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[bioontology-support] Problem with HRDO multilingual label

Ferdinand C Dhombres ferdinand.dhombres at nih.gov
Mon Mar 7 11:17:11 PST 2016


Hi Clement, 

Nice to hear from you on HRDO. I have had many issues with lang tags in bioportal. 
I do not understand the behavior of the browser (which label is chosen). 
I was suggested to create views, for each langage. I must admit I didn’t went into this.

For example, in the ontology file you have this :

    <owl:Class rdf:about="&hrdo;typ_id_6">
        <rdfs:label xml:lang="en">group of diseases</rdfs:label>
        <rdfs:subClassOf rdf:resource="&hrdo;typ_id_0"/>
        <skos:prefLabel xml:lang="en">group of diseases</skos:prefLabel>
        <skos:prefLabel xml:lang="fr">groupe de maladies</skos:prefLabel>
    </owl:Class>

And in the browser you have this (the label in the tree is french, don’t know why) :



However in HRDO v2, rdfs:labels are english and I used skos:prefLabel / altLabel to support the 6 langages of the ontology. 
Please let me know if I can be of any help to you or to the bioportal team.

Best regards, 

Ferdinand.




 
 
Dr Ferdinand C Dhombres, MD, PhD
 
NIH, NLM (National Library of Medicine)
Lister Hill National Center for Biomedical Communications
BG 38A RM 9N912B MSC 3826
8600 ROCKVILLE PIKE
BETHESDA MD 20894-3826
 
phone 	+1 (301) 435-3225
mobile 	+1 (301) 549-8103
mail 	ferdinand.dhombres at nih.gov
skype 	fdhombres

> On Feb 26, 2016, at 7:50 PM, Michael Dorf <mdorf at stanford.edu> wrote:
> 
> 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 <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 <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 <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 <http://www.lirmm.fr/~jonquet>
>>  
>>                 University of Montpellier                          Tel:                   +33/4 67 14 97 43
>>                 LIRMM                                                            Fax:                     +33/4 67  41 85 00           
>>                 161 rue Ada                                                   Skype:                 clementpro
>>                 34095 Montpellier Cdx 5                            Twitter:             @jonquet_lirmm <http://twitter.com/jonquet_lirmm>
>>                 France                                                            Google:                jonquet.lirmm at gmail.com <mailto:jonquet.lirmm at gmail.com>
>> ----------------------------------------------------------------------------------------------------------------------
>> <image001.png> 
>>  
>>  
>>  
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