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EBISPOT / OLS

Ontology Lookup Service from SPOT at EBI
http://www.ebi.ac.uk/ols
Apache License 2.0
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Short Form remove the first numerical value of the IRI fragment #541

Open Ayllonbe opened 2 years ago

Ayllonbe commented 2 years ago

I do not know if I can modify from my side but I was looking for the documentation and I did not see anything. I have a local OLS (for testing) and I introduce my ontology correctly. However, my ontology has identifier like TOTO:1TOEP. The issue that I have with OLS is to how force him to keep the full fragment value in the short form. That means that I expect to have 1TOEP in the short form instead of TOEP.

Thank you

serjoshua commented 2 years ago

hi @Ayllonbe may I know what parts of OLS you experience this? or maybe a screenshot of the issue on your end.

henrietteharmse commented 2 years ago

Can you please provide a minimal complete example ontology that illustrates the problem you are experiencing?

Ayllonbe commented 2 years ago

Yes, sorry to answer that late. The main issue is found in the _shortterm tag. This tag is generated based on the IRI. I did explore a bit the code and I do not know if the issue is from your side or rather from OWL API. If it is the later, it is not a real issue from them since they are following the XML convention QName.

In my case I have an IRI as follows: https://ontology.toto.net/ontology/MyOntology/1TOEP, but then the short_form only representd TOEP instead 1TOEP. That behaviour is shown in all the API calls results but also in the browser, if I tap 1TOEP I have not autocompletation results but removing the 1 I have the TOEP.

henrietteharmse commented 2 years ago

@Ayllonbe Can you please provide a minimal complete example ontology that illustrates the problem you are experiencing?

Ayllonbe commented 2 years ago

You can find attached the ontology (an example one). When I load it into my OLS (Local one and unfourtunately I cannot provide screenshot since my computer is working very weird and give me black screenshot), then the tag short_form in the JSON file is TEST instead of 2TEST

<?xml version="1.0"?>
<rdf:RDF xmlns="http://www.semanticweb.org/ayllona/ontologies/2022/0/untitled-ontology-21#"
     xml:base="http://www.semanticweb.org/ayllona/ontologies/2022/0/untitled-ontology-21"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
    <owl:Ontology rdf:about="http://www.semanticweb.org/ayllona/ontologies/2022/0/untitled-ontology-21"/>

    <!-- 
    ///////////////////////////////////////////////////////////////////////////////////////
    //
    // Classes
    //
    ///////////////////////////////////////////////////////////////////////////////////////
     -->

    <!-- https://ontology.basf.net/ontology/2022/BASF_TEST/test#3TEST -->

    <owl:Class rdf:about="https://ontology.basf.net/ontology/2022/BASF_TEST/test#3TEST"/>

    <!-- https://ontology.basf.net/ontology/BASF_TEST/2TEST2 -->

    <owl:Class rdf:about="https://ontology.basf.net/ontology/BASF_TEST/2TEST2"/>
</rdf:RDF>

<!-- Generated by the OWL API (version 4.2.8.20170104-2310) https://github.com/owlcs/owlapi -->