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BioC: a minimalist approach to interoperability for biomedical text processing
2013
Database: The Journal of Biological Databases and Curation
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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
2014
Database: The Journal of Biological Databases and Curation
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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
2016
International Conference on Biomedical Ontology
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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
2014
Database: The Journal of Biological Databases and Curation
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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
2014
Database: The Journal of Biological Databases and Curation
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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
2016
Database: The Journal of Biological Databases and Curation
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., 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
2017
Database: The Journal of Biological Databases and Curation
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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
2016
PLoS ONE
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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
2013
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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
2022
Frontiers in Digital Health
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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
2014
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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
2014
BMC Bioinformatics
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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
2022
Zenodo
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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
2016
eGEMs
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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
2021
Journal of Medical Internet Research
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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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