Menu
▾
▴
Re: [Obi-protocol-application-branch] [Obi-devel] Protocol Application review: consistency/style of restriction
|
From: Frank G. <fg...@gm...> - 2009-07-30 15:52:46
|
On Thu, Jul 30, 2009 at 4:45 PM, James Malone <ma...@eb...> wrote:
> If this is important it should be added to the tracker and assigned a
> priority 9 and we can add it to the call monday and assign the task. I'm
> not sure how critical it is, if anyone thinks so could you do that please
> (if it given 9 I will add it to agenda). If it's not critical we should
> probably still add it so it's not lost.
>
This is the way we define roles, feed_role is missing the realised in
feeding_process restriction. You dont need to state it again in the process,
we can infer it.
Frank
>
> Cheers,
>
> James
>
>
> Frank Gibson wrote:
>
>>
>>
>> On Thu, Jul 30, 2009 at 4:11 PM, Philippe Rocca-Serra <ro...@eb...<mailto:
>> ro...@eb...>> wrote:
>>
>> Frank, Bjoern
>>
>> +1
>>
>> Frank, I believe we still need to state process 'animal feed'
>> realizes feed_role
>>
>>
>> I think you need to have this relation on the role so the. feed_role
>> is_realized_by some animal_feeding_process
>>
>> Frank
>>
>>
>>
>>
>>
>> since the has_specified_input relation does not imply anything
>> about the realization of a role born by the continuant being specified
>>
>> if this assertion is wrong then the has_specified_input relation
>> needs to be clarified and an example supplied
>>
>> Cheers
>>
>> P
>>
>> Frank Gibson wrote:
>>
>>
>>
>> On Thu, Jul 30, 2009 at 3:46 PM, Bjoern Peters
>> <bp...@li... <mailto:bp...@li...>
>> <mailto:bp...@li... <mailto:bp...@li...>>> wrote:
>>
>>
>> > *animal feeding* has currently the following restriction:
>> realizes some
>> > 'feed role' , which should probably be replaced by:
>> >
>> I believe the above is the best we can do
>>
>>
>> Ok, so the class as it is is wrong, it probably shoudl be
>>
>> animal feeding
>> has_specified_input some organism
>> has_specified_input some (material has_role feed_role)
>> has_specified_ouput some fatter_organism
>>
>> The output here has to indicate that the organims has been fed.
>>
>> Frank
>>
>>
>>
>>
>> > realizes some ('feed role' and (inheres_in some
>> 'material_entity'))....
>> >
>> >
>> Not sure what the .. is. If you want to connect it to
>> 'is_specified_participant', that won't work.
>> > or should it be
>> >
>> > has_specified_input some (material_entity and (realizes some
>> 'feed role'))
>> >
>> >
>> This does not work, as 'realizes' needs a process on the
>> left hand
>> side, not a material entity. What does work is 'has_role'.
>> > Classifier likes either but I guess it is more than a simple
>> question of style. Bjoern had pointed to frequent abuse of
>> 'has_specified_input' relation.
>> > I have found myself confronted with this issue with several
>> classes already (e.g. elution...)
>> > s already (e.g. elution with a restriction such as
>> has_specified_input some ('{molecular entities, molecular
>> entity}'
>> and (has_role some 'solvent role')))
>> >
>> >
>>
>> I agree that we need to have one consistent way of modeling
>> this. I
>> don't believe we can logically exactly say that an entity is a
>> specified
>> participant of a process and the role it realizes.
>> >
>> --
>> 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
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports
>> 2008 30-Day
>> trial. Simplify your report design, integration and
>> deployment -
>> and focus on
>> what you do best, core application coding. Discover what's
>> new with
>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Obi-protocol-application-branch mailing list
>> Obi...@li...
>> <mailto:Obi...@li...>
>> <mailto:
>> Obi...@li...
>> <mailto:Obi...@li...>>
>>
>>
>> https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch
>>
>>
>>
>>
>> -- Frank Gibson, PhD
>> http://peanutbutter.wordpress.com/
>>
>>
>>
>> -- Philippe Rocca-Serra, PhD
>>
>> Technical Coordinator
>> www.ebi.ac.uk/net-project <http://www.ebi.ac.uk/net-project>
>>
>> The European Bioinformatics Institute email: ro...@eb...
>> <mailto:ro...@eb...>
>> EMBL Outstation - Hinxton direct: +44 (0)1223 492 553
>> Wellcome Trust Genome Campus fax: +44 (0)1223 492 620
>> Cambridge CB10 1SD, UK room: A3-141
>> --
>>
>>
>>
>>
>> --
>> Frank Gibson, PhD
>> http://peanutbutter.wordpress.com/
>> ------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day trial. Simplify your report design, integration and deployment - and
>> focus on what you do best, core application coding. Discover what's new with
>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Obi-devel mailing list
>> Obi...@li...
>> https://lists.sourceforge.net/lists/listinfo/obi-devel
>>
>>
>
>
> --
> European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton,
> Cambridge, CB10 1SD, United Kingdom
> Tel: + 44 (0) 1223 494 676
> Fax: + 44 (0) 1223 492 468
>
--
Frank Gibson, PhD
http://peanutbutter.wordpress.com/
|
