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[bioontology-support] Problem with HRDO multilingual label

Ferdinand C Dhombres ferdinand.dhombres at nih.gov
Tue May 3 17:12:33 PDT 2016


Hi Michael, 

Thank you much for having this fixed, it feels much better to browse HRDO with the proper labels !
I am sure Clement will test the API soon.

Ferdinand, 



> On May 3, 2016, at 7:59 PM, Michael Dorf <mdorf at stanford.edu> wrote:
> 
> Hi Clement and Ferdinand,
> 
> Just wanted to let you know that this problem has been fixed. Both the UI and the API services will now use an "EN" prefLabel rather than a random one, if multiple choices are present.
> 
> http://bioportal.bioontology.org/ontologies/HRDO/?p=classes <http://bioportal.bioontology.org/ontologies/HRDO/?p=classes>
> 
> Thanks!
> 
> Michael
> 
> 
>> On Mar 7, 2016, at 18:18, Clement Jonquet <jonquet at lirmm.fr <mailto:jonquet at lirmm.fr>> wrote:
>> 
>> Hi Ferdinand, 
>>  
>> NCBO has reported and tracked the bug ;)
>> We will let you know how it goes. 
>> This is an issue we have also in our local instances in Montpellier… so I am interested.
>>  
>> Clement
>>  
>> De : Ferdinand C Dhombres [mailto:ferdinand.dhombres at nih.gov <mailto:ferdinand.dhombres at nih.gov>] 
>> Envoyé : lundi 7 mars 2016 11:17
>> À : Clement Jonquet <jonquet at lirmm.fr <mailto:jonquet at lirmm.fr>>
>> Cc : support at bioontology.org <mailto:support at bioontology.org>; Michael Dorf <mdorf at stanford.edu <mailto:mdorf at stanford.edu>>
>> Objet : Re: [bioontology-support] Problem with HRDO multilingual label
>>  
>> 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) :
>> <image001.png>
>>  
>>  
>> 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 <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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>>>  
>> 
>>  
> 

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