Evaluating the VIPER pedigree visualisation: detecting inheritance inconsistencies in genotyped pedigrees.

Paterson, Trevor; Graham, Martin; Kennedy, Jessie; Law, Andy

Abstract

VIPER (Visual Pedigree Explorer) is a tool for exploring large complex animal pedigrees and their associated genotype data. The tool combines a novel, space-efficient visualisation of the pedigree structure with an inheritance-checking algorithm. This allows users to explore the apparent errors within the genotype data in the full context of the family and pedigree structure. Ultimately, the aim is to develop an interactive software application that will allow users to identify, confirm and then remove errors from the pedigree structure and scored genotypes. This paper describes an evaluation of how VIPER displays the different scales and types of data set that can occur, along with a description of the further interface functionality necessary to meet the challenges such data presents. This is followed by an examination of a range of possible pedigree genotype errors by replicating these errors in controlled simulated data sets and showing how they are manifested in the VIPER interface and observed by a domain expert. The data sets used include both real and artificially generated data, the advantage of the latter being that they produce known effects in the visualization which the domain expert can then interpret as being useful or unhelpful as they see fit.

Citation

Paterson, T., Graham, M., Kennedy, J., & Law, A. (2011, October). Evaluating the VIPER pedigree visualisation: detecting inheritance inconsistencies in genotyped pedigrees. Presented at 1st IEEE Symposium on Biological Data Visualization

• Conference Name: 1st IEEE Symposium on Biological Data Visualization
• Start Date: Oct 23, 2011
• End Date: Oct 24, 2011
• Publication Date: 2011
• Deposit Date: Nov 2, 2011
• Publicly Available Date: Dec 31, 2011
• Peer Reviewed: Peer Reviewed
• Pages: 119-126
• Book Title: 2011 IEEE Symposium on Biological Data Visualization (BioVis)
• ISBN: 978-1-4673-0003-2
• DOI: https://doi.org/10.1109/BioVis.2011.6094056
• Keywords: Pedigree visualisation; error visualisation; Interfacedesign; utility evaluation
• Public URL: http://researchrepository.napier.ac.uk/id/eprint/4714
• Publisher URL: http://dx.doi.org/10.1109/BioVis.2011.6094056
• Contract Date: Nov 2, 2011