Cathy H. Vijay-Shanker, K. Aydın, Ferhat Hüsünbeyi, Zehra Melce Özgür, Arzucan Shin, Soo-Yong Kwon, Dongseop Dolinski, Kara Tyers, Mike Wilbur, W. John Comeau, Donald C. Database (Oxford) Original Article BioC is a simple XML format for text, annotations and relations, and was developed to achieve interoperability for biomedical text processing. Following the success of BioC in BioCreative IV, the BioCreative V BioC track addressed a collaborative task to build an assistant system for BioGRID curation. In this paper, we describe the framework of the collaborative BioC task and discuss our findings based on the user survey. This track consisted of eight subtasks including gene/protein/organism named entity recognition, protein–protein/genetic interaction passage identification and annotation visualization. Using BioC as their data-sharing and communication medium, nine teams, world-wide, participated and contributed either new methods or improvements of existing tools to address different subtasks of the BioC track. Results from different teams were shared in BioC and made available to other teams as they addressed different subtasks of the track. In the end, all submitted runs were merged using a machine learning classifier to produce an optimized output. The biocurator assistant system was evaluated by four BioGRID curators in terms of practical usability. The curators’ feedback was overall positive and highlighted the user-friendly design and the convenient gene/protein curation tool based on text mining. Database URL: http://www.biocreative.org/tasks/biocreative-v/track-1-bioc/ Oxford University Press 2016-09-01 /pmc/articles/PMC5009341/ /pubmed/27589962 http://dx.doi.org/10.1093/database/baw121 Text en Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.
spellingShingle Original Article
Kim, Sun
Islamaj Doğan, Rezarta
Chatr-Aryamontri, Andrew
Chang, Christie S.
Oughtred, Rose
Rust, Jennifer
Batista-Navarro, Riza
Carter, Jacob
Ananiadou, Sophia
Matos, Sérgio
Santos, André
Campos, David
Oliveira, José Luís
Singh, Onkar
Jonnagaddala, Jitendra
Dai, Hong-Jie
Su, Emily Chia-Yu
Chang, Yung-Chun
Su, Yu-Chen
Chu, Chun-Han
Chen, Chien Chin
Hsu, Wen-Lian
Peng, Yifan
Arighi, Cecilia
Wu, Cathy H.
Vijay-Shanker, K.
Aydın, Ferhat
Hüsünbeyi, Zehra Melce
Özgür, Arzucan
Shin, Soo-Yong
Kwon, Dongseop
Dolinski, Kara
Tyers, Mike
Wilbur, W. John
Comeau, Donald C.
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID
title BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID
title_full BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID
title_fullStr BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID
title_full_unstemmed BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID
title_short BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID
title_sort biocreative v bioc track overview: collaborative biocurator assistant task for biogrid
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009341/
https://www.ncbi.nlm.nih.gov/pubmed/27589962
http://dx.doi.org/10.1093/database/baw121
work_keys_str_mv AT kimsun biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT islamajdoganrezarta biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT chatraryamontriandrew biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT changchristies biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT oughtredrose biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT rustjennifer biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT batistanavarroriza biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT carterjacob biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT ananiadousophia biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT matossergio biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT santosandre biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT camposdavid biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT oliveirajoseluis biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT singhonkar biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT jonnagaddalajitendra biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT daihongjie biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT suemilychiayu biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT changyungchun biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT suyuchen biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT chuchunhan biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT chenchienchin biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT hsuwenlian biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT pengyifan biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT arighicecilia biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT wucathyh biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT vijayshankerk biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT aydınferhat biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT husunbeyizehramelce biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT ozgurarzucan biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT shinsooyong biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT kwondongseop biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT dolinskikara biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT tyersmike biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT wilburwjohn biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid
AT comeaudonaldc biocreativevbioctrackoverviewcollaborativebiocuratorassistanttaskforbiogrid