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[bioontology-support] [BioPortal] Feedback from satyasahoo

John Graybeal jgraybeal at stanford.edu
Thu Oct 21 15:02:02 PDT 2021


Hello Satya,

BioPortal creates the class names by default based on skos:prefLabel. If it can not find skos:prefLabel, it will use rdfs:label if it is present (*not* 'rdfs:Label', I expect that will not work). If that is not present, it uses the short local identifier component at the end of the IRI as the label.

The only adjustment you can make to that is to specify the preferred label identifier as whatever IRI you want. So if you defined a property in your ontology called http://mydomain.example/prefixIRI, and declared for each term
 <myOnt:thisTerm> http://mydomain.example/prefixIRI "My label string" .
then that would work.

But I think that I may be misunderstanding your use of "prefixIRI"  in this context. You may be referring to what I would call the 'fragment' or 'IRI fragment', the final part of the IRI that is the unique phrase occurring after the final separator (typically the '#' or '/') at the end of the II prefix. This expression 'fragment' is common in IRI and URL parsing and web references, so I'll use it here.

As you can see in my description above, if nothing else is available as the preferred label, BioPortal will use the IRI fragment as the label. This only works if BioPortal does not see any rdfs:label at all (so, no skos:prefLabel and no skos:altLabe can be present, because they are both rdfs:labels). There is no way to specify the fragment be used as the label.

Based on my understanding of the SKOS W3C standard, I do not recommend using rdfs:label for synonyms/alternate names of the classes. SKOS has design a pattern expressly for this purpose: skos:prefLabel for the preferred name (if any), and skos:altLabel for any other names including synonyms. I believe that most semantic tools will adopt this usage as they present preferred and alternate names for ontology terms, and this pattern works nicely with internationalization as well as using language tags. Reference https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#seclabel for a clear and detailed definition.

John

On Oct 18, 2021, at 6:39 AM, Satya Sahoo <satya_sanket at hotmail.com<mailto:satya_sanket at hotmail.com>> wrote:

Good Morning, John:
Thank you for resolving this issue! We will work on revising the customized local property to use IRI instead of just text. The visualization of the classes in BioPortal works now.

If possible, can you please clarify if BioPortal can use the entity prefixIRI instead of the rdfs:Label to generate the class names (similar to Protege rendering option using Entity )?

We have consistently used the prefixIRI to assign class names in EpSO and rdfs:Label to model synonyms/alternate names of the classes.

I appreciate your time and help!

Sincerely,
Satya


________________________________
From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Sunday, October 17, 2021 5:04 PM
To: support at bioontology.org<mailto:support at bioontology.org> <support at bioontology.org<mailto:support at bioontology.org>>
Cc: satyasahoo at ieee.org<mailto:satyasahoo at ieee.org> <satyasahoo at ieee.org<mailto:satyasahoo at ieee.org>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from satyasahoo

Hello Dr. Sahoo,

Thank you for your patience with this problem.  We have fixed the ontology and it is now correctly visible in BioPortal.

Details about the problem can be found in the ticket https://github.com/ncbo/bioportal-project/issues/216. In brief, the customized default property setting fields are meant to be specialized settings that are IRIs (unique identifiers), but they had been filled with regular text strings. (Examples of the unique identifiers can be found in the help text below each field.)

These invalid settings were causing the final parsing stage (using rapper) to fail. When we removed them we were able to parse the ontology successfully.

John

On Oct 14, 2021, at 12:45 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: satyasahoo
Email: satyasahoo at ieee.org<mailto:satyasahoo at ieee.org>
Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FEPSO

Feedback:
Good Afternoon,
We continue to experience parsing errors with the Epilepsy and Seizure Ontology (EpSO) OWL file.
The previous submission also experienced similar BioPortal parsing error documented as Issue#216: https://github.com/ncbo/bioportal-project/issues/216.
The BioPortal issue tracker noted that the EpSO OWL file was correctly parsed in the BioPortal staging environment (https://stage.bioontology.org/ontologies/EPSO?p=classes).
The latest release of EpSO (version 2.1) OWL is experiencing same error "Error Rdf Labels").
We request your help in addressing this error at the earliest as we have received community feedback regarding their inability to visually browse EpSO in the BioPortal "Classes" and "Properties" tabs.
Thank you for your time and consideration!
Sincerely,
Satya Sahoo, PhD FAMIA
CWRU School of Medicine
https://bmhinformatics.case.edu/

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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



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