Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Problem with HRDO multilingual label

Michael Dorf mdorf at stanford.edu
Tue May 3 16:59:23 PDT 2016


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

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]
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

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
                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>





_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20160503/43b92488/attachment-0001.html>


More information about the bioontology-support mailing list