Filters








24 Hits in 3.7 sec

The CHEMDNER corpus of chemicals and drugs and its annotation principles

Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M Lowe, Roger A Sayle, Riza Batista-Navarro (+41 others)
<span title="">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5aubiwi6v5beng6iqzj577kiaa" style="color: black;">Journal of Cheminformatics</a> </i> &nbsp;
The CHEMDNER corpus and annotation guidelines are available at:  ...  We propose a standard for required minimum information about entity annotations for the construction of domain specific corpora on chemical and drug entities.  ...  as part of Journal of Cheminformatics Volume 7 Supplement 1, 2015: Text mining for chemistry and the CHEMDNER track.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1758-2946-7-s1-s2">doi:10.1186/1758-2946-7-s1-s2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25810773">pmid:25810773</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4331692/">pmcid:PMC4331692</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7lpufmelsjfa7jbx6rxkam7tka">fatcat:7lpufmelsjfa7jbx6rxkam7tka</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190319042449/https://core.ac.uk/download/pdf/78495834.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5e/d8/5ed8da3070ea03f222532a1e31f13b41916ee5d2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1758-2946-7-s1-s2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4331692" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

DrugProt corpus chemicals and drugs annotation guidelines [CHEMDNER - Biocreative IV]

Obdulia Rabal, Martin Krallinger
<span title="2021-06-15">2021</span> <i title="Zenodo"> Zenodo </i> &nbsp;
Please, cite: @article{krallinger2015chemdner, title={The CHEMDNER corpus of chemicals and drugs and its annotation principles}, author={Krallinger, Martin and Rabal, Obdulia and Leitner, Florian and Vazquez  ...  Annotation guidelines (and data selection criteria) used for the annotations of chemical entities of the CHEMDNER, ChemProt and DrugProt corpora.  ...  It also includes trademark and commercial names of chemicals and drugs.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.4957519">doi:10.5281/zenodo.4957519</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3ltiuyqkpfgpxewwqtn4rhfdku">fatcat:3ltiuyqkpfgpxewwqtn4rhfdku</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210623051916/https://zenodo.org/record/4957519/files/CEM_guidelines.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/cb/c7/cbc7c26a03dcbc12b4b19942d7ca0f6540a6df57.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.4957519"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

Exploring Word Embedding for Drug Name Recognition

Isabel Segura-Bedmar, Víctor Suárez-Paniagua, Paloma Martínez
<span title="">2015</span> <i title="Association for Computational Linguistics"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vlnqh2i2c5blrdw4c3q6loh2yu" style="color: black;">Proceedings of the Sixth International Workshop on Health Text Mining and Information Analysis</a> </i> &nbsp;
To evaluate our approach and compare it with previous work, we conducted a series of experiments on the dataset of SemEval-2013 Task 9.1 Drug Name Recognition.  ...  We trained the Word2vec tool over two different corpus: Wikipedia and MedLine.  ...  Acknowledgments This work was supported by TrendMiner project [FP7-ICT287863] and by eGovernAbility-Access project (TIN2014-52665-C2-2-R).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18653/v1/w15-2608">doi:10.18653/v1/w15-2608</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/acl-louhi/Segura-BedmarSM15.html">dblp:conf/acl-louhi/Segura-BedmarSM15</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/inleb6b2z5ed3e5wbhtstqi2uq">fatcat:inleb6b2z5ed3e5wbhtstqi2uq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200508223158/https://www.aclweb.org/anthology/W15-2608.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/09/29/09296e93eaf997498d499f804cc1ba2e54bcd09c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18653/v1/w15-2608"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Automated Extraction of Information From Texts of Scientific Publications: Insights Into HIV Treatment Strategies

Nadezhda Biziukova, Olga Tarasova, Sergey Ivanov, Vladimir Poroikov
<span title="2020-12-22">2020</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a> </i> &nbsp;
The precision of the chemical NEs recognition is over 0.91; recall is 0.86, and the F1-score (harmonic mean of precision and recall) is 0.89; the precision of recognition of proteins and genes names is  ...  To test the applicability of our approach, we have applied it for the extraction of (i) potential HIV inhibitors and (ii) a set of proteins and genes potentially responsible for viremic control in HIV-positive  ...  The results of five-fold cross-validation for annotated corpora CHEMDNER and ChemProt are represented in Table 2 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2020.618862">doi:10.3389/fgene.2020.618862</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33414815">pmid:33414815</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7783389/">pmcid:PMC7783389</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qo4lvrtyjzgshbdp7xpo7r3zum">fatcat:qo4lvrtyjzgshbdp7xpo7r3zum</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201226032300/https://fjfsdata01prod.blob.core.windows.net/articles/files/618862/pubmed-zip/.versions/1/.package-entries/fgene-11-618862/fgene-11-618862.pdf?sv=2018-03-28&amp;sr=b&amp;sig=mDp2TFXJ8vz0L6xZVQU2%2F%2F7eUjACbgFATeRbGM0Ma2A%3D&amp;se=2020-12-26T03%3A23%3A26Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fgene-11-618862.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3b/de/3bde3acb3e333e74530b6ebd24ee5ec695a9909f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2020.618862"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7783389" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Proceedings of the BioCreative V.5 Challenge Evaluation Workshop

Martin Krallinger, Alfonso Valencia
<span title="2022-05-05">2022</span> <i title="Zenodo"> Zenodo </i> &nbsp;
Proceedings of the BioCreative V.5 Challenge Evaluation Workshop  ...  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  ...  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 Language Technology for  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.6519885">doi:10.5281/zenodo.6519885</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gzzr6ogkwvfe3eglv6anrzt5s4">fatcat:gzzr6ogkwvfe3eglv6anrzt5s4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220506094017/https://zenodo.org/record/6519885/files/BioCreative_V.5_Proceedings.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2d/1e/2d1e5f063c38c06f01ef897b6b6c7e037fa4397b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.6519885"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

PharmacoNER Tagger: a deep learning-based tool for automatically finding chemicals and drugs in Spanish medical texts

Jordi Amengol-Estapé, Felipe Soares, Montserrat Marimon, Martin Krallinger
<span title="2019-06-30">2019</span> <i title="Korea Genome Organization"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/acfgmfmleze4rfuugy66fpl4ky" style="color: black;">Genomics &amp; Informatics</a> </i> &nbsp;
Automatically detecting mentions of pharmaceutical drugs and chemical substances is key for the subsequent extraction of relations of chemicals with other biomedical entities such as genes, proteins, diseases  ...  In the domain of medical texts, for chemical entity recognition (CER), techniques based on hand-crafted rules and graph-based models can provide adequate performance.  ...  Evaluation Data For evaluating PharmacoNER tagger, we used the SPACCC dataset, a manually annotated corpus of 1,000 clinical cases written in Spanish and annotated with mentions of chemical compounds  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5808/gi.2019.17.2.e15">doi:10.5808/gi.2019.17.2.e15</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31307130">pmid:31307130</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6808625/">pmcid:PMC6808625</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/aeoje3snjbgzjjkbkjhvr7srgq">fatcat:aeoje3snjbgzjjkbkjhvr7srgq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208083226/https://genominfo.org/upload/pdf/gi-2019-17-2-e15.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8e/72/8e72905b67ef0d4deb2b9270e542fbeeb0668e5e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5808/gi.2019.17.2.e15"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6808625" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Collaborative relation annotation and quality analysis in Markyt environment

Martín Pérez-Pérez, Gael Pérez-Rodríguez, Florentino Fdez-Riverola, Anália Lourenço
<span title="2017-01-01">2017</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
It enables the management of multi-user and multi-round annotation projects, including inter-annotator agreement and consensus assessments.  ...  Also, Markyt supports the description of entity and relation annotation guidelines on a project basis, being flexible to partial word tagging and the occurrence of annotation overlaps.  ...  Acknowledgements The SING group thanks CITI (Centro de Investigació n, Transferencia e Innovació n) from University of Vigo for hosting its IT infrastructure.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bax090">doi:10.1093/database/bax090</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29220479">pmid:29220479</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5737204/">pmcid:PMC5737204</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/f7v2x5ge3rb3teckhmlpvcjs3y">fatcat:f7v2x5ge3rb3teckhmlpvcjs3y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190222161201/http://pdfs.semanticscholar.org/37d1/a125c9308309d617503f198868258fa96f39.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/37/d1/37d1a125c9308309d617503f198868258fa96f39.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bax090"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737204" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

DrugProt corpus genes and proteins annotation guidelines [GPRO - Biocreative 5.2]

Obdulia Rabal, Martin Krallinger
<span title="2021-06-15">2021</span> <i title="Zenodo"> Zenodo </i> &nbsp;
Annotation guidelines used for the annotations of gene and protein-related objects of the CHEMDNER, ChemProt and DrugProt corpora.  ...  c}}o, An{\'a}lia}, journal={Database}, volume={2016}, year={2016}, publisher={Oxford Academic}} Related Resources: Web DrugProt corpus Relations annotation guidelines Chemicals and drugs annotation guidelines  ...  The annotation carried out for the CHEMDNER GPRO task was exhaustive for the types of GPRO mentions that were previously specified.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.4957577">doi:10.5281/zenodo.4957577</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ex6xz2fmlfa3vo3zphfors3qqa">fatcat:ex6xz2fmlfa3vo3zphfors3qqa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210616123833/https://zenodo.org/record/4957577/files/GPRO_guidelines.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fc/49/fc491f2ed03bf957e9f1d4d354b674f2073e3507.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.4957577"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

PALM-IST: Pathway Assembly from Literature Mining - an Information Search Tool

Sapan Mandloi, Saikat Chakrabarti
<span title="2015-05-19">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
It also analyzes scientific collaboration by extraction and creation of "co-authorship network," for a given search context.  ...  ABNER 10 , ABGene 11 , LingPipe (Alias-i. 2008) are some of the entity recognition tools whose goal is to identify biological terms like gene name, drug name within biomedical literature.  ...  We validated the performance of the bio-entity recognition component of PALM-IST using various gold standard corpuses 39 (GSC) such as BioCreative corpus 39 , NCBI Disease corpus 40 , CHEMDNer corpus  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep10021">doi:10.1038/srep10021</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25989388">pmid:25989388</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4437304/">pmcid:PMC4437304</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rxqm5ds54nfklfjtcf5ekwzc24">fatcat:rxqm5ds54nfklfjtcf5ekwzc24</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200315104422/https://www.nature.com/articles/srep10021.pdf?error=cookies_not_supported&amp;code=0d88cd58-9087-439a-998a-8f64d90af549" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/03/ae/03aecfe0d68318d80ffbb7809abeb30e2da59de6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep10021"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4437304" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

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)
<span title="2014-06-30">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
The ease of use, broad support and rapidly growing number of tools demonstrate the need for and value of the BioC format.  ...  BioC is a new simple XML format for sharing biomedical text and annotations and libraries to read and write that format.  ...  /drug, disease and chemical/gene-specific action term mentions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bau053">doi:10.1093/database/bau053</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24980129">pmid:24980129</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4074764/">pmcid:PMC4074764</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tez7f6bevzbmrlqj4cxub2yf7a">fatcat:tez7f6bevzbmrlqj4cxub2yf7a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719025241/http://www.zora.uzh.ch/id/eprint/104530/1/bau053.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ec/81/ec8107090f0732cf73df95b0e7fcb78e73a15114.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bau053"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4074764" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Towards the Construction of a Gold Standard Biomedical Corpus for the Romanian Language

Maria Mitrofan, Verginica Barbu Mititelu, Grigorina Mitrofan
<span title="2018-11-23">2018</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/73aeke3k45ddlpuyeivcdlmtmu" style="color: black;">Data</a> </i> &nbsp;
In order to automatically annotate the corpus with POS tags, we used a Romanian tag set which has 715 labels, while diseases, anatomy, procedures and chemicals and drugs labels were manually annotated  ...  The automatic annotation of the corpus has been manually checked. The corpus is publicly available and can be used to facilitate the development of NLP algorithms for the Romanian language.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/data3040053">doi:10.3390/data3040053</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tzvm2rg5pnhrhieirjbhmazdg4">fatcat:tzvm2rg5pnhrhieirjbhmazdg4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190503215842/https://res.mdpi.com/data/data-03-00053/article_deploy/data-03-00053.pdf?filename=&amp;attachment=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d8/4b/d84bf26c24a796d7ebc7d1fc41d7b54754d8f25d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/data3040053"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a>

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)
<span title="2013-09-18">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
Acknowledgement The authors thank the anonymous reviewers for their useful suggestions in improving this manuscript. .................................................................................  ...  The second document collection whose adaptation to the BioC format will be examined is the dataset currently prepared for the CHEMDNER task of BioCreative IV on chemical compound and drug name recognition  ...  This set consists of annotated mentions of chemical compounds and drugs in text, designed for a classical named entity recognition task.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bat064">doi:10.1093/database/bat064</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24048470">pmid:24048470</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3889917/">pmcid:PMC3889917</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/m5q3ltrfobg4fgkash3katpkia">fatcat:m5q3ltrfobg4fgkash3katpkia</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170812145031/https://dash.harvard.edu/bitstream/handle/1/11879601/3889917.pdf?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/9f/77/9f77ce09c654eea0ab46dbe468201049524d359f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bat064"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889917" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Named Entity Recognition and Relation Detection for Biomedical Information Extraction

Nadeesha Perera, Matthias Dehmer, Frank Emmert-Streib
<span title="2020-08-28">2020</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4dl6zyzmsrhczjurbzfc3hrzn4" style="color: black;">Frontiers in Cell and Developmental Biology</a> </i> &nbsp;
The number of scientific publications in the literature is steadily growing, containing our knowledge in the biomedical, health, and clinical sciences.  ...  In this paper, we review practices for Named Entity Recognition (NER) and Relation Detection (RD), allowing, e.g., to identify interactions between proteins and drugs or genes and diseases.  ...  Interestingly, BANNER-CHEMDNER has shown an 85.68% and an 86.47% F-score on the testing sets of CHEMDNER Chemical Entity Mention (CEM) and Chemical Document Indexing (CDI) sub-tasks and shown a remarkable  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fcell.2020.00673">doi:10.3389/fcell.2020.00673</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32984300">pmid:32984300</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7485218/">pmcid:PMC7485218</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/khclwjfykjfi3jktvrbuliwidm">fatcat:khclwjfykjfi3jktvrbuliwidm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200829204007/https://fjfsdata01prod.blob.core.windows.net/articles/files/519578/pubmed-zip/.versions/1/.package-entries/fcell-08-00673/fcell-08-00673.pdf?sv=2015-12-11&amp;sr=b&amp;sig=P1qEw6WjATEJZxmj62dVp5yZfkKQDgfYLwQCvCHfDz0%3D&amp;se=2020-08-29T20%3A40%3A36Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fcell-08-00673.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fc/93/fc93fd5802598d8034056b94f53b6f76c32a3805.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fcell.2020.00673"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7485218" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A hybrid deep-learning approach for complex biochemical named entity recognition [article]

Jian Liu, Lei Gao, Sujie Guo, Rui Ding, Xin Huang, Long Ye, Qinghua Meng, Asef Nazari, Dhananjay Thiruvady
<span title="2020-12-20">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Named entity recognition (NER) of chemicals and drugs is a critical domain of information extraction in biochemical research.  ...  abbreviations, polysemes, and low-frequency entities, compared with the state-of-the-art approaches.  ...  Research Funds for the Central Universities of China, and Natural Science Foundation of Anhui Province.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2012.10824v1">arXiv:2012.10824v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qsf5hawehjh23mzqp73t4hn6mi">fatcat:qsf5hawehjh23mzqp73t4hn6mi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201225064351/https://arxiv.org/ftp/arxiv/papers/2012/2012.10824.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/29/fc/29fc19082d1afcd060f9e8048d577fa2532694ba.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2012.10824v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

A rule-based named-entity recognition method for knowledge extraction of evidence-based dietary recommendations

Tome Eftimov, Barbara Koroušić Seljak, Peter Korošec, Francisco M Couto
<span title="2017-06-23">2017</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
They are focused on, for example extracting gene mentions, proteins mentions, relationships between genes and proteins, chemical concepts and relationships between drugs and diseases.  ...  In practice, this means that a daily intake of 25 g of a dietary fiber is set as a DRV because it is adequate for adults, while consuming greater than 25 g of dietary fiber per day may reduce the risk  ...  us with the manual evaluation of the obtained results.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0179488">doi:10.1371/journal.pone.0179488</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28644863">pmid:28644863</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5482438/">pmcid:PMC5482438</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mskfqcfxvjfutg3iwcasvub25e">fatcat:mskfqcfxvjfutg3iwcasvub25e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724175617/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0179488&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/11/62/1162c416c4f0ac5d20cb2d636b1424435ca4bced.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0179488"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5482438" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 24 results