[MOBY-dev] sequence datatypes

[Paul Gordon]

Hi Nassib,

I looked at the presentation, and I'm not sure why you can't just use a 
VirtualSequence instead.  You can then have all of the combinations you 
want, as long as you register the namespaces:

<VirtualSequence articleName="foo" namespace="renci_global" id="bar">
<Integer articleName="Length" namespace="" id="">1500</Integer>
</VirtualSequence>

<VirtualSequence articleName="foo" namespace="renci_user" id="baz">
<Integer articleName="Length" namespace="" id="">1500</Integer>
</VirtualSequence>

<VirtualSequence articleName="foo" namespace="NCBI_gi" id="123456">
<Integer articleName="Length" namespace="" id="">1500</Integer>
</VirtualSequence>

<DNASequence articleName="foo" namespace="any" id="qux">
<Integer articleName="Length" namespace="" id="">1500</Integer>
<String articleName="SequenceString" namespace="" id="">ATG...</String>
</DNASequence>

etc., etc.
> Hi,
>
> I'd like to start explaining a little bit about our use of biomoby and
> also request feedback...
>
> We're using biomoby mainly with taverna workflows, and gradually
> migrating current web services over to become biomoby services (under
> biomoby.renci.org).  The workflows we develop are talking to services
> that for the most part are based here within our servers.  As a result
> we end up passing a very large amount of duplicated sequence data over
> the network between taverna and services, often more data than taverna
> is happy about.  To get around this we have started passing sequences
> by reference using a FASTA-like format that is non-standard but fits
> well into our system and the taverna UI.  I'm calling this the "RENCI
> sequence" format, and it's basically similar to GenBank, while
> allowing an "abbreviated" (truncated) form that consists of only a
> partial header line with at least one namespace/id.  (The architecture
> is described in http://www.renci.org/~nassar/sequence_registry.ppt )
>
> We've added some new datatypes under "RenciSequence" for this purpose,
> analogous to the existing "GenericSequence".  In general we are using
> the existing biomoby datatypes, but for sequences our format seems
> unusual enough that we thought it needed its own datatype to avoid
> confusion.
>
> Nassib
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
>