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Re: Experiment Ontology

From: Kei Cheung <kei.cheung@yale.edu>
Date: Mon, 03 Dec 2007 13:00:16 -0500
To: Matthias Samwald <samwald@gmx.at>
Cc: public-semweb-lifesci@w3.org, Susie M Stephens <STEPHENS_SUSIE_M@LILLY.COM>
Message-id: <47544430.8070908@yale.edu>

This is great!

I have a microarray experiment description (that has to do with 
Alzheimer Disease) extracted from NINDS microarray consortium:


I just wonder how this example would fit this experiment ontology (as 
well as others such as OBI) As shown in this example, we record 
information such as organ type, organ region, cell type (layer II 
pyramidal neuron), etc. NINDS microarry consortium uses different array 
platforms (e.g., agilent, Affymetrix, and cDNA)  for different organisms 
so one may need to divide chips into groups corresponding to different 
platform types. Each group can then be further divided into subgroups 
corresponding to different organisms.

We also would like to capture gene lists (not the raw gene lists but the 
ones (much shorter) that indicate what genes are over/under expressed 
under certain experimental conditions). Such gene lists would usually be 
extracted from the literature. Also the analysis package (including 
version) that was used to generate a gene list should be identified. One 
possible use of these gene lists is to compare them to identify genes 
are differentially expressed under the same/similar experimental 
condition across different microarray experiments. This would help 
identify true signals from noises.

Hope it helps.



Matthias Samwald wrote:
> 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.
> cheers,
> Matthias Samwald
Received on Monday, 3 December 2007 18:00:31 UTC

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