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[bioontology-support] Problem with HRDO multilingual label

Vincent Emonet vincent.emonet at lirmm.fr
Wed Mar 9 01:04:30 PST 2016


HI,

The problem is that for a Class the prefLabel is considered as "unique". 
So there can be only one
https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/models/class.rb#L45
Note that if you set " enforce:[:existence, :list]" it will get the list 
of all the prefLabel for this concept (if it has many of it)

So when this is time to retrieve the prefLabel it is taking the first it 
finds (without taking care of language or the fact that there could be 
multiple skos:prefLabel or rdfs:label)

But I don't know how it retrieves the property used by the submission to 
define its prefLabel (how it knows that the prefLabel property is 
rdfs:label, or skos:prefLabel or anything else)
I guess that it should be using "attribute :prefLabelProperty, enforce: 
[:uri]" of the ontology submission: 
https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/models/ontology_submission.rb#L19

Have a good day,

Vincent Emonet

On 07/03/2016 20:17, Ferdinand C Dhombres wrote:
> 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 <mailto:ferdinand.dhombres at nih.gov>
> skype fdhombres
>
>> On Feb 26, 2016, at 7:50 PM, Michael Dorf <mdorf at stanford.edu 
>> <mailto: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
>>> 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 theSIFR <http://www.lirmm.fr/sifr/>andAgroPortal 
>>> <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/%7Ejonquet>
>>> *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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>>
>
>
>
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