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[bioontology-support] Error rdf

Berrios, Daniel C. (ARC-SCR)[UNIVERSITIES SPACE RESEARCH ASSN] daniel.c.berrios at nasa.gov
Fri Sep 18 16:29:47 PDT 2020


OK yeah I see those in Protégé.  I wonder how they got there? These classes were imported using OBO Robot.  Maybe a bug in Robot.

Thanks


Dan Berrios, MD PhD MPH
USRA/NASA Ames Research Center
650 604 0470 (office)
415 902 5099 (cell)

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Sent: Friday, September 18, 2020 4:21 PM
To: Berrios, Daniel C. (ARC-SCR)[UNIVERSITIES SPACE RESEARCH ASSN] <daniel.c.berrios at nasa.gov>
Cc: support at bioontology.org
Subject: [EXTERNAL] Re: [bioontology-support] Error rdf

Hello Dan,

I looked at the processing log files on our production server. BioPortal can’t load RBO.owl because the ontology source file has 26 occurrences of invalid values in xml:lang attributes. One such example can be found on line 53,078 (DNA microarray class):

 <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0400148<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.obolibrary.org_obo_OBI-5F0400148&d=DwMGaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=lMBbvRfSFsl1rSjmXwHXNwmVt5WcW6khsHyfPBrH_Xk&m=c-zbBJdELzTo4mwUCS2w7cMV0VinATv2nFVA654dZYQ&s=6LWKQKoPJnDn9PGLQ5DxEXzUbd2wXO4Vh9FcXG5RIQ8&e=>">
    …
    <obo:IAO_0000119 xml:lang="2008/03/03">Web:<http://en.wikipedia.org/wiki/DNA_microarray&gt<https://urldefense.proofpoint.com/v2/url?u=http-3A__en.wikipedia.org_wiki_DNA-5Fmicroarray-26gt&d=DwMGaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=lMBbvRfSFsl1rSjmXwHXNwmVt5WcW6khsHyfPBrH_Xk&m=c-zbBJdELzTo4mwUCS2w7cMV0VinATv2nFVA654dZYQ&s=bMXOm6el-Lg3NWSwn4XpUBosAWsSLOxgvaNlR6Nnvks&e=>;</obo:IAO_0000119>
    <rdfs:label xml:lang="en">DNA microarray</rdfs:label>
</owl:Class>

All of these occurrences need to be corrected to use a valid value, e.g., xml:lang=“en”. After making these changes, I believe the system will be able to consume the ontology without issues.

Kind regards,
Jennifer



On Sep 18, 2020, at 3:54 PM, Berrios, Daniel C. (ARC-SCR)[UNIVERSITIES SPACE RESEARCH ASSN] <daniel.c.berrios at nasa.gov<mailto:daniel.c.berrios at nasa.gov>> wrote:

I tried updating our ontology with a new version downloaded directly from WebProtege, but it’s given “rdf error” message in BioPortal twice now…. Can you give more detail?

http://bioportal.bioontology.org/ontologies/RBO<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioportal.bioontology.org_ontologies_RBO&d=DwMGaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=lMBbvRfSFsl1rSjmXwHXNwmVt5WcW6khsHyfPBrH_Xk&m=c-zbBJdELzTo4mwUCS2w7cMV0VinATv2nFVA654dZYQ&s=FkM-FUH2Z2mGrohUZ6KBtH_14u1SxVD2JlxErzC1NB8&e=>

Thanks


Dan Berrios, MD PhD MPH
USRA/NASA Ames Research Center
650 604 0470 (office)
415 902 5099 (cell)

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