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Protein Structures and Information Extraction from Biological Texts: The PASTA System

R. Gaizauskas, G. Demetriou, P. J. Artymiuk, P. Willett
<span title="2003-01-01">2003</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;
PASTA is the first information extraction (IE) system developed for the protein structure domain and one of the most thoroughly evaluated IE system operating on biological scientific text to date.  ...  Results: We describe the Protein Active Site Template Acquisition (PASTA) system, which addresses these problems by performing automatic extraction of information relating to the roles of specific amino  ...  The authors would like to thank Ruth Spriggs and Darren South for their expert assistance in tagging terminology and filling templates.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/19.1.135">doi:10.1093/bioinformatics/19.1.135</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12499303">pmid:12499303</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oynciggvina5pkpwzhzm55yil4">fatcat:oynciggvina5pkpwzhzm55yil4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20070128195027/http://bioinformatics.oxfordjournals.org:80/cgi/reprint/19/1/135.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/7e/09/7e0973cfaaffe5eb1a601be15eb5d280419dbc34.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/19.1.135"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Utilizing text mining results

G. Demetriou, R. Gaizauskas
<span title="">2002</span> <i title="Association for Computational Linguistics"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5n6volmnonf5tn6xputi5f2t3e" style="color: black;">Proceedings of the ACL-02 workshop on Natural language processing in the biomedical domain -</a> </i> &nbsp;
We describe the development of PASTAWeb, a WWWbased interface to the extraction output of PASTA, an IE system that extracts protein structure information from MEDLINE abstracts.  ...  Information Extraction (IE), defined as the activity to extract structured knowledge from unstructured text sources, offers new opportunities for the exploitation of biological information contained in  ...  IE system that extracts information about amino acid residues in protein structures and their roles in protein active sites directly from the published literature.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3115/1118149.1118160">doi:10.3115/1118149.1118160</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/acl/DemetriouG02.html">dblp:conf/acl/DemetriouG02</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iqshlg3pxzfs5bbmv5ytz234pe">fatcat:iqshlg3pxzfs5bbmv5ytz234pe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20040908042933/http://acl.ldc.upenn.edu:80/W/W02/W02-0311.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/32/73/3273bf6d1487458d6908436232bd454ba02e9451.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3115/1118149.1118160"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

ISMB 2003 Text Mining SIG Meeting Report

Christian Blaschke, Alexander Yeh, Lynette Hirschman, Alfonso Valencia
<span title="">2003</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eaz5kv6drnd7hlqjuszvrhtqnm" style="color: black;">Comparative and Functional Genomics</a> </i> &nbsp;
Society for Computational Biology) for organizing the logistics and the infrastructure, and the EU projects ORIEL (Contract number: IST-2001-32688) and TEMBLOR (Contract number: VEQLRT 2001 00015) for  ...  Acknowledgements The organizers of the workshop would like to thank especially all the speakers for their presentations, Marc Light for co-organizing the event, Steven Leard and the ISCB (The International  ...  PASTA, for Protein Active Site Template Acquisition system, is a text mining system for the automatic extraction of information relating to protein structures from the biological literature.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cfg.338">doi:10.1002/cfg.338</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18629019">pmid:18629019</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2447301/">pmcid:PMC2447301</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vmqqau3myrgsfdfhwotqljapje">fatcat:vmqqau3myrgsfdfhwotqljapje</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180726044320/http://downloads.hindawi.com/journals/ijg/2003/106735.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/ca/db/cadb8c02889e2e8e30634483c72a9ff884a3e8de.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cfg.338"> <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/PMC2447301" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Text mining and ontologies in biomedicine: Making sense of raw text

I. Spasic, S. Ananiadou, J. McNaught, A. Kumar
<span title="2005-01-01">2005</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
information, extract facts, discover implicit links and generate hypotheses relevant to user needs.  ...  The volume of biomedical literature is increasing at such a rate that it is becoming difficult to locate, retrieve and manage the reported information without text mining, which aims to automatically distill  ...  Acknowledgments The National Centre for Text Mining (NaCTeM), UK is sponsored by the JISC. AK expresses his gratitude to Alexander von Humboldt Foundation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/6.3.239">doi:10.1093/bib/6.3.239</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16212772">pmid:16212772</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ehw3jx2imze2xd2vfe4nuaqcgy">fatcat:ehw3jx2imze2xd2vfe4nuaqcgy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100613044814/http://webster.cs.uga.edu/%7Ekochut/Teaching/8350/Papers/Ontologies/TextMining-RawText.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/fb/f4/fbf45f623bce30f2679d36299d149ce986e66314.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/6.3.239"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

A Relation Mining and Visualization Framework for Automated Text Summarization [chapter]

Muhammad Abulaish, Jahiruddin, Lipika Dey
<span title="">2009</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
In this paper, we present a relation mining and visualization framework to identify important semi-structured information components using semantic and linguistic analysis of text documents.  ...  The novelty of the paper lies in identifying key snippet from text to validate the interaction between a pair of entities.  ...  The PASTA system [1] is a more comprehensive system that extracts relations between proteins, species and residues. Ono et al.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-11164-8_40">doi:10.1007/978-3-642-11164-8_40</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zhmy73n5hzantij27k67cdkxjm">fatcat:zhmy73n5hzantij27k67cdkxjm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190505025409/https://link.springer.com/content/pdf/10.1007%2F978-3-642-11164-8_40.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/bf/82/bf8228ac11f3f0b921c58ff6442e0a2e530bb579.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-11164-8_40"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Distributed modules for text annotation and IE applied to the biomedical domain

H KIRSCH, S GAUDAN, D REBHOLZSCHUHMANN
<span title="">2006</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jyf7co46pvdybh6jhdipt5d3im" style="color: black;">International Journal of Medical Informatics</a> </i> &nbsp;
Curation is timeconsuming and can be supported by information extraction methods. We present a server which identifies biological facts in scientific text and presents the annotation to the curator.  ...  Such information extraction (IE) tools have to meet a number of demands. First protein and gene names (PGNs) have to be identified in the text.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ijmedinf.2005.06.011">doi:10.1016/j.ijmedinf.2005.06.011</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16085453">pmid:16085453</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dw4m4tkywjho7p7q63g25egzya">fatcat:dw4m4tkywjho7p7q63g25egzya</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809034317/http://wing.comp.nus.edu.sg/~antho/W/W04/W04-1208.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/cc/a6/cca67c075b7d007d54788aea22bf6236cf390761.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ijmedinf.2005.06.011"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Tagging gene and protein names in biomedical text

L. Tanabe, W. J. Wilbur
<span title="2002-08-01">2002</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;
The fundamental task of identifying gene and protein names is a necessary first step towards making full use of the information encoded in biomedical text.  ...  Automated text processing can aid in the comprehension and synthesis of this valuable information.  ...  Browne for providing the Penn Treebank tags for SPECIALIST lexicon entries, and Donald C. Comeau for the list of low frequency trigrams in MEDLINE.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/18.8.1124">doi:10.1093/bioinformatics/18.8.1124</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12176836">pmid:12176836</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d3jvnmobhzfkvast23flyg6sua">fatcat:d3jvnmobhzfkvast23flyg6sua</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100610001821/http://www.hlt.utdallas.edu/~vh/Courses/Fall06/Papers/Tagging%20gene%20and%20protein%20names.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/89/2c/892cbe33671040d6c719811004752ed3ff1b7c8e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/18.8.1124"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Biological relation extraction and query answering from MEDLINE abstracts using ontology-based text mining

Muhammad Abulaish, Lipika Dey
<span title="">2007</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ueo4clepdnbdzhqnuojj57edri" style="color: black;">Data &amp; Knowledge Engineering</a> </i> &nbsp;
The fuzzy biological relations extracted from a text corpus along with other relevant information components like biological entities occurring within a relation, are stored in a database.  ...  The system extracts all frequently occurring biological relations among a pair of biological concepts through text mining.  ...  The PASTA system is a more comprehensive system that extracts relations between proteins, species and residues [23] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.datak.2006.06.007">doi:10.1016/j.datak.2006.06.007</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/up7ix3kl6zh5tagigoxvsvhtde">fatcat:up7ix3kl6zh5tagigoxvsvhtde</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808061347/http://www.abulaish.com/uploads/DKE07.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/e7/31/e73190b747624d4bb25ee29464aebe7e423b961c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.datak.2006.06.007"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

@Note: A workbench for Biomedical Text Mining

Anália Lourenço, Rafael Carreira, Sónia Carneiro, Paulo Maia, Daniel Glez-Peña, Florentino Fdez-Riverola, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha
<span title="">2009</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p4kk6lusgrhyxecgig72iasi5q" style="color: black;">Journal of Biomedical Informatics</a> </i> &nbsp;
Its main functional contributions are the ability to process abstracts and full-texts; an information retrieval module enabling PubMed search and journal crawling; a pre-processing module with PDF-to-text  ...  We present @Note, a platform for BioTM that aims at the effective translation of the advances between three distinct classes of users: biologists, text miners and software developers.  ...  Acknowledgments We thank Alberto Simões and José João Almeida for helping deploy the text rewriting system and their expert suggestions in Natural Language Processing issues.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2009.04.002">doi:10.1016/j.jbi.2009.04.002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19393341">pmid:19393341</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zqgrd47mg5dovjnzd2fjhvsoda">fatcat:zqgrd47mg5dovjnzd2fjhvsoda</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170815132237/http://repositorium.sdum.uminho.pt/bitstream/1822/9416/1/Lourenco_JBI%255B1%255D.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/dd/22/dd22e34f0d717f91cf6fdeb74dc85b4b744f164d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2009.04.002"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Text Mining Improves Prediction of Protein Functional Sites

Karin M. Verspoor, Judith D. Cohn, Komandur E. Ravikumar, Michael E. Wall, Neil R. Smalheiser
<span title="2012-02-29">2012</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;
The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important.  ...  The overlap of predictions with annotations improved when the text-based and structure-based methods agreed.  ...  Acknowledgments We gratefully acknowledge Kevin Nagel for sharing the annotated text corpus he developed for his dissertation work with us and giving us permission to redistribute it.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0032171">doi:10.1371/journal.pone.0032171</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22393388">pmid:22393388</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3290545/">pmcid:PMC3290545</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4564uparzzb6ldzy2wxjpap2w4">fatcat:4564uparzzb6ldzy2wxjpap2w4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171003054112/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0032171&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/88/df/88df8770b38c9bd71ffc57e599298b601c1e6549.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0032171"> <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/PMC3290545" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Text Mining for Biology and Biomedicine Sophia Ananiadou and John McNaught (editors) (University of Manchester and UK National Centre for Text Mining) Boston and London: Artech House, 2006, xi+286 pp; hardbound, ISBN 1-58053-984-X, £53.00

Nikiforos Karamanis
<span title="">2007</span> <i title="MIT Press - Journals"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/e4yflo6sufcufjwloald7xudm4" style="color: black;">Computational Linguistics</a> </i> &nbsp;
Protein structure and information extraction from biological texts: The PASTA system. Bioinformatics, abbreviations from MEDLINE. Journal of the American Medical Information Association, 9:612--620.  ...  of two extant systems, GeneWays (Rzhetsky et al. 2004) and PASTA (Gaizauskas et al. 2003).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1162/coli.2007.33.1.135">doi:10.1162/coli.2007.33.1.135</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/a3qw5watpzd33isdbsberobgoq">fatcat:a3qw5watpzd33isdbsberobgoq</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/details/sim_computational-linguistics_2007-03_33_1/page/136" title="read fulltext microfilm" 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> Archive [Microfilm] <div class="menu fulltext-thumbnail"> <img src="https://archive.org/serve/sim_computational-linguistics_2007-03_33_1/__ia_thumb.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1162/coli.2007.33.1.135"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mitpressjournals.org </button> </a>

A concept-driven biomedical knowledge extraction and visualization framework for conceptualization of text corpora

Jahiruddin, Muhammad Abulaish, Lipika Dey
<span title="">2010</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p4kk6lusgrhyxecgig72iasi5q" style="color: black;">Journal of Biomedical Informatics</a> </i> &nbsp;
The system is also integrated with a biomedical named entity recognizer, ABNER, to tag genes, proteins and other entity names in the text.  ...  The system stores the extracted information components in a structured repository which is integrated with a query-processing module to handle biomedical queries over text documents.  ...  The PASTA system is a more comprehensive system that extracts relations between proteins, species and residues [22] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2010.09.008">doi:10.1016/j.jbi.2010.09.008</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20870033">pmid:20870033</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4gypd7qg2rbk5fvxnxkxurnnju">fatcat:4gypd7qg2rbk5fvxnxkxurnnju</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170924195116/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/1b0/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMTUzMjA0NjQxMDAwMTQwMQ%3D%3D.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/13/e8/13e8f3fa0842371a16d4a9d755204357a32d46ff.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2010.09.008"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

A shallow parser based on closed-class words to capture relations in biomedical text

Gondy Leroy, Hsinchun Chen, Jesse D Martinez
<span title="">2003</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p4kk6lusgrhyxecgig72iasi5q" style="color: black;">Journal of Biomedical Informatics</a> </i> &nbsp;
It uses heuristics and a noun phraser to capture entities of interest in the text. Cascaded finite state automata structure the relations between individual entities.  ...  A shallow parser that captures the relations between noun phrases automatically from free text has been developed and evaluated.  ...  We thank Ryan Falsey and Kerri Kislin from the Arizona Cancer Center for their suggestion, ideas, and evaluations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1532-0464(03)00039-x">doi:10.1016/s1532-0464(03)00039-x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/14615225">pmid:14615225</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/brfkh5e72rcitbrvrlgmjq5nf4">fatcat:brfkh5e72rcitbrvrlgmjq5nf4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190413041709/https://core.ac.uk/download/pdf/82588585.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/a7/14/a71419936bb1a377517c22db85417cdcef9a1dec.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1532-0464(03)00039-x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Two Applications of Information Extraction to Biological Science Journal Articles: Enzyme Interactions and Protein Structures

Kevin Humphreys, George Demetriou, Robert Gaizauskas
<span title="">1999</span> <i title="WORLD SCIENTIFIC"> Biocomputing 2000 </i> &nbsp;
pathways; and PASTA, concerned with protein structure.  ...  DARPA Message Understanding Conferences MUCs, has proved successful at extracting information primarily from newswire texts and primarily in domains concerned with human activity.  ...  PASTA is funded under the UK BBSRC EPRSC BioInformatics Programme BIF08754 and is a collaboration between the Departments of Computer Science, Information Studies and Molecular Biology and Biotechnology  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9789814447331_0048">doi:10.1142/9789814447331_0048</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/g3inqml3vjdbzipqdhcfzo5p6i">fatcat:g3inqml3vjdbzipqdhcfzo5p6i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20060624141000/http://www.ccs.neu.edu:80/home/futrelle/bionlp/psb2000/humphreys.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/13/c9/13c98a57653f521a9fd61ed47f7fa9d711f2467f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9789814447331_0048"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> worldscientific.com </button> </a>

Comparison of Text Mining Models for Food and Dietary Constituent Named-Entity Recognition

Nadeesha Perera, Thi Thuy Linh Nguyen, Matthias Dehmer, Frank Emmert-Streib
<span title="2022-03-16">2022</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tjwucdga6zfftlebfsmbvxjiyy" style="color: black;">Machine Learning and Knowledge Extraction</a> </i> &nbsp;
Biomedical Named-Entity Recognition (BioNER) has become an essential part of text mining due to the continuously increasing digital archives of biological and medical articles.  ...  While there are many well-performing BioNER tools for entities such as genes, proteins, diseases or species, there is very little research into food and dietary constituent named-entity recognition.  ...  The pipeline structure for the model contains three feature extraction steps where rich text articles are cleaned, tagged for parts-of-speech (POS) labels and cleaned semantically.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/make4010012">doi:10.3390/make4010012</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/akf5buq3vngctn23irxwjtwfei">fatcat:akf5buq3vngctn23irxwjtwfei</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220318144730/https://mdpi-res.com/d_attachment/make/make-04-00012/article_deploy/make-04-00012-v2.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/13/30/13304652268dcf96ecc5f1516b74f5557402c18a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/make4010012"> <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>
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