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[bioontology-support] Questions about eagle-i on bioportal.

Carlo Torniai torniai at ohsu.edu
Tue Apr 24 12:42:11 PDT 2012


Hi Thrish,
Sorry for the late reply.
The issue is that Bioportal should just look at the purl.
And the purl (which point to the released version) has never changed.
Maybe we can chat about it while at the workshop.
C


From: Trish Whetzel <whetzel at stanford.edu<mailto:whetzel at stanford.edu>>
Date: Fri, 20 Apr 2012 14:03:50 -0700
To: Carlo Torniai <torniai at ohsu.edu<mailto:torniai at ohsu.edu>>, Paul R Alexander <palexander at stanford.edu<mailto:palexander at stanford.edu>>
Cc: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>, Trish Whetzel <plwhetzel at gmail.com<mailto:plwhetzel at gmail.com>>, Melissa Haendel <haendel at ohsu.edu<mailto:haendel at ohsu.edu>>, Scott Hoffmann <hoffmasc at ohsu.edu<mailto:hoffmasc at ohsu.edu>>
Subject: Re: [bioontology-support] Questions about eagle-i on bioportal.

Hi Carlo,

If the ontology is set-up to load from a URL, BioPortal will check the contents of the file at that URL nightly and if a file with new content is found that file will be loaded. It looks like there were some changes in the structure of the ERO SVN directory in between when these two ERO versions were released, which may have caused some issues. Which entries of the "03/02/2012" would you like removed?

As far as displaying "dc:" at the root, I do see that in the 03/02/2012 version and in other OWL ontologies. Paul, do you know if this is something that can be filtered out of the display?

Trish


On Apr 12, 2012, at 12:40 PM, Carlo Torniai wrote:


I have few questions.

Yesterday we released a new version of our ontology
http://bioportal.bioontology.org/ontologies/3016

I was checking today on bioportal in order to update with the new release and with my surprise I've noticed that the page reports not only a new release but a bunch of other changes to our previous release that we never made.

Now I would like  to understand where the list of versions is coming from.
Because for the release what we do is JUST to redirect
http://purl.obolibrary.org/obo/ero.owl to the latest released version in our SVN (as other ontolgies such Obi or uberon do) have done this JUST yesterday.
So what are all the other versions that bioportal is showing on our page?

Like this one:
2012-03-02<http://bioportal.bioontology.org/ontologies/47195?p=terms>   04/08/2012      04/08/2012      Ontology<http://rest.bioontology.org/bioportal/ontologies/download/47195?apikey=4ea81d74-8960-4525-810b-fa1baab576ff&userapikey=a92e4ab2-f2d5-4822-a2f0-7db7a5f96ef3>


Where they come from? We really don't want them there.
If you please can explain to me what's the process that bioportal goes through and if there is something we should do in order to have JUST the actual released version.

Another thing:
Now I've noticed that there is a funky display of dc: in the root of bioportal ontology browser.
http://bioportal.bioontology.org/ontologies/47218?p=terms

It wasn’t' there before and we haven't change anything related to it. Also no versions of protégé are showing it (under thing we just have ObsoleteClass and entity).

Do you have any idea why this is showing up?
Thanks for your help,

Dr. Carlo Torniai
Assistant Professor
Ontology Development Group, OHSU Library
http://tinyurl.com/ondevgroup
Department of Medical Informatics and Clinical Epidemiology
Oregon Health & Science University

Skype:ctorniai
503-418-2499

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Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
http://www.bioontology.org

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