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

Tiago Rodrigues Antao

doi:10.1186/1471-2105-11-s12-s10

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

Tiago Rodrigues Antao

Tropical Disease Biology

Liverpool School of Tropical Medicine

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	S10
Pages (from-to)	S10
Journal	BMC Bioinformatics
Volume	11
Issue number	SUPPL. 12
DOIs	https://doi.org/10.1186/1471-2105-11-s12-s10
Publication status	Published - 21 Dec 2010

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title = "interPopula: a Python API to access the HapMap Project dataset.",

abstract = "BackgroundThe 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.ResultsinterPopula 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.ConclusionsinterPopula is a straightforward and flexible Python API that facilitates the construction of scripts and applications that require access to the HapMap dataset.",

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

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