The UCSC ENCODE Data Coordination Center

University Of California Santa Cruz, Santa Cruz CA

Investigators

Linked publications & trials

Abstract

[unreadable] DESCRIPTION (provided by applicant): We propose establishing the UCSC ENCODE Data Coordination Center to collect, organize, store, and provide access to data from the ENCODE project and other related projects, based on the well-established UCSC Genome Browser. The UCSC browser is a robust, flexible platform that integrates a variety of features that make accessing genomic data both convenient and information-rich. As such, it has attained a high level of acceptance throughout the biology, bioinformatics, and biomedical research communities. During the pilot phase of the ENCODE project, involving 1% of the genome, UCSC has been the repository of sequence-based data. Through participation in the pilot phase, we have established cost-effective, high-throughput approaches for incorporating and displaying ENCODE data, and we have developed an effective interface to the consortium for uploading data files and methods documentation to our FTP site. Through ongoing expansion and improvement of our ENCODE browser, we have laid the groundwork for data management in the whole-genome phase of the project. UCSC's specific aims for participation as the ENCODE DCC are as follows: 1) coordinate closely with the ENCODE data providers to collect, store, and manage ENCODE sequence-based functional element data and related metadata; 2) provide and maintain a long-term storage system for data from the ENCODE Consortium and related genomic projects; 3) provide the ENCODE and public research communities with freely-available mechanisms to access, search, and analyze the ENCODE data; 4) employ good software engineering practices to ensure that the ENCODE data are of the highest possible quality; and 5) foster collaboration with the biomedical community. [unreadable] [unreadable] Fundamental to understanding human biology and disease is the ability to identify and locate the functional elements in the human genome sequence. Both the effective presentation of experimental data and the ability to analyze sequence data using computational methods will help elucidate genomic function. Because the UCSC Genome Browser serves both of these purposes, it offers the ideal platform for ENCODE data. [unreadable] [unreadable] [unreadable]