Re: relationships between parts, molecules, and cells in BAMS

John B.

This question of parts and their relationship with a whole has been 
addressed in other venues, especially in ISO 10303 which deals with product 
data exchange. I think Part 41 addressed some of the issues.

Briefly, and I am relying on my memory here, the idea was that a whole could 
be put together many different ways and decomposed many different ways. 
Parts could be described as a "bag" with an arbitrary number of instances 
that are used in the whole, e.g., a sandwich could have 0,1 or more pieces 
of cheese, 0,1 more pieces of ham, etc. Or a "set" in which one of each 
instance of the set must occur in the whole, e.g., a car has four and only 
four wheels. Or an "array" [I think that was the name] in which the 
instances of the array were put together in a specific order, e.g. take an 
ethanol molecule then add an hydroxyl group. There was some pretty powerful 
thinking that went into this, so it might be worth looking at.

ISO 10303 is a pretty expensive standard, but a copy of the relevant 
sections probably can be obtained from someone still at NIST, which I left 
about 3 years ago.

John Rumble
Vice President
Information International Associates
Oak Ridge TN
www.infointl.com
jrumble@iiaweb.com
jumbleusa@earthlink.net
301 963 7903 (Home Office in Gaithersburg MD)
301 502 5729 (Cell)
865 298 1251 (Oak Ridge Office)
----- Original Message ----- 
From: "John Barkley" <jbarkley@nist.gov>
To: <mbota@almaak-01.usc.edu>
Cc: <public-semweb-lifesci@w3.org>
Sent: Tuesday, March 20, 2007 6:52 AM
Subject: relationships between parts, molecules, and cells in BAMS


>
> hi Mihail,
>
> Per Alan's email (enclosed below), we have some questions regarding the 
> relations between elements of BAMS, i.e., part/part, part/source, 
> part/target, part/molecules in region, part/cell, and cell/molecules in 
> cell.
>
> 1. For the part/part relation, the xml (swanson-98.xml) relates parts to 
> each other in a tree structure. The part element attribute 
> is_part_of_idrefs indicates a part's parent. Should we assume that this 
> tree structure is an expression of the dataset's view of the world and is 
> relatively immutable?
>
> 2. For each of the other relations: part/source, part/target, 
> part/molecules in region, part/cell, and cell/molecules in cell, should we 
> assume that these are representations of the dataset's current scientific 
> observations, and are not intended to be exhaustive?
>
> Please excuse the crudity of my description of the dataset. I am not a 
> neuroscientist.
>
> thanks,
>
> jb
>
>
>
> ----- Original Message ----- 
> From: "Alan Ruttenberg" <alanruttenberg@gmail.com>
> To: "John Barkley" <jbarkley@nist.gov>; <public-semweb-lifesci@w3.org>
> Sent: Monday, March 19, 2007 4:31 PM
> Subject: Re: bams class style model
>
>
>>
>> Just had a discussion with John, summary:
>>
>> Minor, stylistic: Class names are often written as singular e.g.
>> Cells -> Cell.
>>
>> Single URI for each class, based on the id. The name of the thing
>> goes to the label, and an annotation property records the abbreviation.
>>
>> part_has_cell, cell_has_molecule_within,
>> part_has_molecule_in_region,  become subproperties of ro:location_of
>> (from relation ontology)
>>
>> We had a discussion of the allValuesFrom restrictions.
>> The first was re: his previous mail. He was using separate
>> allValuesFrom which were being interpreted as a conjunction. Instead
>> he would
>> change these to a single allValueFrom of the union.
>> The second question was whether the allValuesFrom was appropriate.
>> It seemed appropriate in some cases, not in others.
>> For the part/part relations, we assumed that the atlas was
>> exhaustive, so the restriction makes sense.
>> We're not as sure about source/target, part/cell, cell/molecule
>> relations. These are probably not exhaustive, so
>> someValueFrom alone would seem to make more sense. He will ask
>> Mikhail and adjust the model accordingly.
>>
>> The "by_" classes will be removed.
>>
>> -Alan
>>
>
>
>
>

Received on Thursday, 22 March 2007 16:16:04 UTC