JGA

About JGA

JGA is a controlled-access archive for sharing, under certain conditions, analysis data produced by research that uses human-derived biospecimens. Submitting or using raw data such as sequence data requires review and approval by the Data Access Committee (DAC). Both Data Submission and Data Use require compliance with the NBDC Guidelines for Human Data Sharing and the NBDC Security Guidelines for the Handling of Human Data. In addition, every dataset carries a Policy that defines its conditions of use, and the data may be used only for research purposes and under conditions that satisfy that Policy.

JGA is a controlled-access archive of the same kind as the European Genome-phenome Archive (EGA), operated by the European Bioinformatics Institute (EBI), and the database of Genotypes and Phenotypes (dbGaP), operated by the National Center for Biotechnology Information (NCBI). Because data submission and data use review must be conducted in accordance with the laws and regulations of each country or region, no mechanism exists for exchanging data itself among JGA, EGA, and dbGaP (FAQ). In addition, none of these archives can issue access tokens for reviewers.

Among the metadata, Study, Dataset, and Policy objects are openly browsable by anyone through DDBJ Search. Raw read data such as sequence files, and other metadata, can only be accessed by users whose Data Use application has been approved.

NOTE

In the Submit Navigator, selecting "Human" + "Prefer restricted access" / "Contains a personal identifier" / "Research under laws and ethics guidelines" guides you through the path from the Data Submission application at the NBDC Human Database to registration in JGA.

Data Submission

Data accepted

For data derived from human individuals, only data that has already been de-identified is accepted; data containing information that could re-identify research participants is not accepted.

Data type	Main format	Linked object	Notes
NGS reads	FASTQ (gzip / bzip2)	Data	Paired-end reads use the `/1` and `/2` suffixes
Aligned reads	BAM	Data	BAM containing unaligned reads is recommended; do not recompress
454 reads	SFF	Data	Submit uncompressed
Variants	VCF	Analysis	VCF is recommended for sequence variations
Microarray	Genotyping / SNP / expression intensity data	Analysis	GEA-compliant format is recommended
Metabolome	Compliant with the MetaboBank submission format	Analysis
Proteome	Compliant with SDRF-Proteomics	Analysis

File-level constraints include: do not include spaces in file names, do not submit multiple files bundled into a ZIP archive, and do not recompress BAM files with gzip or similar tools, since BAM is already a compressed format.

Prerequisites for Data Submission

See the NBDC Human Database page.

Submission flow

See here for the detailed procedure.

flowchart TD
  S1["Log in to the NBDC Human Database application system (recommended browsers: Chrome, Firefox)"]
  S2[Create a Data Submission Group]
  S3[Enter the information required for the Data Submission application and attach ethics-related documents]
  S4["Review by the Data Access Committee (approx. 2 weeks)"]
  S5[Notification of the Submission ID after approval]
  S6["Prepare metadata (in English)* and data files"]
  S7[Upload metadata and data files]
  S8[Accession numbers issued after curator validation]
  S9[Notify the Data Access Committee secretariat once the data publication date is decided]
  S10[Publication of the NBDC Human Database dedicated site and data release]
  S1 --> S2 --> S3 --> S4 --> S5 --> S6 --> S7 --> S8 --> S9 --> S10

* If data submitters want to validate the XML in advance, they can run excel2xml via Singularity.

Data structure

JGA does not adopt the BioProject / BioSample model used by DRA. Instead it has its own entity model, extending the metadata model of the Sequence Read Archive. It consists of seven metadata object types — Study, Sample, Experiment, Data, Analysis, Dataset, Policy — plus a Submission that represents the registration transaction, and each of these receives an independent accession number.

Object	Role
Submission	Unit of the registration transaction; data is released at this unit
Study	Overview of the whole research project; this unit is used for citation in papers
Sample	Description of a de-identified individual sample (typically one sample = one individual)
Experiment	Describes the experimental method, such as library preparation and platform for NGS or array experiments
Data	Primary data files such as raw NGS read data
Analysis	Analysis data files such as VCF, derived data, and summary statistics
Dataset	Distribution unit subject to a Data Use application; linked to one Policy
Policy	Description of the Policy that defines the conditions of data use

Data users specify the data they wish to use at the Dataset level. When different Policies apply within the same Study, the data must be split into separate Datasets, one per Policy.

Accession numbers

After the Data Submission application is approved, a Submission ID (e.g. JSUB000353) is issued and a registration directory is created on the JGA server. Accession numbers are issued once the curator completes XML conversion and xsd validation of the metadata and the data is stored in the archive.

Prefix	Object	Digits	Example
`JGA`	Submission	6	`JGA000001`
`JGAS`	Study	6	`JGAS000001`
`JGAN`	Sample	9	`JGAN000000001`
`JGAX`	Experiment	9	`JGAX000000001`
`JGAR`	Data	9	`JGAR000000001`
`JGAZ`	Analysis	9	`JGAZ000000001`
`JGAD`	Dataset	6	`JGAD000001`
`JGAP`	Policy	6	`JGAP000001`

TIP

Using the Study ID (JGAS######) for citation in papers is recommended.

flowchart TD
  S1["Log in to the NBDC Human Database application system (recommended browsers: Chrome, Firefox)"]
  S2[Create a Data Use Group]
  S3[Enter the information required for the Data Use application and attach the research plan, security checklist, evidence, and other documents]
  S4["Review by the Data Access Committee (approx. 2 weeks)"]
  S5[Notification of approval or rejection]
  S6[If approved, access to the data is granted]
  S7[Access the data and download it to the server specified in the Data Use application]
  S1 --> S2 --> S3 --> S4 --> S5 --> S6 --> S7

JGA official page (Japanese)
JGA official page (English)
JGA Submission guide
JGA Submission step-by-step (EN)
FAQ: data exchange among JGA / dbGaP / EGA
submission-excel2xml (Excel-to-XML converter)
JGA XML schema (xsd)
Example JGA Dataset search on DDBJ Search
NBDC Human Database (review of Data Submission and Data Use applications; publication of submitted data overviews and dataset pages)