[MOBY-dev] findService and the hierarchy

[Martin Senger]

> 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

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger