[Biojava-l] Re: CORBADEV: LSR news - new RFP about biomolecular entities

[Philip Lijnzaad]

[ Dear biocorba, biojava and bioxml folks, this mail replies to a request for
  additional CORBA data types to be standardized by the OMG Life Sciences
  Research group. That is, we are trying to establish _which_ biological
  entities related to sequence analysis need to be standardized, not _how_
  (that's the next part). Please feel free to respond, and my apologies if
  you're not interested. Philip Lijnzaad ] 

On Tue, 19 Sep 2000 10:47:57 +0100 (BST), 
"Martin" == Martin Senger <senger@ebi.ac.uk> writes:

Martin> The OMG LSR prepared a draft for a new RFP dealing with additional
Martin> biomolecular sequence analysis entities - those who were not covered
Martin> by the origibal BSA sumbissions. The RFP will be issued this
Martin> December, and the initial responses are due to the end of March
Martin> 2001. The draft is (or shorly will be) available as the OMG document
Martin> lifesci/00-09-10 (or it is available on my desk in room A-235).

Martin> The objective of the RFP is to define entities which can be used and
Martin> produced by sequence analysis as defined in BSA spec. The RFP asks
Martin> for the following entities:

Martin>    Biomolecular sequence alphabet
Martin>    Fuzzy locations
Martin>    Weight matrices
Martin>    Patterns, including profiles and HMMs
Martin>    Phylogenetic trees
Martin>    Assembly (including trace and quality data)
Martin>    Composite annotations (which may be the first step to define a gene)
Martin>    Gene (still under discussion if this is appropriate to put here)
Martin>    Taxonomy
Martin>    GeneticCode extensions, including initiators and terminators
Martin>    BioSequence extensions, inclusing sequence alphabet

Martin> The LSR is prepared to accept also submissions dealing only with some
Martin> of the listed entities. Later the various submissions will merge
Martin> together to cover most of (and ideally all) entities.

Martin> At the moment, it is a good time to ask for other entities to be
Martin> added into the RFP. 

I have just two suggestions for addition:

- a type for representing floating point information on sequence positions,
  such as hydrophobicity plots. I am not going to insist on this, because the
  (nearly) obvious solution is to just use a IDL::float. Or was that double ...

- a type for representing things like dotplots; this is fairly common in
  sequence analysis, and requesting it might just avoid the quagmire of
  different plot and/or image formats (vector based or bit based or even
  plain matrices of grey-(or colour? which colour model?) values). But this
  maybe out of scope, Architecture Board-wise. 

Furthermore, a few comments:

- I think we should put Gene in, but only if the RfP states its own
  definition of what a Gene is, and then ask to provide IDL for this _OR_ to
  clearly state what _they_ think a Gene should be. Just requesting
  "something for representing genes" hasn't worked, so maybe the RfP should
  take a shot at it so submitters can follow up.  This is not meant to shy
  away dissenting submitters, but to prod the LSR, the RfP authors and the
  submitters into something workable.

- Taxonomy and Phylogeny should prolly be on one line.

Hope this helps,

                                                                      Philip

-- 
When C++ is your hammer, everything looks like a thumb. (Steven Haflich)
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