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. You can also watch a Video tutorial Author Guidelines.

1. If your publication includes research/data about Drosophila melanogaster, then ensure your title/abstract says so!

• include the text 'Drosophila' or 'Drosophila melanogaster' or 'D. melanogaster' in the title and/or abstract. This will ensure your publication is identified and indexed for inclusion in FlyBase.

2. Unambiguously identify the genes or genetic reagents (alleles, deficiencies, transgenes, insertions etc) 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 BDSC or VDRC
• The reference in which the reagent was first generated
• Reagents are best reported using the FlyBase author reagent table. We encourage you to complete and submit this table for publication along with your manuscript.

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

• 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.
• In these cases, a valid FlyBase symbol and FBid will be assigned during curation and processing by FlyBase.

4. Clearly state the FlyBase release (e.g. FB2020_06) used when referring to data obtained from FlyBase

• Data are updated in FlyBase approximately every 2 months and so are subject to change
• The FlyBase release number is found in the header and footer of every FlyBase page

5. Similarly, when reporting genomic location data, 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 JBrowse and in the Release Notes
• For those preferring a more stable reference annotation set for their work, we recommend the NCBI RefSeq set (submitted annually by FlyBase) as shown on our archives page

6. 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

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

• These formats facilitate computational integration of large data sets
• 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.

8. After publication, use the FlyBase Fast-Track Your Paper tool.

• This accelerates getting the data from your paper into FlyBase
• Shortly after being indexed in PubMed, the corresponding author should receive an email from FlyBase with a personalised hyperlink to the tool
• If you do not receive an email, click the Fast-Track Your Paper icon on the FlyBase homepage.

9. Finally, please contact us at any stage of the publication process if you have any other queries relating to integration or display of your data in FlyBase.