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[bioontology-support] BioPortal not allowing uploads

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Jul 16 20:57:01 PDT 2020


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<http://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<mailto: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<mailto: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<mailto: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
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