Import data from BioMart

 You can import annotation data to GenomeJack from BioMart (with MySQL). This document describes how to extract the data from the Ensembl mirror database. GenomeJack keeps the imported data. Therefore, there is no need to reconnect to MySQL once you import the data.
【Note】
 There is another way that you can directly connect to the Ensembl MySQL server.
  1. Please click [File] > [Import BioMart Data...] and enter the database information that you can get from the Import From BioMart Database dialog. You must enter all information except for a password and port number.

    connectBioMart_jpg

  2. If there is some aligned data between genomes that you choose, a list of BioMart data will be shown in the Select Genome dialog. Please choose the database you want to import, and then click [OK].

    selectBioMartTarget_jpg

  3. If there is some aligned data between genomes that you choose, the list of BioMart data will be shown in the Select Method Link Species Set dialog. Please choose the database you want to import, and then click [OK].

    selectBioMartMethod_jpg

  4. The result of the comparison will be displayed on the genome (In this case, the reference genome is human and the target genome is of mouse).

    importFromBioMartEnd_jpg

    Note

    • In the system of GenomeJack, the data classified into “chromosome” of coord_system_name in dnafrag is recognized. Because BioMart data contains only chromosome number (e.g. 1 or 2), you may have to convert the numbers into chr1,2, etc, or chromosome1, 2, etc.