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An evaluation of statistical approaches to MEDLINE indexing

Y Yang
1996 Proceedings : a conference of the American Medical Informatics Association. AMIA Fall Symposium  
This paper applies two statistical learning algorithms, the Linear Least Squares Fit (LLSF) mapping and a Nearest Neighbor classifier named ExpNet, to a large collection of MEDLINE documents.  ...  Whether or not high accuracy classification methods can be scaled to large applications is crucial for the ultimate usefulness of such methods in text categorization.  ...  In the MEDLINE database, for example, articles are indexed using Medical Subject Headings (MeSH) for the purposes of retrieval.  ... 
pmid:8947688 pmcid:PMC2233015 fatcat:6ol3ci44mbfwhcvua42woighpy

Words or concepts: the features of indexing units and their optimal use in information retrieval

Y Yang, C G Chute
1993 Proceedings. Symposium on Computer Applications in Medical Care  
Words or Concepts, which are a better choice for indexing the contents of documents? The answer depends on what method is used for retrieval.  ...  This paper studies the effects of using canonical concepts versus document words in different retrieval systems with a testing collection of MEDLINE documents.  ...  Hersh for generously providing the testing data. This work is supported in part by NIH support grants LM-07041, LM-05416, and AR30582.  ... 
pmid:8130562 pmcid:PMC2850662 fatcat:rbub75vgkveezoupxqsjrbapra

An application of Expert Network to clinical classification and MEDLINE indexing

Y Yang, C G Chute
1994 Proceedings. Symposium on Computer Applications in Medical Care  
The total training and testing time on the patient-record text collection (6134 texts) was 4 minutes for ExpNet versus 96 minutes for LLSF; on the MEDLINE document collection (2344 documents), the total  ...  Evaluations in patient-record text classification and MEDLINE document indexing show a performance of ExpNet in recall and precision comparable to the Linear Least Squares Fit (LLSF) mapping method, and  ...  Kent Bailey for fruitful discussions about the original idea, and Geoffrey Atkin for programming. This work is supported in part by NIH grants LM-07041, LM-05416, and AR30582.  ... 
pmid:7949911 pmcid:PMC2247915 fatcat:nwazt6xymvbfhdnunz4c3bvzae

Words, concepts, or both: optimal indexing units for automated information retrieval

W R Hersh, D H Hickam, T J Leone
1992 Proceedings. Symposium on Computer Applications in Medical Care  
The consistently best methods are those that use indexing based on the words that occur in the available text of each document.  ...  This study compares the retrieval effectiveness of five different methods for automated (machine-assigned) indexing using three test collections.  ...  INTRODUCTION One of the biggest controversies in the information science field concerns the optimal units for representing the content of a document.  ... 
pmid:1482951 pmcid:PMC2248024 fatcat:h5dhg7cx4jgbxpbdo56wilm75m

The dimensions of indexing

W John Wilbur, Won Kim
2003 AMIA Annual Symposium Proceedings  
Indexing of documents is an important strategy intended to make the literature more readily available to the user.  ...  Here we describe several dimensions of indexing that are important if indexing is to be optimal. These dimensions are coverage, predictability, and transparency.  ...  Clearly the indexing vocabulary forms the basis for a language in which queries must be expressed and documents represented.  ... 
pmid:14728266 pmcid:PMC1480214 fatcat:qjqs25tanfegzlsrhqv3dkch5e

Evaluation of SAPHIRE: an automated approach to indexing and retrieving medical literature

W Hersh, D H Hickam, R B Haynes, K A McKibbon
1991 Proceedings. Symposium on Computer Applications in Medical Care  
An analysis of SAPHIRE, an experimental information retrieval system featuring automated indexing and natural language retrieval, was performed on MEDLINE references using data previously generated for  ...  a MEDLINE evaluation.  ...  In the long run, we hope to identify and validate a set of techniques for optimal information retrieval in the biomedical domain. Bibliography MeSH) vocabulary or individual text words.  ... 
pmid:1807718 pmcid:PMC2247642 fatcat:jk35ahbaand45pd4c4lupk4bfu

Balancing Manual and Automatic Indexing for Retrieval of Paper Abstracts [chapter]

Kwangcheol Shin, Sang-Yong Han, Alexander Gelbukh
2004 Lecture Notes in Computer Science  
The search engine supplied with MEDLINE uses Boolean retrieval model with only MeSH keywords used for indexing.  ...  MEDLINE is a widely used very large database of abstracts of research papers in medical domain. Abstracts in it are manually supplied with keywords from a controlled vocabulary called MeSH.  ...  Expert annotators of the National Library of Medicine databases, based on indexed content of documents, assign subject headings to each MEDLINE document for the users to be able to effectively retrieve  ... 
doi:10.1007/978-3-540-30120-2_26 fatcat:45eh3zmz6zccnn34lvbohbnuh4

SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts

Gobeill Julien, Caucheteur Déborah, Michel Pierre-André, Mottin Luc, Pasche Emilie, Ruch Patrick
2020 Nucleic Acids Research  
They cover MEDLINE and PubMed Central Open Access enriched by nearly 2 billion of mapped biomedical entities, and are daily updated.  ...  Indeed, SIBiLS allow fully customizable search in semantically enriched contents, based on keywords and/or mapped biomedical entities from a growing set of standardized and legacy vocabularies.  ...  National Library of Medicine and National Institute of Health for improving access to PubMed and PubMedCentral.  ... 
doi:10.1093/nar/gkaa328 pmid:32379317 pmcid:PMC7319474 fatcat:wnwek6k6fngerlm2txpqc4r2si

TXTGate: profiling gene groups with text-based information

Patrick Glenisson, Bert Coessens, Steven Van Vooren, Janick Mathys, Yves Moreau, Bart De Moor
2004 Genome Biology  
By means of tailored vocabularies, term- as well as gene-centric views are offered on selected textual fields and MEDLINE abstracts used in LocusLink and the Saccharomyces Genome Database.  ...  Subclustering and links to external resources allow for in-depth analysis of the resulting term profiles.  ...  We acknowledge Peter Antal for starting up this research direction.  ... 
doi:10.1186/gb-2004-5-6-r43 pmid:15186494 pmcid:PMC463076 fatcat:iijxrcxvr5hffkpfnpwl4hbhvq

Searching for information on the Internet using the UMLS and Medical World Search

H H Suarez, X Hao, I F Chang
1997 Proceedings : a conference of the American Medical Informatics Association. AMIA Fall Symposium  
Medical World Search's usage by medical information seekers is summarized. future directions for research are outlined.  ...  After discussing some of the previous uses of the UMLS for medical information retrieval, we describe the Medical World Search system.  ...  Ted Shortliffe for his suggestions of potential medical professional user groups, and Dr. Malet for his suggestions about improving Medical World Search.  ... 
pmid:9357740 pmcid:PMC2233554 fatcat:mfsz5weu3va47gebnrw4pztrzq

Predicting Medical Subject Headings Based on Abstract Similarity and Citations to MEDLINE Records

Adam K. Kehoe, Vetle I. Torvik
2016 Proceedings of the 16th ACM/IEEE-CS on Joint Conference on Digital Libraries - JCDL '16  
Our approach can be applied broadly to documents with abstracts that are similar to (or cite) MEDLINE abstracts, which would help linking and searching across bibliographic databases beyond MEDLINE.  ...  MEDLINE records.  ...  Furthermore, all MeSH are not equally represented in MEDLINE so optimizing a classifier for each term should further improve performance.  ... 
doi:10.1145/2910896.2910920 dblp:conf/jcdl/KehoeT16 fatcat:utoprlglhfahpfpsvllr2jjpkm

Surveying the traumatic stress literature: The effective use of bibliographic databases in preparing reviews and meta-analyses

Fred Lerner, Jessica L. Hamblen
2010 Journal of Traumatic Stress  
This commentary offers suggestions for identifying the literature to be searched, designing a suitable search strategy, using a controlled vocabulary, and describing the bibliographic methodology underlying  ...  Careful selection of bibliographic databases and the use of well-designed search strategies based on the controlled vocabularies contained in published thesauri are essential to ensure retrieval of all  ...  Even the most careful indexer will be unable to index a document that does not come to his or her attention.  ... 
doi:10.1002/jts.20580 pmid:20979218 fatcat:s6kwighi6zgkhncs63kkdk6mba

An information retrieval system for expert and consumer users

Rena Peraki, Euripides G. M. Petrakis, Angelos Hliaoutakis
2012 2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)  
Relying on term extraction by natural language processing, the system supports automatic categorization as well as, indexing and retrieval of medical documents by user profile (novice users and experts  ...  The requirements for the design and implementation of a medical information retrieval system for expert and consumer users are discussed.  ...  Fig. 3 . 3 A two-layered indexing structure for Medline documents. • PMC: A corpus of 5,819 full documents from PubMed 17 indexed in MedLine selected out of 60 Journals.  ... 
doi:10.1109/bibe.2012.6399664 dblp:conf/bibe/PerakiPH12 fatcat:whcbr6jb2bb3tpa6ds3xmbr7my

The NLM Indexing Initiative

A R Aronson, O Bodenreider, H F Chang, S M Humphrey, J G Mork, S J Nelson, T C Rindflesch, W J Wilbur
2000 Proceedings. AMIA Symposium  
The objective of NLM's Indexing Initiative (IND) is to investigate methods whereby automated indexing methods partially or completely substitute for current indexing practices.  ...  We describe the current state of the project and discuss our plans for the future.  ...  Tybaert for their essential contributions to this research effort.  ... 
pmid:11079836 pmcid:PMC2243970 fatcat:qdmxvq3zv5cfhcevqvssqlsdia

Searching biomedical databases on complementary medicine: the use of controlled vocabulary among authors, indexers and investigators

Linda S Murphy, Sibylle Reinsch, Wadie I Najm, Vivian M Dickerson, Michael A Seffinger, Alan Adams, Shiraz I Mishra
2003 BMC Complementary and Alternative Medicine  
Conclusions: Searching biomedical databases for CAM is challenging due to inconsistent use of controlled vocabulary and indexing procedures in different databases.  ...  The optimal retrieval of a literature search in biomedicine depends on the appropriate use of Medical Subject Headings (MeSH), descriptors and keywords among authors and indexers.  ...  Acknowledgements This project was supported in part by the University of California Irvine (UCI) College of Medicine 41 st Trust; The Susan Samueli Center for Complementary and Alternative Medicine at  ... 
doi:10.1186/1472-6882-3-3 pmid:12846931 pmcid:PMC166167 fatcat:vqiurlipgjgzxn7t7wjvddkv4m
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