Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Jennifer Leigh Vendetti vendetti at stanford.edu
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:

format-version
data-version
date
etc.

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.

Jennifer


On Apr 26, 2016, at 1:11 AM, sherin <yangxl74 at gmail.com<mailto:yangxl74 at gmail.com>> 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 pir.georgetown.edu<http://pir.georgetown.edu>,
which is the current release.

Thank you!



--
View this message in context: http://ncbo-support.2288202.n4.nabble.com/bioontology-support-Error-Rdf-message-for-PRotein-Ontology-other-issues-tp4654077p4654739.html
Sent from the NCBO Support mailing list archive at Nabble.com<http://nabble.com>.
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20160427/fed2f7b6/attachment-0001.html>


More information about the bioontology-support mailing list