Submission to JGA

Submission Guide*

The JGA accepts only de-identified data approved by NBDC. The users apply for data submission directly to the NBDC and the JGA will only accept submissions once the information of a successful application process has been passed from the NBDC to the JGA.

It should be clear from the original consent agreements affiliated to your samples if your data should be subject to controlled access. All data submitted to the JGA has controlled access, which means that access to the data submitted is subject to approval by NBDC as a part of a formal application procedure.

Controlled access does not correspond to holding a release prior to publication. All the DDBJ archival resources including the JGA enable you to hold a submission before publication.

Accession numbers are issued to metadata objects with following prefixes.

プレフィックスメタデータオブジェクト数字の桁数
JGASubmission11JGA00000000001
JGASStudy11JGAS00000000001
JGANSample11JGAN00000000001
JGAXExperiment11JGAX00000000001
JGARData11JGAR00000000001
JGAZAnalysis11JGAZ00000000001
JGADData set11JGAD00000000001
JGAPPolicy11JGAP00000000001

Currently, there is no requirement for authors to use a specific JGA accession in their publications. We would recommend that authors use the JGAS (study) accession, which would provide the reader/user with a complete overview of the study and a set of links to all the data from that study.

An example of accession number citation: "Genotype data has been deposited at the Japanese Genotype-phenotype Archive (JGA, http://trace.ddbj.nig.ac.jp/jga), which is hosted by the DDBJ, under accession number JGASXXXXXXXXX."

Sequence data file (raw/unaligned and aligned)*

Supported JGA data submission formats are described below. If you have data in any other format or have any questions please contact the JGA.

Data files should be de-multiplexed prior to submission so that each data object is submitted with files containing data for a single sample only.

BAM format

BAM format is the preferred JGA data submission format. All JGA submitters are encouraged to submit their data using BAM files.

All submitted BAM files must be readable with SAMtools and Picard. Currently, BAM files must be de-multiplexed prior submission.

The BAM files are nearly optimal in terms of compression and should be submitted uncompressed.

Fastq format

Primary sequence data submissions of single and paired reads are accepted as Fastq files that meet the following the requirements:

  • Quality scores must be in Phred scale. For example, quality scores from early Solexa pipelines must be converted to use this scale. Both ASCII and space delimitered decimal encoding of quality scores are supported. We will automatically detect the Phred quality offset of either 33 or 64.
  • No technical reads (adapters, linkers, barcodes) are allowed.
  • Single reads must be submitted using a single Fastq file.
  • Paired reads must split and submitted using two Fastq files. The read names must have a suffix identifying the first and second read from the pair, for example '/1' and '/2'; (regular expression for the reads "^(.*)([\\.|:|/|_])([12])$").
  • The first line for each read must start with '@'.
  • The base calls and quality scores must be separated by a line starting with '+'.
  • The Fastq files must be compressed using gzip or bzip2.
Example of Fastq file containing single reads:
@read_name
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
...
Example of Fastq file containing paired reads:
@read_name/1
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
@read_name/2
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
...

SFF format

The recommended submission format for the 454 platform is SFF.

The SFF files are nearly optimal in terms of compression and should be submitted uncompressed.

Array based (Genotypes, SNP, Expression)

The JGA accepts processed data from all types of array based technologies, such as genotypes, gene expression, methylations, etc.

We are very flexible regarding these submissions and would accept all types of files affiliated to the array experiment into the JGA array.

We recommend that both raw data (CELs) and analysis files be submitted, which will enable potential users of the data to recreate your results cited in the paper as well as view the described results.

The JGA also archives any sample-associated phenotype information.

Variation data file

The JGA supports submissions of sequence variations in VCF format. The vcf files are accepted as secondary analysis object.

Other data files

Analysis can refer to multiple Data and Sample objects and summary data summarizing data files of these objects can be registered to the Analysis. Example analysis files are listed below.

  • A reference sequence GFF3 file assembled by using multiple sequence files in a objects.
  • A table file summarizes normalized array data files in Arrays.
  • A phenotype table file summarizes phenotype information of Samples.

Metadata*

The JGA data model is created by extending the Sequence Read Archive's model. The JGA metadata are composed of the XML objects.

JGA XML schema: JGA.xsd.zip

Example: single policy.
Example: single policy.
Example: separate policies for control and case.
Example: separate policies for control and case.

Summary information for public display

When JGA submissions are released, following metadata objects will be public on the JGA and NBDC websites to display summary of submissions.

Submission:
All fields excluding submitters' contact information.
Study:
All fields.
Data set:
All fields, number of samples, and filesize.
Policy:
All fields.

Submission

The submission XML is used to describe the submission transaction. It contains contact details of the submitter.

XML schema: JGA.submission.xsd

Study

The study XML describes your study in detail. It contains a title, a study type and an abstract, as it would appear in the publication. After publication, the study can be updated to include the PubMed ID of the paper containing the submitted data.

XML schema: JGA.study.xsd

Sample

The sample XML describes each of the samples used in your submission. A sample generally corresponds to a participant. Whilst the mandatory fields are minimal we highly recommend to describe the sample in as much detail as possible.

XML schema: JGA.sample.xsd

Experiment

The experiment XML is used to describe each unique set of experimental setup details. This includes the library preparation details, sequencing and microarray platforms. The experiment XML can represent both sequencing and array experiments.

XML schema: JGA.experiment.xsd

Data

The data XML describes the data files and their relationship with the experiments. The data XML serves as a file container.

XML schema: JGA.data.xsd

Analysis

The Analysis XML can be used to submit analyzed and summarized data to JGA. Sample phenotype files can also be submitted. Variation data can be submitted as VCF files. Only one VCF file can be submitted in each analysis and the samples used within the VCF files must be associated with JGA Samples. Optimally the VCF file would be associated with an INSDC reference assembly and sequences either by using accessions or by using commonly used labels.

XML schema: JGA.analysis.xsd

Data set

The dataset XML describes the data files, defined by the Data XML and Analysis XML, that make up the dataset and links the collection of data files to a specified Policy (Data Access Agreement). Submitters do not need to create data set when single policy is associated with all data files. Please consider the number of datasets that your submission consists of, for example, a case control study is likely to consist of at least two datasets.

In general, policy is determined by informed consent with participants.

XML schema: JGA.dataset.xsd

Policy

The Policy XML describes the Data Access Agreement (DAA). If only NBDC policy is associated with a submission, submitters do not need to create a new policy.

If additional policies are needed, you need to register a policy to NBDC and reference issued JGAP number from submitting data set.

XML schema: JGA.policy.xsd

Update submissions*

To update your submissions, please contact to the JGA team.