SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata

Benjamin C. Hitz, Laurence D. Rowe, Nikhil R. Podduturi, David I. Glick, Ulugbek K. Baymuradov, Venkat S. Malladi, Esther T. Chan, Jean M. Davidson, Idan Gabdank, Aditi K. Narayana, Kathrina C. Onate, Jason Hilton, Marcus C. Ho, Brian T. Lee, Stuart R. Miyasato, Timothy R. Dreszer, Cricket A. Sloan, J. Seth Strattan, Forrest Y. Tanaka, Eurie L. HongJ. Michael Cherry

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome Project. The current database exceeds 6500 experiments across more than 450 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the H. sapiens andM. musculus genomes. All ENCODE experimental data, metadata, and associated computational analyses are submitted to the ENCODE Data Coordination Center (DCC) for validation, tracking, storage, unified processing, 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 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/ (for the generic database) and http://github.com/ENCODE-DCC/encoded/ to store genomic data in the manner of ENCODE. The core database engine, SnoVault (which is completely independent of ENCODE, genomic data, or bioinformatic data) has been released as a separate Python package.

Original languageEnglish (US)
Article numbere0175310
JournalPloS one
Volume12
Issue number4
DOIs
StatePublished - Apr 2017
Externally publishedYes

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Encyclopedias
Metadata
DNA
Databases
Software
Genes
Boidae
Human Genome Project
genomics
Python
genome
Bioinformatics
engines
Computational Biology
Application programming interfaces (API)
bioinformatics
Chromatin
chromatin
Websites
Cells

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Hitz, B. C., Rowe, L. D., Podduturi, N. R., Glick, D. I., Baymuradov, U. K., Malladi, V. S., ... Cherry, J. M. (2017). SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata. PloS one, 12(4), [e0175310]. https://doi.org/10.1371/journal.pone.0175310

SnoVault and encodeD : A novel object-based storage system and applications to ENCODE metadata. / Hitz, Benjamin C.; Rowe, Laurence D.; Podduturi, Nikhil R.; Glick, David I.; Baymuradov, Ulugbek K.; Malladi, Venkat S.; Chan, Esther T.; Davidson, Jean M.; Gabdank, Idan; Narayana, Aditi K.; Onate, Kathrina C.; Hilton, Jason; Ho, Marcus C.; Lee, Brian T.; Miyasato, Stuart R.; Dreszer, Timothy R.; Sloan, Cricket A.; Strattan, J. Seth; Tanaka, Forrest Y.; Hong, Eurie L.; Cherry, J. Michael.

In: PloS one, Vol. 12, No. 4, e0175310, 04.2017.

Research output: Contribution to journalArticle

Hitz, BC, Rowe, LD, Podduturi, NR, Glick, DI, Baymuradov, UK, Malladi, VS, Chan, ET, Davidson, JM, Gabdank, I, Narayana, AK, Onate, KC, Hilton, J, Ho, MC, Lee, BT, Miyasato, SR, Dreszer, TR, Sloan, CA, Strattan, JS, Tanaka, FY, Hong, EL & Cherry, JM 2017, 'SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata', PloS one, vol. 12, no. 4, e0175310. https://doi.org/10.1371/journal.pone.0175310
Hitz, Benjamin C. ; Rowe, Laurence D. ; Podduturi, Nikhil R. ; Glick, David I. ; Baymuradov, Ulugbek K. ; Malladi, Venkat S. ; Chan, Esther T. ; Davidson, Jean M. ; Gabdank, Idan ; Narayana, Aditi K. ; Onate, Kathrina C. ; Hilton, Jason ; Ho, Marcus C. ; Lee, Brian T. ; Miyasato, Stuart R. ; Dreszer, Timothy R. ; Sloan, Cricket A. ; Strattan, J. Seth ; Tanaka, Forrest Y. ; Hong, Eurie L. ; Cherry, J. Michael. / SnoVault and encodeD : A novel object-based storage system and applications to ENCODE metadata. In: PloS one. 2017 ; Vol. 12, No. 4.
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