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[bioontology-support] Minimal TTL file for SKOS

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Apr 4 17:02:26 PDT 2019


Hi Dan,


On Apr 4, 2019, at 8:05 AM, Davis, Daniel (NIH/NLM) [C] <daniel.davis at nih.gov<mailto:daniel.davis at nih.gov>> wrote:

The attached file, simple-ontology.ttl, is an effort to understand how to use BioPortal effectively.  It raises certain questions about how to upload SKOS.   It is accompanied by a simple-ontology.nt, which proves that it is well-formed as it can  be converted from TTL and NT and back and forth.

This gives rise to certain questions:

  *   Is TTL supported, or must the file be in RDF/XML or some similar format.


End users most commonly submit ontologies to us in OWL or OBO, with a lesser number of SKOS submissions (roughly 27 out of the 930 ontologies in our repository).

For OWL ontologies, RDF/XML or any of the other syntaxes work, e.g., OWL/XML, Manchester OWL Syntax, etc.

That said, we use the OWL API [1] during the first step of the parsing process, which will read TTL files. I uploaded your ontology in our staging environment to see how they system would react. It passed the initial portion of the parsing process with the OWL API, but failed the second step of the process where we load the triples into our backend triplestore. I investigated the error message and found that you need to have dots at the end of your prefix declarations in order for the parsing process to succeed. For example, instead of this:

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

… you need this:

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .

After adding dots at the end of of all seven of your prefix declarations and re-submitting, the parsing step succeeded. I’ve included a screen shot below of how the class tree appears in our staging environment.



  *   Must the prefix used in the TTL file for subjects match that claimed in the Submit New Ontology wizard?


Apologies - I don’t follow what you’re asking here.



  *   Does BioPortal have support for both “skos:hasTopConcept” and “skos:topConceptOf”.


No, just hasTopConcept at the moment. If you haven’t already seen it, we have a wiki page that describes what we’re currently able to handle:

https://www.bioontology.org/wiki/SKOSSupport

Kind regards,
Jennifer

[1] http://owlcs.github.io/owlapi/


[cid:37921F92-08AB-43EA-8DF5-5B28DA6357D8 at stanford.edu]


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