Difficulties in finding DNA mutations and associated phenotypic data in web resources using simple, uncomplicated search terms, and a suggested solution

Elizabeth A Webb,Timothy D Smith,Richard GH Cotton

doi:10.1186/1479-7364-5-3-141

Abstract

DNA mutation data currently reside in many online databases, which differ markedly in the terminology used to describe or define the mutation and also in completeness of content, potentially making it difficult both to locate a mutation of interest and to find sought-after data (eg phenotypic effect). To highlight the current deficiencies in the accessibility of web-based genetic variation information, we examined the ease with which various resources could be interrogated for five model mutations, using a set of simple search terms relating to the change in amino acid or nucleotide. Fifteen databases were investigated for the time and/or number of mouse clicks; clicks required to find the mutations; availability of phenotype data; the procedure for finding information; and site layout. Google and PubMed were also examined. The three locus-specific databases (LSDBs) generally yielded positive outcomes, but the 12 genome-wide databases gave poorer results, with most proving not to be search-able and only three yielding successful outcomes. Google and PubMed searches found some mutations and provided patchy information on phenotype. The results show that many web-based resources are not currently configured for fast and easy access to comprehensive mutation data, with only the isolated LSDBs providing optimal outcomes. Centralising this information within a common repository, coupled with a simple, all-inclusive interrogation process, would improve searching for all gene variation data.

Highlights

Data on genetic changes are being generated at an ever-increasing rate and mutations are being collected and catalogued in many different web-based databases
The way in which gene variations are collected at present is either in general databases which contain genome-wide data or in locus-specific databases (LSDBs), where the emphasis is on collecting data pertaining to one single gene
Ability to find mutations using amino acid-related search terms As shown in Table 3, all mutations were able to be found using the specified search terms only in HGMD, MUTdb, UniProt and their respective LSDBs; mutation 3 was incorrectly numbered in HGMD as codon 617

Summary

Introduction

Data on genetic changes are being generated at an ever-increasing rate and mutations (variations which cause genetic diseases1) are being collected and catalogued in many different web-based databases This information is used, and will increasingly be accessed, by clinicians and healthcare workers seeking to determine the significance of a mutation found to be present in any particular patient. To test the current situation for these types of web searches, we sought to examine the ease of use of both genome-wide databases and LSDBs. We searched for five representative mutations using a variety of straightforward search terms relating to the amino acid or nucleotide change (not requiring knowledge of special parameters such as accession or other numbers) and measuring the time and number of computer mouse clicks (CMCs) taken to find the mutation. Since Google and PubMed are used as resources for obtaining information about specific genetic changes, these were searched using the same search criteria

Methods

Results

Discussion