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Author Name Disambiguation in MEDLINE

Vetle I Torvik, Neil R Smalheiser
<span title="2009-07-01">2009</span> <i title="Association for Computing Machinery"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gvg3htf2zjex5j7pnaz4tzal6a" style="color: black;">ACM Transactions on Knowledge Discovery from Data</a> </i> &nbsp;
Here we test the hypothesis that the Author-ity model will suffice to disambiguate author names for the vast majority of articles in MEDLINE.  ...  RESULTS: Pairwise comparisons were computed for all author names on all 15.3 million articles in MEDLINE (2006 baseline), that share last name and first initial, to create Author-ity 2006, a database that  ...  Acknowledgments We sincerely thank Wei Zhang for programming assistance, Clement Yu for advice on computational issues, and Jeff Baer for permission to use Community of Science data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20072710">pmid:20072710</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2805000/">pmcid:PMC2805000</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iy6qajnpyrh7ddmw2i3srlimfy">fatcat:iy6qajnpyrh7ddmw2i3srlimfy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209224900/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2805000&amp;blobtype=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/0f/ed/0fedf71bde00ea99ae5a536beb800d3c530574e1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805000" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Author name disambiguation in MEDLINE

Vetle I. Torvik, Neil R. Smalheiser
<span title="2009-07-01">2009</span> <i title="Association for Computing Machinery (ACM)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gvg3htf2zjex5j7pnaz4tzal6a" style="color: black;">ACM Transactions on Knowledge Discovery from Data</a> </i> &nbsp;
We also thank the US National Library of Medicine (NLM) for providing the 2006 baseline release of MEDLINE.  ...  ACKNOWLEDGMENTS We sincerely thank Wei Zhang for programming assistance, Clement Yu for advice on computational issues, and Jeff Baer for permission to use Community of Science data.  ...  MEDLINE (hence creating a gold standard of article pairs arising from the same individual).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1552303.1552304">doi:10.1145/1552303.1552304</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4vd5yjoccfdc7l4a2mqn6ypxti">fatcat:4vd5yjoccfdc7l4a2mqn6ypxti</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100620171905/http://arrowsmith.psych.uic.edu/arrowsmith_uic/tutorial/torvik_tkdd_2009.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/15/27/152788a40a09cd5b9b979034df608a5cb3909f79.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1552303.1552304"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

The Effect of Word Sense Disambiguation Accuracy on Literature Based Discovery

Judita Preiss, Mark Stevenson
<span title="">2015</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6g37zvjwwrhv3dizi6ffue642m" style="color: black;">Proceedings of the ACM Ninth International Workshop on Data and Text Mining in Biomedical Informatics - DTMBIO &#39;15</a> </i> &nbsp;
Evaluation of the LBD output is carried out using timeslicing approach, where hidden knowledge is generated from articles published prior to a certain cutoff date and a gold standard extracted from publications  ...  The accuracy of each WSD approach is determined by comparing its output against a standard benchmark.  ...  Acknowledgements The work described in this paper was funded by the Engineering and Physical Sciences Research Council (EP/J008427/1).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/2811163.2811185">doi:10.1145/2811163.2811185</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/cikm/PreissS15.html">dblp:conf/cikm/PreissS15</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tlqpdpclrzdzvoh74q5hdfpgwa">fatcat:tlqpdpclrzdzvoh74q5hdfpgwa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171008141439/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/090/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjExODYvczEyOTExLTAxNi0wMjk2LTEucGRm.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/7f/7a/7f7abeb872abcc1f255b6e5aa299c5918a5b9c58.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/2811163.2811185"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

The effect of word sense disambiguation accuracy on literature based discovery

Judita Preiss, Mark Stevenson
<span title="">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bnylrk2y7bfnrn7u2f2vjkx7ta" style="color: black;">BMC Medical Informatics and Decision Making</a> </i> &nbsp;
Evaluation of the LBD output is carried out using timeslicing approach, where hidden knowledge is generated from articles published prior to a certain cutoff date and a gold standard extracted from publications  ...  The accuracy of each WSD approach is determined by comparing its output against a standard benchmark.  ...  Acknowledgements The work described in this paper was funded by the Engineering and Physical Sciences Research Council (EP/J008427/1).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12911-016-0296-1">doi:10.1186/s12911-016-0296-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27455071">pmid:27455071</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4959388/">pmcid:PMC4959388</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ay3wmj2njjalnpa4bpi3xmddfq">fatcat:ay3wmj2njjalnpa4bpi3xmddfq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210427172527/http://usir.salford.ac.uk/id/eprint/58771/1/s12911-016-0296-1.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/d0/60/d06066dcf81b0521a47d683420e53383941e3d76.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12911-016-0296-1"> <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/PMC4959388" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

LINNAEUS: A species name identification system for biomedical literature

Martin Gerner, Goran Nenadic, Casey M Bergman
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
LINNAEUS uses a dictionary-based approach (implemented as an efficient deterministic finite-state automaton) to identify species names and a set of heuristics to resolve ambiguous mentions.  ...  The task of recognizing and identifying species names in biomedical literature has recently been regarded as critical for a number of applications in text and data mining, including gene name recognition  ...  We therefore also provide a new gold-standard corpus of full-text articles with manually annotated mentions of species names.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-11-85">doi:10.1186/1471-2105-11-85</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20149233">pmid:20149233</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2836304/">pmcid:PMC2836304</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eru576q7u5befdadlzwjhw3mqi">fatcat:eru576q7u5befdadlzwjhw3mqi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170819123551/https://www.biomedcentral.com/content/pdf/1471-2105-11-85.pdf&amp;keyword=species-names" 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/e1/03/e1039346942874c59d89028bb934b72524827b8c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-11-85"> <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/PMC2836304" 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 mature use of semantic resources for biomedical analyses

D Rebholz-Schuhmann, F Rinaldi, S Pyysalo, N Collier, U Hahn
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iasjcyzzyncgnohh3aitx65bhq" style="color: black;">Journal of Biomedical Semantics</a> </i> &nbsp;
This solution improves the disambiguation of the names of genes and proteins in the GENIA corpus.  ...  a large-scale analysis of the whole of Medline to collect and characterise associations of genes and proteins through syntactic parsing.  ...  SVM classification performed better than a Naives Bayes classifier delivering evidence for a high degree of correlation between pre-diagnostic social media signals and gold standard laboratory data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-2-s5-i1">doi:10.1186/2041-1480-2-s5-i1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22166304">pmid:22166304</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3239298/">pmcid:PMC3239298</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gyyjdxtguzdd5cnlzdqzu3kqii">fatcat:gyyjdxtguzdd5cnlzdqzu3kqii</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160101021223/http://www.zora.uzh.ch/60993/1/2041-1480-2-S5-I1.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/87/e6/87e676bed840cc26dcd769df2cee330c3fe18fcd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-2-s5-i1"> <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/PMC3239298" 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 large scale, corpus-based approach for automatically disambiguating biomedical abbreviations

Hong Yu, Won Kim, Vasileios Hatzivassiloglou, John Wilbur
<span title="2006-07-01">2006</span> <i title="Association for Computing Machinery (ACM)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a2o77szzyngfjiyr6oftvf2ts4" style="color: black;">ACM Transactions on Information Systems</a> </i> &nbsp;
provide training data for disambiguating the abbreviations that are not linked to a full form within a text.  ...  In this study, we have developed supervised approaches to identifying the full forms of ambiguous abbreviations within the context they appear.  ...  GOLD STANDARD We selected a total of 300 MEDLINE abstracts that incorporate the 60 abbreviations we would use for evaluating our automatic biomedical disambiguation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1165774.1165778">doi:10.1145/1165774.1165778</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ynevzx5ydnbu7bwf5nutzvemky">fatcat:ynevzx5ydnbu7bwf5nutzvemky</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110401184641/https://pantherfile.uwm.edu/hongyu/www/files/articles/p380-yu.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/98/54/9854d3ce48428e4524ba72ca3965391ba0f1c06d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1165774.1165778"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

Harmonization of gene/protein annotations: towards a gold standard MEDLINE

David Campos, Sérgio Matos, Ian Lewin, José Luís Oliveira, Dietrich Rebholz-Schuhmann
<span title="2012-03-13">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
However, little effort has been spent on a systematic analysis of methods harmonizing the annotation results and measuring against a combination of Gold Standard Corpora (GSCs).  ...  We demonstrate that our solution delivers reliable annotation results across the GSCs and it is an important contribution towards a homogeneous annotation of MEDLINE abstracts.  ...  ACKNOWLEDGEMENT We have to thank to the members of the CALBC project: David Milward, Peter Corbett, Udo Hahn, Ekatarina Buyko, Katrin Tomanek, Jan Kors, Erik van Mulligen and Ning Kang.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts125">doi:10.1093/bioinformatics/bts125</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22419783">pmid:22419783</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ihh7bn22bvfppkxm7nlyqrfiai">fatcat:ihh7bn22bvfppkxm7nlyqrfiai</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20150813231950/http://bioinformatics.oxfordjournals.org/content/28/9/1253.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/76/d4/76d4158293022e848800e8602d3b4fe439debe68.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts125"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Exploiting citation networks for large-scale author name disambiguation

Christian Schulz, Amin Mazloumian, Alexander M Petersen, Orion Penner, Dirk Helbing
<span title="2014-09-25">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/63pnypuhi5fehog53lylgzct3q" style="color: black;">EPJ Data Science</a> </i> &nbsp;
We present a novel algorithm and validation method for disambiguating author names in very large bibliographic data sets and apply it to the full Web of Science (WoS) citation index.  ...  machine in less than a day.  ...  Acknowledgements The authors would like to thank Tobias Kuhn and Michael Maes for useful feedback.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1140/epjds/s13688-014-0011-3">doi:10.1140/epjds/s13688-014-0011-3</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jeerekybrjb3dabmddmxvqx6gq">fatcat:jeerekybrjb3dabmddmxvqx6gq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171121092712/https://core.ac.uk/download/pdf/33751022.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/7c/8a/7c8ac97aa2b90b16217363e82d3a8a55bef944a8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1140/epjds/s13688-014-0011-3"> <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>

Facts from Text—Is Text Mining Ready to Deliver?

Dietrich Rebholz-Schuhmann, Harald Kirsch, Francisco Couto
<span title="2005-02-15">2005</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tsaumnzpkvdmvdi3blhl5clb24" style="color: black;">PLoS Biology</a> </i> &nbsp;
Publishers and authors have to agree on standards though.  ...  If appropriate quality control is provided, and if authors receive due credit for their deposition of facts into databases, we might well see a shift towards original papers describing new creative ideas  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pbio.0030065">doi:10.1371/journal.pbio.0030065</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15719064">pmid:15719064</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC548955/">pmcid:PMC548955</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/z3twrjzisjexpo3iztqzyojws4">fatcat:z3twrjzisjexpo3iztqzyojws4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190504205003/https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.0030065&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/1c/80/1c80a716d5e52f3500e3b8b7caeae3b3ebd88211.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pbio.0030065"> <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/PMC548955" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </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.  ...  This remains a challenging task due to the irregularities and ambiguities in gene and protein nomenclature.  ...  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>

A probabilistic similarity metric for Medline records: A model for author name disambiguation

Vetle I. Torvik, Marc Weeber, Don R. Swanson, Neil R. Smalheiser
<span title="">2004</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/irrfofzyh5dn5jykwm6u5zvb5e" style="color: black;">Journal of the American Society for Information Science and Technology</a> </i> &nbsp;
(prevalence in the literature, middle initial, and suffix).  ...  We have created a free, public service ("Author-ity": http://arrowsmith.psych.uic.edu) that takes as input an author's name given on a specific article, and gives as output a list of all articles with  ...  We also thank the National Library of Medicine for graciously providing us with the 2002 baseline release of Medline.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/asi.20105">doi:10.1002/asi.20105</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q2ci6dhkh5fuzn6pltgmdaygrq">fatcat:q2ci6dhkh5fuzn6pltgmdaygrq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20070225202359/http://arrowsmith.psych.uic.edu:80/arrowsmith_uic/tutorial/torvik_jasist_2005.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/bd/7ebdbacf977c516c12956e7d71c1403d66681755.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/asi.20105"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes

Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, Stella Zevio, Clement Jonquet
<span title="2018-11-06">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Conclusions: We show the web service performs comparably to other knowledge-based annotation approaches in recognizing entities in biomedical text and reach state-of-the-art levels in clinical context  ...  Despite a wide adoption of English in science, a significant amount of biomedical data are produced in other languages, such as French.  ...  Névéol in particular) for their authorization to use the corpora (Quaero and 2017 Task 1), the European Hospital Georges Pompidou for the evaluation of ConText on a clinical corpus, as well as all users  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-018-2429-2">doi:10.1186/s12859-018-2429-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30400805">pmid:30400805</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6218966/">pmcid:PMC6218966</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dmwmnr4qs5fbfgcz2obqualfpq">fatcat:dmwmnr4qs5fbfgcz2obqualfpq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427070533/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2429-2" 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/81/d9/81d9e803461f3efb886d8bb6fd5dfc968412c1b1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-018-2429-2"> <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/PMC6218966" 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 Method for Harmonization of Clinical Abbreviation and Acronym Sense Inventories

Lisa V Grossman, Elliot G Mitchell, George Hripcsak, Chunhua Weng, David K Vawdrey
<span title="2018-11-07">2018</span> <i title="Elsevier"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p4kk6lusgrhyxecgig72iasi5q" style="color: black;">Journal of Biomedical Informatics</a> </i> &nbsp;
Future work should address quality issues in source inventories and explore additional approaches to establishing synonymy.  ...  Develop an automated method to harmonize sense inventories from different regions and specialties towards the development of a comprehensive inventory.  ...  Acknowledgements This work was supported by the National Library of Medicine (T15LM007079, R01LM006910, PI: Hripcsak; R01LM009886, PI: Weng) and the Agency for Healthcare Research and Quality (R01HS21816  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2018.11.004">doi:10.1016/j.jbi.2018.11.004</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30414475">pmid:30414475</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6474250/">pmcid:PMC6474250</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vfj32f3a3jhtlncl6fa5iy6e7m">fatcat:vfj32f3a3jhtlncl6fa5iy6e7m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200506192236/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6474250&amp;blobtype=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/e9/83/e9838ed52d7fec5ab39d593d273f219110908225.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2018.11.004"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6474250" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

"Understanding" Medical School Curriculum Content Using KnowledgeMap

J. C. Denny
<span title="2003-03-28">2003</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 number of "gold standard" concepts in each lecture document identified by either KM or MetaMap, and the cause of each failure or relative success in a random subset of documents.  ...  Results: For 4,281 "gold standard" concepts, MetaMap matched 78% and KM 82%. Precision for "gold standard" concepts was 85% for MetaMap and 89% for KM.  ...  The author pair previously had identified the ''gold standard'' meaningful terms and composite phrases in the study documents.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1197/jamia.m1176">doi:10.1197/jamia.m1176</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12668688">pmid:12668688</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC181986/">pmcid:PMC181986</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pfeibe33rrfo7mrcdejmcn5lbm">fatcat:pfeibe33rrfo7mrcdejmcn5lbm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170901014546/https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/jamia/10/4/10.1197/jamia.M1176/2/10-4-351.pdf?Expires=1504258186&amp;Signature=fgiPjPrUIFc2fDQAkqrqhtleBYru-GUCk4LQrqYqB18MoctYqh2eAjCdDvpUSJhHQWv8yuwoVOIbZnJlx-0PtGc6bCq6wyGV3VithK-hdv8TbF8ZJWFzCGnHgvkE3IUjEDKlj8nOC-nse1IGS085O7dznRIdEmThpVsoIgCo62MFwZ1GSsEVjkwkH0r2FJatHWVKdJCGCSfvixHoON3PxV8z4jgOG1-9IzRRndPZTz1cdxdPWKu4SZQmxFfK3pZntLG7cXrX8YWLJTlJhoNnIWiBDnOZBG-GZ1C5Q6Xxc4qLzd~LM2LSWSe4S44IFdTZ0Wk1vmYV19k3-m5jPYTI0A__&amp;Key-Pair-Id=APKAIUCZBIA4LVPAVW3Q" 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/a4/dc/a4dc3de95a4ea17a498bc6d94d785ec1f9eb867b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1197/jamia.m1176"> <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/PMC181986" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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