RT Journal Article
SR Electronic
T1 SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 044578
DO 10.1101/044578
A1 Benjamin C. Hitz
A1 Laurence D. Rowe
A1 Nikhil R. Podduturi
A1 David I. Glick
A1 Ulugbek K. Baymuradov
A1 Venkat S. Malladi
A1 Esther T. Chan
A1 Jean M. Davidson
A1 Idan Gabdank
A1 Aditi K. Narayanan
A1 Kathrina C. Onate
A1 Marcus C. Ho
A1 Brian T. Lee
A1 Stuart R. Miyasato
A1 Timothy R. Dreszer
A1 Cricket A. Sloan
A1 J. Seth Strattan
A1 Forrest Y. Tanaka
A1 Eurie L. Hong
A1 J. Michael Cherry
YR 2016
UL http://biorxiv.org/content/early/2016/03/19/044578.1.abstract
AB The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort[1–6] to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome Project[7][1]. The current database exceeds 5500 experiments across more than 350 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the H. sapiens and M. musculus genomes. All ENCODE experimental data, metadata, and associated computational analyses are submitted to the ENCODE Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. As the volume of data increases, the identification and organization of experimental details becomes increasingly intricate and demands careful curation. The ENCODE DCC[8–10] has created a general purpose software system, known as SnoVault, that supports metadata and file submission, a database used for metadata storage, web pages for displaying the metadata and a robust API for querying the metadata. The software is fully open-source, code and installation instructions can be found at: http://github.com/ENCODE-DCC/snovault [need to register this ASAP]. The core database engine, SnoVault (which is completely independent of ENCODE, genomic data, or bioinformatic data) has been released as a separate Python package.Database URL https://www.encodeproject.org/