title: SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata.
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 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.
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Benjamin C
authors.identifier: http://orcid.org/0000-0003-3361-3594
authors.initials: BC
authors.lastname: Hitz
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Laurence D
authors.initials: LD
authors.lastname: Rowe
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Nikhil R
authors.initials: NR
authors.lastname: Podduturi
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: David I
authors.initials: DI
authors.lastname: Glick
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Ulugbek K
authors.initials: UK
authors.lastname: Baymuradov
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Venkat S
authors.initials: VS
authors.lastname: Malladi
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Esther T
authors.initials: ET
authors.lastname: Chan
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Jean M
authors.initials: JM
authors.lastname: Davidson
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Idan
authors.initials: I
authors.lastname: Gabdank
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Aditi K
authors.initials: AK
authors.lastname: Narayana
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Kathrina C
authors.initials: KC
authors.lastname: Onate
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Jason
authors.initials: J
authors.lastname: Hilton
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Marcus C
authors.initials: MC
authors.lastname: Ho
authors.affiliation: University of California Santa Cruz, Baskin School of Engineering, Center for Biomolecular Science and Engineering, Santa Cruz, California, United States of America.
authors.forename: Brian T
authors.initials: BT
authors.lastname: Lee
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Stuart R
authors.initials: SR
authors.lastname: Miyasato
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Timothy R
authors.initials: TR
authors.lastname: Dreszer
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Cricket A
authors.initials: CA
authors.lastname: Sloan
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: J Seth
authors.initials: JS
authors.lastname: Strattan
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Forrest Y
authors.initials: FY
authors.lastname: Tanaka
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: Eurie L
authors.initials: EL
authors.lastname: Hong
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.
authors.forename: J Michael
authors.initials: JM
authors.lastname: Cherry
mesh_terms: D000818:Animals; D004247:DNA / Q000235:genetics; D030541:Databases, Genetic; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D000071253:Metadata; D051379:Mice; D012984:Software
chemical_list: D004247:DNA