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[bioontology-support] Problem with HRDO multilingual label

Clement Jonquet jonquet at lirmm.fr
Thu Feb 25 17:13:32 PST 2016


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
<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> &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
<http://data.bioontology.org/ontologies/HRDO/classes/http%3A%2F%2Fwww.limics
.org%2Fhrdo%2Frdfns%23typ_id_17?include=all&display_context=false&display_li
nks=false> &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  <http://www.lirmm.fr/sifr/> SIFR and
<http://agroportal.lirmm.fr/> AgroPortal projects

Visiting faculty, Stanford University

 

 <mailto:jonquet at lirmm.fr> 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:
<http://twitter.com/jonquet_lirmm> @jonquet_lirmm

                France
Google:                 <mailto:jonquet.lirmm at gmail.com>
jonquet.lirmm at gmail.com

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