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[bioontology-support] MS ontology

Trish Whetzel whetzel at stanford.edu
Wed Jun 17 08:26:20 PDT 2009


That can be done either by subscribing to the RSS feed for MS, which  
will be updated for each new note or new item added to an existing  
note or to see all terms with notes, these are displayed on the  
ontology metadata page, http://bioportal.bioontology.org/ontologies/40152 
. Since there are no notes on MS, this section is blank. The  
Biomedical Resource Ontology (http://bioportal.bioontology.org/ontologies/39977 
) contains notes as an example.

Trish


On Jun 17, 2009, at 8:17 AM, Eric Deutsch wrote:

> I guess what I’m interested in is how I can get a list of all notes  
> without having to click on every term to see if someone added a note  
> to it. How do I do that?
>
> Thanks,
> Eric
>
>
> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> Sent: Wednesday, June 17, 2009 7:09 AM
> To: Eric Deutsch
> Cc: support at bioontology.org
> Subject: Re: [bioontology-support] MS ontology
>
> Yes, these are stored in a database backend and the table is self- 
> referential so the note entries are nested and ordered as displayed  
> in the Web interface. They are also date stamped and marked by the  
> user who entered the note.  Alerts of new Notes or new threads to an  
> existing Note is currently via RSS, with email alerts to be added in  
> the future.
>
> There is also discussion of exposing access to the Notes via a web  
> service so that if someone using an annotation application, for  
> example, wanted to add a note or propose a new term they could do  
> that at the time of annotation via the web service.
>
> Trish
>
>
> On Jun 16, 2009, at 11:02 PM, Eric Deutsch wrote:
>
>
> Hmm, no, I did not know this existed, although now I see it.  
> Assuming a number of people write in notes, is there a way to  
> extract and collate notes? Or collect notes newer than date X for  
> review?
>
> Thanks,
> Eric
>
>
> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> Sent: Tuesday, June 16, 2009 10:47 PM
> To: Eric Deutsch
> Subject: Re: [bioontology-support] MS ontology
>
> Sure, no problem. BTW, have you considered using the Notes feature  
> for dialog on terms or term proposals?
>
> Trish
>
>
> On Jun 16, 2009, at 9:33 PM, Eric Deutsch wrote:
>
>
>
> Great, thank you!
>
> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> Sent: Tuesday, June 16, 2009 1:24 PM
> To: 'Eric Deutsch'; support at bioontology.org
> Subject: RE: [bioontology-support] MS ontology
>
> Thanks. The newest file is in the queue for loading.
>
> Trish
>
> From: Eric Deutsch [mailto:edeutsch at systemsbiology.org]
> Sent: Tuesday, June 16, 2009 1:01 PM
> To: 'Trish Whetzel'; support at bioontology.org
> Cc: 'Eric Deutsch'
> Subject: RE: [bioontology-support] MS ontology
>
> Hi Trish, it’s all there in the header:
>
> .
> .
> remark: namespace: MS
> remark: version: 2.13.0
> remark: release date: 2009-06-11
> .
> .
>
> Thanks!
> Eric
>
>
>
> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> Sent: Tuesday, June 16, 2009 11:57 AM
> To: 'Eric Deutsch'; support at bioontology.org
> Subject: RE: [bioontology-support] MS ontology
>
> Sounds good.
>
> One question on the ontology metadata, I see that the release date  
> is specified here “remark: release date: 2009-06-11”, however where  
> is the ontology version stated?
>
> Trish
>
>
> From: Eric Deutsch [mailto:edeutsch at systemsbiology.org]
> Sent: Tuesday, June 16, 2009 11:29 AM
> To: 'Trish Whetzel'; support at bioontology.org
> Cc: 'Eric Deutsch'
> Subject: RE: [bioontology-support] MS ontology
>
> Hi Trish, thanks. If you’re happy to do so, why don’t we email support at bioontology.org 
>  whenever there’s a new version and have you take care of it. Later  
> we’ll try to come up with an easier solution.
>
> Thank you!
> Eric
>
>
> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> Sent: Tuesday, June 16, 2009 10:31 AM
> To: 'Eric Deutsch'; support at bioontology.org
> Subject: RE: [bioontology-support] MS ontology
>
> Hi Eric,
>
> Thanks for the pointer to the new file. Currently there are 2 ways  
> that the file can be updated for ontologies that are not within the  
> obo sourceforge cvs directory.  The ways to update the file in  
> BioPortal are either for us to load the file when there is a new  
> version given some sort of alert of the new file (email, RSS, etc)  
> or someone from PSI can load the file. It is very easy to load a new  
> version and takes only ~5 minutes from downloading the file from the  
> source location to uploading into BioPortal.  Do you have a  
> preference on how the file is updated; we are happy to load the file  
> given notice of a new version.
>
> Trish
>
>
> From: bioontology-support-bounces at lists.stanford.edu [mailto:bioontology-support-bounces at lists.stanford.edu 
> ] On Behalf Of Eric Deutsch
> Sent: Monday, June 15, 2009 1:49 PM
> To: support at bioontology.org
> Cc: Eric Deutsch
> Subject: [bioontology-support] MS ontology
>
> Hi, I notice that the MS ontology:
>
> http://bioportal.bioontology.org/ontologies/39281
>
> is quite out of date. The latest is much newer an available from our  
> CVS:
>
> http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo
>
> Can we get the BioPortal site updated?
>
> What needs to happen for our ontology to get automatically updated  
> whenever we can a new version?
>
> Thanks!
> Eric
>
>
>
>
>
> Trish Whetzel, PhD
> Outreach Coordinator
> The National Center for Biomedical Ontology
> Ph: 650-721-2378
> whetzel at stanford.edu
> http://www.bioontology.org
>
>
>
>

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