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An Overview of Terminological Resources available for French bioNLP
2013
Conference and Labs of the Evaluation Forum
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Herein, we review the extent of this coverage as well as the sources and methods for additional material available for French. ...
Terminological resources in languages other than English are playing a critical role in all kinds of medical administrative solutions in countries where English is not an official language, or not the ...
authors acknowledge travel funding from the EU STREP project grant 296410 ("Mantra") under the 7th EU Framework Programme within Theme "Intelligent Content and Semantics", "Challenge 4: Technologies for ...
dblp:conf/clef/NeveolRZ13
fatcat:vu24vgo5xzei3pr2rhf4fquwuu
BioNLP shared Task 2013 - An Overview of the Bacteria Biotope Task
2013
Workshop on Biomedical Natural Language Processing
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This paper presents the Bacteria Biotope task of the BioNLP Shared Task 2013, which follows BioNLP-ST-11. ...
Bacteria locations are crucial knowledge in biology for phenotype studies. The paper details the corpus specifications, the evaluation metrics, and it summarizes and discusses the participant results. ...
Acknowledgments This work has been partially supported by the Quaero program, funded by OSEO, the French state agency for innovation and the INRA OntoBiotope Network. ...
dblp:conf/bionlp/BossyGRBN13
fatcat:xr76d7vwlvbidjzpvksfihmzzy
First Steps towards Building a Medical Lexicon for Spanish with Linguistic and Semantic Information
2019
Proceedings of the 18th BioNLP Workshop and Shared Task
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We greatly thank the institutions who gave permission to include their data in MedLexSp, and also thank the anonymous reviewers for their valuable comments. ...
We provide a resource to be distributed for research purposes in the BioNLP community. ...
Graeco-Latin components are very productive for coining medical terms; thus, several BioNLP systems integrate morphology-based lexical resources. ...
doi:10.18653/v1/w19-5017
dblp:conf/bionlp/Llanos19
fatcat:4eo6tyrkvzf5djuxx6vfknrxty
Medical information retrieval: introduction to the special issue
2016
Information retrieval (Boston)
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Acknowledgments We thank the co-editors of the journal Charles Clarke, Tetsuya Sakai and Arjen de Vries for their guidance during the editing of this special issue. ...
This workshop gave an overview of the current research directions taken in the medical IR domain. ...
• Roberts et al. (2016) present an overview of the TREC Clinical Decision Support (CDS) track. ...
doi:10.1007/s10791-015-9277-8
fatcat:vup6o3ddcfhynap2wi7smikwfm
Overview of the gene regulation network and the bacteria biotope tasks in BioNLP'13 shared task
2015
BMC Bioinformatics
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The Bacteria Track tasks remain publicly open; the BioNLP-ST website provides an online evaluation service, the reference corpora and the evaluation tools. ...
The Bacteria Track was motivated by a need to develop specific BioNLP tools for fine-grained event extraction in bacteria biology. ...
Acknowledgements This work has been partially supported by the Quaero program funded by OSEO, the French state agency for innovation, the Program Investing in the Future, Grant n°ANR-10-IDEX-0003-02» funded ...
doi:10.1186/1471-2105-16-s10-s1
pmid:26202448
pmcid:PMC4511173
fatcat:keakzqti2bftpdbtaoi6nhv2pu
CODER: Knowledge infused cross-lingual medical term embedding for term normalization
[article]
2021
arXiv
pre-print
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2021 pre-print arXiv:2011.02947v2 fatcat:mt7jthkohren3fo4tbtfjyhyxyOther Versions
Our codes and models are available at https://github.com/GanjinZero/CODER. ...
CODER is designed for medical term normalization by providing close vector representations for different terms that represent the same or similar medical concepts with cross-lingual support. ...
an existing terminology system, such as the Unified Medical Language System (UMLS) [5] or SNOMED Clinical Terms (SNOMED-CT) [13] . ...
arXiv:2011.02947v3
fatcat:lyecgcxewzghhgsm3ujsy74o3u
Semantic annotation in biomedicine: the current landscape
2017
Journal of Biomedical Semantics
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As a result, the meaning of those mentions is unambiguously and explicitly defined, and thus made readily available for automated processing. ...
We also examine potential directions for further improvements of today's annotators which could make them even more capable of meeting the needs of real-world applications. ...
Availability of data and materials Data sharing is not applicable to this article as no datasets were generated or analysed during the current study. ...
doi:10.1186/s13326-017-0153-x
pmid:28938912
pmcid:PMC5610427
fatcat:jby2gq576vfdfmf4lsusahjrrm
The Recent Advances in Automatic Term Extraction: A survey
[article]
2023
arXiv
pre-print
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As units of knowledge in a specific field of expertise, extracted terms are not only beneficial for several terminographical tasks, but also support and improve several complex downstream tasks, e.g., ...
ATE systems, along with annotated datasets, have been studied and developed widely for decades, but recently we observed a surge in novel neural systems for the task at hand. ...
The overview of different evaluation metrics in ATE task. ...
arXiv:2301.06767v1
fatcat:aof447u2bzantl3omjhr7nbsn4
Text mining resources for the life sciences
2016
Database: The Journal of Biological Databases and Curation
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In this survey, we give an overview of the text mining resources that exist in the life sciences to help researchers, especially those employed in biocuration, to engage with text mining in their own work ...
Text mining resources for the life sciences. Abstract Text mining is a powerful technology for quickly distilling key information from vast quantities of biomedical literature. ...
Funding This work is jointly supported by the EC/H2020 project: an Open Mining INfrastructure for TExt and Data (OpenMinTeD) Grant ID: 654021 and the BBSRC project: Enriching Metabolic PATHwaY models with ...
doi:10.1093/database/baw145
pmid:27888231
pmcid:PMC5199186
fatcat:nb5eby565jdcrho63yporkcjaa
Biomedical term extraction: overview and a new methodology
2015
Information retrieval (Boston)
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Terminology extraction is an essential task in domain knowledge acquisition, as well as for Information Retrieval (IR). ...
languages (English, French, and Spanish). ...
Keywords Automatic Term Extraction · Biomedical Terminology Extraction · Natural Language Processing · BioNLP · Text Mining · Web Mining · Graphs
Introduction The huge amount of biomedical data available ...
doi:10.1007/s10791-015-9262-2
fatcat:eccc224wqjbv5bsr46b7pgypue
NeuroElectro: a window to the world's neuron electrophysiology data
2014
Frontiers in Neuroinformatics
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NeuroElectro is a valuable resource for experimental physiologists attempting to supplement their own data, for computational modelers looking to constrain their model parameters, and for theoreticians ...
The behavior of neural circuits is determined largely by the electrophysiological properties of the neurons they contain. ...
When manually curating the text-mined content for some of the most commonly reported electrophysiological properties, we accounted for an investigator's calculation of an electrophysiological measurement ...
doi:10.3389/fninf.2014.00040
pmid:24808858
pmcid:PMC4010726
fatcat:wnnfyv7brnb4lpnbhtv76lo2oq
Can reproducibility be improved in clinical natural language processing? A study of 7 clinical NLP suites
2020
JAMIA Journal of the American Medical Informatics Association
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Frameworks based on WMS match more than 50% of features (26 features for LAPPS Grid, 22 features for OpenMinted) compared to 18 features for current clinical NLP framework (cTakes, CLAMP) and 17 features ...
Clinical natural language processing (NLP) pipelines are routinely leveraged for the secondary use of data. ...
While resources for languages other than English are available in spaCy, ScispaCy does not offer resources outside of English. ...
doi:10.1093/jamia/ocaa261
pmid:33319904
pmcid:PMC7936396
fatcat:63l3hlzuvnar5nbhdeqowck6t4
Pre-trained Language Models in Biomedical Domain: A Systematic Survey
[article]
2023
arXiv
pre-print
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2023 pre-print arXiv:2110.05006v3 fatcat:2dtoy4d6ozcn3ew5hcfmbkxikiOther Versions
It expects a survey that not only systematically reviews recent advances of biomedical PLMs and their applications but also standardizes terminology and benchmarks. ...
At last, we illustrate various limitations and future trends, which we hope can provide inspiration for the future research of the research community. ...
We draw an overview for these models in Fig. 1 . ...
arXiv:2110.05006v4
fatcat:tgz5zgzmizasphlgsxur3kereu
Making UIMA Truly Interoperable with SPARQL
2013
Linguistic Annotation Workshop
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We alleviate this problem by introducing a conversion mechanism based on SPARQL, a query language for the data retrieval and manipulation of RDF graphs. ...
Commonly, this problem has been solved programmatically by implementing UIMA components that perform the alignment of two type systems, an arduous task that is impractical with a growing number of type ...
The triples are composed of resources and/or literals with the latter available only as objects. ...
dblp:conf/acllaw/RakA13
fatcat:cgvpvhj5ibcsff5ngma3h6hioi
Information Extraction from Electronic Medical Records using Natural Language Processing Techniques
2020
Journal of Applied Sciences and Environmental Management
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The system promises to assist health organizations in making informed decisions with the flood of key information data available in their domain. ...
The cross-industry standard process for data mining methodology was applied in an experiment with an EMR dataset from PubMed todemonstrate the framework. ...
Acknowledgement: The authors appreciate the contributions of Dr. Magnus Ogaraku of the Federal University Lokoja Health Services for providing some expert validation functions for this research. ...
doi:10.4314/jasem.v24i6.13
fatcat:u6hgdntpezdktfdcj7arbpb7lu
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