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Re: actions related to collections

From: Jun Zhao <jun.zhao@zoo.ox.ac.uk>
Date: Wed, 18 Apr 2012 22:41:05 +0100
Message-Id: <F5292147-9452-4E02-B09F-5DD6E51DE5D8@zoo.ox.ac.uk>
Cc: "<public-prov-wg@w3.org>" <public-prov-wg@w3.org>
To: Luc Moreau <L.Moreau@ecs.soton.ac.uk>
Luc and all,

Apology if I destroyed any proper threading!

I want to say that I absolutely agree that the current collection structure will be very useful for describing some type of provenance. I have no doubt about its usefulness and the necessity for its relatively more restrictive structure.

However, Satya and I are trying to provide some examples to show the need for some alternative more relaxed collection structure from DM, like set.

I don't like proposing people to use rdf collection or bag. Actually the sioc use case doesn't need to use such rdf constructs. If sioc can support this in their vocab, why can't ours? It's a very simple membership relationship I am pushing for. No orders, no list, just a set of stuff.

Out of interest, what do we lose if we get the key as optional in the model?

Jun

Sent from my iPad

On 18 Apr 2012, at 22:20, Luc Moreau <L.Moreau@ecs.soton.ac.uk> wrote:

> Hi Satya,
> 
> Therefore, in your cell line example, I suppose you don't want/cannot enumerate the cells, and
> therefore express insertion into/removal from the cell line?
> 
> You may still want to distinguish the states of the cell line at two different instances and
> relate them by derivation?
> 
> Luc
> 
> On 18/04/12 21:33, Satya Sahoo wrote:
>> 
>> Hi Luc,
>> 
>> Do I understand correctly that those two collections do not change: a cell line has a given number of cells, and the cohort involves a set of patients.
>> 
>> A cohort remains static during the period of study. The number of cells may increase (by cell division) or decrease (by cell death).
>> 
>> Thanks.
>> 
>> Best,
>> Satya
>>  
>> So, yes, I understand that removal/insertion are not necessary for such static collections.  
>> 
>> Regards,
>> Luc
>> 
>> 
>> On 18/04/12 17:35, Satya Sahoo wrote:
>>> 
>>> Hi all,
>>> The issue I had raised last week is that collection is an important provenance construct, but the assumption of only key-value pair based collection is too narrow and the relations derivedByInsertionFrom, Derivation-by-Removal are over specifications that are not required.
>>> 
>>> I have collected the following examples for collection, which only require the definition of the collection in DM5 (collection of entities) and they don't have (a) a key-value structure, and (b) derivedByInsertionFrom, derivedByRemovalFrom relations are not needed:
>>> 1. Cell line is a collection of cells used in many biomedical experiments. The provenance of the cell line (as a collection) include, who submitted the cell line, what method was used to authenticate the cell line, when was the given cell line contaminated? The provenance of the cells in a cell line include, what is the source of the cells (e.g. organism)? 
>>> 
>>> 2. A patient cohort is a collection of patients satisfying some constraints for a research study. The provenance of the cohort include, what eligibility criteria were used to identify the cohort, when was the cohort identified? The provenance of the patients in a cohort may include their health provider etc.
>>> 
>>> Hope this helps our discussion.
>>> 
>>> Thanks.
>>> 
>>> Best,
>>> Satya
>>> 
>>> 
>>> On Thu, Apr 12, 2012 at 5:06 PM, Luc Moreau <L.Moreau@ecs.soton.ac.uk> wrote:
>>> 
>>> Hi Jun and Satya,
>>> 
>>> Following today's call, ACTION-76 [1] and ACTION-77 [2] were raised against you, as we agreed.
>>> 
>>> Cheers,
>>> Luc
>>> 
>>> [1] https://www.w3.org/2011/prov/track/actions/76
>>> [2] https://www.w3.org/2011/prov/track/actions/77
>>> 
>>> 
>> 
Received on Wednesday, 18 April 2012 21:56:40 GMT

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