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[bioontology-support] BioPortal not allowing uploads

Kuttichi Keloth, Vipina vk396 at njit.edu
Fri Jul 17 07:15:12 PDT 2020


Hi Jennifer,

Thank you so much. I was not aware of this. I loaded it in Protege and
there were no issues.
I will make sure to correct these in future uploads.

Thank you.
Vipina


On Thu, Jul 16, 2020 at 11:57 PM Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hello Vipina,
>
> There are 2,535 occurrences in your ontology source file where the value
> of rdf:about has a leading space character. One such example can be seen on
> line 156,587:
>
> <owl:Class rdf:about=" http://purl.obolibrary.org/obo/CIDO_UMLS_C5203670”>
>
> The ontology parsing library we use internally considers these leading
> space characters illegal:
>
>
> Detailed logs:
>
> --------------------------------------------------------------------------------
> Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser at 985696
>     Stack trace:
> org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException:
> [line=156589:column=79] IRI '
> http://purl.obolibrary.org/obo/CIDO_UMLS_C5203670' cannot be resolved
> against current base IRI http://purl.obolibrary.org/obo/cido.owl reason
> is: Illegal character in scheme name at index 0: %20http://
> purl.obolibrary.org/obo/CIDO_UMLS_C5203670
>  org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:76)
>
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:221)
>
>
> I ran a search and replace over the file to remove these leading space
> characters and uploaded the modified version of your ontology as a new
> submission. It’s fully processed and available in BioPortal now. If you
> want to submit updates, you’ll need to correct these leading space
> characters in your original source file.
>
> Kind regards,
> Jennifer
>
>
>
> On Jul 16, 2020, at 2:29 PM, Kuttichi Keloth, Vipina <vk396 at njit.edu>
> wrote:
>
> Thank you. I was able to upload some time back ( CIDIT_V1_2). But I guess
> there is a processing error.
> It shows under the submissions - uploaded,* Error rdf.*
>
> *Could you please reprocess it?*
>
> *Thank you.*
> *Vipina*
>
> On Thu, Jul 16, 2020 at 5:25 PM Michael Dorf <mdorf at stanford.edu> wrote:
>
>> Hi Vipina,
>>
>> Thank you for your report. Apologies for that. There was a system glitch
>> that required clearing of our internal cache repositories. The ontology
>> submission page is now back to operational. Let us know if you are still
>> experiencing issues.
>>
>> Thank you!
>>
>> Michael
>>
>> > On Jul 16, 2020, at 11:45 AM, Kuttichi Keloth, Vipina <vk396 at njit.edu>
>> wrote:
>> >
>> > Hi,
>> >
>> > I guess you are notified about the issue. The submit ontology page
>> returns an error.
>> >
>> > Could you please look into this?
>> >
>> > Thank you.
>> > Vipina
>> > _______________________________________________
>> > bioontology-support mailing list
>> > bioontology-support at lists.stanford.edu
>> > https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>> _______________________________________________
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> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>
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