Dear Surajit,

I'm looking at the MaxTox.owl you've attached earlier this week. The 
reasoner classifies it well, so technically it is correct, but I'm 
lacking some additional knowledge about the problem you wish to solve 
with this ontology, may you give me some more explanations so that i  so 
that I can get your point while creating it.

It is surprising for me to see that you have chosen to create a class 
called RatTD50 as a Dataset subclass. Normally the concrete datasets or 
features are individuals and they are not part of the ontology, but of 
some external resource and they have their URL. What is your reason to 
design it this way?

Best,
ivelina






surajit ray wrote:
> Hi Nina,
>
> I have created a basic ontology for the Maxtox model. Could please go
> through it briefly when you have the time - and suggest improvements as well
> as how we can fit this into the existing Ontology of Opentox. Just
> indications will do (I understand you are already under a deadline
> pressure...)
>
> I have just started learning protege so a few concepts may have gone awry. I
> have tried my best to get the gist of our prediction system into the
> attached ontology.
>
> Thanks in advance
>
> Cheers
> Surajit
>
> On Tue, Feb 2, 2010 at 11:45 AM, Nina Jeliazkova <nina at acad.bg> wrote:
>
>   
>>  Hi Surajit,
>>
>>
>> surajit ray wrote:
>>
>> Hi Nina,
>>
>>  Are we officially supposed to use the restlet2 m7 ?
>>
>>  The library and particular release are choice of the developer, so the
>> answer is - it is up to you.
>>
>>  At this point I have few questions about this interaction
>> a) Once a time consuming calculation is over - should the server notify an
>> attached client about the result OR just sit with the data at a specified
>> URL till it is fetched by the client ?
>>
>> The client sends GET requests and verifies if the result is ready (200 OK).
>> Have a look at the API  at  http://opentox.org/dev/apis/api-1.1/AsyncTask
>>
>> When returning 303 (redirect) for an uncomplete task and making use of
>> Refresh field, it is very easy to implement browser -like client to
>> periodically check the task status. Browsers will automatically try to fetch
>> the content after time interval, specified in Refresh:
>>
>>  (In the REST interface is it allowable for the server to contact a
>> connected client ?)
>>
>> No.  REST is using HTTP protocol for communication and there is no any
>> notion of an "attached" client.  The client sends GET/PUT/POST/DELETE
>> request, receives an answer and there is no permanent between them after the
>> response is sent.
>> Unless you implement your client to behave as server as well, there is no
>> way of server to tell the client anything, besides answering client request.
>>
>>  b) Should the server identify the client requesting the computation and
>> authenticate before delivering the data OR give it to any client requesting
>> the URI of the predicted/computed values ?
>>
>> We've decided to postpone everything, concerning authentication and
>> authorization after the end of February, and currently all the services are
>> open to everybody (I know it sounds scary :)
>>
>>  c) How long should the computed values be retained on the server OR
>> should there be REST interface for destroying (and hence freeing up
>> resources) a set of computed values ?
>>
>> It depends on your implementation.
>>
>> For example ambit services store everything in a database and keep the
>> results forever, unless a delete operation is performed on specific
>> resource.  REST way of deleting a resource is sending DELETE request
>> (instead of POST or PUT, which are generaly for create/update).  For most of
>> OpenTox resources DELETE operation is defined in the API (see wiki), but not
>> everybody has implemented the full set of the API.
>>
>> d) Should there be an "account" like system for every client on the server
>>
>> See answer in (b).
>>
>> ? If yes - should the data generated by a client be attached to that
>> "account" or available to all ?
>>
>> There might be public and private data, but at this moment we consider
>> everything is public and will decide on details after finalizing
>> deliverables at the end of this month.
>>
>>  Should the computed data persist indefinitely in each of these "accounts"
>> ?
>>
>>  Again, it depends on your implementation.
>>
>> Best regards,
>> Nina
>>
>>  Cheers
>> Surajit
>>
>> On Tue, Feb 2, 2010 at 3:31 AM, Nina Jeliazkova <nina at acad.bg> wrote:
>>
>>     
>>> Hi Pantelis,
>>>
>>> There is a standard Java class java.util.concurrent.ExecutorService ; it
>>> could be configured to work as a pool of fixed or variable number of
>>> threads.
>>>
>>> There is a Restlet TaskService , which is wraps the ExecutorService.
>>> I've found it behaved weird and switched to the standard Java class.
>>>
>>> You might look at ambit code at
>>>
>>>
>>> https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-www/src/main/java/ambit2/rest/AmbitApplication.java
>>>
>>> https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-www/src/main/java/ambit2/rest/task
>>>
>>> For each asynchronous task, it creates a Callable class, which returns
>>> Reference. Each tasks has an unique identifier (UUID) and the set of
>>> tasks is stored in a ConcurrentMap. There is a timer, which removes
>>> completed tasks few hours after completion.
>>>
>>> Hope this helps,
>>> Nina
>>>
>>>
>>> chung wrote:
>>>       
>>>> Hi Nina,
>>>>  I'm trying to make some improvements on the services so except for the
>>>> migration from restlet2 m3 to m7 I was thinking of introducing some
>>>> execution pool (e.g. an ExecutorService or -why not- something
>>>> 'homemade') and establish a queue for the incoming requests (especially
>>>> those characterized as time-consuming and memory-consuming ones). This
>>>> way I will be able to manage all running tasks on the server and make
>>>> some performance improvements I hope. Is there some standard way of
>>>> doing this? Could you suggest some executor or some utility to manage
>>>> the running threads and do you know if there is some way to specify the
>>>> maximum number of running threads for Restlet?
>>>>
>>>> Best Regards,
>>>> Pantelis
>>>>
>>>>
>>>> On Tue, 2010-01-26 at 14:21 +0200, Nina Jeliazkova wrote:
>>>>
>>>>         
>>>>> Hello All,
>>>>>
>>>>> Following the data type discussions and proposal earlier this month,
>>>>>           
>>> now
>>>       
>>>>> support for NumericFeature and NominalFeature are implemented in IDEA
>>>>> services.
>>>>>
>>>>> Please note all features are explicitly declared to be subclass of
>>>>> ot:Feature as well. While this is redundant and can be derived from the
>>>>> ontology with a help of a reasoner, it does make the client
>>>>> implementation somewhat easier.
>>>>>
>>>>> Examples from CPDBAS dataset at
>>>>> http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/9
>>>>>
>>>>> <http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12122>
>>>>>       a       ot:Feature , ot:NominalFeature ;
>>>>>       dc:identifier
>>>>> "http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12122"^^xsd:anyURI ;
>>>>>       dc:title "ActivityOutcome_CPDBAS_SingleCellCall" ;
>>>>>       ot:acceptValue "inactive" , "active" ;
>>>>>       ot:hasSource
>>>>> <http://ambit.uni-plovdiv.bg:8080/ambit2/reference/11847> ;
>>>>>       ot:units "" ;
>>>>>       =       ot:ActivityOutcome_CPDBAS_SingleCellCall .
>>>>>
>>>>>
>>>>> <http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12124>
>>>>>       a       ot:Feature , ot:NumericFeature ;
>>>>>       dc:identifier
>>>>> "http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12124"^^xsd:anyURI ;
>>>>>       dc:title "STRUCTURE_MolecularWeight" ;
>>>>>       ot:hasSource
>>>>> <http://ambit.uni-plovdiv.bg:8080/ambit2/reference/11847> ;
>>>>>       ot:units "" ;
>>>>>       =       ot:STRUCTURE_MolecularWeight .
>>>>>
>>>>>
>>>>> Bug reports are of course welcome at the usual place
>>>>>
>>>>> http://sourceforge.net/tracker/?group_id=191756
>>>>>
>>>>> Best regards,
>>>>> Nina
>>>>>
>>>>>           
>>>>>>             
>>>>>>>               
>>>>>> 1) Feature data types:
>>>>>> Proposal (based on Pantelis suggestions and Protege guide) at
>>>>>> http://opentox.org/data/documents/development/RDF%20files/Datatypes.
>>>>>> Updated opentox.owl at
>>>>>>
>>>>>>             
>>> http://opentox.org/data/documents/development/RDF%20files/OpenToxOntology/view
>>>       
>>>>>>
>>>>>>             
>>>>> _______________________________________________
>>>>> Development mailing list
>>>>> Development at opentox.org
>>>>> http://www.opentox.org/mailman/listinfo/development
>>>>>
>>>>>
>>>>>           
>>>> _______________________________________________
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>>>>         
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>>>       
>>
>> --
>> Surajit Ray
>> Partner
>> www.rareindianart.com
>>
>>
>>
>>     
>
>
>   
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