[MOBY-dev] decomposition of BioMoby Objects in Taverna

[Edward Kawas]

Hi Jerzy,

That option is indeed unavailable. It can be something that we add in the
future.

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jerzy Orlowski
Sent: September-26-08 1:29 AM
To: moby-dev at lists.open-bio.org
Subject: [MOBY-dev] decomposition of BioMoby Objects in Taverna

Hi

I think there is one important option missing in BioMoby plugins in Taverna.

Suppose I have a MobyService that returns an AminoAcidSequence. I want 
to extract the sequence on my AminAcidSequence (it is a String object) 
and use it as input for another MobyServices that eats String as its input.

The only way I can do it now is to use a Parser which decomposes 
AminoAcidSequence to basic types and then construct my String from these 
basic elements 
(namespace,id,aminoacid_'Length',aminoacid_'Length'_id,aminoacid_'Length'_ns
,aminoacid_'SequenceString',aminoacid_'SequenceString'_id 
and aminoacid_'SequenceString'_ns).
This is not very difficult in this case, but imagine what would happen 
if I parse an object which is composed of for example 
WieghtedAminoSequences and try to get AminoAcidSequence out of it...

In fact current BioMobyObjectProcessors  are processors for constructing 
MobyObjects (with basic types as input ports and composite types as 
output ports). There should be another type of 
BioMobyObjectDeconstructingProcessors for deconstructing MobyObjects 
(with composite types as input ports and basic types as output ports).

Please inform me if such option already exists somewhere and I missed it.

Jerzy Orlowski
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