TP Atlas
2013/12/16HTTPS Site: https://dbarchive.biosciencedbc.jp/data/tp_atlas/
The database of achievements of Targeted Proteins Research Program mapped on pathway diagrams.
README Content
1. Database Component
2. Data Description
2.1 README
| Data name | README |
| Description of data contents | HTML file to describe "TP Atlas" data. |
| File | README_e.html(English) |
2.2 Main
| Data name | Main |
| Description of data contents | It is a summary table of achievements in the Targeted Proteins Research Program (TPRP)-structural biology project in Japan; including background, highlight and references of each project. |
| File | tp_atlas_en.zip (20.1 KB) |
| Data item | Description |
|---|---|
| Project ID | Project ID |
| Project Theme | Theme of the project |
| Project Theme (short) |
Theme of the project (short ver.) |
| Principal Investigator | Principal Investigator of the project |
| Affiliation | Affiliation of the project |
| Backgrounds | Backgrounds of the project |
| Highlights | Highlights of the project |
| Outline | Outline of the project |
| Review | Reviews or original papers on the project (In the cases of multiple items, they are arranged in the same order as PubMed ID.) |
| PubMed ID | PubMed ID (In the cases of multiple items, they are arranged in the same order as Review.) |
| CSML File | Name of the Network data (CSML file) (Linked to the Network data in the Simple Search site.) |
2.3 Protein
| Data name | Protein |
| Description of data contents | It is a summary table of protein information in individual projects; such as protein name, abbreviation, organism and terms for searching protein information on other websites. |
| File | tp_atlas_protein.zip (49.8 KB) |
| Data item | Description |
|---|---|
| Project ID | Project ID |
| Sub Group | Sub group of the protein |
| Symbol | Symbol of the protein |
| Synonym | Synonym of the protein |
| Wiki | Search term in wikipedia |
| Full Name | Full name of the protein |
| Other Names | Other names of the protein |
| TaxId | Taxon identifer in UniProt Taxonomy |
| Organism | Organism of the protein |
| Entrez | Gene ID in NCBI Gene |
| UniProt | UniProt KB accession number |
| GNP |
Gene ID in GNP (Genome Network Platform) (NCBI Gene ID) |
| Struct. PDB | PDB ID in PDBj (Protein Data Bank Japan) |
| Struct. P3K | PDB ID in Protein 3000 Structure Gallery |
| Struct. TPRP | PDB ID in TP Structure Gallery |
| PPI GNP | Gene ID in PPI in GNP (NCBI Gene ID) |
| PCI | PDB ID in PCI |
| TP Article | PMID (PubMed ID) in PubMed |
| Press Release | TP press release ID |
2.4 Network File
| Data name | Network File |
| Description of data contents | Network diagrams (in CSML format) for each project. One project has one pathway file originally drawn by Cell Illustrator. |
| File | tp_atlas_csml.zip (2.02 MB) |
About CSML format file
- For CSML (Cell System Markup Language), see also the CSML website.
- CSML files may be graphically viewed on Cell Illustrator Online Player. These files may also be graphically edited and simulated at Cell Illustrator Online. For these pieces of software, see also the Cell Illustrator website or the Cell Illustrator Online website.
2.5 Image File
| Data name | Image File |
| Description of data contents | Network diagrams (in PNG format) for each project. One project has one pathway file originally drawn by Cell Illustrator. |
| File | tp_atlas_png.zip (6.93 MB) |
3. License
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: "TP Atlas © Targeted Proteins Research Program 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.
Yata 1111, Mishima, Shizuoka 411-8540, JAPAN
Platform for Drug Discovery, Informatics, and Structural Life Science
Research Organization of Information and Systems
National Institute of Genetics
E-mail: p4d-info[at]nig[dot]ac[dot]jp
4. Update History
| Date | Update contents |
|---|---|
| 2013/12/16 | The email address in the contact information is corrected. |
| 2013/11/19 | TP Atlas English archive site is opened. |
| 2008/4/1 | TP Atlas (http://www.tanpaku.org/tpatlas/) is opened. |
5. Literature
-6. Contact address
When you have any question about "TP Atlas", contact the following:
Yata 1111, Mishima, Shizuoka 411-8540, JAPAN
Platform for Drug Discovery, Informatics, and Structural Life Science
Research Organization of Information and Systems
National Institute of Genetics
Hideaki Sugawara
E-mail: p4d-info[at]nig[dot]ac[dot]jp