EBISPOT / OLS

Ontology Lookup Service from SPOT at EBI
http://www.ebi.ac.uk/ols
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search does not find rdfs:label values with language tags other than "en" #647

Open KonradHoeffner opened 1 year ago

KonradHoeffner commented 1 year ago

Our users need to find our classes with different language labels, however we can find the class below only by searching for "Upper arm", while "Brachium" and "Oberarm" return no results. How can we support this with OLS?

<owl:Class rdf:about="https://ols.imise.uni-leipzig.de/ontologies/anno#Upper_arm">
<rdfs:subClassOf rdf:resource="https://ols.imise.uni-leipzig.de/ontologies/anno#Upper_Limb"/>
<rdfs:label xml:lang="la">Brachium</rdfs:label>
<rdfs:label xml:lang="de">Oberarm</rdfs:label>
<rdfs:label xml:lang="en">Upper arm</rdfs:label>
</owl:Class>
serjoshua commented 1 year ago

Hi Konrad,

We are looking into this.

serjoshua commented 1 year ago

Hello Konrad,

Do you happen to know a specific ontology in OLS where we can test this scenario on? I am testing a term in OBI for example and the search seems to work even with ZH (Chinese) characters.

KonradHoeffner commented 1 year ago

The strange thing is that most ontologies in OLS do not seem to use language tags. I tried APO, ARO, AEO, AMPHX, ADO and AFO from the first page and got 0 hits for "lang" inside the downloaded ontology files. However I consider language tags to be very useful and important and I don't understand why they are not used there. Especially in the medical and biological domains where latin is used heavily.

I finally found some language tags inside CIDO, however they are all English.

Then I tried the Vertebrate Taxonomy Ontology and found labels in many different languages but without any language tags:

   <owl:Class rdf:about="http://purl.obolibrary.org/obo/VTO_0001564">
       <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VTO_0001562"/>
       <vto:has_rank rdf:resource="http://purl.obolibrary.org/obo/TAXRANK_0000006"/>
       <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ATO:0007160</oboInOwl:hasDbXref>
       <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://amphibiaweb.org/species/4074</oboInOwl:hasDbXref>
       <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">vto-namespace</oboInOwl:hasOBONamespace>
       <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Atylodes genei</oboInOwl:hasRelatedSynonym>
       <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Barna barlangi-sz</oboInOwl:hasRelatedSynonym>
       <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Euroopa koopaojalik</oboInOwl:hasRelatedSynonym>
       <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Geotritone di Gen�</oboInOwl:hasRelatedSynonym>
       <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Geotritone iglesiente</oboInOwl:hasRelatedSynonym>
       <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hydromantes genei (Temminck &amp; Schlegel, 1838)</oboInOwl:hasRelatedSynonym>
       <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Salamandra cavernicola de Cerde�a</oboInOwl:hasRelatedSynonym>
       <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Salamandra genei</oboInOwl:hasRelatedSynonym>
       <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sardinian Cave Salamander</oboInOwl:hasRelatedSynonym>
       <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sardischer Schleuderzungensalamander</oboInOwl:hasRelatedSynonym>
       <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Speleomantes genei</oboInOwl:hasRelatedSynonym>
       <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sp�l�rpes de Gen�</oboInOwl:hasRelatedSynonym>
       <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">VTO:0001564</oboInOwl:id>
       <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hydromantes genei</rdfs:label>
   </owl:Class>

Ultimately, I haven't found any ontology in the main OLS that uses non-English language tags.

KonradHoeffner commented 1 year ago

However you can try it at our own OLS instance with the SNIK ontology, which does contain labels in multiple languages, for example (here in RDF Turtle form):

:EntityType
    a owl:Class ;
    rdfs:comment "An entity type is any kind of information that is consumed, produced or modified by a task. These can be documents, data structures, objects, roles, specified by data types or even paper based artifacts."@en ;
    rdfs:label "Objekttyp"@de, "entity type"@en ;
    rdfs:subClassOf :Top ;
    owl:disjointWith :Function, :Role .

Now when you search https://ols.imise.uni-leipzig.de/ontologies/snik (currently included, may drop out of our OLS in the future, just given to replicate the error), you can find meta:EntityType with its English label "entity type" but not with its German label "Objekttyp".

You can find the full ontology at https://github.com/snikproject/ontology/blob/master/meta.ttl (the SNIK download in our OLS doesn't work currently).

henrietteharmse commented 1 year ago

@KonradHoeffner Myself and Josh have looked into this. Honestly I would expect this to work in the current OLS, but Josh has loaded your SNIK ontology locally and the multi-lang labels are clearly not in the Solr index. Unfortunately we cannot spent more time on this currently as we need to focus on getting OLS4 out. We will ensure that this is addressed in OLS4.

KonradHoeffner commented 1 year ago

@henrietteharmse thank you for looking into this and for testing it with the SNIK ontology! I will use a script to remove the language tags as a workaround and then switch to OLS4.