Re: [SO-devel] Changes for sequence_variation terms

[Lincoln S. <ls...@cs...>]

Does this make sequence_variant and sequence_alteration siblings? That
doesn't sound right.

It seems to me that the two ideas of a change and the nature of the change
are orthogonal to each other, such that the genetic properties are
attributes of the change and should be combined via cross products. Let's
take a simple case where the two genetic properties are "fixed" for a fixed=
,
species-specific change, and "polymorphic", for a population polymorphism.
Hence I can see something like the following:

sequence_alteration
   deletion
   insertion
   inversion
   substitution
   translocation

polymorphic sequence_alteration
   polymorphic deletion
   polymorphic insertion
   polymorphic inversion
   polymorphic substitution
   polymorphic translocation

fixed sequence_alteration
   fixed deletion
   fixed insertion
   fixed inversion
   fixed substitution
   fixed translocation

The problem that I see is what to call rare or experimentally-induced
mutations, which nevertheless can be transmitted as alleles. If we aren't
careful we will be drawn into definitions of "rare polymorphism" and "commo=
n
polymorphism."

Lincoln

On 7/25/07, Karen Eilbeck <ei...@fr...> wrote:
>
> Hi
>
> At the recent immunology workshop we decided to add new terms (allele,
> genotype etc. ) to sequence_variant, which already had kinds of variation=
 as
> its children (insertion, inversion etc). This has caused some problems:
> allele and insertion should not be siblings.
>
> One term is being used to describe  two phenomena; differences that relat=
e
> to populations, and differences between two sequences.
>
> We need to modify the ontology.
>
> The way I think this should be is that sequence_variant should be the ter=
m
> that is the parent of allele etc. It needs a new definition.
>
> We need a new term sequence_alteration to capture the actual changes in
> the sequence between a variant and the reference sequence. (alteration is
> the neutral term suggested by HGVS.)
>
> This would be the new structure:
>
> sequence_variant
>
>             allele
>
>             genotype
>
>             haplotype
>
>             polymorphic_sequence_variant
>
>
>
> sequence_alteration
>
>             deletion =96 change definition
>
>             deletion_junction - remove
>
>             insertion
>
>             insertion_site - remove
>
>             inversion
>
>             substitution
>
>             translocation
>
>             translocation_site - remove
>
>
>
> These are my first stabs at defining these terms:
>
> A sequence_variant is a non exact copy of a sequence_feature or genome
> exhibiting one or more sequence_alteration.
>
> A sequence_alteration is a sequence_feature whose extent is the deviation
> from another sequence.
>
> Comments, better definitions etc would be appreciated,
> Karen
>
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--=20
Lincoln D. Stein
Cold Spring Harbor Laboratory
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