PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods
2016/07/29Web Site: http://pgdbj.jp/pages/index.html?dir=&page=mk&ln=en
FTP Site: ftp://ftp.biosciencedbc.jp/archive/pgdbj-dna-marker-linkage-map/
The database of general information, DNA markers, QTLs, DB links and genome analysis methods of plants including model plants.
README Content
1. Database Component
2. Data Description
2.1 README
| Data name | README |
| Description of data contents | HTML file to describe "PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods" data. |
| File | README_e.html(English) |
2.2 Registered plant list
| Data name | Registered plant list |
| Description of data contents | The list of organisms handled in this database. It includes that basic explanation of the organism, links to the DNA marker list, the QTL list, the list of related databases and/or the genomic analysis information. |
| File | pgdbj_dna_marker_linkage_map_plant_species_list_en.zip (20.0 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Scientific name | Scientific name |
| Taxonomy ID | Taxonomy ID of NCBI |
| Family | Family |
| Genus | Genus |
| Species | Species |
| Common name | Common name |
| Synonym | Synonym |
| Links (NCBI) | Links (NCBI) |
| Links (DFCI) | Links (DFCI) |
| Resource information | Resource information |
| Reference | Reference |
| Commentary | Commentary |
| Scientific name authority | Scientific name authority |
| Variety | Variety |
| Marker list | Presence or absence of Marker list in this DB (link to the Marker list in simple search page) |
| QTL list | Presence or absence of QTL list in this DB (link to the QTL list in simple search page) |
| Plant DB link | Presence or absence of Plant DB link in this DB (link to the Plant DB link list in simple search page) |
| Genome analysis methods | Presence or absence of Genome analysis methods information in this DB (link to the Genome analysis methods information in simple search page) |
2.3 Marker list
| Data name | Marker list |
| Description of data contents | The list of DNA markers, including following information: marker name, organism name, type of marker, sequence of marker and related papers. |
| File | pgdbj_dna_marker_linkage_map_plant_marker_list.zip (1.6 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| Scientific name | Scientific name |
| Scientific name authority | Scientific name authority |
| Name | Common name |
| Family | Family |
| Marker | Marker name |
| Marker type | Marker type |
| Taxonomy ID | Taxonomy ID of NCBI |
| Journal name | Journal name of reference |
| Published year | Published year of reference |
| DOI | DOI of reference |
| PMID | PMID of reference |
| Sequence information | Sequence information |
| Typing method | Typing method |
| Forward primer | Forward primer |
| Reverse primer | Reverse primer |
2.4 QTL list
| Data name | QTL list |
| Description of data contents | The list of QTLs, including following information: organism name, papers and trait. |
| File | pgdbj_dna_marker_linkage_map_plant_qtl_list.zip (22.6 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Scientific name | Scientific name |
| Scientific name authority | Scientific name authority |
| Name | Common name |
| Family | Family |
| Taxonomy ID | Taxonomy ID of NCBI |
| QTL name | QTL name |
| Population name | Population name |
| Population type | Population type |
| Population size | Population size |
| Trait | Trait |
| Gene, description | Comments |
| Journal name | Journal name of reference |
| Published year | Published year of reference |
| DOI | DOI of reference |
| PMID | PMID of reference |
2.5 Plant DB link
| Data name | Plant DB link |
| Description of data contents | The list of Databases related in Plant Science, which includes databases of DNA markers, QTLs, and information of organisms. |
| File | pgdbj_dna_marker_linkage_map_plant_db_link_en.zip (36.3 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Database ID | Database ID |
| Database name | Database name |
| Species | Species mentioned in the Database |
| Family name | Family name |
| Common name | Common name |
| Country | Country |
| Institute | Institute |
| URL | URL of database |
| Research/General | Distinction between Research and General |
| Class | Class of database |
2.6 Genome analysis methods
| Data name | Genome analysis methods |
| Description of data contents | The current status and related information of the genomic analysis about each organism (March, 2014). In the case of organisms carried out genomic analysis, the details of analytical method, references and information of genomic database are shown in this list. |
| File | pgdbj_dna_marker_linkage_map_genome_analysis_methods_en.zip (5.8 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Scientific name | Scientific name |
| Status | Status of genome analysis |
| Chromosome number | Chromosome number |
| Genome size | Genome size |
| Year | Year of genome analysis |
| Sequencing method | Sequencing method |
| Read counts | Read counts |
| Covered genome region | Covered genome region |
| Sequencing depth | Sequencing depth |
| Assembly method | Assembly method |
| Number of scaffolds | Number of scaffolds |
| Contig counts | Contig counts |
| Gene annotation method | Gene annotation method |
| Number of predicted genes | Number of predicted genes |
| Genome database | Genome database information |
| Assembly release | Assembly release |
| Annotation release | Annotation release |
| Reference1 (DOI) | Reference1 (DOI) |
| Reference1 (PMID) | Reference1 (PMID) |
| Reference2 (DOI) | Reference2 (DOI) |
| Other reference (DOI) | Other reference (DOI) |
3. License
Last updated : 2014/04/03
You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.
The license for this database is specified in the Creative Commons Attribution-Share Alike 2.1 Japan.
If you use data from this database, please be sure attribute this database as follows: "PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods © Satoshi Tabata (Kazusa DNA Research Institute) licensed under CC Attribution-Share Alike 2.1 Japan".
The summary of the Creative Commons Attribution-Share Alike 2.1 Japan is found here.
With regard to this database, you are licensed to:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- freely create and distribute database and other derivative works based on part or whole of the data from this database,
under the license, as long as you comply with the following conditions:
- You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any derivative work.
- You must distribute any derivative work based on part or whole of the data from this database under the license.
- You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.
Satoshi Tabata
Kazusa DNA Research Institute
2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 JAPAN
Contact Form
4. Update History
| Date | Update contents |
|---|---|
| 2016/07/29 | Database Description page is updated.
|
| 2014/10/10 | PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods English archive site is opened. |
| 2012/08/08 | PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods is opened. |
5. Literature
Erika Asamizu, Hisako Ichihara, Akihiro Nakaya, Yasukazu Nakamura, Hideki Hirakawa, Takahiro Ishii, Takuro Tamura, Kaoru Fukami-Kobayashi, Yukari Nakajima and Satoshi TabataPlant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases.
Plant Cell Physiol (2014) 55 (1): e8
PMID: 24363285
6. Contact address
When you have any question about "PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods", contact the following:Kazusa DNA Research Institute
2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 JAPAN
Contact Form