%0 Journal Article
%T Deafness mutation mining using regular expression based pattern matching
%A Christopher M Frenz
%J BMC Medical Informatics and Decision Making
%D 2007
%I BioMed Central
%R 10.1186/1472-6947-7-32
%X A Perl based utility was developed to allow the use of regular expressions in Pubmed searches, thereby improving the accuracy of the searches.This utility was then utilized to create a comprehensive listing of all DFN deafness mutations discussed in Pubmed records containing the keywords "human ear".Biological research has yielded a vast amount of research data, which can often provide novel insights when the data can be viewed in an aggregated fashion, and thus recent studies have employed computational methods of information extraction from the biomedical literature. These studies have dealt with a wide range of information extractions, including the names of genes and proteins[1], intermolecular relationships [2], and molecular biological descriptors [3].Pubmed currently catalogs citation and abstract information for over 4,400 biomedical research journals and houses a citation database of over 12.8 million citations[4]. With any database of this size the return of relevant query results is often a difficult task, given the large number of potential matches there likely are for any single query term. These difficulties are compounded even further, given that Pubmed records are all natural language records and searches cannot readily be conducted using a predefined set of terms, as is the case for many relational databases. Thus Pubmed employs a word-matching algorithm, which seeks to match query words to the contents of citation records, and will return all records containing that word in their order of publication starting with the most recent.For certain types of queries, such as mutations, basic word matching is an ineffective search strategy, since an effective query cannot be specified as a single word, but rather is better expressed as a textual pattern, such as [Residue] [Position] [MutantResidue] [5]. The use of textual pattern matching, however, has a wide array of uses that extend beyond the location of mutations within Pubmed records, and include the a
%U http://www.biomedcentral.com/1472-6947/7/32