CellDesigner Help

You can connect to the databases from Species name or ID specified in the notes of the components. (New to 2.2)
Currently we support the connections to the following databases:

• From Species Name
  • DBGET (a simple database retrieval system for a diverse range of molecular biology databases. )
  • SGD (Saccharomyces Genome Database)
  • iHOP (Information Hyperlinked over Proteins) (New to 2.5)
  • Genome Network Platform (New to 4.0)
• From ID described in the Notes
  • PubMed (New to 3.1)
  • Entrez Gene (New to 3.2)
    
• Retrieve models from BioModels.net (New to 3.1)

Connect to the databases from Species Name

1. Select the component (Species, Reaction or Compartment)
   then select [Database] -> [Connect to SGD], [Connect to DBGET], [Connect to iHOP] or [Connect to Genome Network Platform].

According to the name of the Species, the web browser will pop up and open the relevant page.

Note: In case of DBGET, search is conducted according to the format of the name.If the name is written as "2.1.3.1", "EC2.1.3.1", "EC: 2.1.3.1", and "EC 2.1.3.1" for EC number, while the name start with "C", "C00010", "C 00010", "C: 00010" , search for compound ID.

target	format
EC number	"2.1.3.1", "EC2.1.3.1", "EC: 2.1.3.1", and "EC 2.1.3.1"
compound ID	"C00010", "C 00010", "C: 00010"

Connect to PubMed / Entrez Gene via the ID written in the Notes of the components

1. Specify the PubMed ID in the notes of Species, Reaction, or Compartment as follows;

PMID: 12345 PMID: 67890

Gene ID: 493761 GeneID: 22954


Note: This function does not work for Protein notes and Model note.


2. Select the component (Species, Reaction or Compartment) then [Database] -> [Connect to PubMed]
   
   The web browser will pop up and open the relevant page specified by the PubMed ID / Gene ID.
   
   Note: When you use Windows XP + Internet Explorer, and if there are multiple PubMed ID specified in the note, the relevant pages will be displayed in the single window. To browse all the pages, press [Back] button of the browser.