Pig Genome Database: A Networked Information Hub to Facilitate Comprehensive Genetic Analysis

The availability of an annotated pig genome provides new opportunities for genetic analyses. Although the pig genome information is freely available from Ensembl, NCBI, UCSC, and other resources, it is still a challenge for users to make use of this information to perform complex genetic analysis. In addition, much of the historic pig genomics information is fragmented in various forms/databases. It’s time-consuming to assemble all these information to understand multiple genetic factors in a networked fashion. We developed the Pig Genome Database (PGD) in an attempt to overcome these difficulties. Firstly, we designed the PGD to seamlessly bridge genome information from different databases. The database we brought together include NCBI Gene DB, ANEXDB, Animal QTLdb, Animal CorrDB, GO, and OMIA. Secondly, we have tied several tools together to serve the purpose of seamless data transfer between applications. The tools included Ensembl gene structure browser, BioMART, GBrowse, SNPlotz, Expiditor, CateGOrizer, and VCmap. Thirdly, we designed the PGD to be and open-end tool in the sense for extending its capability for new data types (e.g. Nextgen sequencing data) and tools (e.g. API access). The PGD is still in the process for further development. It is our aim to collaboratively utilize all databases and tools to form a networked database resources federation, maximize the potentials of existing database tools, thereby to facilitate information integration for comprehensive genetic analysis.