Re: [SO-devel] Changes for sequence_variation terms

[Suzanna L. <su...@be...>]

Hi Karen,

So essentially you are saying,

sequence_variant is for describing differences that relate to =20
populations &
sequence_alteration is for the kinds of modifications
(that is, an alteration may give rise to a variant)

also, when you say "remove" for deletion_junction and insertion_site =20
you are referring to that branch of the ontology only, correct? (not =20
removing them utterly)

-S

On Jul 25, 2007, at 10:55 PM, Karen Eilbeck wrote:

> Hi
>
> At the recent immunology workshop we decided to add new terms =20
> (allele, genotype etc. ) to sequence_variant, which already had =20
> kinds of variation as its children (insertion, inversion etc). This =20=

> has caused some problems: allele and insertion should not be siblings.
>
> One term is being used to describe  two phenomena; differences that =20=

> relate 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 =20
> the term that is the parent of allele etc. It needs a new definition.
>
> We need a new term sequence_alteration to capture the actual =20
> changes in the sequence between a variant and the reference =20
> 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 =20
> genome exhibiting one or more sequence_alteration.
>
> A sequence_alteration is a sequence_feature whose extent is the =20
> deviation from another sequence.
>
> Comments, better definitions etc would be appreciated,
>
> Karen
> ----------------------------------------------------------------------=20=

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