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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 (+44 others)
2016 Database: The Journal of Biological Databases and Curation  
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.  ...  Acknowledgements We would like to acknowledge all the users and team members who have participated in this activity throughout BioCreative. Conflict of interest. None declared.  ... 
doi:10.1093/database/baw119 pmid:27589961 pmcid:PMC5009325 fatcat:ldpn6gjxircjlibqtysi57cztq

Overview of the Interactive Task in BioCreative V

Qinghua Wang, Fabio Rinaldi, Et Al
2015
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 point.  ...  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 point.  ...  Acknowledgment We would like to acknowledge all the users and team members who have participated in this activity.  ... 
doi:10.5167/uzh-116471 fatcat:elfvz7vs3zcx3obt33nak26rii

BioCreative-IV virtual issue

C. N. Arighi, C. H. Wu, K. B. Cohen, L. Hirschman, M. Krallinger, A. Valencia, Z. Lu, J. W. Wilbur, T. C. Wiegers
2014 Database: The Journal of Biological Databases and Curation  
Acknowledgments This issue is dedicated to the memory of our friend and colleague Phoebe Roberts who contributed significantly to the BioCreative effort in the past years.  ...  We would like to thank the the BioCreative User Advisory Group and the task co-organizers Donald Comeau, Rezarta Islamaj Dogan, Obdulia Rabal, Julen Oyarzabal, Allan Davis, Carolyn Mattingly, Kimberly  ...  Owing to the relevance for the chemistry community, the overview and results for this task will be presented in a separate publication published in the Journal of Chemoinformatics.  ... 
doi:10.1093/database/bau039 pmid:24852177 pmcid:PMC4030502 fatcat:ov6v6jhv3vdinasqvot5zrm5cu

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 (+23 others)
2016 Database: The Journal of Biological Databases and Curation  
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.  ...  Acknowledgements The authors would like to thank Cecilia Arighi for providing resources for the user questionnaire.  ...  Overview of BioCreative V BioC track. The track consists of named entity recognition (NER), protein-protein interaction (PPI), genetic inter- action (GI) and visual tool tasks.  ... 
doi:10.1093/database/baw121 pmid:27589962 pmcid:PMC5009341 fatcat:bqe4o77fizadhf5e3xese3i23y

The BEL information extraction workflow (BELIEF): evaluation in the BioCreative V BEL and IAT track

Sumit Madan, Sven Hodapp, Philipp Senger, Sam Ansari, Justyna Szostak, Julia Hoeng, Manuel Peitsch, Juliane Fluck
2016 Database: The Journal of Biological Databases and Curation  
Participation in the BioCreative V Interactive task (IAT) track with BELIEF revealed a systems usability scale (SUS) of 67.  ...  Based on the BioCreative V BEL track evaluation, we show that the BELIEF Pipeline automatically extracts relationships with an F-score of 36.4% and fully correct statements can be obtained with an Fscore  ...  We are also very grateful for the support of the BioCreative IAT team, who provided us with the opportunity to take part in the IAT and organized the whole task.  ... 
doi:10.1093/database/baw136 pmid:27694210 pmcid:PMC5045868 fatcat:fkuoxt7j6ffnxoknhsqmqjvdrq

Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task

Chih-Hsuan Wei, Yifan Peng, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Jiao Li, Thomas C. Wiegers, Zhiyong Lu
2016 Database: The Journal of Biological Databases and Curation  
Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task.  ...  To this end, we organized a challenge task through BioCreative V to automatically extract CDRs from the literature.  ...  BioCreative V, 2015) CID P R F Best team result 55.67 58.44 57.03 Crowdsourcing a 56.10 76.50 64.70 All teams combined (18 teams) 76.45 53.28 62.80 a Table 4 . 4 Overview of how  ... 
doi:10.1093/database/baw032 pmid:26994911 pmcid:PMC4799720 fatcat:til4dwhyszcftgixdtlxldxnei

CU-UD: text-mining drug and chemical-protein interactions with ensembles of BERT-based models [article]

Mehmet Efruz Karabulut, K. Vijay-Shanker, Yifan Peng
2021 arXiv   pre-print
BioCreative VII track 1 DrugProt task aims to promote the development and evaluation of systems that can automatically detect relations between chemical compounds/drugs and genes/proteins in PubMed abstracts  ...  Our system obtained 0.7708 in precision and 0.7770 in recall, for an F1 score of 0.7739, demonstrating the effectiveness of using ensembles of BERT-based language models for automatically detecting relations  ...  R ESULTS OF OUR SYSTEMS ON D RUG P ROT TEST SET Overview of the BioCreative VI chemical-protein interaction Track.  ... 
arXiv:2112.03004v1 fatcat:svpjh324uzcm3gsdot4nctvuzi

Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL)

Juliane Fluck, Sumit Madan, Sam Ansari, Alpha T. Kodamullil, Reagon Karki, Majid Rastegar-Mojarad, Natalie L. Catlett, William Hayes, Justyna Szostak, Julia Hoeng, Manuel Peitsch
2016 Database: The Journal of Biological Databases and Curation  
Those text excerpts were evaluated and manually annotated as true or false supportive in the course of the BioCreative V BEL track task.  ...  Success in extracting biological relationships is mainly dependent on the complexity of the task as well as the availability of high-quality training data.  ...  One of the authors, Majid Rastegar-Mojarad participated in the BioCreative V BEL track and is one of the developers of the second method described in the method part.  ... 
doi:10.1093/database/baw113 pmid:27554092 pmcid:PMC4995071 fatcat:e43tl6edwnfldgugogqeny3x3u

Relation Extraction for Protein-protein Interactions Affected by Mutations

Ziling Fan, Luca Soldaini, Arman Cohan, Nazli Goharian
2018 Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '18  
Evaluation of the result using BioCreative VI PM track testing dataset proves the effectiveness of the features proposed in my method.  ...  Information about protein-protein interaction and mutations affecting the interaction is essential in understanding biological processes and is one of the key aims in PM research.  ...  Thank her for leading me to do this research project; thank her for taking large amount of time and energy for instructing me, helping me reviewing and revising the thesis.  ... 
doi:10.1145/3233547.3233617 dblp:conf/bcb/FanSCG18 fatcat:424d4dzeubgh3fbf2kbzwn32xe

BioCreative V CDR task corpus: a resource for chemical disease relation extraction

Jiao Li, Yueping Sun, Robin J. Johnson, Daniela Sciaky, Chih-Hsuan Wei, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Thomas C. Wiegers, Zhiyong Lu
2016 Database: The Journal of Biological Databases and Curation  
Recently in BioCreative V, a new challenge was organized for the tasks of disease named entity recognition (DNER) and chemical-induced disease (CID) relation extraction.  ...  BioCreative V CDR task corpus: a resource for chemical disease relation extraction.  ...  Acknowledgment We would like to thank Yifan Peng for his help on the manuscript. Conflict of interest. None declared.  ... 
doi:10.1093/database/baw068 pmid:27161011 pmcid:PMC4860626 fatcat:fyf2efylgfemxibwpj6ek2qiwa

Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II

Z. Lu, L. Hirschman
2012 Database: The Journal of Biological Databases and Curation  
To close this gap and better understand all aspects of literature curation, we invited submissions of written descriptions of curation workflows from expert curated databases for the BioCreative 2012 Workshop  ...  Despite the continuing advances in biomedical text mining and the pressing needs of biocurators for better tools, few existing text-mining tools have been successfully integrated into production literature  ...  Acknowledgements We would like to thank the other BioCreative 2012 organizers for helpful discussion and the Track II teams for their participation. Conflict of interest. None declared.  ... 
doi:10.1093/database/bas043 pmid:23160416 pmcid:PMC3500522 fatcat:tkyl4ik7tfdjflroojq6axjtkq

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

C. N. Arighi, B. Carterette, K. B. Cohen, M. Krallinger, W. J. Wilbur, P. Fey, R. Dodson, L. Cooper, C. E. Van Slyke, W. Dahdul, P. Mabee, D. Li (+29 others)
2013 Database: The Journal of Biological Databases and Curation  
This analysis will help to plan for a more intense study in BioCreative IV.  ...  In terms of inter-annotator agreement, the factors that contributed to significant differences for some of the systems included the expertise of the biocurator on the given curation task, the inherent  ...  Acknowledgements The authors would like to thank all the teams and the biocurators who participated in this activity. Conflict of interest. None declared.  ... 
doi:10.1093/database/bas056 pmid:23327936 pmcid:PMC3625048 fatcat:hofjvjt55fhcre55nfsa6s2qcm

Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine

Rezarta Islamaj Doğan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C Panyam, Karin Verspoor, Hongfang Liu (+15 others)
2019 Database: The Journal of Biological Databases and Curation  
The goal of BioCreative VI Precision Medicine Track was to extract this particular type of information and was organized in two tasks: (i) document triage task, focused on identifying scientific literature  ...  influence of genetic variants in these interactions.  ...  Acknowledgements We thank the BioGRID database curators Rose Oughtred, Jennifer Rust, Christie S. Chang and Lorrie Boucher for annotating the evaluation data set. Conflict of interest. None declared.  ... 
doi:10.1093/database/bay147 pmid:30689846 pmcid:PMC6348314 fatcat:jvsf4xwr7jbbnb75d3oqczrjrq

Does constituency analysis enhance domain-specific pre-trained BERT models for relation extraction? [article]

Anfu Tang, Claire Nédellec
2021 arXiv   pre-print
The DrugProt track at BioCreative VII provides a manually-annotated corpus for the purpose of the development and evaluation of relation extraction systems, in which interactions between chemicals and  ...  in which the syntactic information is infused.  ...  Overview of with 15, 27, 39 examples in the train set respectively (though the BioCreative VI chemical-protein interaction Track.  ... 
arXiv:2112.02955v1 fatcat:xjdbtgfr2fg77fkcfi7m2gymea

Assisting manual literature curation for protein-protein interactions using BioQRator

D. Kwon, S. Kim, S.-Y. Shin, A. Chatr-aryamontri, W. J. Wilbur
2014 Database: The Journal of Biological Databases and Curation  
In the BioCreative IV edition, BioQRator was tailored for protein-protein interaction (PPI) annotation by migrating information from PIE the search.  ...  Database URL: http://www.bioqrator.org/ V C The Author(s)  ...  The authors also would like to thank Cecilia N. Arighi for valuable comments on implementing the BioQRator interface. Conflict of interest. None declared.  ... 
doi:10.1093/database/bau067 pmid:25052701 pmcid:PMC4105708 fatcat:etgsfppxmrfxplp2n2t2mic2oq
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