Re: [bioontology-support] questions over a few issues in uploading an ontology

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Re: [bioontology-support] questions over a few issues in uploading an ontology

jvendetti
Hello Peter,


I have made an upload to BioPortal (after discussion with John Graybeal) - this is the (private) ontology I have loaded (under the user ID: i2s) (I have attached a screen grab so it is clearer what account I am referring to):
https://bioportal.bioontology.org/ontologies/I2SV

I had a few upload issues and was wondering if you might be able to answer some questions for me thanks.

(1) My first upload to BioPortal attracted an error: "Uploaded, Error Rdf" and nothing much seemed to happen - I ran the file through the check webpage and it passed, which I wasn't sure what to make of (https://bioportal.bioontology.org/validate_ontology_file)


I’m familiar with the existence of the check webpage that you refer to, but it’s not something we’ve actively maintained. If you’re working with RDF, I would suggest 3rd party validators instead, e.g., the W3C’s RDF Validator.



- so, I went and rechecked and redid the Excel file, targeting a few things I thought might have been causing issues, then redid the SKOS convert (TURTLE file attached) and uploaded it again to BioPortal again - this time that seemed to produce a class output that I was expecting to see but this second upload also seemed to attract some kind of error - "Parsed, Indexed, Metrics, Annotator, Error Diff", but the classes propagated.

My question is does the "Error Diff" need responding too and if so, how do I respond to it?


There's no action needed here. The BioPortal application attempted to generate a diff to the previous submission, but the diff failed because the previous submission never processed successfully. BioPortal’s code should admittedly be improved here - the application shouldn’t attempt to generate a diff if it can’t find any previous valid submissions.



(2) Although this may impact on version control, is it possible to delete a file from the submissions list (I am thinking of the first file i uploaded with the "Uploaded, Error Rdf" notice)?


Yes this is possible, though you need to contact us to request the deletion. If this is what you’d like us to do, just confirm and I can take care of it.



(3) Somehow or the other, there are now two 'definitions' on the main page for the I2SV ontology (when there should be one) and I am unsure why this is happening - would you know how I can fix that?


Apologies - I didn’t follow what you mean here about duplicate definitions. Are you referring to this Summary page: https://bioportal.bioontology.org/ontologies/I2SV? I couldn’t find any duplicate text here, but I could be missing something.



(4) ASCII is coming through in the SKOS convert; for example:


This is an Excel to SKOS conversion that you’re doing? Just curious.


*  'Arnstein’s ladder' (which should be Arnstein's ladder) - can I get rid of this by editing the TURTLE file by replacing with the equivalent symbol (eg., ’ is ')?


BioPortal is reading the label value directly from the skos:prefLabel for that concept in the ontology source file. I downloaded the source file for the latest submission and see the label you’re referring to on line 105:

skos:prefLabel "Arnstein’s ladder"@en .

I believe if you edit the TTL file and re-upload to BioPortal, the application will honor/display whatever label value you place here.


* In order to reduce ASCII turning up, I had swapped a space for a dash in the top-concept (between the word 'implementation' and 'sciences', and I could not work out why this was happening - 'Integration and implementation-sciences') - would you know how I can stop that dash appearing?


The dash displays in BioPortal because it exists in the skos:prefLabel for that concept on line 906:

skos:prefLabel "Integration and implementation-sciences"@en;

You should be able to modify the prefLabel value to remove the dash, then re-upload to BioPortal.

Kind regards,
Jennifer


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