#1 viewing the MathML labels and the class names


Many of the term names also include very long bits of mathML make visualizing the ontology (Jambalaya, OntoViz in Protege) very very difficult, as it seems to be luck which rdfs:label is used in Protege (3.4 beta). You can only choose one over the other if you set the default language to "en" for one of them. If there is some way to have a mathML annotation property (possible in OWL, but not sure about OBO) it would make visualizing the ontology much more straightforward and easier for your users. I think this is because it is chance which of the two rdfs:labels Protege chooses to display. I have emailed them asking if they know a way to force the string rather than the XML to be displayed, but haven't had a response yet. However, I'm not sure why you have two rdfs:labels. Maybe it's due to the conversion to OWL? If they are meant to be synonyms, then perhaps you should choose one, like the string, as the rdfs:label, and the mathML as a synonym.


  • Nicolas Le Novère

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    A first step would be to separate the "name" and the "definition", keeping the OWL "label" for the OBO "name". Several OBO ontologies expressed in OWL just use an element "definition" to store this definition. Such an element could maybe contain text and other XML constructs (such as MathML)?

  • Allyson Lister

    Allyson Lister - 2008-05-14

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    That sounds like a good idea. By the way, I have had a response from Tania Tudorache in the Protege-owl mailing list, which might help you:

    So, let's say that the
    class Pizza has two rdfs:label (no language): one label "Pizza 1" and
    one label "Pizza 2". If you set the display slot for owl:Class to be
    rdfs:label as described here [1], then the class Pizza will be displayed
    as {Pizza1, Pizza2}.

    So, if you have multiple values for the rdfs:label, then all of them
    will be displayed in curly brackets.

    However, if you have a language defined for one of the labels (lets say,
    rdf:label="Pizza 1" for language "en"), and you set the default language
    in the metadata tab to be "en", then you will see only "Pizza 1".

    So, if in your ontology, the string rdf:label has a language associated
    to it, then all you have to do is to set the default language.

    There is another thing: the display settings are stored in the pprj file
    (not in the owl file) so if you want to preserve the display settings
    over different protege sessions, you need to open the pprj file, not the
    owl file.