Disappearing edges when creating KG about pheknowlator HOT 6 CLOSED

Hi @callahantiff, not sure if this is the right place but I was tracking this issue while updating to v3.1.2 and after updating, owltools is throwing exceptions in the Ontology_Cleaning.ipynb notebook. I checked on command line and the owltools package in pkt_kg/ seems to be throwing errors as well. I can open a new issue if you'd like but thought might be relevant here. Thanks!

Hey @sanyabt - thanks for your message. It's odd that owltools is acting up. Nothing that was changed related to the original issue filed above touched owltools. So, I am wondering if it's a dependencies thing. I did see owlnets throwing warnings a while ago but it had no impact on the code running.

Could you please provide the error message you are getting and what you ran that triggered it?

For the sake of completeness, would you by chance be willing to try replacing your current version of owltools with one from a prior release? You can access the file from the zipped source_code (here, for example).

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Thank you for letting me know! It might just be an owl tools or dependency issue on my environment then in which case I'm sorry for worrying you! I'll try running the notebook again with the new and old version of owl tools and let you know. Was planning to do it today but didn't get the time. Thanks again for checking!!

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Hey @GuarinoValentina!

Thanks so much for using PheKnowLator and for reaching out. I reviewed your message and believe that I know where the problem is. I think it will be easier (and certainly more fun) if we set-up a virtual meeting to discuss. I will reach out to you via email to set something up.

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Everything should be fixed with the latest release v3.1.2. Thank you again for brining this to my attention, I hope it didn't cause you too much trouble. I am going to close this issue. Please feel free to re-open or make a new issue if you encounter anything else. Thanks so much!

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Hi @callahantiff, not sure if this is the right place but I was tracking this issue while updating to v3.1.2 and after updating, owltools is throwing exceptions in the Ontology_Cleaning.ipynb notebook. I checked on command line and the owltools package in pkt_kg/ seems to be throwing errors as well. I can open a new issue if you'd like but thought might be relevant here. Thanks!

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Hey @sanyabt -- just an update. I had a chance to run the Ontology_Cleaning.ipynb notebook today and was able to run it from start to finish without any issues.

This is good news overall; I was worried that it is was going to be something scary that required replacing owltools (which would be a big job given how much it's used in pkt). That said, I want to help you get things running on your end if I can!

Keep me posted!

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