I was exploring the ChEBI Ontology workflow (https://www.knime.com/blog/exploring-a-chemistry-ontology-with-knime).
The owl file is very big and I cannot run the workflow on my laptop. Thus, I was wondering whether would it be possible to obtain a smaller owl file?
PS: I have already increased my memory.
Thank you in advance for your support!
Not really a KNIME question at all - but there are “lite” and other sized versions of that ontology here: ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/
It’s cool to see people interested in ontologies but a pity the example isn’t working on your laptop.
As it was already mentioned there is another “lite” version of the ontology, that is much smaller, but this will not work in my example workflow from the blog post, as I was filtering properties that will be missing then - so you will get another errors.
What is exactly the error message you are getting, is it already while loading the example workflow? Or later during the execution? The chebi file is included in the workflow folder, if it is the loading you could remove it (it’s about 500 Mb) so you will be at least able to see the workflow.
Also, are you interested only in chemistry ontologies? or might other examples be interesting? There are several public SPARQL Endpoints available where you just send a query and will get a very quick reply without the need to load the whole ontology into KNIME.
Sorry, the link is not working. Could you please send it
The link should work when you copy and paste into your webbrowser. Maybe its due to the ftp server where the files are located at ebi.
Alright, I got it. Thank you a lot for the answer.
Anyway, slowely, I managed to executed the workflow. However, at the second-last component (step 4), the node “Network Analyzer” is not configured correctly. I tried to pplay a bit with it but I did not manage. Could you please provide me the right configurations of that node?
(the forum software is not marking up FTP links correctly - it seems)
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