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

被引：8

作者：

Hitz, Benjamin C. ^{[1
]}

Rowe, Laurence D. ^{[1
]}

Podduturi, Nikhil R. ^{[1
]}

Glick, David I. ^{[1
]}

Baymuradov, Ulugbek K. ^{[1
]}

Malladi, Venkat S. ^{[1
]}

Chan, Esther T. ^{[1
]}

Davidson, Jean M. ^{[1
]}

Gabdank, Idan ^{[1
]}

Narayana, Aditi K. ^{[1
]}

Onate, Kathrina C. ^{[1
]}

Hilton, Jason ^{[1
]}

Ho, Marcus C. ^{[1
]}

Lee, Brian T. ^{[2
]}

Miyasato, Stuart R. ^{[1
]}

Dreszer, Timothy R. ^{[1
]}

Sloan, Cricket A. ^{[1
]}

Strattan, J. Seth ^{[1
]}

Tanaka, Forrest Y. ^{[1
]}

Hong, Eurie L. ^{[1
]}

Cherry, J. Michael ^{[1
]}

机构：

[1] Stanford Univ, Dept Genet, Sch Med, Stanford, CA 94305 USA

[2] Univ Calif Santa Cruz, Baskin Sch Engn, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA

来源：

PLOS ONE | 2017年 / 12卷 / 04期

关键词：

REGULATORY INFORMATION; CHROMATIN; PRINCIPLES; ANNOTATION; EXPRESSION; ELEMENTS; MOUSE;

D O I：

10.1371/journal.pone.0175310

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

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 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, 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.

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