A recent advance in the automatic indexing of the biomedical literature

Journal of Biomedical Informatics

Volumn 42, Issue 5, 2009, Pages 814-823

  Névéol, Aurélie ^a   Shooshan, Sonya E ^a   Humphrey, Susanne M ^a   Mork, James G ^a   Aronson, Alan R ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

*Evaluation Studies as Topic; *MEDLINE; Abstracting and Indexing as Topic *methods statistics numerical data; Artificial Intelligence; Dictionaries, Medical; Medical Subject Headings; Natural Language Processing

Indexed keywords

AUTOMATIC ASSIGNMENT; BIBLIOGRAPHIC DATABASE; BIOMEDICAL CITATIONS; BIOMEDICAL LITERATURE; BIOMEDICAL TEXT; DICTIONARIES, MEDICAL; EXPLOSIVE GROWTH; MACHINE LEARNING METHODS; MEDICAL SUBJECT HEADINGS; MEDLINE; NATIONAL LIBRARY OF MEDICINES; NATURAL LANGUAGE PROCESSING;

ABSTRACTING; ARTIFICIAL INTELLIGENCE; AUTOMATIC INDEXING; COMPUTATIONAL LINGUISTICS; INFORMATION SERVICES; LINGUISTICS; NATURAL LANGUAGE PROCESSING SYSTEMS;

INDEXING (OF INFORMATION);

ACCURACY; ARTICLE; AUTOMATION; BIOMEDICINE; DATA ANALYSIS; DATA SYNTHESIS; INFORMATION PROCESSING; LANGUAGE PROCESSING; MACHINE LEARNING; PRIORITY JOURNAL; STATISTICAL ANALYSIS;

ABSTRACTING AND INDEXING AS TOPIC; ARTIFICIAL INTELLIGENCE; DICTIONARIES, MEDICAL; EVALUATION STUDIES AS TOPIC; HUMANS; MEDICAL SUBJECT HEADINGS; MEDLINE; NATURAL LANGUAGE PROCESSING; USER-COMPUTER INTERFACE;

EID: 70349440994     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2008.12.007     Document Type: Article

References (24)

1. Aronson A.R., Mork J.G., Gay C.W., Humphrey S.M., and Rogers W.J. The NLM indexing initiative's medical text indexer. Stud Health Technol Inform 107 Pt 1 (2004) 268-272
2. Névéol A., Shooshan S.E., Humphrey S.M., Rindflesch T.C., and Aronson A.R. Multiple approaches to fine-grained indexing of the biomedical literature. Pac Symp Biocomput (2007) 292-303
3. Névéol A., Shooshan S.E., Mork J.G., and Aronson A.R. Fine-grained indexing of the biomedical literature: MeSH subheading attachment for a MEDLINE indexing tool. AMIA Annu Symp Proc 11 (2007) 553-557
4. In: Salton G. (Ed). The SMART retrieval system; experiments in automatic document processing (1983), Prentice-Hall, Englewood Cliffs, NJ
5. Deerwester S., Dumais S., Furnas G., Landauer T., and Harshman R. Indexing by latent semantic analysis. J Am Soc Inf Sci 41 6 (1990) 391-407
6. Ruiz M.E., and Srinivasan P. Hierarchical text categorization using neural networks. Inf Retr 5 1 (2002) 87-118
7. Ruch P., Baud R., and Geissbühler A. Learning-free Text Categorization. Proc AIME LNAI 2780 (2003) 199-204
8. Cai L., and Hofmann T. Hierarchical document categorization with support vector machines. Proc CIKM (2004) 396-402
9. Yang Y. An evaluation of statistical approaches to text categorization. Technical report, School of Computer Science, Carnegie Mellon University; 1997. Retrieved on 01/20/2008 at http://reports-archive.adm.cs.cmu.edu/anon/1997/CMU-CS-97-127.ps.
10. Rak R., Kurgan L.A., and Reformat M. Multilabel associative classification categorization of MEDLINE articles into MeSH keywords. IEEE Eng Med Biol Mag 26 2 (2007) 47-55
11. Aronson AR, Bodenreider O, Demner-Fushman D, Fung KW, Lee VK, Mork JG, et al. From indexing the biomedical literature to coding clinical text: experience with MTI and machine learning approaches. ACL 2007, Workshop BioNLP.
12. Lin J., and Wilbur W.J. PubMed related articles: a probabilistic topic-based model for content similarity. BMC Bioinformatics 8 (2007) 423
13. Sohn S., Kim W., Comeau D.C., and Wilbur W.J. Optimal training sets for bayesian prediction of MeSH assignment. J Am Med Inform Assoc 15 4 (2008) 546-553
14. Névéol A., Rogozan A., and Darmoni S.J. Automatic indexing of online health resources for a French quality controlled gateway. Inf Process Manage 42 (2006) 695-709
15. Liu Y., Brandon M., Navathe S., Dingledine R., and Ciliax B.J. Text mining functional keywords associated with genes. Stud Health Technol Inform 107 Pt 1 (2004) 292-296
16. Humphrey S.M. Automatic indexing of documents from journal descriptors: a preliminary investigation. J Am Soc Inf Sci Technol 50 8 (1999) 661-674
17. Humphrey S.M., Lu C.J., Rogers W.J., and Browne A.C. Journal descriptor indexing tool for categorizing text according to discipline or semantic type. AMIA Annu Symp Proc (2006) 960
18. Rindflesch T.C., and Fiszman M. The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text. J Biomed Inform 36 6 (2003) 462-477
19. Bodenreider O., Nelson S.J., Hole W.T., and Chang H.F. Beyond synonymy: exploiting the UMLS semantics in mapping vocabularies. Proc AMIA Symp (1998) 815-819
20. Kim W., Aronson A.R., and Wilbur W.J. Automatic MeSH term assignment and quality assessment. Proc AMIA Symp (2001) 319-323
21. Lancaster F.W. Indexing and abstracting in theory and practice (1991), University of Illinois, Champaign, IL
22. Ting WK, Witten I. Stacking bagged and dagged models. Proc 14th International Conference on Machine Learning; 1997. p. 367-75.
23. Rodriguez-Esteban R., Iossifov I., and Rzhetsky A. Imitating manual curation of text-mined facts in biomedicine. PLoS Comput Biol 2 9 (2006) e118
24. Funk M.E., and Reid C.A. Indexing consistency in MEDLINE. Bull Med Libr Assoc 71 2 (1983) 176-183