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[bioontology-support] ontology loading problem

BARD Jonathan J.Bard at ed.ac.uk
Wed Nov 22 13:25:30 PST 2017


Jennifer

You are right - the last 3 are out of date and, as far as I am concerned, be lost

Thanks for updating the AEO which may still be useful

Regards

Jonathan

--------------------------------------------

Professor Jonathan Bard

Balliol College, Oxford - graduate advisor
Dept. Physiology, Anatomy & Genetics
   Oxford - visiting member
45 Charlbury Road, OX2 6UX UK
T= 44/0 1865 315185, M = 07741477720





On 22 Nov 2017, at 20:24, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Jonathan,

All of the URLs you listed below are part of a SourceForge site where the root seems to have been removed and results in a 404 error:

http://obo.cvs.sourceforge.net/

I noticed these are all OBO ontologies, so I looked on the OBO Foundry website and was able to find this updated download URL for the Anatomical Entity Ontology:

http://purl.obolibrary.org/obo/aeo.owl

The other 3 ontologies are marked as obsolete on the OBO Foundry website, so I was unable to find alternative download URLs. If you’d like, I could modify these entries in BioPortal to stop checking the SourceForge URLs on a daily basis for new versions. This would prevent BioPortal from sending you email about load failures. The ontologies are otherwise fine and displaying as normal in the BioPortal application.

Kind regards,
Jennifer


On Nov 22, 2017, at 1:35 AM, BARD Jonathan <J.Bard at ed.ac.uk<mailto:J.Bard at ed.ac.uk>> wrote:

I have had 4 emails (below) about my ontologies not loading

These should all be stable as they haven’t been touched by me for a few years

Is the problem at your end?

Jonathan

--------------------------------------------

Professor Jonathan Bard

Balliol College, Oxford - graduate advisor
Dept. Physiology, Anatomy & Genetics
   Oxford - visiting member
45 Charlbury Road, OX2 6UX UK
T= 44/0 1865 315185, M = 07741477720

BioPortal failed to load Anatomical Entity Ontology (AEO) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/aeo.obo.

BioPortal failed to load Human Developmental Anatomy Ontology, abstract version 1 (EHDAA) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo.

BioPortal failed to load Human Developmental Anatomy Ontology, timed version (EHDA) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-staged.obo.

BioPortal failed to load Minimal Anatomical Terminology (MAT) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/multispecies/minimal_anatomical_terminology.obo.



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