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Nic Walker and Andrew Devereau, University of Manchester, Manchester, UK.
Assessment of the quality of bio-informatics tools is a difficult yet essential requirement for the genetics testing community. There is a wide variety of third party developed tools in use by genetics testing laboratories, yet currently there is no facility available that assesses the status and utility of the products. Previous analyses have suggested that a community based assessment tool would be a valuable asset to develop, and progress towards this goal has been undertaken in the form of a controlled wiki environment[1]. A survey identified tools commonly used in the testing community, and of these, sequence analysis tools were identified as a priority for quality assessment. This report describes the development of the quality assessment approach for use in assessing sequence analysis tools.
In our original report we showed how a table of features had been developed using a wiki to allow different tools to be compared side-by-side and the results displayed on a website. A wiki is a website for collaborative editing of content: it allows users (either any user or only those registered to do so) to edit and add to the website content and can thus be used to develop resources by a community of users. We originally used the MediaWiki application (www.mediawiki.org) to develop the assessment tool for sequence analysis software. However as we developed this approach we found that editing tabulated data in MediaWiki was going to be too complex for users. We therefore looked for a wiki application with easier table editing features and chose TWiki. This has a page editor similar to a word processor and also has a specific table editor which allows data to be edited directly within the table. Access to the wiki tool requires only a web browser. Users can view the data but will need to register with the wiki administrator to edit data. Table 1 shows the entry point to the wiki and the root classification of bioinformatics tools.
Table 1. Top level categorisation of bioinformatics tools in the wiki
The current content of the wiki and table structure for sequence analysis tools is shown in Table 2. This feature table concentrates on the tool's development - its developer, version, funding basis etc.; its scope and capacity; and finally its quality assessment. The latter has been based on the approach used in the technology assessment of Mutation Surveyor (www.softgenetics.com) undertaken at NGRL Manchester in 2005[2]. We have chosen to represent these results as columns detailing standard accuracy values, sensitivity, and positive predictive value where applicable to the particular tool. The four data sets that the performance measures were calculated from are available to any users to allow for standardised assessment for SNP detection algorithms.
Currently the sequence analysis tools hold representative information on products from Softgenetics® ABI, Beckman Coulter and Phenosystems®, based on experience in their use at the Manchester NGRL. Two areas of the wiki are targeted for development due to their perceived relevance to the genetics testing community; further assessment of SNP detection algorithms and the formation of structures for presenting core genetic database quality information.
To further the relevance of the repository, collaboration in the genetics testing community is vital for detailing product information, and secondly performing and reporting accuracy quality measures based on the standard data sets made available via the wiki.
Table 2. Feature list and assessment measures for sequence analysis tools
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