dominance designations

Mike Cherry CHERRY at FRODO.MGH.HARVARD.EDU
Sat Sep 18 13:41:33 EST 1993


>Kathy Barton (barton at vms2.macc.wisc.edu) wrote:
> ...
>        In Arabidopsis this might work as ap1-36(ts) or gl1-43(d). Note
>that numerical allele designations are kept. It is a simple, flexible
>system that has worked well for the worm folks and a set of standard
>suffixes could be agreed upon for Arabidopsis. As for compatibility with
>databases, the worm community was responsible for developing the database
>on which AAtdb is based. Presumably this means that such a system can be
>accomodated by AAtdb.

Yes AAtDB is based on the ACEDB software developed by Durbin and
Thierry-Mieg. A name is a name and can be used by any database as long
as it is a unique name. However the ACeDB database does not use the
nomenclature mentioned above as the designation of an allele name.
Note I am not an expert in the nomenclature for C. elegans. I have
simply explored its representation within the ACeDB database. The
above nomenclature appears to only be used for the description of
loci, not alleles and often used in the description of phenotypes. For
example there are only four occurances of "(d)" in the current allele
class of ACEDB, release 1-21:

Allele : "n1305"
Phenotype        "Dpy,Egl, sup of lin-12(d)"

Allele : "n1313"
Phenotype        "sup lin-12(d), viable"

Allele : "n1314"
Phenotype        "sup lin-12(d), viable"

Allele : "n1317"
Phenotype        "sup lin-12(d), viable"

This usage is as a comment field within ACeDB. The "(d)" is found
within remarks in several other classes of ACeDB and found most within
the abstracts and titles of papers. Note that "lin-12" is the name of
the locus in ACeDB, and "lin-12(d)" is only used in free text fields
of the database.

You are free to infer why the suffixes are not part of the names
within ACeDB.

Mike



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