[MOBY-dev] findService and the hierarchy

[Edward Kawas]

Hi Andreas,

I believe that the results are correct.

There are no services in the default registry that consume
Annotated_GO_Term. 1 service that consumes its parent (GO_Term) and 689
services that strictly consume Object.

When you set the flag, includeParentDatatype, the behaviour is like doing a
findservice for services that consume Annotated_GO_Term or any parent type
up to and including Object with includeParentDatatype=false. 

Does this make sense?

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
Sent: August-03-08 11:33 PM
To: Core developer announcements
Subject: Re: [MOBY-dev] findService and the hierarchy

Martin Senger wrote:

> I posted my results - now it is up to Eddie or Mark to draw
> conclusion from that results... 


could any of you two state something about that ?

Thanks
Andreas

Andreas Groscurth wrote:
> i like to bring this up for discussion again ;-)
>
> thanks
>
> Martin Senger wrote:
>>> In my opinion when searching for services consuming 
>>> Annotated_GO_Term via
>>> the findService method i should also include the service which 
>>> consumes a
>>> GO_Term datatype, as this is the parent datatype (per default
>>> 'includeParentDatatype' is true)....
>>>
>>>     
>>
>> I assume that by "I should also include" you actually meant "the 
>> registry
>> response should also include". Is my understanding correct?
>>
>> If so, I am afraid that it is not the issue of the jMoby library but the
>> registry itself. Eddie or Mark can confirm or reject this hypothesis.
>>
>> The BioMoby API allows to specify two XML tags when calling findService
>> method: the
>>
>> <expandObjects>X</expandObjects>
>> and
>> <expandServices>X</expandServices>
>>
>> Where X can be either 1 or 0.
>>
>> The jMoby's findService() method sets these two tags according to the 
>> two
>> boolean parameters that the method can get:
>>
>> boolean includeChildrenServiceTypes
>> and
>> boolean includeParentDataTypes
>>
>> I have tried to call the findService, with the Annotated_GO_Term input,
>> using all combinations of these two tags (you can do it using the Moby
>> command-line client with the optioins -nc and/or -np). The results are
>> either no service or 713 services:
>>
>> expandObjects     expandServices    # of found services
>> 1                 1                 713
>> 0                 0                 0
>> 1                 0                 713
>> 0                 0                 0
>>
>> I have feeling that this is not a correct result. Could Eddie or Mark
>> perhaps comment on it?
>>
>> [I vaguely remember that we had this conversation about these tags 
>> with Mark
>> years(!) ago - but I do not recall what was the conclusion. I only, and
>> again vaguely, remember to have this issue in my to-do list - which 
>> would
>> indicate that something could be done in the jMoby library.]
>>
>> Cheers,
>> Martin
>>
>>   
>
>


-- 
=====================================================
  Dipl. Bioinf. Andreas Groscurth
  Bioinformatics Software Developer
  Plant Computational Biology group
  Max-Planck Institute for plant breeding research
  Carl-von-Linne Weg 10
  50829 Cologne
  Germany
  +49(0) 221 5062449
=====================================================

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