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

Trish Whetzel whetzel at stanford.edu
Fri Apr 27 14:44:57 PDT 2012


Hi Carlo, 

I've removed the extra entries. 

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	04/11/2012	04/11/2012	Ontology
> 
> 2012-03-02	03/02/2012	03/06/2012	Ontology
> 
> 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>
> Date: Tue, 24 Apr 2012 12:42:11 -0700
> To: Trish Whetzel <whetzel at stanford.edu>, Paul R Alexander <palexander at stanford.edu>
> Cc: "support at bioontology.org" <support at bioontology.org>, Trish Whetzel <plwhetzel at gmail.com>, Melissa Haendel <haendel at ohsu.edu>, Scott Hoffmann <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>
> Date: Fri, 20 Apr 2012 14:03:50 -0700
> To: Carlo Torniai <torniai at ohsu.edu>, Paul R Alexander <palexander at stanford.edu>
> Cc: "support at bioontology.org" <support at bioontology.org>, Trish Whetzel <plwhetzel at gmail.com>, Melissa Haendel <haendel at ohsu.edu>, Scott Hoffmann <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	04/08/2012	04/08/2012	Ontology
>> 
>> 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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>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 
> 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
> 

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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