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...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
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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 |
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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 |
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