DDBJ Search
About DDBJ Search
- DDBJ Search is a search system for INSDC BioProject/BioSample/SRA and JGA/GEA/MetaboBank by accession number and keyword.
- Revision history search is not provided.
- DDBJ Search is, as well as a simple web form, available by WebAPI program which calls up the data directly.
- DDBJ flat file data retrieval is unavailable in DDBJ Search, please refer getentry.
Search from Web Browser
URL : https://ddbj.nig.ac.jp/search
Search by keywords
- Accession number and keywords are searchable.
- Wildcards (*,?) cannot be used.
1) Accession numbers
- Input the Accession Number.
- Performs a forward-matching, case-insensitive search.
- Multiple number search and range search are not available.
Example:
PRJDB1000
SAMD00020000
2) Keywords
- Input the term or letters of the metadata of BioProject, BioSample, SRA, JGA , GEA and MetaboBank records.
- Contents of Title and Description are searchable.
- Performs a forward-matching, case-insensitive search.
- AND/OR search is not available.
Example:
Homo sapiens
metagenome
Selection by faceted Menu
- You can narrow down your query by using the faceted menu (Database, Type, Organism, Published Date) on the left side of the page.
1) Database
- There are six items to choose from: BioProject, BioSample, SRA, JGA, GEA and MetaboBank.
2) Type
- There are fourteen items to choose from: bioproject, biosample, sra-submission, sra-study, sra-sample, sra-experiment, sra-run, sra-analysis, jga-dataset, jga-study, jga-policy, jga-dac, gea and metabobank.
3) Organism
- You can choose from a list of organism names.
- In the Organism keyword field, you can input the name of organism listed in the facet menu (the top 100 organisms). For other organism names, please use the keyword search at the top left side of the page.
4) Published Date
- You can set a range of data published dates (Date Published).
Output format
- The search results by keyword and selected facet items are displayed.
- Details information of the record is displayed by cricking each record ID.
- The following metadata items are displayed.
- Each item may not be displayed if it has no value.
1) Common Item
| Identifier | Accession number |
| Type | Data type, one of the following values: bioproject, biosample, sra-submission, sra-study, sra-sample, sra-experiment, sra-run, sra-analysis, jga-dataset, jga-study, jga-policy, jga-da, gea, metabobank |
| sameAs | Number (ID) of equivalent records in other databases |
| Organism | Organism name (value in NCBI Taxonomy database) |
| Title | Short title |
| Description | Description of the contents |
| Properties | The metadata of this record represented in JSON format. The “+” icon at the upper right of the black frame allows you to switch between full view and partial view. The icon to the left of the icon allows you to copy the contents. |
| dbXrefs | Links to the related accession numbers in the INSDC databases (BioProject, BioSample, SRA, Assembly, conventional sequence data, master record of bulk sequence data (WGS/TLS/TSA), NCBI taxonomy), the DDBJ databases (GEA, MetaboBank, JGA), the NBDC human database and the NCBI PubMed database.* |
| Download | Link to download file |
| Status | Status of INSDC data publication |
| Accessibility | State of restricted access to data** |
| Date Created | Date of data submitted |
| Date Modified | Date of last data published |
| Date Published | Date of first data published |
* The maximum number of accession numbers listed is 100. In case of there are accession numbers more than 100, whole list can get by the JSON format from cricking “dedicated API” in the upper right position.
** Controlled-access indicates restricted access data for samples from human individuals that require an application to the NBDC human database to obtain raw data and detailed metadata.
2) Type-specific items
bioproject
| Project type | Umbrella BioProject (if the BioProject is an Umbrella BioProject) |
| parentBioprojects | List of umbrella projects of this project |
| childBioprojects | List of child projects of this project |
| Organization | Name of the implementing organization of this project |
| Publication | Literature information related to this project |
| Grant | Project budget information |
| External link | URLs of resources directly related to the project (Examples: GEA, MetaboBank, GEO, GOLD) |
biosample
| Host | The natural (as opposed to laboratory) host to the organism from which the sample was obtained |
| Strain | Microbial or eukaryotic strain name |
| Isolate | Identifier of the specific individual or sample |
| Geo Loc Name | Geographical origin of the sample |
| Collection Date | Time of sampling |
| Attributes | Sample package’s attribute information |
sra-sample
| Geo Loc Name | Geographical origin of the sample |
| Collection Date | Time of sampling |
| Attributes | Sample package’s attribute information |
sra-experiment
| Library Strategy | Sequencing technique intended for this library |
| Library Source | Library source specifies the type of source material that is being sequenced |
| Library Selection | Method used to select and/or enrich the material being sequenced |
| Library Layout | Layout of reads in sequencing data files |
| Library Name | Submitter’s name for this library |
| Library Construction Protocol | Protocol by which the sequencing library was constructed |
| Platform | Sequencing instrument used |
| Instrument Model | Sequencing instrument model |
gea
| Experiment Type | The type of experimental method |
metabobank
| Study Type | The type of the study content |
| Experiment Type | The type of experimental method |
| Submission Type | The type of this submission (Examples: LC-MS, GC-MS) |
Limit（upper limit of the data acquisition）
10000 recoreds
Download files
| [BioProject/BioSample] metadata | JSON, JSON-LD |
| [SRA] metadata | XML |
| [SRA] fastq | FASTQ |
| [SRA] sra | SRA |
| [SRA] analysis data | DATA |
Search by WebAPI
DDBJ Search is available from WebAPI program, as well as a simple web form, which calls up the data directly. For details, see below.
https://github.com/ddbj/ddbj-search-api(in Japanease)
How to Create Links to BioProject/BioSample/SRA/JGA Records
You can create links to individual BioProject, BioSample, SRA, JGA, GEA and MetaboBank records.
Format:
https://ddbj.nig.ac.jp/search/entry/{Type name}/{Accession number}
Example:
https://ddbj.nig.ac.jp/search/entry/bioproject/PRJDB1000
https://ddbj.nig.ac.jp/search/entry/sra-experiment/SRX10474797
https://ddbj.nig.ac.jp/search/entry/gea/E-GEAD-282
https://ddbj.nig.ac.jp/search/entry/metabobank/MTBKS201