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Ontobee is a linked data server for ontologies. See: http://www.ontobee.org.
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Terms in MICRO are missing in Ontobee #158

Closed kbeckenrode closed 3 years ago

kbeckenrode commented 3 years ago

A branch from Ontology of Prokaryotic Phenotypic and Metabolic Characters (MICRO) is not found by Ontobee:

distinctively shaped prokaryotic cell, obo link, and all of its children cannot be found.

Let me know if I can provide any futher information

yongqunh commented 3 years ago

Hi Kelly,

It appears that MICRO is not yet in Ontobee. Is it an OBO library ontology?

Best, Oliver

From: Kelly Eckenrode notifications@github.com Sent: Friday, October 30, 2020 2:06 PM To: OntoZoo/ontobee ontobee@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [OntoZoo/ontobee] Terms in MICRO are missing in Ontobee (#158)

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A branch from Ontology of Prokaryotic Phenotypic and Metabolic Characters (MICRO) is not found by Ontobee:

distinctively shaped prokaryotic cell () and all of its children cannot be found.

Let me know if I can provide any future information

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kbeckenrode commented 3 years ago

Hi Oliver,

The MICRO ontology is a OBO library ontology.Here is the link to it Ontology of Prokaryotic Phenotypic and Metabolic Characters

Talk to you soon! Thanks for your guidance.

yongqunh commented 3 years ago

I see. We will check this out. Thanks, Oliver

From: Kelly Eckenrode notifications@github.com Sent: Sunday, November 1, 2020 12:21 PM To: OntoZoo/ontobee ontobee@noreply.github.com Cc: He, Oliver yongqunh@med.umich.edu; Comment comment@noreply.github.com Subject: Re: [OntoZoo/ontobee] Terms in MICRO are missing in Ontobee (#158)

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Hi Oliver,

The MICRO ontology is a OBO library ontology.Here is the link to it Ontology of Prokaryotic Phenotypic and Metabolic Charactershttp://www.obofoundry.org/ontology/micro.html

Talk to you soon! Thanks for your guidance.

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yongqunh commented 3 years ago

This has now been fixed by Edison Ong.

The problem wasa caused by the invalid language definition in Micro ontology:

  1. MICRO_0000541 & MICRO_0000543

    ...

  2. MICRO_0001571

    ...

  3. MICRO_0001781

    ... ---

You can see the xml:lang definition is incorrect. In particular, MICRO_0001781 has an extremely long definition and makes Virtuoso unable to process it.

After fixing it, Ontobee daily auto-update script should be able to correctly update Micro ontology.

yongqunh commented 3 years ago

Note that we corrected the problem and stored a local copy of Micro, and Ontobee was specified to use the local version.

Please let us know once the MICRO developers fixed the problem so that we can change it back to auto-update.

Thanks, Edison & Oliver