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[bioontology-support] OGMS loading issue

Aevermann, Brian baeverma at jcvi.org
Wed Aug 12 12:39:30 PDT 2020


Thanks for all your help! I will fix the issues in the OWL file at github so that it parses correctly in the future.

Thanks again!

b


—
Brian Aevermann
Bioinformatics Analyst
J. Craig Venter Institute
4120 Capricorn Lane
La Jolla, CA 92037
858-200-1873

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: Tuesday, August 11, 2020 at 5:22 PM
To: "Aevermann, Brian" <baeverma at jcvi.org>
Cc: "support at bioontology.org" <support at bioontology.org>
Subject: Re: [bioontology-support] OGMS loading issue

Hi Brian,



On Aug 11, 2020, at 10:45 AM, Aevermann, Brian <baeverma at jcvi.org<mailto:baeverma at jcvi.org>> wrote:

I have recently updated the OGMS ontology via github and the file for the new release has been uploaded to bioportal; however, there are issues. I pushed my release about a week ago but the new version is not displaying in bioportal. Next to the file it says rdf errors, and I would like to know how to fix this situation.


I found the following issues with the latest submission of ogms.owl:

1). On lines 33 and 39, there’s an invalid value in the xml:lang attribute:

<rdfs:comment xml:lang="jcvi.org<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fjcvi.org%2F&data=02%7C01%7Cbaeverma%40jcvi.org%7C93a1f98ac1f548608ae308d83e55b87b%7C24d967f13ed84448baa6560ec572acb3%7C0%7C0%7C637327885194731146&sdata=3U4loHJHhX2WTcKH%2FT%2Fgdkjicp7sy6KpiUa%2BPIVp%2BAE%3D&reserved=0>. be sure to include a google-account username with your request (this will be the username associated with a gmail address). we use google apps for sharing and development purposes.”>

Valid values for xml:lang are two letter language abbreviations, e.g.:

xml:lang=“en”

2). The parsing log contained a number of "URI error - illegal Unicode escape \u0020 in URI” errors. The underlying cause of this error is an invalid XML namespace declaration on line 11:

xmlns:rdf1="http://www.w3.org/2002/07/owl#versionIRI<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.w3.org%2F2002%2F07%2Fowl%23versionIRI&data=02%7C01%7Cbaeverma%40jcvi.org%7C93a1f98ac1f548608ae308d83e55b87b%7C24d967f13ed84448baa6560ec572acb3%7C0%7C0%7C637327885194731146&sdata=VjdKLFfSM%2BI%2FD%2FzV%2B%2FEjYDT5PxdM%2F6V2sGDycb3vY5U%3D&reserved=0> rdf:"

… i.e., there should be no spaces in the URI portion of the declaration.

I modified the source file pulled from GitHub to set the above mentioned xml:lang tags to “en”. I also deleted the invalid XML namespace declaration on line 11, and replaced line 50:

<rdf1:resource>http://purl.obolibrary.org/obo/ogms/2020-07-06/ogms.owl</rdf1:resource><https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fogms%2F2020-07-06%2Fogms.owl%253C%2Frdf1%3Aresource%253E&data=02%7C01%7Cbaeverma%40jcvi.org%7C93a1f98ac1f548608ae308d83e55b87b%7C24d967f13ed84448baa6560ec572acb3%7C0%7C0%7C637327885194741104&sdata=JZY27360bMoyC4HBxIJazghHLE%2BaYR%2F9qdnzcVyQP%2BE%3D&reserved=0>

… with this:

<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ogms/2020-07-06/ogms.owl<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fogms%2F2020-07-06%2Fogms.owl&data=02%7C01%7Cbaeverma%40jcvi.org%7C93a1f98ac1f548608ae308d83e55b87b%7C24d967f13ed84448baa6560ec572acb3%7C0%7C0%7C637327885194741104&sdata=wurQZeBzDMbRZG7v%2FomDaXDWSdygvweU31z4zTDOPJw%3D&reserved=0>"/>

I reprocessed the ontology after making these modifications, and BioPortal completed the parsing / loading process successfully. If you’d like future versions to load successfully, you’ll need to fix the GitHub version that BioPortal is configured to check nightly.




Also the version name is not being updated when I release. The last several releases have been labelled 2018-11-27. I don’t know where that label is coming from. Any clues would be appreciated.


It’s read from the owl:versionInfo property. The last 3 OWL files submitted contained:

<owl:versionInfo>2018-11-27</owl:versionInfo>

When I reprocessed the latest submission today, the new version information was correctly set during the parsing process.

Kind regards,
Jennifer

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