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[bioontology-support] Problem with HRDO multilingual label

Michael Dorf mdorf at stanford.edu
Fri Feb 26 16:50:04 PST 2016


Hi Clement,

I've confirmed with Manuel that this indeed is a bug. We should select a prefLabel with "en" language when the property skis:prefLabel is defined as an array. I've created a ticket to track this issue (NCBO-1662 - An incorrect prefLabel is chosen when multiple language prefLabel(s) are defined). We'll do our best to address it in a timely manner.

Thanks,

Misha


On Feb 25, 2016, at 17:13, Clement Jonquet <jonquet at lirmm.fr<mailto:jonquet at lirmm.fr>> wrote:

Dear BioPortal team,

Looking into an issue on one our AgroPortal OWL ontology that have label defined in skos in multiple language we figure out a bug that is in fact happening in the NCBO BioPortal e.g. on HRDO

Why is this concept prefLabel Spanish
http://data.bioontology.org/ontologies/HRDO/classes/http%3A%2F%2Fwww.limics.org%2Fhrdo%2Frdfns%23pat_id_10463?include=all&display_context=false&display_links=false

Where as this one is in French
http://data.bioontology.org/ontologies/HRDO/classes/http%3A%2F%2Fwww.limics.org%2Fhrdo%2Frdfns%23typ_id_17?include=all&display_context=false&display_links=false

And other will be in English.

While BioPortal is not multiligual (yet!) everyone assume that if a multilingual ontology is uploaded, only the english labels will be display in the tree (or as defaultprefLabel).

The issue seems to come from the fact that multiple skos:prefLabel are defined with different languages e.g.,

<owl:Class rdf:about="&hrdo;typ_id_17">
        <rdfs:label xml:lang="en">biological anomaly</rdfs:label>
        <rdfs:subClassOf rdf:resource="&hrdo;typ_id_4"/>
        <skos:prefLabel xml:lang="en">biological anomaly</skos:prefLabel>
        <skos:prefLabel xml:lang="fr">anomalie biologique</skos:prefLabel>
    </owl:Class>

FYI:

The ontology has for perfLabelProperty skos:prefLabel
http://data.bioontology.org/ontologies/HRDO/latest_submission?include=all

FYI2:
I think this is not happening with OWL ontologies using multiple rdfs:label
To be double checked.

FYI3:
The problem is propagated to the Annotator that match only the terms selected as prefLabel…
It means that a text with “anomalie biologique et biological anomaly” this is the French expression that generate the annotation

FYI4:
The problem is not propagated to the Search service that uses all the properties of classes
E.g., a search for “Eales disease” does return the class “
Enfermedad de Eales”

FYI5:
Protégé parse the ontology properly, without mixing the languages

Could you look into this issue or tell us where to look at to fix the problem ?

Al the best
Clement

---------------------------------------------------------------------------------------------------------------------------
Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor
Coordinator of the SIFR<http://www.lirmm.fr/sifr/> and AgroPortal<http://agroportal.lirmm.fr/> projects
Visiting faculty, Stanford University

jonquet at lirmm.fr<mailto:jonquet at lirmm.fr>
http://www.lirmm.fr/~jonquet

                University of Montpellier                          Tel:                   +33/4 67 14 97 43
                LIRMM                                                            Fax:                     +33/4 67  41 85 00
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