Re: [Obi-instrument-branch] material and artefact_object as defined classes

[Philippe]

Dear obi-instrumenters,biomaterials,

For those using Protege 3.3.1 please check the FAQ, and the Biomaterial branch list
I have made a short tutorial for this version.

https://wiki.cbil.upenn.edu/obiwiki/index.php/FAQ

Melanie, could you send me an editable verison of your document so we can merge these docs and I will be able to add the corresponding screenshots (wiki sucks for this things)

Thanks

Phil

Melanie Courtot wrote:

>Dear obi-instrumenters,
>
>We went ahead this morning and updated the owl file for biomaterial. At
>the same time, we updated the device branch, and created artefact_object
>as a defined class.
>If there is any problem we can always revert, we just thought it would be
>easier to see the changes in practice.
>
>I started writing down a doc that you will find here
>http://obi-biomaterial.googlegroups.com/web/MaterialDocumentation.pdf
>
>This is not expected to be the final version, so please feel free to comment.
>
>Our goal is to have a final version for the next biomaterial call on
>Friday. This will then be circulated on the dev list for general comments,
>and if everything goes well will be added under our methodology section in
>the future.
>
>Thanks,
>Melanie
>
>
>
>-------------------------------------------------------------------------
>This SF.net email is sponsored by: Microsoft
>Defy all challenges. Microsoft(R) Visual Studio 2008.
>http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>_______________________________________________
>Obi-instrument-branch mailing list
>Obi-instru...@lists.sourceforge.net
>https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch
>
>

[Melanie Courtot]

Hi all,

I added the original doc under https://wiki.cbil.upenn.edu/obiwiki/index.php/BiomaterialTermNeedsCalls#February_8.2C_2008
Please update as needed.

Philippe, I believe that a document describing the differences in activating the reasoned depending the version of protege should be distinct of this one, or it will get confusing, but feel free to re use anything you need :-)

Thanks,
Melanie

[Philippe]

Hi Franck, Alan,

I guess this can be discussed during the Biomaterial call on friday with
Susanna. The classes Organisation and Person have been thrown in more as
placeholder (maybe my hunch here) rather that definitive locations. We
need additional work on the definitions. Input is more than welcome.

I would say that Organization is a group of persons + a set of rules +
possibly an hosting site.

One a somehow related issues (hence inclusion of role- branch) while
going the current classes, I have the following:
Investigation_site and Trial_site are currently roles, which feels a bit
odd since we have a class 'Site' from BFO. Do we really need those roles ?

I guess we could constraint Investigation so that when declaring an
investigation, one must report information about the site. The filler
could be 'Organization' (but could also be a term from ENVO-GAZ if
applicable).

I think it would probably be better to have Processes constrained so
that they have to unfold in a physical location. This leads to possibly
having to discuss where we need relations such as:
Process || located_in (could be 'happens_in') || Site . Reverse
relation could be Site || is_host_for || Process. Tocheck if this holds
true at class level.

Cheers

Phil

Alan Ruttenberg wrote:

>Organization's definition is of a group of people. Since people are
>made of stuff, they are a material in this ontology. An aggregate of
>them is similarly stuff.
>-Alan
>
>On Feb 11, 2008, at 12:02 PM, frank gibson wrote:
>
>
>
>>Hi Melanie
>>
>>In regards to the artifact object assertion. Is their a reason why
>>organization is asserted under material?
>>
>>Thanks
>>
>>Frank

>>--
>>Frank Gibson
>>Research Associate
>>Room 2.19, Devonshire Building
>>School of Computing Science,
>>University of Newcastle upon Tyne,
>>Newcastle upon Tyne, NE1 7RU
>>United Kingdom
>>Telephone: +44-191-246-4933
>>Fax: +44-191-246-4905

[Alan Ruttenberg]

On Feb 12, 2008, at 3:30 AM, frank gibson wrote:

> Hi Alan
>
> So the definitions as they stand fit with their assertion. I am fine
> with person being a material. However, an organisation is more than
> the sum of its parts.

Yes, I think you are right. Probably should have, at a minimum,
"group of people", and then make organization a defined class in
terms of that and some sort of role so as to differentiate these
groups from some random group of people you see sitting at a table or
walking down the street. The definition should reflect that which
people are in the group can change over time and still retain identity.

Thinking aloud, I think we might have some similar sort of situation
as with generically and specifically dependent plans, but now with
generically and specifically dependent roles. Something like each
member of the organization having a role: member of organization x.
The organization then defined by those people who have role "member
of organization x.". The aggregate then having the role "organization
x" which is generically dependent on the members.

> As Phillipe eludes to, it has people, it also has goals,
> objectives, infrastructure etc.

I'm not sure of the difference between goals and objectives. We have
plans/realizable information entities in denrie (below generically
dependent continuants) that can inhere in the people in the
organization at any given time, which I think covers this.

We might need some idea of control/ownership in OBI to model
acquisition - buying something includes, among other things, transfer
of ownership. I think, if this were not an organization, that "owner
of x" would be a role. With the organization there is this
generically dependent business again.

> I suppose it depends how far we need to model an organisation
> within OBI, we may not require
> anything more than names and associated roles such as vendor or
> manufacture. So until we have a need to identify an organisation than
> anything more than a collection of people, I am fine with where it is.

OK. Makes sense to me too (especially after thinking about the issues
a bit more ;-).

>
> Frank
>
> On Feb 11, 2008 6:00 PM, Melanie Courtot <cou...@ebi.ac.uk> wrote:
>> Hi all,
>>
>> Agreed with Alan. I will add this to the list of corrections for the
>> document.
>> We can review these during the call on Friday, and amend the document
>> accordingly.
>>
>> Thanks,
>> Melanie

>> ---------------------------------------------------------------------

[Alan Ruttenberg]

Good point. Any ideas how to modify the definition?
-Alan

On Feb 12, 2008, at 8:57 AM, Helen Parkinson wrote:

> I think organization can be one person, e.g. in the case of someone
> who
> is self employed and has a company,
>
> cheers
> Helen

> --
> Helen Parkinson, PhD
> ArrayExpress Production Coordinator,
> Microarray Informatics Team,
> EBI
>
> EBI 01223 494672
> Skype: helen.parkinson.ebi

[Melanie Courtot]

After this morning's dev call (notes to come later), I believe we agreed that we will have person and organization/population in the sense aggregate of persons under material. Any of those could then bear an organisation_role (to be defined by the role branch on friday's call at 1pm EST, everybody welcome, we will be using centra).

The idea is to distinguish between the physical part of the organization concept and the social role which can be played by one person or an aggregate of persons.

Does that sound right for everybody?

Melanie

[Smith, Barry]

The organization and the person would still, then, be different.
This is because the organization can cease to exist while the person
still goes bravely marching on.
The organization exists because there is a special role the person plays.
BS

At 08:57 AM 2/12/2008, Helen Parkinson wrote:
>I think organization can be one person, e.g. in the case of someone
>who is self employed and has a company,
>
>cheers
>Helen
>
>Alan Ruttenberg wrote:
>>