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

Sun Kim, Rezarta Islamaj Doğan, Andrew Chatr-Aryamontri, Christie S Chang, Rose Oughtred, Jennifer Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han ChuChien Chin Chen, Wen-Lian Hsu, Yifan Peng, Cecilia Arighi, Cathy H Wu, K Vijay-Shanker, Ferhat Aydın, Zehra Melce Hüsünbeyi, Arzucan Özgür, Soo-Yong Shin, Dongseop Kwon, Kara Dolinski, Mike Tyers, W John Wilbur, Donald C Comeau

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

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/.

Original languageEnglish
JournalDatabase : the journal of biological databases and curation
Volume2016
DOIs
Publication statusPublished - Sep 1 2016

Fingerprint

Proteins
proteins
Genes
Communications Media
Text processing
mass media
Data Mining
Information Dissemination
artificial intelligence
Interoperability
XML
Learning systems
Classifiers
genes
Visualization
Databases
Feedback
Communication
organisms
methodology

Keywords

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Intramural
  • Research Support, U.S. Gov't, Non-P.H.S.

Cite this

Kim, S., Islamaj Doğan, R., Chatr-Aryamontri, A., Chang, C. S., Oughtred, R., Rust, J., ... Comeau, D. C. (2016). BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database : the journal of biological databases and curation, 2016. https://doi.org/10.1093/database/baw121

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.

In: Database : the journal of biological databases and curation, Vol. 2016, 01.09.2016.

Research output: Contribution to journalArticle

Kim, S, Islamaj Doğan, R, Chatr-Aryamontri, A, Chang, CS, Oughtred, R, Rust, J, Batista-Navarro, R, Carter, J, Ananiadou, S, Matos, S, Santos, A, Campos, D, Oliveira, JL, Singh, O, Jonnagaddala, J, Dai, H-J, Su, EC-Y, Chang, Y-C, Su, Y-C, Chu, C-H, Chen, CC, Hsu, W-L, Peng, Y, Arighi, C, Wu, CH, Vijay-Shanker, K, Aydın, F, Hüsünbeyi, ZM, Özgür, A, Shin, S-Y, Kwon, D, Dolinski, K, Tyers, M, Wilbur, WJ & Comeau, DC 2016, 'BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID', Database : the journal of biological databases and curation, vol. 2016. https://doi.org/10.1093/database/baw121
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. In: Database : the journal of biological databases and curation. 2016 ; Vol. 2016.
@article{87c1c25df6c54225a4204f02986bc287,
title = "BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID",
abstract = "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/.",
keywords = "Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Research Support, N.I.H., Intramural, Research Support, U.S. Gov't, Non-P.H.S.",
author = "Sun Kim and {Islamaj Doğan}, Rezarta and Andrew Chatr-Aryamontri and Chang, {Christie S} and Rose Oughtred and Jennifer Rust and Riza Batista-Navarro and Jacob Carter and Sophia Ananiadou and S{\'e}rgio Matos and Andr{\'e} Santos and David Campos and Oliveira, {Jos{\'e} Lu{\'i}s} and Onkar Singh and Jitendra Jonnagaddala and Hong-Jie Dai and Su, {Emily Chia-Yu} and Yung-Chun Chang and Yu-Chen Su and Chun-Han Chu and Chen, {Chien Chin} and Wen-Lian Hsu and Yifan Peng and Cecilia Arighi and Wu, {Cathy H} and K Vijay-Shanker and Ferhat Aydın and H{\"u}s{\"u}nbeyi, {Zehra Melce} and Arzucan {\"O}zg{\"u}r and Soo-Yong Shin and Dongseop Kwon and Kara Dolinski and Mike Tyers and Wilbur, {W John} and Comeau, {Donald C}",
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",
month = "9",
day = "1",
doi = "10.1093/database/baw121",
language = "English",
volume = "2016",
journal = "Database : the journal of biological databases and curation",
issn = "1758-0463",
publisher = "Oxford University Press",

}

TY - JOUR

T1 - BioCreative V BioC track overview

T2 - collaborative biocurator assistant task for BioGRID

AU - Kim, Sun

AU - Islamaj Doğan, Rezarta

AU - Chatr-Aryamontri, Andrew

AU - Chang, Christie S

AU - Oughtred, Rose

AU - Rust, Jennifer

AU - Batista-Navarro, Riza

AU - Carter, Jacob

AU - Ananiadou, Sophia

AU - Matos, Sérgio

AU - Santos, André

AU - Campos, David

AU - Oliveira, José Luís

AU - Singh, Onkar

AU - Jonnagaddala, Jitendra

AU - Dai, Hong-Jie

AU - Su, Emily Chia-Yu

AU - Chang, Yung-Chun

AU - Su, Yu-Chen

AU - Chu, Chun-Han

AU - Chen, Chien Chin

AU - Hsu, Wen-Lian

AU - Peng, Yifan

AU - Arighi, Cecilia

AU - Wu, Cathy H

AU - Vijay-Shanker, K

AU - Aydın, Ferhat

AU - Hüsünbeyi, Zehra Melce

AU - Özgür, Arzucan

AU - Shin, Soo-Yong

AU - Kwon, Dongseop

AU - Dolinski, Kara

AU - Tyers, Mike

AU - Wilbur, W John

AU - Comeau, Donald C

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 - 2016/9/1

Y1 - 2016/9/1

N2 - 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/.

AB - 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/.

KW - Journal Article

KW - Research Support, N.I.H., Extramural

KW - Research Support, Non-U.S. Gov't

KW - Research Support, N.I.H., Intramural

KW - Research Support, U.S. Gov't, Non-P.H.S.

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85037580282&origin=resultslist&sort=plf-f&src=s&sid=2cf3fc6ad797b7bd2d82bd0ec0fd4bec&sot=a&sdt=a&sl=31&s=AU-ID%28%22Su%2c+Chiayu%22+22939281200%29&relpos=7&citeCnt=1&searchTerm=

UR - https://www.scopus.com/results/citedbyresults.uri?sort=plf-f&cite=2-s2.0-85037580282&src=s&imp=t&sid=ac348583fdf48692a1efccbb0f9008e0&sot=cite&sdt=a&sl=0&origin=recordpage&editSaveSearch=&txGid=3039ab3f2fb1efb365560880f4cc6ee0

U2 - 10.1093/database/baw121

DO - 10.1093/database/baw121

M3 - Article

C2 - 27589962

VL - 2016

JO - Database : the journal of biological databases and curation

JF - Database : the journal of biological databases and curation

SN - 1758-0463

ER -