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relationships between parts, molecules, and cells in BAMS

From: John Barkley <jbarkley@nist.gov>
Date: Tue, 20 Mar 2007 06:52:24 -0400
Message-ID: <154101c76add$d8076b30$8a3a0681@ncsl.nist.gov>
To: <mbota@almaak-01.usc.edu>
Cc: <public-semweb-lifesci@w3.org>

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 

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 



----- 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 Tuesday, 20 March 2007 10:53:37 UTC

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