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Re: Experiment Ontology

From: Matthias Samwald <samwald@gmx.at>
Date: Sun, 2 Dec 2007 23:24:43 +0100
Message-ID: <F8BD027F3E80406F8690C054968F54C8@tessellate>
To: <public-semweb-lifesci@w3.org>, "Susie M Stephens" <STEPHENS_SUSIE_M@LILLY.COM>

Hi Susie,

Susie wrote:
> It would be great if you could take a look at it and provide comments. The
> ontology is available at:
> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/Experiment_Ontology

* Some of the entities/properties are missing a rdfs:label or have an empty 
label (a string with lenght 0).
* Some of the entities could be taken from existing ontologies like OBI, RO 
or some of the OBO Foundry ontologies. This would save work and makes 
integration with other data sources and ontologies much easier. By the way, 
there seem to be several groups working on ontologies for mircoarray 
experiments, or are at least planning to do that. It would be great if these 
groups could work together.
* The class 'Chip type' should be removed and be replaced by subclasses of 
'chip', e.g., 'chip (human)', 'chip (mouse)' etc.
* Some of the object properties appear like they are intended to be datatype 
properties (e.g., 'has proteome id').
* Many of the datatype properties could be replaced with object properties, 
possibly referring to third party ontologies -- of course this would require 
a richer ontology and more work spent on creating mappings. 'has molecular 
function' could refer to entities from the gene ontology, 'has associated 
organ' could refer to an ontology about anatomy and so on.
* Object properties and their ranges are quite redundant. Property 'has 
reagent' has range 'Reagent', property 'has treatment' has range'Treatment' 
and so on. Maybe the ontology could be designed in such a way that there are 
only some generic properties such as 'has part'. This would make the 
ontology much easier to maintain, query and understand in the long term.
* It is unclear how 'Gene list' is intended to be used.
* 'Hardware' and 'Software' should not be subclasses of 'Protocol'.

Many of the datatype properties in this ontology look very interesting and 
might provide requirements for other ontologies. It would be great if some 
of them could be described/commented in more detail so that we know more 
about the requirements that motivated the creation of these properties.

I hope that was somewhat helpful.

Matthias Samwald
Received on Sunday, 2 December 2007 22:25:12 UTC

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