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[bioontology-support] [BioPortal] Feedback from Shaker El-Sappagh

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Oct 4 11:47:03 PDT 2018


Hello Dr. El-Sappagh,

I tracked down the issue that prevented our system from parsing your ontology. FASTO.owl has an import statement of:

<Import>http://www.owl-ontologies.com/OntoFood.owl</Import>

The above URL appears to have been hijacked by spammers, and results in a corrupt ontology import where an annotation property contains HTML tags. You can reproduce this behavior in the Protege ontology editor by opening FASTO.owl and using the drop down box at the top of the application to navigate to what should be the OntoFood import. What you see in the application is the failed / mostly empty import with a single annotation property with HTML tags as content:


[cid:2E73723B-4416-4AA4-A7F9-9E5D1EC0B749 at stanford.edu]
BioPortal is unable to load a corrupt import like this into our backend triplestore. As a test, I removed the OntoFood import statement and resubmitted your ontology, which then parsed successfully:

[cid:23F88B49-B3A1-4AC7-9208-A5208B868DC9 at stanford.edu]

I’m not sure if you are the maintainer of OntoFood. One suggestion I have would be to use Protege to change the ontology name (Refactor -> Change ontology IRI…). After doing this, you might also consider merging your ontologies into one OWL file (Refactor -> Merge ontologies…), and upload the resulting merged OWL file to BioPortal.

We've been keeping a detailed account of the parsing problems in our issue tracker:

https://github.com/ncbo/bioportal-project/issues/98

Kind regards,
Jennifer




On Oct 1, 2018, at 5:32 AM, Shaker El-Sappagh <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.

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, sh.elsappagh at gmail.com.


On Friday, September 28, 2018, 10:11:02 AM GMT+9, Jennifer Leigh Vendetti <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”

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:

http://www.co-ode.org/ontologies/ont.owl#DDO_0000002

After making this modification, I believe our system will be able to parse the ontology.

Kind regards,
Jennifer



> On Sep 24, 2018, at 8:31 PM, Shaker El-Sappagh <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:
>
> http://bioportal.bioontology.org/ontologies/FASTO
>
> 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, sh.elsappagh at gmail.com.
>
>
> On Tuesday, September 25, 2018, 3:35:12 AM GMT+9, Jennifer Leigh Vendetti <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:
>
> http://ncbo-support.2288202.n4.nabble.com/bioontology-support-How-to-handle-imported-ontologies-on-bioportal-tp4654202p4654212.html
>
> 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,
> Jennifer
>
>
>
>> On Sep 24, 2018, at 8:49 AM, support at bioontology.org wrote:
>>
>> Name: Shaker El-Sappagh
>>
>> Email: Shaker_elsapagh at yahoo.com
>>
>> Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FFASTO
>>
>>
>> Feedback:
>>
>> Please, I have uploaded my FASTO ontology. It has not worked yet.
>>
>> Best regards .
>>
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>


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