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Improving the dictionary lookup approach for disease normalization using enhanced dictionary and query expansion

Jitendra Jonnagaddala, Toni Rose Jue, Nai-Wen Chang, Hong-Jie Dai
2016 Database: The Journal of Biological Databases and Curation  
-W. and Dai,H.-J. Improving the dictionary lookup approach for disease normalization using enhanced dictionary and query expansion.  ...  Among all the proposed methods, conditional random fields (CRFs) and dictionary lookup method are widely used for named entity recognition and normalization respectively.  ...  Acknowledgement We would like to thank the organizers of BioCreative V CDR Track for providing us, with the corpus and sample code to develop REST APIs.  ... 
doi:10.1093/database/baw112 pmid:27504009 pmcid:PMC4976299 fatcat:bproo6ouo5hjlgmukudmhvo6ay

Automatic Coding of Death Certificates to ICD-10 Terminology

Jitendra Jonnagaddala, Feiyan Hu
2017 Conference and Labs of the Evaluation Forum  
We deployed an approach to tackle the task by solely using dictionary lookup, also known as dictionary matching or dictionary projection.  ...  The advantages of a dictionary look up method include speed and no need for training data. We present our results of 3 different experimental settings each of which has 2 individual runs.  ...  We would like to thank the organizers of CLEF eHealth 2017 Task 1 for providing us, with the ICD10 coded text content from death certificates.  ... 
dblp:conf/clef/JonnagaddalaH17 fatcat:akykcrid45dk7la5lj5a5nlwwa

Leveraging both Structured and Unstructured Data for Precision Information Retrieval

Yanshan Wang, Ravikumar Komandur Elayavilli, Majid Rastegar-Mojarad, Hongfang Liu
2017 Text Retrieval Conference  
We first query the unstructured fields (i.e., the fields of title and abstract) and utilize information in structured fields from top-ranked documents as feedback for query expansion.  ...  The extracted entities were indexed in different fields and treated as structured data for retrieval. Second, we used multi-field querying in a Pseudo Relevance Feedback (PRF) model.  ...  Acknowledgments The authors gratefully acknowledge the support from the National Library of Medicine (NLM) grant R01LM11934.  ... 
dblp:conf/trec/WangERL17 fatcat:a6q4t4pxnfdcdpm6otc4mduakq

Variations on language modeling for information retrieval

Wessel Kraaij
2005 SIGIR Forum  
Variations on Language Modeling for Information Retrieval W. Kraaij -Enschede: Neslia Paniculata. Thesis Enschede -With ref. With summary ISBN 90-75296-09-6  ...  We also compared naive query expansion and a re-weighted variant for dictionary based query expansion (vc1/vc1ow).  ...  be used for effective query expansion.  ... 
doi:10.1145/1067268.1067291 fatcat:h23lp5aqfvfu5iecwnihfme244

Anchor text mining for translation of Web queries

Wen-Hsiang Lu, Lee-Feng Chien, Hsi-Jian Lee
2004 ACM Transactions on Information Systems  
The obtained experimental results have shown that the proposed approach is effective in extracting translations of unknown queries, is easy to combine with the probabilistic retrieval model to improve  ...  the cross-language retrieval performance, and is very useful when the considered language pairs lack a sufficient number of anchor texts.  ...  ACKNOWLEDGMENTS The authors would like to thank Prof. Mark Sanderson and the anonymous reviewers for their valuable comments and suggestions. Many thanks are given to Mr.  ... 
doi:10.1145/984321.984324 fatcat:75mnaq3qmza6vdduluhn3yhm5m

pGenN, a Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature

Ruoyao Ding, Cecilia N. Arighi, Jung-Youn Lee, Cathy H. Wu, K. Vijay-Shanker, Willy John Wilbur
2015 PLoS ONE  
Gene normalization is critical for improving the coverage of annotation in the databases, and is an essential component of many text mining systems and database curation pipelines.  ...  The system consists of three steps: dictionary-based gene mention detection, species assignment, and intra species normalization. We have developed new heuristics to improve each of these phases.  ...  Ross for the editorial assistance for the manuscript, and Mengxi Lv for participating in the evaluation of pGenN. Author Contributions  ... 
doi:10.1371/journal.pone.0135305 pmid:26258475 pmcid:PMC4530884 fatcat:6gphkqhqnzfgbkzbzshp2ge4ha

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
2011 Bioinformatics  
Here we present the GNAT Java library for text retrieval, named entity recognition, and normalization of gene and protein mentions in biomedical text.  ...  The library can be used as a component to be integrated with other text-mining systems, as a framework to add user-specific extensions, and as an efficient stand-alone application for the identification  ...  In step (3) , Gnat recognizes names referring to both genes and species using a dictionary-based approach.  ... 
doi:10.1093/bioinformatics/btr455 pmid:21813477 pmcid:PMC3179658 fatcat:ayz2mevokre5jk622udycr5tom

DeepSuggest: Using Neural Networks to Suggest Related Keywords for a Comprehensive Search of Clinical Notes

Soheil Moosavinasab, Emre Sezgin, Huan Sun, Jeffrey Hoffman, Yungui Huang, Simon Lin
2021 ACI Open  
DeepSuggest can supplement established ontologies for query expansion.  ...  Human intelligence is then used to further refine or pivot their query. Results DeepSuggest learns the semantic and linguistic relationships between the words from a large collection of local notes.  ...  Using Both Knowledge Bases and Word Embedding."  ... 
doi:10.1055/s-0041-1729982 fatcat:3unqqo6ppnaljnc3rph7bu2ug4

Factors affecting the effectiveness of biomedical document indexing and retrieval based on terminologies

Duy Dinh, Lynda Tamine, Fatiha Boubekeur
2013 Artificial Intelligence in Medicine  
In addition, our experimental results show that document expansion using preferred terms in combination with query expansion using terms from top ranked expanded documents improve the biomedical IR effectiveness  ...  Through this study, we presented many factors affecting the effectiveness of biomedical IR system including term weighting, query expansion, and document expansion models.  ...  Acknowledgements We would like to thank people at the IRIT laboratory who develop and maintain the OSIRIM platform, which is an infrastructure of several interconnected computers for undertaking experimental  ... 
doi:10.1016/j.artmed.2012.08.006 pmid:23092678 fatcat:2ss3cba3njfhzpk76rbd6isuga

Text mining processing pipeline for semi structured data D3.3

Jenny Copara, Nona Naderi, Alexander Kellmann, Gurinder Gosal, William Hsiao, Douglas Teodoro
2021 Zenodo  
In this deliverable, we present the methodology used to develop the different text mining tools created by the dedicated SFU, UMCG, EBI, and HES-SO/SIB groups for specific CINECA cohorts.  ...  Named entity recognition and normalization enable the automatic conversion of free text into standard medical concepts.  ...  This allows researchers to do complex queries using ontology expansion and synonyms -for example, searching for heart diseases will return samples annotated with myocardial infarction using ontology expansion  ... 
doi:10.5281/zenodo.5795433 fatcat:kqwmgbfbqbbrjbuhkrr2spxkza

Building a biomedical ontology recommender web service

Clement Jonquet, Mark A Musen, Nigam H Shah
2010 Journal of Biomedical Semantics  
The number and variety of biomedical ontologies is large, and it is cumbersome for a researcher to figure out which ontology to use.  ...  The system uses textual metadata or a set of keywords describing a domain of interest and suggests appropriate ontologies for annotating or representing the data.  ...  We also thank Helen Parkinson (European Biomedical Institute), Stephen Granite (Johns Hopkins University) and Wei-Nchih Lee (Stanford University) for the help in the Recommender evaluation.  ... 
doi:10.1186/2041-1480-1-s1-s1 pmid:20626921 pmcid:PMC2903720 fatcat:d7mxashoyjhsbphqqlpsi3ugxq

Knowledge-based extraction of adverse drug events from biomedical text

Ning Kang, Bharat Singh, Chinh Bui, Zubair Afzal, Erik M van Mulligen, Jan A Kors
2014 BMC Bioinformatics  
Fifty abstracts were used for training, the remaining abstracts were used for testing.  ...  Conclusion: A knowledge-based approach can be successfully used to extract adverse drug events from biomedical text without need for a large training set.  ...  Acknowledgements This study was partially supported by the European Commission  ... 
doi:10.1186/1471-2105-15-64 pmid:24593054 pmcid:PMC3973995 fatcat:33ubfhzeg5d3tcx5o267scjyca

Medical Query Expansion using UMLS

K. Saravana Kumar, K. Deepa
2016 Indian Journal of Science and Technology  
In this work, we proposed a method that deals with enriching the user query with the use of UMLS. The enriched user query after expansion is used to get accurate documents with less amount of time.  ...  Internet users have grown in recent years and they demand answers for many through online. Searching and retrieving documents is one of the most frequent thing most of the people do today.  ...  The search can be improved by using UMLS query expansion 22 .  ... 
doi:10.17485/ijst/2016/v9i14/77644 fatcat:azrcept4bjezno3alpm23it4by

DNorm: disease name normalization with pairwise learning to rank

R. Leaman, R. Islamaj Dogan, Z. Lu
2013 Bioinformatics  
Methods: In this article we introduce the first machine learning approach for DNorm, using the NCBI disease corpus and the MEDIC vocabulary, which combines MeSH Õ and OMIM.  ...  Motivation: Despite the central role of diseases in biomedical research, there have been much fewer attempts to automatically determine which diseases are mentioned in a text-the task of disease name normalization  ...  ACKNOWLEDGEMENTS The authors thank Chih-Hsuan Wei for his help preparing the demonstration Web site and loading DNorm results into PubTator, both Alan Aronson and Jim Mork for help with  ... 
doi:10.1093/bioinformatics/btt474 pmid:23969135 pmcid:PMC3810844 fatcat:sxi527ibbvdybgwbeirey2nah4

BioCreative II Workshop Proceedings

Lynette, Martin, Alfonso
2007 Zenodo  
by dictionary lookup 135 Gene Mention and Gene Normalization Based on Machine Learning and Online Resources 141 Me and my friends: gene mention normalization with background knowledge 145 Context-Aware  ...  Gene Mentions 101 BioCreative II Gene Mention Tagging System at IBM Watson 105 Rich Feature Set, Unifi cation of Bidirectional Parsing and Dictionary Filtering for High F-Score Gene Mention Tagging 109  ...  The hierarchical pattern matching algorithm gives higher flexibility than traditional rule-based approach and maintains high precision by using most specific pattern level.  ... 
doi:10.5281/zenodo.4274543 fatcat:3sa3fvgngffjrblxzgswof42tq
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