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[bioontology-support] "Error Rdf" message for PRotein Ontology (& other issues)

Jennifer Leigh Vendetti vendetti at
Tue Apr 26 18:25:50 PDT 2016

Hello sherin,

The last time the Protein Ontology showed an “Error Rdf” status in BioPortal, we located a syntax error on line 11 in the OBO source file.  This line:

property_value: obo-date "05:01:2016 13:20”

… causes the following parsing error to occur:

Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser at 7b50df34
    Stack trace:
spaces not allowed: '05:01:2016 13:20’

According to the OBO specification, header tags should appear in this order:


I modified the OBO file to record the date as such:

format-version: 1.2
data-version: 48.0.
date: 05:01:2016 13:20
saved-by: ceci
auto-generated-by: OBO-Edit 2.0
synonymtypedef: PRO-common-name "Label appended to organism-specific terms in place of scientific name" EXACT
synonymtypedef: PRO-short-label "Unique short label for PRO terms for display purposes" EXACT
synonymtypedef: PSI-MOD-label "Unique short label curated by PSI-MOD" EXACT
default-namespace: protein
remark: Use reasoner in OBO Edit to see the correct hierarchy.
ontology: pr
!property_value: obo-date "05:01:2016 13:20”

Notice the new location where the date is specified, and that I commented out the line that caused issues.  After making that modification, the ontology parsed in BioPortal without errors.

I don’t know if the folks that generate this OBO file have modified their process to incorporate this fix.


On Apr 26, 2016, at 1:11 AM, sherin <yangxl74 at<mailto:yangxl74 at>> wrote:

Hello Darren,

we also met "Error Rdf" when we uploaded the PRotein Ontology to the
Bioportal  installed on the local sever. I want to know  whether you have
fixed the error.

The owl file of PRotein Ontology was downloaded from<>,
which is the current release.

Thank you!

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