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[bioontology-support] MS ontology

Eric Deutsch edeutsch at systemsbiology.org
Wed Jun 17 08:17:41 PDT 2009


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/controll
edVocabulary/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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