[Obi-protocol-application-branch] call tomorrow is on

[Bjoern Peters]

Agenda for tomorrow:

* Develop the plan how we will tackle the core terms:

My first draft:

- review the current state of each term, and capture issues in editor
notes
- complete metadata for each, including multiple examples (=subclasses,
like BFO does)
- write mini use cases that cover all terms, resolve issues
- write up a document defining the terms and how they build on each
other that could be used as a result section of the manuscript. I would
like to follow the style of a paper from Barry and Richard:
http://ontology.buffalo.edu/08/phenotype/Terminology_for_Clinical_Phenotypes.pdf

Here is the current list of core terms, additions still welcome:

* objective driven process (and objective)
* planned process (and plan)
* protocol application (and protocol)
* assay
* analyte measuring assay
* material transformation
* material separation
* material administration
* manufacturing process
* investigation
* study

-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Obi-protocol-application-branch mailing list
Obi-protocol-ap...@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch

[frank gibson]

Are we on centra or skype?

Frank

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

[Bjoern Peters]

Centra for Jennifer's benefit

[Bjoern Peters]

We looked at investigation design, study design and investigation, to
identify overlap / definitions for each. Based on this, we removed
'investigation design', updated the definition for investigation, and
added the logical definitions (linking to planning, documenting and
doing). A number of issues are captured in editor notes, including
several I have just added. As I had to redo all edits manually, it could
be that I missed some from the call (let me know if that is the case).

Please review the file, specifically 'investigation'.

I thought this was an important and fruitful exercise! We need to do
several of these, and I would like to schedule several longer calls in
the coming two weeks.

I have the following slots available, California time:

* Tomorrow, 1pm - 3pm
* Tuesday 12pm - 3pm
* Extend next Thursday call to two hours?

Can anyone join then?

- Bjoern

> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Obi-protocol-application-branch mailing list
> Obi-protocol-ap...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch
>

------------------------------------------------------------------------------
SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
The future of the web can't happen without you. Join us at MIX09 to help
pave the way to the Next Web now. Learn more and register at
http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/

[Melanie Courtot]

Hi Bjoern,
Sorry I couldn't make it this morning.
I could do tomorrow (that's just after the biomaterial call right?). I
could also do tuesday, but would rather not do 2h thursday: there is
the DT call beforehand, and 3h of call is more than I can handle :)
Thanks,
Melanie

As said previously, I was unclear between investigation design, study
design, plan specification and protocol.

[frank gibson]

On Fri, Dec 5, 2008 at 2:06 AM, Bjoern Peters <bpe...@liai.org> wrote:
> We looked at investigation design, study design and investigation, to
> identify overlap / definitions for each. Based on this, we removed
> 'investigation design', updated the definition for investigation, and
> added the logical definitions (linking to planning, documenting and
> doing). A number of issues are captured in editor notes, including
> several I have just added. As I had to redo all edits manually, it could
> be that I missed some from the call (let me know if that is the case).
>
> Please review the file, specifically 'investigation'.

We still have something called investigation_planning under planning.
What is this for and how does it relate to investigation?

Could we make investigation and planning defined classes? I can only
think, that the only thing that would output a plan_specification
would be a planning_process.

>
> I thought this was an important and fruitful exercise! We need to do
> several of these, and I would like to schedule several longer calls in
> the coming two weeks.
>
> I have the following slots available, California time:
>
> * Tomorrow, 1pm - 3pm
> * Tuesday 12pm - 3pm
> * Extend next Thursday call to two hours?

Could do this, would it be possible to start an hour early rather than
an hour later?

Frank

>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> Build the coolest Linux based applications with Moblin SDK & win great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Obi-protocol-application-branch mailing list
>> Obi-protocol-ap...@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch
>>
>
>

> ------------------------------------------------------------------------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
> The future of the web can't happen without you. Join us at MIX09 to help
> pave the way to the Next Web now. Learn more and register at
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/

> _______________________________________________
> Obi-protocol-application-branch mailing list
> Obi-protocol-ap...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch
>

--

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

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

SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
The future of the web can't happen without you. Join us at MIX09 to help
pave the way to the Next Web now. Learn more and register at
http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/

[frank gibson]

whooops!, did you hit the big shiney reasoner button before you checked in :)

I would go through it but I am going to be offline for the rest of the
day, sorry

Frank

>>> -------------------------------------------------------------------------
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>>> Build the coolest Linux based applications with Moblin SDK & win great prizes
>>> Grand prize is a trip for two to an Open Source event anywhere in the world
>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>> _______________________________________________
>>> Obi-protocol-application-branch mailing list
>>> Obi-protocol-ap...@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch
>>>
>>
>>

>> ------------------------------------------------------------------------------
>> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
>> The future of the web can't happen without you. Join us at MIX09 to help
>> pave the way to the Next Web now. Learn more and register at
>> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/

>> _______________________________________________
>> Obi-protocol-application-branch mailing list
>> Obi-protocol-ap...@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch
>>
>
>
>

> --
> Frank Gibson, PhD
> http://peanutbutter.wordpress.com/
>
> ------------------------------------------------------------------------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
> The future of the web can't happen without you. Join us at MIX09 to help
> pave the way to the Next Web now. Learn more and register at
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/

> _______________________________________________
> Obi-protocol-application-branch mailing list
> Obi-protocol-ap...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch
>

--

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

------------------------------------------------------------------------------
SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
The future of the web can't happen without you. Join us at MIX09 to help
pave the way to the Next Web now. Learn more and register at
http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/

[frank gibson]

I had a quick glance, I think you have used the has_specfied_output in
a couple of places where you should have used the
outputs_specified_data relation

Frank

>>>> -------------------------------------------------------------------------
>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>>>> Build the coolest Linux based applications with Moblin SDK & win great prizes
>>>> Grand prize is a trip for two to an Open Source event anywhere in the world
>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>>> _______________________________________________
>>>> Obi-protocol-application-branch mailing list
>>>> Obi-protocol-ap...@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch
>>>>
>>>
>>>

>>> ------------------------------------------------------------------------------
>>> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
>>> The future of the web can't happen without you. Join us at MIX09 to help
>>> pave the way to the Next Web now. Learn more and register at
>>> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/

>>> _______________________________________________
>>> Obi-protocol-application-branch mailing list
>>> Obi-protocol-ap...@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch
>>>
>>
>>
>>

>> --
>> Frank Gibson, PhD
>> http://peanutbutter.wordpress.com/
>>
>> ------------------------------------------------------------------------------
>> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
>> The future of the web can't happen without you. Join us at MIX09 to help
>> pave the way to the Next Web now. Learn more and register at
>> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/

>> _______________________________________________
>> Obi-protocol-application-branch mailing list
>> Obi-protocol-ap...@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch
>>
>
>
>

> --
> Frank Gibson, PhD
> http://peanutbutter.wordpress.com/
>
> ------------------------------------------------------------------------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
> The future of the web can't happen without you. Join us at MIX09 to help
> pave the way to the Next Web now. Learn more and register at
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/

> _______________________________________________
> Obi-protocol-application-branch mailing list
> Obi-protocol-ap...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch
>

--

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

------------------------------------------------------------------------------
SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
The future of the web can't happen without you. Join us at MIX09 to help
pave the way to the Next Web now. Learn more and register at
http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/

[Fostel, Jennifer (NIH/NIEHS) [C]]

it seems to me that one of the key components of an investigation would
be to implement the design / plan for that investigation. do we need to
state that in the definition?

Frank

>> ---------------------------------------------------------------------
>> ---- This SF.Net email is sponsored by the Moblin Your Move

>> Developer's challenge Build the coolest Linux based applications with

>> Moblin SDK & win great prizes Grand prize is a trip for two to an
>> Open Source event anywhere in the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Obi-protocol-application-branch mailing list
>> Obi-protocol-ap...@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application
>> -branch
>>
>
>
> ----------------------------------------------------------------------

> -------- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las

> Vegas, Nevada.
> The future of the web can't happen without you. Join us at MIX09 to
> help pave the way to the Next Web now. Learn more and register at
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmi

> x.com/ _______________________________________________

> Obi-protocol-application-branch mailing list
> Obi-protocol-ap...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-
> branch
>

--

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

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

SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas,
Nevada.
The future of the web can't happen without you. Join us at MIX09 to
help pave the way to the Next Web now. Learn more and register at
http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.
com/

[Bjoern Peters]

Melanie pointed out the same thing. The 'documenting' class was screwed
up. Fixed it this morning.

[frank gibson]

You may also want to consider if an Investigation has_participant some
person, along with its parts of planning/assay/documenting.

Frank

On Fri, Dec 5, 2008 at 2:06 AM, Bjoern Peters <bpe...@liai.org> wrote:

> We looked at investigation design, study design and investigation, to
> identify overlap / definitions for each. Based on this, we removed
> 'investigation design', updated the definition for investigation, and
> added the logical definitions (linking to planning, documenting and
> doing). A number of issues are captured in editor notes, including
> several I have just added. As I had to redo all edits manually, it could
> be that I missed some from the call (let me know if that is the case).
>
> Please review the file, specifically 'investigation'.
>

> I thought this was an important and fruitful exercise! We need to do
> several of these, and I would like to schedule several longer calls in
> the coming two weeks.
>
> I have the following slots available, California time:
>
> * Tomorrow, 1pm - 3pm
> * Tuesday 12pm - 3pm
> * Extend next Thursday call to two hours?
>

> Can anyone join then?
>
> - Bjoern
>
>
>

>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> Build the coolest Linux based applications with Moblin SDK & win great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Obi-protocol-application-branch mailing list
>> Obi-protocol-ap...@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch
>>
>
>

> ------------------------------------------------------------------------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
> The future of the web can't happen without you. Join us at MIX09 to help
> pave the way to the Next Web now. Learn more and register at
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/

> _______________________________________________
> Obi-protocol-application-branch mailing list
> Obi-protocol-ap...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch
>

--

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

------------------------------------------------------------------------------
SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
The future of the web can't happen without you. Join us at MIX09 to help
pave the way to the Next Web now. Learn more and register at
http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/

[frank gibson]

was there any consensus on extra or extended calls this week?

Frank

On Fri, Dec 5, 2008 at 2:06 AM, Bjoern Peters <bpe...@liai.org> wrote:
> We looked at investigation design, study design and investigation, to
> identify overlap / definitions for each. Based on this, we removed
> 'investigation design', updated the definition for investigation, and
> added the logical definitions (linking to planning, documenting and
> doing). A number of issues are captured in editor notes, including
> several I have just added. As I had to redo all edits manually, it could
> be that I missed some from the call (let me know if that is the case).
>
> Please review the file, specifically 'investigation'.
>
> I thought this was an important and fruitful exercise! We need to do
> several of these, and I would like to schedule several longer calls in
> the coming two weeks.
>
> I have the following slots available, California time:
>
> * Tomorrow, 1pm - 3pm
> * Tuesday 12pm - 3pm
> * Extend next Thursday call to two hours?
>
> Can anyone join then?
>
> - Bjoern
>
>
>

>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> Build the coolest Linux based applications with Moblin SDK & win great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Obi-protocol-application-branch mailing list
>> Obi-protocol-ap...@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch
>>
>
>

> ------------------------------------------------------------------------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
> The future of the web can't happen without you. Join us at MIX09 to help
> pave the way to the Next Web now. Learn more and register at
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/

> _______________________________________________
> Obi-protocol-application-branch mailing list
> Obi-protocol-ap...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch
>

--

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

------------------------------------------------------------------------------
SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
The future of the web can't happen without you. Join us at MIX09 to help
pave the way to the Next Web now. Learn more and register at
http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/

[Bjoern Peters]

I wouIdn't call it a consensus, but still believe we need the extra
time. Therefore I will do two calls for this week:
- today 1-3pm (California time)
- Thursday: extended call 9 - 11
Calls will be on Centra, and focus on going through the remaining core
terms.

[Bjoern Peters]

I agree with two of Frank's suggestions below, and accordingly I removed
'investigation planning' (not needed) and made planning a defined class.

--
Bjoern Peters
Assistant Member
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters

[Bjoern Peters]

According to Jennifer's suggestion, I specifically refer to the study
design in the textual definition of investigation now.

--
Bjoern Peters
Assistant Member
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters