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BioC: a minimalist approach to interoperability for biomedical text processing

D. C. Comeau, R. Islamaj Dogan, P. Ciccarese, K. B. Cohen, M. Krallinger, F. Leitner, Z. Lu, Y. Peng, F. Rinaldi, M. Torii, A. Valencia, K. Verspoor (+3 others)
2013 Database: The Journal of Biological Databases and Curation  
Acknowledgement The authors thank the anonymous reviewers for their useful suggestions in improving this manuscript. .................................................................................  ...  Our approach to these problems is what we would like to call a 'minimalist' approach. How 'little' can one do to obtain interoperability?  ...  Our approach to these problems, a 'minimalist' approach, is focused on an XML format, described in a DTD, to share common information.  ... 
doi:10.1093/database/bat064 pmid:24048470 pmcid:PMC3889917 fatcat:m5q3ltrfobg4fgkash3katpkia

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  
BioC is a new simple XML format for sharing biomedical text and annotations and libraries to read and write that format.  ...  Abstract BioC is a new simple XML format for sharing biomedical text and annotations and libraries to read and write that format.  ...  This led to the success of Track 3 and demonstrates a new approach for the text mining community in general.  ... 
doi:10.1093/database/bau053 pmid:24980129 pmcid:PMC4074764 fatcat:tez7f6bevzbmrlqj4cxub2yf7a

BioCconvert: A Conversion Tool Between BioC and PubAnnotation

Donald C. Comeau, Rezarta Islamaj Dogan, Sun Kim, Chih-Hsuan Wei, W. John Wilbur, Zhiyong Lu
2016 International Conference on Biomedical Ontology  
BioC is a simple XML data format for text, annotations, and relations. PubAnnotation is a repository of text annotations focused on the life science literature.  ...  A conversion tool between BioC XML and the JSON import / export format of PubAnnotation has been developed, BioCconvert.  ...  BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford), 2013, bat064. doi:10.1093/database/bat064. [2] Canada, 2012. [7] Sohn, S., Comeau, D.  ... 
dblp:conf/icbo/ComeauDKWWL16 fatcat:iy7smsk3dzaw3golkxfbvptlti

BioC implementations in Go, Perl, Python and Ruby

W. Liu, R. Islamaj Do an, D. Kwon, H. Marques, F. Rinaldi, W. J. Wilbur, D. C. Comeau
2014 Database: The Journal of Biological Databases and Curation  
As part of a communitywide effort for evaluating text mining and information extraction systems applied to the biomedical domain, BioC is focused on the goal of interoperability, currently a major barrier  ...  BioC is a simple XML format, specified by DTD, for exchanging data for biomedical natural language processing.  ...  BioC (1) has been gaining momentum as a solution to the interoperability challenge-an interchange format for biomedical natural language processing tools.  ... 
doi:10.1093/database/bau059 pmid:24961236 pmcid:PMC4067548 fatcat:7bqvo7wgk5c6pofj5flgon6ubq

tmBioC: improving interoperability of text-mining tools with BioC

Ritu Khare, Chih-Hsuan Wei, Yuqing Mao, Robert Leaman, Zhiyong Lu
2014 Database: The Journal of Biological Databases and Curation  
In response, BioC is a recent proposal that offers a minimalistic approach to tool interoperability by stipulating minimal changes to existing tools and applications.  ...  Abstract The lack of interoperability among biomedical text-mining tools is a major bottleneck in creating more complex applications.  ...  in BioC XML format for the BioCreative IV GO task.  ... 
doi:10.1093/database/bau073 pmid:25062914 pmcid:PMC4110697 fatcat:2wg4mnf4jjgmpnpaonlxt7xqky

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  
., Chatr-Aryamontri, A. et al. 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.  ...  BioC is a minimalist approach to interoperability for biomedical text mining.  ... 
doi:10.1093/database/baw121 pmid:27589962 pmcid:PMC5009341 fatcat:bqe4o77fizadhf5e3xese3i23y

The BioC-BioGRID corpus: full text articles annotated for curation of protein–protein and genetic interactions

Rezarta Islamaj Doğan, Sun Kim, Andrew Chatr-aryamontri, Christie S. Chang, Rose Oughtred, Jennifer Rust, W. John Wilbur, Donald C. Comeau, Kara Dolinski, Mike Tyers
2017 Database: The Journal of Biological Databases and Curation  
To facilitate the development of practical text-mining strategies, a new challenge was organized in BioCreative V for the BioC task, the collaborative Biocurator Assistant Task.  ...  To this end, the BioGRID database systematically curates the biomedical literature for genetic and protein interaction data.  ...  Acknowledgements The authors would like to thank the BioCreative V organizers and the BioCreative V BioC task participants.  ... 
doi:10.1093/database/baw147 pmid:28077563 pmcid:PMC5225395 fatcat:s7dpik24cfct3ihiz3sbghbbdq

PubMedPortable: A Framework for Supporting the Development of Text Mining Applications

Kersten Döring, Björn A. Grüning, Kiran K. Telukunta, Philippe Thomas, Stefan Günther, Robert Guralnick
2016 PLoS ONE  
The BioCreative community supports these developments with yearly open challenges, which led to a standardised XML text annotation format called BioC.  ...  PubMed provides access to the largest open biomedical literature repository, but there is no unified way of connecting its data to natural language processing tools.  ...  Introduction Large progress has been made in the field of text mining and natural language processing (NLP) in the biomedical domain [1] .  ... 
doi:10.1371/journal.pone.0163794 pmid:27706202 pmcid:PMC5051953 fatcat:z6376blmpjefznfuao7v6momui

PyBioC: a python implementation of the BioC core

Hernani Marques, Fabio Rinaldi
2013
PyBioC: a python implementation of the BioC core Hernani Marques, Fabio Rinaldi Motivation BioC 1 (1) is a recently proposed framework which aims at providing a simple and yet powerful approach for the  ...  We plan to switch gradually to a BioC compatibile internal format and for this purpose we have decided to provide an independent implementation of the BioC core in python.  ... 
doi:10.5167/uzh-91881 fatcat:asz252yqlzejtbat3ufwvfsd4u

Auto-CORPus: A Natural Language Processing Tool for Standardizing and Reusing Biomedical Literature

Tim Beck, Tom Shorter, Yan Hu, Zhuoyu Li, Shujian Sun, Casiana M. Popovici, Nicholas A. R. McQuibban, Filip Makraduli, Cheng S. Yeung, Thomas Rowlands, Joram M. Posma
2022 Frontiers in Digital Health  
The BioC format is a community-driven simple data structure for sharing text and annotations, however there is limited access to biomedical literature in BioC format and a lack of bioinformatics tools  ...  convenient machine-interpretable outputs to support biomedical text analytics.  ...  BioC: a minimalist approach to interoperability for biomedical text processing. Database. (2013) 2013:bat064. doi: 10.1093/database/bat064 PubMed Abstract | CrossRef Full Text | Google Scholar 6.  ... 
doi:10.3389/fdgth.2022.788124 pmid:35243479 pmcid:PMC8885717 fatcat:fx5juyzi35cgdm3rlrcvhchike

BioC Implementations in Go, Perl, Python and Ruby

Wanli Liu, Rezarta Islamaj Doğan, Dongseop Kwon, Hernani Marques, Fabio Rinaldi, W John Wilbur, Donald C Comeau
2014
As part of a communitywide effort for evaluating text mining and information extraction systems applied to the biomedical domain, BioC is focused on the goal of interoperability, currently a major barrier  ...  BioC is a simple XML format, specified by DTD, for exchanging data for biomedical natural language processing.  ...  BioC (1) has been gaining momentum as a solution to the interoperability challenge-an interchange format for biomedical natural language processing tools.  ... 
doi:10.5167/uzh-107014 fatcat:h6loirltvrfzhdf7r7wem4y55i

OntoGene web services for biomedical text mining

Fabio Rinaldi, Simon Clematide, Hernani Marques, Tilia Ellendorff, Martin Romacker, Raul Rodriguez-Esteban
2014 BMC Bioinformatics  
Text mining services are rapidly becoming a crucial component of various knowledge management pipelines, for example in the process of database curation, or for exploration and enrichment of biomedical  ...  We present an approach towards providing advanced text mining capabilities through web services, using a recently proposed standard for textual data interchange (BioC).  ...  This article has been published as part of BMC Bioinformatics Volume 15 Supplement 14, 2014: Semantic, social, mobile applications for bioinformatics and biomedical laboratories: selected works from the  ... 
doi:10.1186/1471-2105-15-s14-s6 pmid:25472638 pmcid:PMC4255746 fatcat:oufaw2qdcfhjraterrruhy7l4q

Proceedings of the BioCreative V.5 Challenge Evaluation Workshop

Martin Krallinger, Alfonso Valencia
2022 Zenodo  
We would like to thank Matthias Herzog for technical support and Milena Kraus for her support of mapping the semantic types. Acknowledgments  ...  for funding.  ...  We describe the latest developments of Neji, a modular framework for biomedical text processing and concept recognition, including the in-built support for REST webservices.  ... 
doi:10.5281/zenodo.6519885 fatcat:gzzr6ogkwvfe3eglv6anrzt5s4

v3NLP Framework: Tools to Build Applications for Extracting Concepts from Clinical Text

Guy Divita, Marjorie Carter, Le-Thuy Tran, Doug Redd, Qing T. Zeng, Scott Duvall, Matthew H. Samore, Adi V. Gundlapalli
2016 eGEMs  
There are scale-up and scale-out functionalities to process large numbers of records.  ...  concepts from clinical text.  ...  We acknowledge the staff, resources and facilities of the VA Salt Lake City IDEAS Center 2.0 for providing a rich and stimulating environment for NLP research.  ... 
doi:10.13063/2327-9214.1228 pmid:27683667 pmcid:PMC5019303 fatcat:hbsndtmntvgxnd3mhvkl3y2vga

A Fine-Tuned Bidirectional Encoder Representations From Transformers Model for Food Named-Entity Recognition: Algorithm Development and Validation

Riste Stojanov, Gorjan Popovski, Gjorgjina Cenikj, Barbara Koroušić Seljak, Tome Eftimov
2021 Journal of Medical Internet Research  
In the last 2 decades, a large amount of work has been done in natural language processing and machine learning to enable biomedical information extraction.  ...  However, machine learning in food science domains remains inadequately resourced, which brings to attention the problem of developing methods for food information extraction.  ...  Neither the European Union institutions and bodies nor any person acting on their behalf may be held responsible for the use that may be made of the information contained herein.  ... 
doi:10.2196/28229 pmid:34383671 pmcid:PMC8415558 fatcat:hwbxqhvjcrf25mt4mqpxn3gpgy
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