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

Carlo Torniai torniai at ohsu.edu
Tue Apr 24 14:22:22 PDT 2012


Thanks  Trish,
We will  monitor if there are some future changes that are reported in Bioportal that are not related to actual eagle-i releases.
Let us know if any of your developers need some more information from us.
Best,
Carlo



From: Trish Whetzel <whetzel at stanford.edu<mailto:whetzel at stanford.edu>>
Date: Tue, 24 Apr 2012 14:17:13 -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" <support at bioontology.org<mailto:support at bioontology.org>>, 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,

The additional versions can be removed. BioPortal is set-up to check the contents of the file at the provided URL nightly and if a file with changed content is found at that URL the file will be loaded. As for why additional files were pulled, perhaps one of the NCBO developers can provide more details on this.

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?

Best,
Trish


On Apr 24, 2012, at 4:01 PM, Carlo Torniai wrote:

Hi Trish,
So the only version that should appear on the Bioportal about eagle-I are:
2012-04-09<http://bioportal.bioontology.org/ontologies/47218?p=terms>   04/11/2012      04/11/2012      Ontology<http://rest.bioontology.org/bioportal/ontologies/download/47218?apikey=4ea81d74-8960-4525-810b-fa1baab576ff&userapikey=a92e4ab2-f2d5-4822-a2f0-7db7a5f96ef3>

2012-03-02<http://bioportal.bioontology.org/ontologies/47012?p=terms>   03/02/2012      03/06/2012      Ontology<http://rest.bioontology.org/bioportal/ontologies/download/47012?apikey=4ea81d74-8960-4525-810b-fa1baab576ff&userapikey=a92e4ab2-f2d5-4822-a2f0-7db7a5f96ef3>

Also Bioportal should just look at my purl, and don’t' care of what's happening on my SVN (as I explained0.
Whatever I reorganize or change the directory that the purl resolves to never changes ( unless upon release ) and that's the only thing I'm expecting Bioportal to report.
Please let me know how can we make sure that Bioportal won't report in the future any wrong information about eagle-I releases.

Thanks,
Carlo



From: Carlo Torniai <torniai at ohsu.edu<mailto:torniai at ohsu.edu>>
Date: Tue, 24 Apr 2012 12:42:11 -0700
To: Trish Whetzel <whetzel at stanford.edu<mailto:whetzel at stanford.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 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<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<http://www.bioontology.org/>

"Like" NCBO on Facebook: http://on.fb.me/bioontology

Follow NCBO on Twitter: http://twitter.com/#!/bioontology

Join in Discussions on LinkedIn: http://linkd.in/ncbo-group


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

"Like" NCBO on Facebook: http://on.fb.me/bioontology

Follow NCBO on Twitter: http://twitter.com/#!/bioontology

Join in Discussions on LinkedIn: http://linkd.in/ncbo-group

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