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This article is part of the supplement: Proceedings of the 11th Annual Bioinformatics Open Source Conference (BOSC) 2010

Open Access Proceedings

interPopula: a Python API to access the HapMap Project dataset

Tiago Antao

Author Affiliations

Liverpool School of Tropical Medicine, L3 5QA, Liverpool, UK

BMC Bioinformatics 2010, 11(Suppl 12):S10  doi:10.1186/1471-2105-11-S12-S10

Published: 21 December 2010

Abstract

Background

The HapMap project is a publicly available catalogue of common genetic variants that occur in humans, currently including several million SNPs across 1115 individuals spanning 11 different populations. This important database does not provide any programmatic access to the dataset, furthermore no standard relational database interface is provided.

Results

interPopula is a Python API to access the HapMap dataset. interPopula provides integration facilities with both the Python ecology of software (e.g. Biopython and matplotlib) and other relevant human population datasets (e.g. Ensembl gene annotation and UCSC Known Genes). A set of guidelines and code examples to address possible inconsistencies across heterogeneous data sources is also provided.

Conclusions

interPopula is a straightforward and flexible Python API that facilitates the construction of scripts and applications that require access to the HapMap dataset.