Excerpts from surajit ray's message of Tue Nov 23 09:12:16 +0100 2010:
> Hi Christoph,
> 
> Scrolling through the mile long RDF file - I could barely make out
> whats going on !

One of the big advantages of XML ;-)

> Could you please outline in a graphical/intuitive
> description as to what exactly is implemented in the RDF ?

You are better off, if you have a look at the Turtle representation (was
attached in the previous post) which is easier to read. 

A dataset with 3 compounds and 3 substructures would have the following
basic structure (assuming that 
	- featureX occurs in compound1 and compound2
	- featureY occurs in compound2
	- featureZ occurs in compound1 and compound3
)

compounds:
	- compound1
	- compound2
	- compound3

data_entries:
	- compound1:
		featureX: true
		featureZ: true
	- compound2:
		featureY: true
		featureX: true
	- compound3:
		featureZ: true

features:
	featureX:
		ot:smarts: cN
		ot:pValue: 0.97
		ot:effect: activating
		ot:hasSource: http://webservices.in-silico.ch/algorithm/fminer/bbrc
		ot:parameters:
			dataset_uri: http://webservices.in-silico.ch/dataset/1
	featureY:
		ot:smarts: ccc
		ot:pValue: 0.96
		ot:effect: deactivating
		ot:hasSource: http://webservices.in-silico.ch/algorithm/fminer/bbrc
		ot:parameters:
			dataset_uri: http://webservices.in-silico.ch/dataset/1
	featureZ:
		ot:smarts: N(O)=O
		ot:pValue: 0.99
		ot:effect: activating
		ot:hasSource: http://webservices.in-silico.ch/algorithm/fminer/bbrc
		ot:parameters:
			dataset_uri: http://webservices.in-silico.ch/dataset/1

> Also I have a question about mutually common relationships like MCSS.
> MCSS is common to both compounds (being compared). So in your
> representation would it be necessary to represent the relationship
> twice ? That is once for each compound - or can it be represented just
> once and be associated with both compounds ?

I would do it like this:

compounds:
	- compound1
	- compound2

data_entries:
	- compound1:
		mcss_feature: true
	- compound2:
		mcss_feature: true

features:
	mcss_feature:
		ot:smarts: c1cccc1(CC)
		ot:hasSource: your_mcss_service_uri

Best regards,
Christoph