FlyBase:Author Guidelines

Advice to authors: how to improve your data in FlyBase

Here, we detail a few small steps you can take, both during the writing process and after publication, to facilitate accurate incorporation of your data into FlyBase. By helping FlyBase get it right, you'll be improving the service to all our users and aiding the dissemination of your research.

1. Unambiguously identify the existing genes or fly lines (alleles, deficiencies, transgenes, insertions) used in your paper by including one of the following:

• Unique FlyBase Identifier - consisting of ‘FB’ and then 7 digits - found on every report page, in the 'FlyBase ID' box in the top right hand corner.
• Approved FlyBase symbol - found on every report page, in the 'Symbol' box in the top left hand corner.
• Stock center ID - e.g., as assigned at Bloomington or the VDRC
• The reference in which the line was first generated.
• This is all best done using the FlyBase author reagent table. We encourage you to complete and submit this table for publication along with your manuscript.

2. Be explicit when you’ve generated a new fly line in your paper and provide details.

• In these cases, a valid FlyBase symbol and FBid will be assigned during curation and processing by FlyBase.
• E.g. For transgenic constructs, provide the name of the vector (e.g. pUAST), the relevant regulatory and coding sequences present, and the relationship to any previously published constructs.

3. Clearly state the FlyBase release (e.g. FB2014_06) used when referring to data obtained from FlyBase

• This is found in the header and footer of every FlyBase page

4. When reporting genomic location, state the genome release used (e.g. D. melanogaster release 6.02) and use genomic coordinates (e.g 2L:12,487,248) or a short unambiguous sequence (>20 bases). Gene-specific landmarks (e.g. transcription start, exon number) are subject to change.

• The current genome release is found in the header of GBrowse or in the Release Notes
• For those preferring a stable reference annotation set for their work, we recommend the NCBI RefSeq set (submitted annually by FlyBase).

5. When naming a gene for the first time, follow the guidelines in our nomenclature document and/or contact us *prior to publication* to check validity

6. Provide supplementary data files in tab separated value (.tsv), spreadsheet (.xls), bed, gff3 or wig (not pdf or image) formats.

• Provide a clear explanation of what each column represents.
• Specify a threshold that distinguishes high confidence results within a larger set. E.g., a cut-off at which a phenotype is judged significant, or the high confidence hits within an RNAi or mass spectometry experiment.

7. After publication, use the Fast-Track Your Paper tool to alert us.

• Shortly after being indexed in PubMed, the corresponding author should receive an email from FlyBase with a hyperlink. You can help get the data from your paper into FlyBase more quickly by clicking on the link in the email and using the Fast-Track Your Paper (FTYP) tool. If you do not receive an email, click the icon on the FlyBase homepage.

8. Finally, please contact us if you have any other queries relating to integration or display of your data.