Richard,

I hope I didn't forgot to send you yesterday the link where OpenTox
resources are defined: 
http://opentox.org/dev/apis/api-1.0/?searchterm=API .

The link  
<http://opentox.org/toxicity-prediction/opentoxservices>http://opentox.org/toxicity-prediction/opentoxservices 
points to resources, implemented according to the API 1.0 documented
above. 

API 1.1. is currently under development:
http://opentox.org/dev/apis/api-1.1/?searchterm=API

Perhaps we need to rename "opentoxservices" to "opentoxresources" to
avoid confusions.

Best regards,
Nina

Nina Jeliazkova wrote:
> richard apodaca wrote:
>   
>> --- On Tue, 9/29/09, Nina Jeliazkova <nina at acad.bg> wrote:
>>
>>   
>>     
>>> Sorry, the correct link to implemented services  is
>>> http://opentox.org/toxicity-prediction/opentoxservices
>>>     
>>>       
>>>> New version, currently under revision
>>>> http://opentox.org/dev/apis/api-1.1/?searchterm=API
>>>>
>>>> One note - if the information above is hard to find
>>>>       
>>>>         
>>> and not obvious
>>>     
>>>       
>>>> where to look for, we indeed would need to reorganize
>>>>       
>>>>         
>>> at least the front
>>>     
>>>       
>>>> page of OpenTox site.
>>>>       
>>>>         
>> Thanks for the link. But it looks like a list of services.
>>   
>>     
> Can you clarify , why do you think so?
>   
>> What I'm actually after is a list of resources, in the REST sense of the word - a domain model if you will.
>>
>> For example, a "resource" in this context might be "Prediction".
>>   
>>     
> Well, not intending to go into terminology discussion, but  Model or
> Algorithm are just resources.  Models can be applied on a dataset or
> substance (this is defined in the API).
>
> I would personally interpret prediction as something that already
> happened, after applying a Model, otherwise it sounds more like an
> "activity" than a "resource".
>   
>> When we talk about making a Prediction, a lot of other concepts go with that. For example, we might perform a Prediction on a Substance or a Dataset. 
>>     
> We apply "Models" on a Substance of a Dataset.  Models are created by
> applying Algorithms on Datasets.
>   
>> That Dataset might be composed of Items, for example. The Substance may in turn be composed of Components. It's these domain concepts and how they're aggregated that make a domain model. Only with a domain model in hand can you start thinking about resources.
>>   
>>     
> Datasets are composed of compounds, and might have descriptors
> (features) defined.  We agreed on a flexible approach, where any
> compound property (descriptor, name, endpoint) is a feature. Feature can
> have meta information, assigning specific meaning (e.g. descriptors).
>   
>> The point is not to get bogged down in the details, but rather to create a common language for toxicity prediction. A language that can be understood by domain experts (Toxicologists, in vivo pharmacologists) and developers alike.
>>
>> So far, I haven't found anything like this for OpenTox. If there is no such thing, how interested would the OpenTox group be in developing one?
>>   
>>     
> It seems to me you are confused by the terms, adopted in OpenTox, which
> are more or less following machine learning vocabulary. Otherwise
> OpenTox resources quite closely follow your suggestions. Does my
> explanations help?
>
> Best regards,
> Nina
>   
>> Best,
>> Rich
>>
>> ___________________________________
>>
>> Richard L. Apodaca
>>
>> http://depth-first.com      Blog
>> http://metamolecular.com    Company
>>   
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>>     
>
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