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High-performance gene name normalization with GENO

J. Wermter, K. Tomanek, U. Hahn
<span title="2009-02-02">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Motivation: The recognition and normalization of textual mentions of gene and protein names is both particularly important and challenging.  ...  Results: We present GENO, a highly competitive system for gene name normalization, which obtains an F-measure performance of 86.4% (precision: 87.8%, recall: 85.0%) on the BIOCREATIVE-II test set, thus  ...  This tagger is based on Conditional Random Fields (Lafferty et al., 2001) and incorporates features which have been shown to work well for biomedical entity recognition (Settles, 2004) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btp071">doi:10.1093/bioinformatics/btp071</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19188193">pmid:19188193</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lxeqm2sd7rctxkqfwdiusuu5ti">fatcat:lxeqm2sd7rctxkqfwdiusuu5ti</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190309115226/http://pdfs.semanticscholar.org/f8e5/19c1fb0efa22a876e372261e71a8ba30261d.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/f8/e5/f8e519c1fb0efa22a876e372261e71a8ba30261d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btp071"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

BioTagger-GM: A Gene/Protein Name Recognition System

M. Torii, Z. Hu, C. H. Wu, H. Liu
<span title="2009-03-01">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/aapnwtybrvghlc35hfimbtdlom" style="color: black;">JAMIA Journal of the American Medical Informatics Association</a> </i> &nbsp;
Measurements: The BioCreAtIvE II Gene Mention (GM) corpus was used to evaluate the proposed method.  ...  Results: BioTagger-GM achieved an F-Measure of 0.8887 on the BioCreAtIvE II GM corpus, which is higher than that of the first-place system in the BioCreAtIvE II challenge.  ...  four systems 0.8821 0.8952 0.8887 GM ϭ gene mention; CRF ϭ conditional random field.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1197/jamia.m2844">doi:10.1197/jamia.m2844</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19074302">pmid:19074302</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2649315/">pmcid:PMC2649315</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cylljvehzzg6nhourtabxt5ieu">fatcat:cylljvehzzg6nhourtabxt5ieu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180727170217/https://watermark.silverchair.com/16-2-247.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAaMwggGfBgkqhkiG9w0BBwagggGQMIIBjAIBADCCAYUGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMWMiTxbnxZWG3Qht2AgEQgIIBVskN9fWDYVj9o0gIqKHIs9A6zDaQ3Onef4014mBfmepJdazfHe_iHBEu-PX7H_E3ZFQluRHNUI297-pnh3-gGLWVgqlHZlWoMcoxRjfPLtazDHzn-Jqk5bGeal_7iImb-kXhuqJrOwBHyQZ4wPpyvZPvkwyO9meCa3kNlnnrD0W55R42l3Ko_QT_lq4OQZE0v7_wZV09GcS3tlgE8doHEbWLQS9uvYnUChYAZZfpHA8aTQAhbYNJ86aSpycANU2miIhsWCyi77QHpg01NSqdjlKQ18qzJR71No9THwB0KEaPP00lYsFaqTpVw2OsDZYtsubbNZBBq7xKDhkE20stmBMDsXiPRxG3UeZC1b31Q4cIyYxahh8asHcYk3tJV6bFbtd4h9rxGeQZkH1YcPm-fzN0Ry3Nmaj9Ugnv9G_2dVIdZ933tmvzAzYutPqA79GUBnpaQcHsVg" 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/16/65/1665f870a6d8f0d1446faf0f38578a8e2be60f58.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1197/jamia.m2844"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2649315" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Overview of BioCreative II gene mention recognition

Larry Smith, Lorraine K Tanabe, Rie Ando, Cheng-Ju Kuo, I-Fang Chung, Chun-Nan Hsu, Yu-Shi Lin, Roman Klinger, Christoph M Friedrich, Kuzman Ganchev, Manabu Torii, Hongfang Liu (+22 others)
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop.  ...  In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions.  ...  This article has been published as part of Genome Biology Volume 9 Supplement 2, 2008: The BioCreative II -Critical Assessment for Information Extraction in Biology Challenge.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2008-9-s2-s2">doi:10.1186/gb-2008-9-s2-s2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18834493">pmid:18834493</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2559986/">pmcid:PMC2559986</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eguamlzmd5ec7btwyq3mr6v4fi">fatcat:eguamlzmd5ec7btwyq3mr6v4fi</a> </span>
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Evaluating Word Representation Features in Biomedical Named Entity Recognition Tasks

Buzhou Tang, Hongxin Cao, Xiaolong Wang, Qingcai Chen, Hua Xu
<span title="">2014</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/icbhosh775h7bgzgot6avm3cua" style="color: black;">BioMed Research International</a> </i> &nbsp;
We selected one algorithm from each of the three types of WR features and applied them to the JNLPBA and BioCreAtIvE II BNER tasks.  ...  Biomedical Named Entity Recognition (BNER), which extracts important entities such as genes and proteins, is a crucial step of natural language processing in the biomedical domain.  ...  Acknowledgments This study is supported in part by Grants CPRIT  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2014/240403">doi:10.1155/2014/240403</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24729964">pmid:24729964</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3963372/">pmcid:PMC3963372</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zhoy6aqxhvf5fcjydkheiwskge">fatcat:zhoy6aqxhvf5fcjydkheiwskge</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190503080801/http://downloads.hindawi.com/journals/bmri/2014/240403.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/52/3f/523f255f90be3f1ae0f151c60cac50467e965ed0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2014/240403"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> hindawi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3963372" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Introducing meta-services for biomedical information extraction

Florian Leitner, Martin Krallinger, Carlos Rodriguez-Penagos, Jörg Hakenberg, Conrad Plake, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tsai, Hsi-Chuan Hung, William W Lau, Calvin A Johnson, Rune Sætre (+20 others)
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
Annotation types cover gene names, gene IDs, species, and protein-protein interactions. The annotations are distributed by the meta-server in both human and machine readable formats (HTML/XML).  ...  S6.2 biomedical researchers and database annotators, and in biomedical language processing. The platform allows direct comparison, unified access, and result aggregation of the annotations.  ...  Also, we should like especially to thank all participants of the second BioCreative challenge and their vital contributions during the discussions at the workshop and in the mailing lists.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2008-9-s2-s6">doi:10.1186/gb-2008-9-s2-s6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18834497">pmid:18834497</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2559990/">pmcid:PMC2559990</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vxtilyugbza73lep66bvclyjem">fatcat:vxtilyugbza73lep66bvclyjem</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810105038/http://clair.si.umich.edu/~radev/papers/122.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/9f/26/9f26511eac364cc0acafce06e61b3ed72d063f21.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2008-9-s2-s6"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559990" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The GNAT library for local and remote gene mention normalization

J. Hakenberg, M. Gerner, M. Haeussler, I. Solt, C. Plake, M. Schroeder, G. Gonzalez, G. Nenadic, C. M. Bergman
<span title="2011-08-03">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
of gene and protein names for data analysis.  ...  Here we present the GNAT Java library for text retrieval, named entity recognition, and normalization of gene and protein mentions in biomedical text.  ...  In addition to the dictionary-based gene NER taggers, we now provide an interface to Banner (Leaman and Gonzalez, 2008) , which uses conditional random fields to recognize candidate gene names.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btr455">doi:10.1093/bioinformatics/btr455</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21813477">pmid:21813477</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3179658/">pmcid:PMC3179658</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ayz2mevokre5jk622udycr5tom">fatcat:ayz2mevokre5jk622udycr5tom</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20151203092614/http://bioinformatics.oxfordjournals.org:80/content/27/19/2769.full.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/d5/d6/d5d6727566086559d593c3850cb6dad045f07b15.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btr455"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179658" 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 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  ... 
<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>

Proceedings of the second biocreative challenge evaluation workshop

Lynette Hirschman, Martin Krallinger, Alfonso Valencia
<span title="2007-04-23">2007</span> <i title="Zenodo"> Zenodo </i> &nbsp;
Proceedings of the Second BioCreative Challenge Evaluation Workshop  ...  of the AIIA-GMT system to the BioCreative III Gene Normalization data.  ...  for evaluation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.6519852">doi:10.5281/zenodo.6519852</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k6q4vrkd65hbthlvwnhy2ufiey">fatcat:k6q4vrkd65hbthlvwnhy2ufiey</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220508015331/https://zenodo.org/record/6519852/files/BioCreative_III_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/f4/9b/f49b7ed11db85b966b557de9263c4e8be67f3119.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.6519852"> <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>

The gene normalization task in BioCreative III

Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner (+16 others)
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
BACKGROUND: We report the Gene Normalization (GN) challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles.  ...  Abstract Background: We report the Gene Normalization (GN) challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles  ...  Zuofeng Li for developing the genetic sequence based gene normalizer and acknowledge the support from the National Library of Medicine, grant numbers 5R01LM009836 to Hong Yu and 5R01LM010125 to Isaac  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-12-s8-s2">doi:10.1186/1471-2105-12-s8-s2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22151901">pmid:22151901</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3269937/">pmcid:PMC3269937</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/26ncvweohrh7nkovlxexjkrpki">fatcat:26ncvweohrh7nkovlxexjkrpki</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501162444/https://www.zora.uzh.ch/id/eprint/58295/1/1471-2105-12-S8-S2.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/ee/2dee7064ac32385e2e60067c508b6a0c21b4d4d9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-12-s8-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/PMC3269937" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

BioCreative II Workshop Proceedings

Lynette, Martin, Alfonso
<span title="2007-04-23">2007</span> <i title="Zenodo"> Zenodo </i> &nbsp;
Gene Mention Task 17 Overview of BioCreative II Gene Normalization 29 Evaluating the Detection and Ranking of Protein Interaction relevant Articles: the BioCreative Challenge Interaction Article Sub-task  ...  81 Combined Conditional Random Fields and n-Gram Language Models for Gene Mention Recognition 85 Tackling the BioCreative2 Gene Mention task with Conditional Random Fields and Syntactic Parsing 89 Named  ...  We are grateful to Indiana University's Research and Technical Services for technical support. The AVIDD Linux Clusters used in our analysis are funded in part by NSF Grant CDA-9601632.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.4274543">doi:10.5281/zenodo.4274543</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3sa3fvgngffjrblxzgswof42tq">fatcat:3sa3fvgngffjrblxzgswof42tq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201116181924/https://zenodo.org/record/4274543/files/BioCreative_2_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] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.4274543"> <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>

IDENTIFYING GENE-SPECIFIC VARIATIONS IN BIOMEDICAL TEXT

ROMAN KLINGER, CHRISTOPH M. FRIEDRICH, HEINZ THEODOR MEVISSEN, JULIANE FLUCK, MARTIN HOFMANN-APITIUS, LAURA I. FURLONG, FERRAN SANZ
<span title="">2007</span> <i title="World Scientific Pub Co Pte Lt"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zudjdcas3bcm3lfnfxnjyl5zty" style="color: black;">Journal of Bioinformatics and Computational Biology</a> </i> &nbsp;
To tackle this challenge, we integrate the ProMiner system developed for the recognition and normalization of gene and protein names with a Conditional Random Field based recognition of variation terms  ...  Remaining challenges associated with this system were the relatively low recall for variation mentions and gene name recognition.  ...  Acknowledgments This work has been partially funded by the MPG-FhG Machine Learning Collaboration (see http://lip.fml.tuebingen.mpg.de/) and in the framework of the European integrated project @neurIST  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/s0219720007003156">doi:10.1142/s0219720007003156</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18172929">pmid:18172929</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nnunmmf7yjbebgdaj2qttoeplu">fatcat:nnunmmf7yjbebgdaj2qttoeplu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922050107/https://pub.uni-bielefeld.de/download/2603456/2675056" 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/ad/3e/ad3e05eb4e871acaab32ccf6e63d8bd4868e7656.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/s0219720007003156"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> worldscientific.com </button> </a>

Incorporating rich background knowledge for gene named entity classification and recognition

Yanpeng Li, Hongfei Lin, Zhihao Yang
<span title="">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Then we combined the dictionary with a conditional random field (CRF) based gene mention tagger, achieving an F-score of 89.05, which improves the performance of the CRF-based tagger by 4.46 with little  ...  Gene named entity classification and recognition are crucial preliminary steps of text mining in biomedical literature. Machine learning based methods have been used in this area with great success.  ...  This work was supported by grant from the Natural Science Foundation of China (No. 60373095 and 60673039) and the National High Tech Research and Development Plan of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-10-223">doi:10.1186/1471-2105-10-223</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19615051">pmid:19615051</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2725142/">pmcid:PMC2725142</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/z7h5n4r3uva5bno3pfxefjaina">fatcat:z7h5n4r3uva5bno3pfxefjaina</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170820051333/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-10-223?site=bmcbioinformatics.biomedcentral.com" 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/80/d2/80d270c5de8e6718c8b2ed25cb48ebd9eeed8344.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-10-223"> <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/PMC2725142" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Automating curation using a natural language processing pipeline

Beatrice Alex, Claire Grover, Barry Haddow, Mijail Kabadjov, Ewan Klein, Michael Matthews, Richard Tobin, Xinglong Wang
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
The tasks in BioCreative II were designed to approximate some of the laborious work involved in curating biomedical research papers.  ...  Although high performance may be obtained on individual tasks such as gene mention recognition and normalization, and document classification, tasks in which a number of components must be combined, such  ...  This article has been published as part of Genome Biology Volume 9 Supplement 2, 2008: The BioCreative II -Critical Assessment for Information Extraction in Biology Challenge.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2008-9-s2-s10">doi:10.1186/gb-2008-9-s2-s10</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18834488">pmid:18834488</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2559981/">pmcid:PMC2559981</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/asmlwci6kze55j3m64gpicdzui">fatcat:asmlwci6kze55j3m64gpicdzui</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170817073734/http://www.research.ed.ac.uk/portal/files/694611/gb_2008_9_s2_s10.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/76/ba/76ba7b4527557f63f8648c8d7c252eda550d4b62.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2008-9-s2-s10"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559981" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

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)
<span title="">2016</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;
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.  ...  The recognition of gene/protein (F-score 70%) and organism mentions (F-score 73%) in text was addressed by training Conditional Random Fields models on lexical and Table 3 .  ...  The gene mention recognizer, a conditional random fields model, was trained on the generated linguistic information and these features were used as the input for the species mention recognizer.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baw121">doi:10.1093/database/baw121</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27589962">pmid:27589962</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5009341/">pmcid:PMC5009341</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bqe4o77fizadhf5e3xese3i23y">fatcat:bqe4o77fizadhf5e3xese3i23y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190221020820/http://pdfs.semanticscholar.org/2b82/2193399be9f0b0471ea6cf84eb25071e6ca8.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/2b/82/2b822193399be9f0b0471ea6cf84eb25071e6ca8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baw121"> <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/PMC5009341" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Cross-species gene normalization by species inference

Chih-Hsuan Wei, Hung-Yu Kao
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Gene names are often ambiguous, in that they can refer to the genes of many species. Therefore, gene normalization is a difficult challenge.  ...  To access and utilize the rich information contained in the biomedical literature, the ability to recognize and normalize gene mentions referenced in the literature is crucial.  ...  This article has been published as part of BMC Bioinformatics Volume 12 Supplement 8, 2011: The Third BioCreative -Critical Assessment of Information Extraction in Biology Challenge.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-12-s8-s5">doi:10.1186/1471-2105-12-s8-s5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22151999">pmid:22151999</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3269940/">pmcid:PMC3269940</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jrot7nsqxvaeferxkoybgrpcr4">fatcat:jrot7nsqxvaeferxkoybgrpcr4</a> </span>
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