[Obi-instrument-branch] instrument calls

[Melanie Courtot]

Hi all,

Due to lots of things happening for all the OBI instrumenters, the
recent calls were attended by Daniel, Frank and myself.

Daniel has now left the EBI, Frank started working for a private
company so won't have as much time as before to dedicate to OBI, and I
won't be able to attend future instruments call either.

We therefore propose to cancel those, unless other editors are willing
to take on.

Frank and myself had a chat during the OBI meeting last week: the
instrument branch is in need of clean up, and in order to try and move
forward with what we think would be the most efficient process we
propose to try and coordinate via emails between the both of us.

Obviously and for the reasons mentioned above this will be a slow
process, so if you have any other suggestion or comment please let us
know :)

Melanie

---
Mélanie Courtot
TFL- BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada

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[Trish Whetzel]

Since it sounds like you will need to intersperse conversations with changes to the owl file, would use of Collaborative Protege be helpful? 

Here are answers to questions brought up at the OBI workshop:
1) Can it do reasoning?
Yes.

2) Can it save all versions?
The edits are simultaneous in Collaborative Protege. There isn't really the concept of versions. Whatever change a user makes, all other users will see immediately. The ontology can be saved at any time in an OWL format and can be submitted to a SVN, if needed.

3) Can changes be rolled back?
No. It is dangerous to do that with simultaneous editing. New version based on Protege 4 has that in plan.

4) Is the OWL file accessible in case there are special edits that need to be done offline that cannot be performed in Protégé?
Yes.

5) Can the file be locked similar to a svn lock so that if offline work is needed, the file will be the same when added back to the server?
No. Edits are simultaneous, so there are no versions. This "locking" feature is planned for the next version.

6) Is this an active project?
Definitely.


Trish

[Allyson Lister]

Hi all,

The idea of trying out collaborative protege sounds good. And, while I don't have much time for TCs right now, doing a little work here and there on the ontology might be something I can make time for, especially since the instrument group is dropping in numbers. So, please include me on whatever next steps you take!

:) Allyson

2009/2/10 Trish Whetzel <plwh...@gmail.com>

Since it sounds like you will need to intersperse conversations with changes to the owl file, would use of Collaborative Protege be helpful? 

Here are answers to questions brought up at the OBI workshop:
1) Can it do reasoning?
Yes.

2) Can it save all versions?
The edits are simultaneous in Collaborative Protege. There isn't really the concept of versions. Whatever change a user makes, all other users will see immediately. The ontology can be saved at any time in an OWL format and can be submitted to a SVN, if needed.

3) Can changes be rolled back?
No. It is dangerous to do that with simultaneous editing. New version based on Protege 4 has that in plan.

4) Is the OWL file accessible in case there are special edits that need to be done offline that cannot be performed in Protégé?
Yes.

5) Can the file be locked similar to a svn lock so that if offline work is needed, the file will be the same when added back to the server?
No. Edits are simultaneous, so there are no versions. This "locking" feature is planned for the next version.

6) Is this an active project?
Definitely.


Trish

On Mon, Feb 9, 2009 at 5:05 PM, Melanie Courtot <mcou...@gmail.com> wrote:

--

Allyson Lister
http://lurena.vox.com

CISBAN, http://www.cisban.ac.uk
Newcastle University

[Alan Ruttenberg]

Another question forgot to ask. How does it interact with imports? We need the imports to reason correctly (and because parts are defined in different branches). We also need to be able to control to which branch edits are made.

Finally, if we do try this it needs to be done in a way that supports our version management - after some session of work, either collaborative or individual, the branch that is edited needs to be checked in.

-Alan

[Frank Gibson]

Hi,

I think in this case, using collaborative protege may be overkill. I
have used it before and I do think using collaborative protege should
be the direction we should be heading in. However, in this case the
editing required is minimal and is really just curating the terms with
the new relations we have and fixing all the imported MSI terms, this
can be handled offline with very little communication.

For anyone that wants to edit the instrument branch the idea is to
review everything under device, add missing funtions, has_supplier and
device_setting and the other device relations and assert the classses
under material entity rather than device.

I will remove the instrument calls from the calendar unless anyone steps up

Frank

--
Frank Gibson, PhD
http://peanutbutter.wordpress.com/

[Trish Whetzel]

Got it, less discussions and decision-making, but more hands-on editing needed.

Trish

[Trish Whetzel]

I can check on that unless Frank has some input from previous usage?

Trish

[Frank Gibson]

I have had any experience using the imports from external ontologies
as we were playing with the single file release. However, the reason
we have branches is to allow concurrant editing, collaborative protege
allows us to do this, therfore making the existance of branch files
redundant, should we choose to adopt this approach.

Frank

--

Frank Gibson, PhD
http://peanutbutter.wordpress.com/

------------------------------------------------------------------------------

[Frank Gibson]

That last message shouls have read "I have not had any...."

Frank