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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  
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  ...  The analysis of this survey highlights how important task completion is to the biocurators' overall experience of a system, regardless of the system's high score on design, learnability and usability.  ...  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

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

A. Chatr-aryamontri, Y. Li, P. Roberts, S. Jimenez, W. J. Wilbur, C. E. Van Slyke, L. Licata, J. Park, M. Haendel, P. Mabee, H. Drabkin, L. Matthews (+20 others)
2013
Here, we report on an effort to bring together text mining tool developers and database biocurators to test the utility and usability of tools.  ...  As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant.  ...  Funding National Science Foundation grant DBI-0850319; National Institutes of Health grant 5G08LM010720-02; The participation of Z.L. and W.J.W. was supported by the Intramural Research Program of the  ... 
doi:10.17615/z71n-my38 fatcat:vyx3nry7o5fwlg576qy3g24nom

BioCreative-2012 Virtual Issue

C. H. Wu, C. N. Arighi, K. B. Cohen, L. Hirschman, M. Krallinger, Z. Lu, C. Mattingly, A. Valencia, T. C. Wiegers, W. John Wilbur
2012 Database: The Journal of Biological Databases and Curation  
task and (III) an interactive text mining and user evaluation task.  ...  The 'Track III Interactive Text Mining' task (15) featured demonstration and evaluation of interactive text mining systems, some of which are currently being used in biocuration workflows.  ... 
doi:10.1093/database/bas049 pmid:23221175 pmcid:PMC3514749 fatcat:quxmdzvqzbcrblrjbszkmbsgky

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  ...  Compared to a survey done in 2009, our 2012 results show that many more databases are now using text mining in parts of their curation workflows.  ...  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

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  ...  workflow, starting with BioCreative III, BioCreative has created a track (Interactive Track) to explore interactions between biocurators and TM interfaces, as part of an investigation of utility, usability  ... 
doi:10.1093/database/bau039 pmid:24852177 pmcid:PMC4030502 fatcat:ov6v6jhv3vdinasqvot5zrm5cu

Text mining for the biocuration workflow

L. Hirschman, G. A. P. C. Burns, M. Krallinger, C. Arighi, K. B. Cohen, A. Valencia, C. H. Wu, A. Chatr-Aryamontri, K. G. Dowell, E. Huala, A. Lourenco, R. Nash (+3 others)
2012 Database: The Journal of Biological Databases and Curation  
the survey for biocuration workflow and text mining.  ...  L.H. was responsible for the initial workshop organization and for the final editing of the article; G.A.P.C.B. interviewed several model organism databases and did the modeling of the workflows in UML  ...  of detailed descriptions of biocuration workflows and identification of insertion points for text mining, from the perspective of biocurators; and Interactive Text Mining (Track 3): an interactive text  ... 
doi:10.1093/database/bas020 pmid:22513129 pmcid:PMC3328793 fatcat:g4foc66eerbq7cvipwolq6pe5y

Community challenges in biomedical text mining over 10 years: success, failure and the future

Chung-Chi Huang, Zhiyong Lu
2015 Briefings in Bioinformatics  
His research focuses on text data mining and its applications for accelerating knowledge discovery. Dr. Lu is an organizer of the BioCreative challenge.  ...  Following the success of the Critical Assessment of protein Structure Prediction (CASP) in bioinformatics research, a number of challenge evaluations have been organized by the text-mining research community  ...  We also thank all the task organizers and participants for their efforts in the community challenges.  ... 
doi:10.1093/bib/bbv024 pmid:25935162 pmcid:PMC4719069 fatcat:z7wlyvovnnbrrkufmqaxycqdyi

Collaborative biocuration--text-mining development task for document prioritization for curation

T. C. Wiegers, A. P. Davis, C. J. Mattingly
2012 Database: The Journal of Biological Databases and Curation  
(Track I); curation workflow (Track II) and text mining/natural language processing (NLP) systems (Track III).  ...  The 'BioCreative Workshop 2012' subcommittee identified three areas, or tracks, that comprised independent, but complementary aspects of data curation in which they sought community input: literature triage  ...  This program is supported by funds from the National Institute of Environmental Health Sciences (ES014065). Conflict of interest. None declared.  ... 
doi:10.1093/database/bas037 pmid:23180769 pmcid:PMC3504477 fatcat:6rbjinpu6bd55lmnd3tb7yosp4

BioC interoperability track overview

D. C. Comeau, R. T. Batista-Navarro, H.-J. Dai, R. Islamaj Do an, A. Jimeno Yepes, R. Khare, Z. Lu, H. Marques, C. J. Mattingly, M. Neves, Y. Peng, R. Rak (+6 others)
2014 Database: The Journal of Biological Databases and Curation  
The interoperability track at the BioCreative IV workshop featured contributions using or highlighting the BioC format.  ...  The interoperability track at the BioCreative IV workshop featured contributions using or highlighting the BioC format.  ...  The 'BioCreative Workshop 2012' Track I/Triage task was organized by CTD and focused on document triaging and ranking (45) .  ... 
doi:10.1093/database/bau053 pmid:24980129 pmcid:PMC4074764 fatcat:tez7f6bevzbmrlqj4cxub2yf7a

The eFIP system for text mining of protein interaction networks of phosphorylated proteins

C. O. Tudor, C. N. Arighi, Q. Wang, C. H. Wu, K. Vijay-Shanker
2012 Database: The Journal of Biological Databases and Curation  
As a participant in the BioCreative-2012 Interactive Text Mining track, the performance of eFIP was evaluated on document retrieval (F-measures of 78-100%), sentence-level information extraction (F-measures  ...  The utility and usability of the eFIP web interface were also evaluated during the BioCreative Workshop.  ...  Acknowledgements We would like to thank the BioCreative organizing committee for providing the venue for eFIP user evaluation, and the curators who took time to participate in the testing and evaluation  ... 
doi:10.1093/database/bas044 pmid:23221174 pmcid:PMC3514748 fatcat:osvnfxj33beg5gfxjk3ur3or34

Using binary classification to prioritize and curate articles for the Comparative Toxicogenomics Database

D. Vishnyakova, E. Pasche, P. Ruch
2012 Database: The Journal of Biological Databases and Curation  
DebugIT is funded by the European Community's Seventh Framework Programme under grant agreement n8 FP7-217139, which is gratefully acknowledged. Conflict of interest. None declared.  ...  The work presented in this article has been partially supported by the DebugIT project (http://www.debugit.eu/).  ...  Data and methods Data overview BioCreative 2012 proposes to explore how text mining methods can successfully be applied to practically help biocuration of a large molecular biology knowledge base.  ... 
doi:10.1093/database/bas050 pmid:23221176 pmcid:PMC3514750 fatcat:ytibxvbnijgtfd6hasaca5jtpe

Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR

K. Van Auken, P. Fey, T. Z. Berardini, R. Dodson, L. Cooper, D. Li, J. Chan, Y. Li, S. Basu, H.-M. Muller, R. Chisholm, E. Huala (+1 others)
2012 Database: The Journal of Biological Databases and Curation  
Acknowledgements We would like to thank the BioCreative Workshop 2012 Steering Committee for the opportunity to participate in the workshop and, in particular, C.  ...  Arighi for advice and support regarding the Task III evaluation.  ...  This latter work was presented as part of the BioCreative 2012 Workshop Track III on Interactive Text Mining.  ... 
doi:10.1093/database/bas040 pmid:23160413 pmcid:PMC3500519 fatcat:xm263mzjpferrgyn4augokxkgm

PharmaCoNER: Pharmacological Substances, Compounds and proteins Named Entity Recognition track

Aitor Gonzalez Agirre, Montserrat Marimon, Ander Intxaurrondo, Obdulia Rabal, Marta Villegas, Martin Krallinger
2019 Proceedings of The 5th Workshop on BioNLP Open Shared Tasks  
A total of 22 teams participated in the sub-track 1, (77 system runs), and 7 teams in the sub-track 2 (19 system runs).  ...  We foresee that the PharmaCoNER annotation guidelines, corpus and participant systems will foster the development of new resources for clinical and biomedical text mining systems of Spanish medical data  ...  Acknowledgments We acknowledge the Encargo of Plan TL (SEAD) to CNIO and BSC for funding, and the scientific committee for their valuable comments and guidance.  ... 
doi:10.18653/v1/d19-5701 dblp:conf/bionlp/Gonzalez-Agirre19 fatcat:epkf2zw5f5adpktuzypltv2q2m

Multiple Features Based Approach to Extract Bio-molecular Event Triggers Using Conditional Random Field

Amit Majumder
2012 International Journal of Intelligent Systems and Applications  
Overview of BioNLP’09 shared task on event Cussens and C.  ...  Text: TRA DD was the only protein that interacted and gene are not distinguished).  ... 
doi:10.5815/ijisa.2012.12.06 fatcat:elq62iki2bfwpd2yc2b6gzztgy

Proceedings of the BioCreative V.5 Challenge Evaluation Workshop

Martin Krallinger, Alfonso Valencia
2022 Zenodo  
Proceedings of the BioCreative V.5 Challenge Evaluation Workshop  ...  Acknowledgment The authors thank the organizers of the BioCreative V. Acknowledgments.  ...  Acknowledgment We acknowledge the OpenMinted (654021) and the ELIXIR-EXCELERATE (676559) H2020 projects, and the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Lan-guage Technology  ... 
doi:10.5281/zenodo.6519885 fatcat:gzzr6ogkwvfe3eglv6anrzt5s4
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