wikipathways-discuss@googlegroups.com

[Qing Zhao]

Hello,

I am currently using PathVisio to generate a gene signaling pathway. However, I am encountering an issue where I am unable to select the downloaded gene database ("Hs_Derby_Ensembl_108.bridge"). The error message I receive is:

Error: Failed to open Gene Database; Could not connect to database. See the error log for details.

Upon checking the error log, I found the following message:

Warning creating a new DataSource with systemCode original and null fullName!

I would greatly appreciate any advice or guidance you could provide on resolving this issue.

Best,

Lexie

[Kristina Hanspers]

Hi Lexie,

You can try using web services instead of the bridgedb database. In PathVisio, go to "Data > Identifier mapping setup". Click "Add" and then select "BridgeRest web service" on the left. For "Base URL", update it to https://webservice.bridgedb.org (note the "s" after http). For "Port", update to 443. Because of a bug in the interface, you then have to click "Cancel", and then reopen the interface by clicking "Add" again. The changes to Base Url and Port should have been saved, and you should now be able to see a list of species under "Species". Select "Homo sapiens" and click OK. 

Hope this helps.

Regards,

Kristina