Dynamic Macrophage Pathway CSML Database

2009/09/07

WebSite: http://gnp.hgc.jp/macrophage/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/dmpd

DMPD collects pathway models of transcriptional regulation and signal transduction in CSML format for dymamic simulation based on the curation of descriptions about LPS and PMA stimulation for macrophage from literature.

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. Literature list concerning differentiation and activation of macrophage and pathways found in the literature
  3. Pathway data concerning differentiation and activation of macrophage
Return to Top

2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "Dynamic Macrophage Pathway CSML Database" data.
File README_e.html(English)
Return to Top

2.2 Literature list concerning differentiation and activation of macrophage and pathways found in the literature

Data name Literature list concerning differentiation and activation of macrophage and pathways found in the literature
Description of data contents

Literature list concerning curated differentiation and activation of macrophage. The list is a CSV format text file.

File dmpd.zip (16KB)
Data items are the following:
Data item Description
PubmedID PubMed ID (PMID) of article
Title Article title
Authors Article author(s)
Publication Journal published the article
Pathway Diagram of the pathway (Blank in the downloaded data)
PNG File Link to the pathway diagram (PNG file) (In the downloaded data, a flag indicating the existence of the diagram is shown.)
SVG File Link to the pathway diagram (SVG file) (In the downloaded data, a flag indicating the existence of the diagram is shown.)
HTML File Link to the pathway information (HTML file) (In the downloaded data, a flag indicating the existence of the information is shown.)
CSML File Link to the pathway information (CSML file) (In the downloaded data, a flag indicating the existence of the information is shown.)
Open .csml file with CIOPlayer Link to open a CSML file on Cell Illustrator Online Player (Blank in the downloaded data.)
Open .csml file with CIO Link to open a CSML file at Cell Illustrator Online (Blank in the downloaded data.)

2.3 Pathway data concerning differentiation and activation of macrophage

Data name Pathway data concerning differentiation and activation of macrophage
Description of data contents

Pathways concerning differentiation and activation of macrophage extracted from the literature list in the CSML format, which is an XML format. One CSML file to an article.

File macrophageCSML.zip (11.6MB)
About CSML format file
Return to Top

3. License

The Standard License specifies the license terms regarding the use of this database and the requirements you must follow in using this database.
The Additional License specifies those items that are exceptionally permitted even though they are generally prohibited in the Standard License.

3.1 Standard License

The Standard License for this database is the license 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: "DMPD (Dynamic Macrophage Pathway CSML Database), Copyright© 2009 The University of Tokyo 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:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. freely create and distribute database and other derivative works based on part or whole of the data from this database,

under the Standard License, as long as you comply with the following conditions:

  1. 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.
  2. You must distribute any derivative work based on part or whole of the data from this database under this License.

3.2 Additional License

1. You must display this Additional License along with the Standard License when distributing any derivative work based on part of whole of the data from this database.

2. When you conduct research by using this database, and describe the research results in an article or paper, you always need to cite this database, and specify the name and URL of this database in the article or paper.

3.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 Standard License and the above Additional License.

Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo
4-6-1 Shirokanedai, Minato-ku, Tokyo
108-8639
Tel: +81-3-5449-5615
FAX: +83-3-5449-5442
E-mail: mlab-adm[at]ims[dot]u-tokyo[dot]ac[dot]jp

3.3 About Providing Links to This Database

You can freely provide links to all contents in this database. But, contents might be changed without notice.

Return to Top

4. Update History

Date Update contents
2010/03/29 DMPD English archive site is opened.
2009/8 Data is updated.
2009/3 DMPD (Dynamic Macrophage Pathway CSML Database)(http://gnp.hgc.jp/macrophage/) is released.
Return to Top

5. Literature

6. Contact address

When you have any question about "Dynamic Macrophage Pathway CSML Database", contact the following:

Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo
4-6-1 Shirokanedai, Minato-ku, Tokyo
108-8639
Tel: +81-3-5449-5615
FAX: +83-3-5449-5442
E-mail: mlab-adm[at]ims[dot]u-tokyo[dot]ac[dot]jp

Return to Top