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An overview of the BioCreative 2012 Workshop Track III: interactive text mining task
2013
Database: The Journal of Biological Databases and Curation
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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
2013
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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
2012
Database: The Journal of Biological Databases and Curation
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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
2012
Database: The Journal of Biological Databases and Curation
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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
2014
Database: The Journal of Biological Databases and Curation
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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
2012
Database: The Journal of Biological Databases and Curation
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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
2015
Briefings in Bioinformatics
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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
2012
Database: The Journal of Biological Databases and Curation
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(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
2014
Database: The Journal of Biological Databases and Curation
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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
2012
Database: The Journal of Biological Databases and Curation
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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
2012
Database: The Journal of Biological Databases and Curation
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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
2012
Database: The Journal of Biological Databases and Curation
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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
2019
Proceedings of The 5th Workshop on BioNLP Open Shared Tasks
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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
2012
International Journal of Intelligent Systems and Applications
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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
2022
Zenodo
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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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