opening RiC in Protégé Web

[sethvanhooland]

Dear colleagues,

I want to visualize the recent version of RiC-O in https://webprotege.stanford.edu/ in the class I'm teaching tomorrow evening, as it's a great tool to walk through the ontology. However, I noticed that the classes from RiC-O-version 0.2 do not appear in the software.

It's a minor thing, as 0.2 does work under a local Protégé install (thanks @wildit for the quick feedback) but if it's an easy fix I think it would be beneficial for many educators who prefer the ease of working with a web-based version of Protégé.

Kind regards, Seth

[florenceclavaud]

I have the same problem (did not notice that before, since I do not use WebProtégé). However, RiC-O 0.2 as an OWL 2 file is correct as far as I know - I had checked and checked it again, and I also use it every day in rdf bases. So we have to investigate further. It may be the file, or WebProtégé. It may take some time to understand this. Anyway thanks to let us know! Let me just note an hypothesis, though it has to be checked : the metadata of RiC-O themselves extensively use HTML (which is correct). Maybe WebProtégé does not like this. My two first cents.

[dpitti]

Were you able to figure why RiC-O was failing to open in WebProtégé. I have never used it, myself.

Thanks, Daniel

On Nov 8, 2021, at 1:00 PM, Florence Clavaud @.***> wrote:

I have the same problem (did not notice that before, since I do not use WebProtégé). However, RiC-O 0.2 as an OWL 2 file is correct as far as I know - I had checked and checked it again, and I also use it every day in rdf bases. So we have to investigate further. It may be the file, or WebProtégé. It may take some time to understand this. Anyway thanks to let us know! Let me just note an hypothesis, though it has to be checked : the metadata of RiC-O themselves extensively use HTML (which is correct). Maybe WebProtégé does not like this. My two first cents.

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[CatarinaAugusta]

Dear Florence and Daniel, We used WebProtegé to start trying out the model in a pilot project. Although we realized that the application didn't import the RIC-O ontology we kind of did it in the wrong way (describing the relations directly in the application). For now all that is left is a file in RDF/XML, because the project doesn't load anymore. When I finish describing the correspondence collection I'm working on (of the portuguese scientist Barros Machado), I'd like to model this data according to the RIC. What program or application do you recommend? I heard that Atom will include the RIC-O ontology, maybe I should wait for the new version release. Best regards, Catarina

[florenceclavaud]

Dear @CatarinaAugusta; sorry, I have left this issue unsolved. Next week, I will do some tests about this, first following my first idea (see my first comment). Maybe you could switch to Protégé Desktop, with which you will have no problem loading, editing or extending RiC-O (I use it every day). Atom is a tool for editing archival metadata, not a tool for developing an ontology. I am not sure the roadmap of Atom actually includes implementing RiC-O. My advice would be to use any tool you have to produce structured data, where the entities described can be assigned a unique identifier (relational database, XML editor...), check the quality/consistency of your data, map the logical model of your data to RiC-O and develop/use a conversion tool to convert the data to RDF (RDF is not a format that you can easily edit as a human, since it is quite 'technical', and you will soon get a lot of triples). Then you can import the RDF data into a graph database (using for example the free GraphDB software) and play (particularly query/update the data using SPARQL). Maybe @wildit can suggest other methods.

[florenceclavaud]

Dear colleagues,

I want to visualize the recent version of RiC-O in https://webprotege.stanford.edu/ in the class I'm teaching tomorrow evening, as it's a great tool to walk through the ontology. However, I noticed that the classes from RiC-O-version 0.2 do not appear in the software.

It's a minor thing, as 0.2 does work under a local Protégé install (thanks @wildit for the quick feedback) but if it's an easy fix I think it would be beneficial for many educators who prefer the ease of working with a web-based version of Protégé.

Kind regards, Seth

Hi @sethvanhooland, at last I had some time for investigating this issue. I have tested the https://webprotege.stanford.edu/ application, and you are right, it is not possible to upload RiC-O 0.2 as the starting point of a new project, because the file includes, as concerns the description of the ontology itself, 3 Dublin Core properties that have XML (XHTML) content, like this one:

<dcterms:abstract rdf:parseType="Literal">
            <html:div xml:lang="en">
                <html:p>RiC-O (Records in Contexts-Ontology) is an OWL ontology [...]. </html:p>
                <html:p>The current official version is <html:strong>v0.2</html:strong>[...].</html:p>
                <html:p>[blah blah]</html:p>
            </html:div>
   </dcterms:abstract>

This is correct; but the https://webprotege.stanford.edu/ instance of WebProtégé does not accept it. I have not installed WebProtégé locally, maybe a more complete configuration would accept this. I have removed the 3 dcterms properties concerned and then I could upload the RiC-O file. I also could upload the file after having declared the HTML namespace locally (i.e. on the html:div above, adding a xmlns:html="http://www.w3.org/1999/xhtml") instead of on the root rdf:RDF element), and it worked too. However, I still get pop-ups with error messages ("not supported") when I browse the hierarchies of classes and properties, without getting any information about what went wrong exactly. I suspect that some OWL features of RiC-O (e.g. owl:propertyChainAxiom or even owl:inverseOf) cause these problems. It seems that instance of WebProtégé does not allow everything. A locally installed instance could probably be configured so that the problems above disappear (see also https://protegewiki.stanford.edu/wiki/WebProtegeUsersGuide#Viewing_and_Editing_OWL_2_Ontologies on this topic.) Protégé Desktop allows all this without doing anything special BTW ;-) Hope this helps!

[florenceclavaud]

Closed as an answer was given with no new comment or reaction.