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      interPopula: a Python API to access the HapMap Project dataset

      research-article
      Author(s): 1 ,
      Publication date (Electronic):
      Journal: BMC Bioinformatics
      Publisher: BioMed Central
      Conference name: The 11th Annual Bioinformatics Open Source Conference (BOSC) 2010
      Conference date: 9–10 July 2010

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          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.

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          Most cited references9

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          The Bioperl toolkit: Perl modules for the life sciences.

          Jason E Stajich, David Block, Kris Boulez … (2002)
          The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.
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            The generic genome browser: a building block for a model organism system database.

            Lincoln D. Stein, Christopher John Mungall, ShengQiang Shu … (2002)
            The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org.
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              The UCSC Genome Browser database: update 2010

              Brooke Rhead, Donna Karolchik, Robert M. Kuhn … (2010)
              The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc.edu/) provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users’ own annotation data. As of September 2009, genomic sequence and a basic set of annotation ‘tracks’ are provided for 47 organisms, including 14 mammals, 10 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms and a yeast. New data highlights this year include an updated human genome browser, a 44-species multiple sequence alignment track, improved variation and phenotype tracks and 16 new genome-wide ENCODE tracks. New features include drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats for large datasets (bigBed and bigWig), a new multiple alignment output tool, links to variation and protein structure tools, in silico PCR utility enhancements, and improved track configuration tools.
              Article 0 comments Cited 260 times – based on 0 reviews     Review now
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                Author and article information

                Conference
                Journal ID (nlm-ta): BMC Bioinformatics
                Title: BMC Bioinformatics
                Publisher: BioMed Central
                ISSN (Electronic): 1471-2105
                Publication date Collection: 2010
                Publication date (Electronic): 21 December 2010
                Volume: 11
                Issue: Suppl 12
                Page: S10
                Affiliations
                [1 ]Liverpool School of Tropical Medicine, L3 5QA, Liverpool, UK
                Article
                Publisher ID: 1471-2105-11-S12-S10
                DOI: 10.1186/1471-2105-11-S12-S10
                PMC ID: 3040524
                PubMed ID: 21210977
                SO-VID: 0aeec7e8-38c6-4646-b350-dfcac73643f4
                Copyright © Copyright ©2010 Antao; licensee BioMed Central Ltd.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Conference name: The 11th Annual Bioinformatics Open Source Conference (BOSC) 2010
                Conference location: Boston, MA, USA
                Conference date: 9–10 July 2010
                History
                Categories
                Subject: Proceedings

                ScienceOpen disciplines: Bioinformatics & Computational biology
                Data availability:
                ScienceOpen disciplines: Bioinformatics & Computational biology

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