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[bioontology-support] [BioPortal] Feedback from Shaker El-Sappagh
Jennifer Leigh Vendetti
vendetti at stanford.edu
Mon Oct 1 08:00:51 PDT 2018
Hello Dr. El-Sappagh,
Thank you for making the requested changes. The ontology parsing process proceeded further than last time, but there is a new error that I am currently investigating. Apologies that I don’t have it tracked down quite yet. I will update you with more information as soon as I’m able.
On Oct 1, 2018, at 5:32 AM, Shaker El-Sappagh <shaker_elsapagh at yahoo.com<mailto:shaker_elsapagh at yahoo.com>> wrote:
Hello Dr. Jennifer,
I hope that you are fine.
Please, I have uploaded the ontology after handling the mentioned error. However, the ontology is still not working.
Kindly, guide me until the ontology become properly work.
Shaker El-Sappagh, PhD.
UWB Wireless Communications Research Center,
Department of Information and Communication Engineering,
Inha University, Incheon, South Korea.
Email: Shaker_elsapagh at yahoo.com<http://us.mc1126.mail.yahoo.com/mc/compose?to=Shaker_elsapagh@yahoo.com>, sh.elsappagh at gmail.com.
On Friday, September 28, 2018, 10:11:02 AM GMT+9, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hello Dr. El-Sappagh,
The error that occurs in our log file is this:
"Illegal Element Name (Element Is Not A QName): http://www.co-ode.org/ontologies/ont.owl#DDO:0000002”<http://www.co-ode.org/ontologies/ont.owl#DDO:0000002%E2%80%9D>
There are 3 occurrences in the FASTO.owl source file of the above URI, where the colon character isn’t allowed in the end fragment (DDO:0000002). The URI will need to be modified to remove the colon character, e.g., you could replace it with an underscore:
After making this modification, I believe our system will be able to parse the ontology.
> On Sep 24, 2018, at 8:31 PM, Shaker El-Sappagh <shaker_elsapagh at yahoo.com<mailto:shaker_elsapagh at yahoo.com>> wrote:
> Dear Dr. Jennifer,
> Thank you for your kind reply.
> Please, I have uploaded my ontology as it is required.You can find the FASTO ontology at this link:
> Thank you for your support.
> Best Regards.
> Shaker El-Sappagh, PhD.
> Post-Doctoral Fellow
> UWB Wireless Communications Research Center,
> Department of Information and Communication Engineering,
> Inha University, Incheon, South Korea.
> Email: Shaker_elsapagh at yahoo.com<mailto:Shaker_elsapagh at yahoo.com>, sh.elsappagh at gmail.com.<mailto:sh.elsappagh at gmail.com.>
> On Tuesday, September 25, 2018, 3:35:12 AM GMT+9, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
> Hello Dr. El-Sappagh,
> It appears you’ve submitted multiple ontology files inside of a RAR file. We don’t support RAR files. Instead, you’ll need to repackage your ontology files inside of a ZIP file. We also have some requirements about how the ZIP file is named so that BioPortal can figure out which of the files is your main ontology file. The naming convention is described in this post in our mailing list archive:
> Let us know once you’ve resubmitted in the proper format, and we’ll have another look at whether the ontology parsed in our system.
> Kind regards,
>> On Sep 24, 2018, at 8:49 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:
>> Name: Shaker El-Sappagh
>> Email: Shaker_elsapagh at yahoo.com<mailto:Shaker_elsapagh at yahoo.com>
>> Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FFASTO
>> Please, I have uploaded my FASTO ontology. It has not worked yet.
>> Best regards .
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
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