Suggestions for authors.

We literature curators stock FlyBase with data recorded from your
articles about genes, alleles and transgenes.  It is important for you,
our users, that the information we gather is filed under the correct
gene, allele or transgene construct.  Sometimes, we are unsure of the
identity of a gene or allele your paper discusses, or which transgene
you used and then we must write to you for clarification.  This
document is to explain what information you need to include to minimize
the amount of checking that we need to do.

Of course this would not be necessary if everyone used valid FlyBase
symbols for all the components in all the Materials and Methods
sections of all papers.  But as we all know, in life and in literature,
things are never as simple as that.  Different groups publish genes and
alleles under a wide variety of names and symbols. This is unlikely ever
to change - and it is not the job of FlyBase to seek to change this.
However, if we are to maintain the links between all of the information
we curate from your papers and the genes or alleles they apply to - a
task we hope you agree is a useful one - then we need to know exactly
which object you are talking about.

For gene symbols where you choose to use an "invalid" symbol, we like it
if you state somewhere (the Materials and Methods section is ideal)
which FlyBase valid gene symbol or CG genome annotation symbol each
gene corresponds to. e.g: "hid (CG5123)" or "hid (FlyBase symbol:W)".

Each object in FlyBase has a unique identifier number, and these can
also be used for making the identity of items explicit e.g. "hid
(FBgn0003997)".  For alleles, an example would be "ck[IIQ106] (FlyBase
symbol:ck[15])" or "ck[IIQ106] (FBal0001696)".

If you were to publish a paper about a newly named gene with molecular
information that indicates that you know which CG your "new" gene
corresponds to, but do not make a statement about that correspondence,
then we will mail you to determine that link.  It saves time for
everybody if these correspondences are stated up front.
FlyBase gives explicit symbols to some objects that the community
does not treat with the same nomenclatural respect that it gives to
genes and alleles, notably Transgene constructs and Transposable
element insertions.  You should use the FlyBase symbol or ID number to
convey the construct you used e.g.  "UAS-TNT (FlyBase
symbol:P{UAS-TeTxLC.tnt})" or "UAS-TNT (FBtp0001264)".

It can be particularly difficult for us to decide, on the basis of
Materials and Methods sections, whether a construct is "new" or has
been previously published.  Accurately referencing constructs that are
not novel secures you a warm place in the hearts of the literature
curators.  For new transgene constructs the name of the transformation
vector used (e.g. pUAST), the selectable marker used and the
relationship to previously published constructs are particularly useful
pieces of information for us.

When describing insertions, for example of enhancer trap elements, the
identity of the transgene construct is important.  For example "a
previously unpublished insertion of P{lArB} into 27C" is much more
informative than "an enhancer trap insertion on the second

You need only tell us the FlyBase symbol which represents each object
you discuss once in each paper. You may prefer to use nicknames rather
than FlyBase nomenclature throughout the rest of your paper, but if you
have followed our guidelines clarity will have been attained.  Any name
used by you that is not a FlyBase valid symbol is stored as a synonym,
so that anyone searching FlyBase using your symbol will find the
FlyBase object they are looking for.

An aside concerning sequence-level data: FlyBase is trying to map many
data types to the genomic sequence.  For such data, it would help 
immeasurably if you would identify an unambiguous sequence reference 
point or feature to which other sequence coordinates can be accurately 
related.  This can simply be a small stretch of unique sequence 10-20bp 
long; transcription and translation start sites do not qualify as 

We hope you find this useful.  If you would like to follow these
guidelines but are unsure about which symbol/identifier number
corresponds to your gene, allele or construct, we would be delighted to
help you figure it out as you put your manuscript together.  Just write
to us at  We can also help with naming
new things.  Our nomenclature document gives general guidelines but we
are always happy to give specific advice for your particular

Best regards,

the FlyBase literature curators.