standards > model/format > DOI:10.25504/FAIRsharing.q72e3w


ready Short Read Archive eXtensible Markup Language

Abbreviation:SRA-XML


General Information
The SRA data model contains the following objects: Study: information about the sequencing project Sample: information about the sequenced samples Experiment: information about the libraries, platform; associated with study, sample(s) and run(s) Run: contains the raw data files Analysis: contains the analysis data files; associated with study, sample and run objects Submission: information about the submission actions include release date. It is used by The Sequence Read Archive (SRA) and the European Nucleotide Archive (ENA) to store raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT.



How to cite this record FAIRsharing.org: SRA-XML; Short Read Archive eXtensible Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.q72e3w; Last edited: March 15, 2018, 11:55 a.m.; Last accessed: Sep 22 2018 7:09 a.m.


Record updated: March 15, 2018, 11:50 a.m. by The FAIRsharing Team.

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Implementing Databases (6)
GenBank
GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis. The complete release notes for the current version of GenBank are available on the NCBI ftp site. A new release is made every two months. GenBank growth statistics for both the traditional GenBank divisions and the WGS division are available from each release.

European Nucleotide Archive
The European Nucleotide Archive (ENA) is a globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and experimental design. Serving both as the database of record for the output of the world's sequencing activity and as a platform for the management, sharing and publication of sequence data, the ENA provides a portfolio of services for submission, data management, search and retrieval across web and programmatic interfaces. The ENA is part of the International Nucleotide Sequence Database Collaboration.

Sequence Read Archive
The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.

Database of Genotypes and Phenotypes
The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype.

Japanese Genotype-phenotype Archive
The Japanese Genotype-phenotype Archive (JGA) is a service for permanent archiving and sharing of all types of individual-level genetic and de-identified phenotypic data resulting from biomedical research projects.

Gene Transcription Regulation Database
Gene Transcription Regulation Database (GTRD) is a database of transcription factor binding sites (TFBSs) identified by ChIP-seq experiments for human and mouse.

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