Re: [SO-devel] New term suggestion

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Lincoln

We already have:

[Term]
id: SO:0000670
name: chromosome_breakage_sequence
def: "A sequence within the micronuclear DNA of ciliates at which chromosome 
breakage and telomere addition occurs during nuclear differentiation." [SO:ma]
is_a: SO:0000669 ! sequence_rearrangement_feature

[Term]
id: SO:0000671
name: internal_eliminated_sequence
def: "A sequence eliminated from the genome of ciliates during nuclear 
differentiation." [SO:ma]
is_a: SO:0000669 ! sequence_rearrangement_feature

[Term]
id: SO:0000672
name: macronucleus_destined_segment
def: "A sequence that is conserved, although rearranged relative to the 
micronucleus, in the macronucleus of a ciliate genome." [SO:ma]
is_a: SO:0000669 ! sequence_rearrangement_feature

Michael

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> From: Lincoln Stein <ls...@cs...>
> To: son...@li...
> Subject: Re: [SO-devel] New term suggestion
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> Cc: Pankaj Jaiswal <pj...@co...>
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> Date: Tue, 21 Feb 2006 13:17:54 -0500
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> 
> Uh oh. What about the rearranged chromosomes in the ciliate macronucleus?
> 
> Lincoln
> 
> 
> On Tuesday 21 February 2006 10:01, Pankaj Jaiswal wrote:
> > Instead of 'chloroplast chromosome', call it 'plastid chromosome'.
> >
> > Having mitochondrial chromosome does make sense. Also consider adding,
> > 'mitochondrial plasmid', these are extra chromosomal linear/circular
> > forms of DNA found in mitos. However here is a problem, e.g. in maize
> > out many types of cytoplasm, the one that gives cytoplasmic male
> > sterility has part of the mitochondrial genome exists as plasmid, where
> > as the one that gives fertile cytoplasm has this fragment integrated in
> > the chromosome. How is SO going to distinguish between the two.
> >
> > In maize there is a big master circle (main chromosome) of the mito
> > chromosome, but there are also small sub circles derived from the master
> > chromosome. Is there a way to handle this.
> >
> > -Pankaj
> >
> > Michael Ashburner (Genetics) wrote:
> > > David
> > >
> > > I think the term 'mitochondrial chromosome' could well be added
> > > and, for completion also 'chloroplast chromosome', as types of
> > > chromosome.
> > >
> > > Karen: What do you think ?
> > >
> > > Michael
> > >
> > >
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> > > Subject: Re: [SO-devel] New term suggestion
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> > > <http://sourceforge.net/mailarchive/forum.php?forum=song-devel> Date:
> > > Tue, 21 Feb 2006 08:05:04 -0500
> > >
> > > Hi Michael,
> > >
> > >>> genome has been suggested as a new term.
> > >>> I am wary of this because a genome is for the most part discontinuous,
> > >>> and stitching it up to make a region of continuous sequence would be
> > >>> somewhat arbitrary.
> > >>>
> > >>> Anyone else have an opinion?
> > >
> > > Just curious...  What about mitochondrial genomes?
> > > We're using "chromosome" in chado for the Dmel mitochondrial genome...
> > >
> > > Best,
> > >
> > > -Dave
> > >
> > > On Tue, 21 Feb 2006 6:33, Michael Ashburner (Genetics) wrote:
> > >>I agree it has no place.
> > >>
> > >>M
> > >>
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> > >>> Subject: [SO-devel] New term suggestion
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> > >>> Date: Thu, 16 Feb 2006 16:25:03 -0700
> > >>> X-Keywords:
> > >>>
> > >>> genome has been suggested as a new term.
> > >>> I am wary of this because a genome is for the most part discontinuous,
> > >>> and stitching it up to make a region of continuous sequence would be
> > >>> somewhat arbitrary.
> > >>>
> > >>> Anyone else have an opinion?
> > >>> --Karen
> > >>>
> > >>> Initial Comment:
> > >>> Suggestion: How about a term "genome" ?
> > >>>
> > >>> It itself is used within other term names, their definitions, and
> > >>>even a
> > >>> relationship (genome_of).   Primarily, I was simply hoping to reason
> > >>> that a
> > >>> chromosome was part_of a genome, but presumably this term would be
> > >>> wide-reaching (many possible "parts")...
> > >>>
> > >>> Possible defs:
> > >>> http://www.google.com/search?oi=defmore&defl=en&q=define:Genome
> > >>>
> > >>>
> > >>>
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> -- 
> Lincoln D. Stein
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