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[bioontology-support] [BioPortal] Feedback from satyasahoo

Satya Sahoo satya_sanket at hotmail.com
Mon Oct 18 06:39:53 PDT 2021


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>
Sent: Sunday, October 17, 2021 5:04 PM
To: support at bioontology.org <support at bioontology.org>
Cc: satyasahoo at ieee.org <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



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