Document Detail


A dictionary to identify small molecules and drugs in free text.
MedLine Citation:
PMID:  19759196     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
MOTIVATION: From the scientific community, a lot of effort has been spent on the correct identification of gene and protein names in text, while less effort has been spent on the correct identification of chemical names. Dictionary-based term identification has the power to recognize the diverse representation of chemical information in the literature and map the chemicals to their database identifiers. RESULTS: We developed a dictionary for the identification of small molecules and drugs in text, combining information from UMLS, MeSH, ChEBI, DrugBank, KEGG, HMDB and ChemIDplus. Rule-based term filtering, manual check of highly frequent terms and disambiguation rules were applied. We tested the combined dictionary and the dictionaries derived from the individual resources on an annotated corpus, and conclude the following: (i) each of the different processing steps increase precision with a minor loss of recall; (ii) the overall performance of the combined dictionary is acceptable (precision 0.67, recall 0.40 (0.80 for trivial names); (iii) the combined dictionary performed better than the dictionary in the chemical recognizer OSCAR3; (iv) the performance of a dictionary based on ChemIDplus alone is comparable to the performance of the combined dictionary. AVAILABILITY: The combined dictionary is freely available as an XML file in Simple Knowledge Organization System format on the web site http://www.biosemantics.org/chemlist.
Authors:
Kristina M Hettne; Rob H Stierum; Martijn J Schuemie; Peter J M Hendriksen; Bob J A Schijvenaars; Erik M van Mulligen; Jos Kleinjans; Jan A Kors
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2009-09-16
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  25     ISSN:  1367-4811     ISO Abbreviation:  Bioinformatics     Publication Date:  2009 Nov 
Date Detail:
Created Date:  2009-11-05     Completed Date:  2010-02-02     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  England    
Other Details:
Languages:  eng     Pagination:  2983-91     Citation Subset:  IM    
Affiliation:
Department of Health Risk Analysis and Toxicology, Maastricht University, Maastricht, The Netherlands. k.hettne@erasmusmc.nl
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MeSH Terms
Descriptor/Qualifier:
Abstracting and Indexing as Topic / methods
Computational Biology / methods*
Dictionaries as Topic
Dictionaries, Chemical*
Information Storage and Retrieval / methods*
Natural Language Processing
Pharmaceutical Preparations / chemistry
Software
Unified Medical Language System
Chemical
Reg. No./Substance:
0/Pharmaceutical Preparations

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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