interPopula: a Python API to access the HapMap Project dataset.

Rodrigues Antao, Tiago (2010) 'interPopula: a Python API to access the HapMap Project dataset.'. BMC bioinformatics, Vol 11 Sup, Issue S 12, S10.

Preview

Text Antao-BMC-2010.pdf - Published Version Download (526kB)

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.

Item Type:	Article
Additional Information:	The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2105/11/S12/S10 Proceedings of the 11th Annual Bioinformatics Open Source Conference (BOSC) 2010 .
Subjects:	QU Biochemistry > Genetics > QU 450 General Works
Faculty: Department:	Groups (2002 - 2012) > Molecular & Biochemical Parasitology Group
Digital Object Identifer (DOI):	https://doi.org/10.1186/1471-2105-11-S12-S10
Depositing User:	Mary Creegan
Date Deposited:	15 Aug 2011 13:01
Last Modified:	06 Feb 2018 13:03
URI:	https://archive.lstmed.ac.uk/id/eprint/2281

Statistics

View details

Actions (login required)

Edit Item