ClueGO: not able to update KEGG pathway database

[Ching Ching WEE]

Hi All

I'm trying to update Ontologies by selecting "GO-update GO categories...".

However, error showed up as shown in the attachment. The same error occur when I chose tp update KEGG. I don't think my internet got problem as I still can surf the other website.

Can anyone help please 

[Scooter Morris]

Looks like the folks at GO have disabled their ftp server.  Start by looking in the ClueGOConfiguration folder outlined in the error message and see if the ftp: URI is embedded in a configuration file.  If it is, try changing it to: http://current.geneontology.org/annotations/tair.gaf.gz.  If not, I would suggest reaching out to the ClueGO authors and ask them to switch to an alternative service.

-- scooter

[Bernhard]

Hi, yes there was a change from http to https for KEGG. We will fix this asap.

Best

[Aura Perez]

Good morning, I just tried to update wikipathways inside cluego for both human and mouse and it got the error saying that either internet is down or the link is no longer working. The error directs me to look into the properties folder but I don't really see a link there directly affecting the wikipathways location

[Scooter Morris]

What link are you using for wikipathways?

-- scooter

[Aura Perez]

The link that appears in the error window is https://wikipathways-data.wcm.wmcloud.org/java-bots/gmt/current/gmt_wp_Homo_sapiens.gmt that is when i tried to update the human one, the mice, is the same but refers to mice of course

. I tried to follow that link in the browser, but I can not find it exactly like that

[Aura Perez]

I should have added that the files in the properties directory that the error message wants me to look into are not gmt files, they end in txt.gz files. When I tried to update the pathway, a new Homo Sapiens_WikiPathways_Pathways_10.08.2023.txt.gz file is create with just 1 kb and after I close the initial window error, another one appears telling me that file is corrupt, that I should delete it, get out of cytoscape and come back to it

[Scooter Morris]

Hi Aura,

I just tried to duplicate the issue you had and see the same error.  I don't think they have the correct filename.  You could try to download the file yourself and install it in the "Organism_Homo Sapiens" directory.  The correct url is: https://wikipathways-data.wmcloud.org/current/gmt/wikipathways-20230810-gmt-Homo_sapiens.gmt

-- scooter

[Aura Perez]

Thank you very much Scooter, I will try that, but at first look the file that you want me to download seems to have a different extension than the ones that I see in the Organism_Homo Sapiens folder, but I will try it

[Aura Perez]

Scooter, it took several trials. After downloading the file, the only way I got it to work was by using the down arrow that is to the right of the ontology/pathways and not by using the update ontologies section right below that. I also had to tell it to import the file and make sure that I chose gmt, as opposed to all files. A new entry was created and it is now calling a Custom ontology with the name of imported file. It seems to be working, thank you

Aurita

On Wednesday, August 16, 2023 at 11:48:09 PM UTC-4 Scooter Morris wrote: