[MOBY-dev] findService and the hierarchy

[Andreas Groscurth]

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
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  50829 Cologne
  Germany
  +49(0) 221 5062449
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