Difference between revisions of "FlyBase:Author Guidelines"

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Here, we list some guidelines that would greatly aid our curation of your papers. Where followed, they will increase not only the number of papers we can curate, but also the accuracy of our curation, so improving our service. Moreover, following these guidelines will enable the readers of your articles to easily and unambiguously identify the specific genes and genetic reagents you refer to and use.
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<big>'''Advice to authors: how to improve your data in FlyBase'''</big>
  
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'''Use unique identifiers'''
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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 [https://www.youtube.com/watch?v=HsoWqclXMng Author Guidelines].
  
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* It is helpful if you state somewhere in your paper (for example, in parentheses upon its first mention in the text) the FlyBase valid symbol, annotation ID, or FlyBase identifier (FBid) for the genes to which you refer. For example, when discussing the gene 'chpd', state that it is known in FlyBase as amn, CG11937 or FBgn0000076.
 
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* FlyBase also gives unique valid symbols and FBid's to all other genetic objects. These include: alleles (e.g. amn[1], FBal0000500), aberrations (e.g. Df(2L)BSC4, FBab0029533), transgenic constructs (e.g. P{UAS-dpp.S}, FBtp0011928) and transgenic insertions (e.g. P{UAS-dpp.S}42B.4, FBti0001019). We also recommend that you use or mention the valid FlyBase symbol or FBid when using or referring to such genetic reagents - the Materials and Methods section is an ideal place to do this.
 
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* FBid's are found within the General Information section at the top of all report pages in FlyBase.
 
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* You need only tell us once the valid FlyBase symbol or FBid that represents each object you discuss in your paper. Any symbol/name used by you that is not a valid FlyBase symbol/name is stored as a synonym, so that anyone searching FlyBase using your symbol will still find it.
 
  
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'''Be explicit'''
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'''1. If your publication includes research/data about ''Drosophila melanogaster'', then ensure your title/abstract says so!'''
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* 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.
  
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* Sometimes, it can be difficult for us to decide whether a reagent (allele, construct, etc.) described in a paper is "new" or has been previously published. If it is new, please be explicit in stating this. (In these cases, a valid FlyBase symbol and FBid will be assigned post-publication during curation and processing by FlyBase.)
 
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* If you characterise a gene, and identify a CG annotation that belongs to that gene, state this explicitly in the text of the paper so we can attribute the identification to you.
 
  
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'''Be complete'''
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'''2. Unambiguously identify the genes or genetic reagents (alleles, deficiencies, transgenes, insertions etc) used in your paper by including one of the following:'''
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* 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.
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* Approved FlyBase symbol - found on every report page, in the 'Symbol' box in the top left hand corner.
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* Stock center ID - e.g., as assigned at [https://bdsc.indiana.edu/ BDSC] or [https://shop.vbc.ac.at/vdrc_store/ VDRC]
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* The reference in which the reagent was first generated
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* Reagents are best reported using the FlyBase '''[[FlyBase:Author_Reagent_Table|author reagent table]]'''. We encourage you to complete and submit this table for publication along with your manuscript.
  
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* When describing insertions, for example, the identity of the transgenic construct is important. "A previously unpublished insertion of P{lArB} into 27C" is much more informative than "an enhancer trap insertion on the second chromosome".
 
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* 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.
 
  
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'''3. Be explicit when you’ve generated a new fly line in your paper and provide details.'''
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* 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.
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* In these cases, a valid FlyBase symbol and FBid will be assigned during curation and processing by FlyBase.
  
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We hope you find these guidelines useful. If you are unsure about which symbol/FBid corresponds to your gene, allele or construct (etc), or what symbol/name would be appropriate for a new genetic object you describe, we would be delighted to help you as you put your manuscript together, prior to publication. Our nomenclature document gives general guidelines, but don't hesitate to contact us if you have any further questions.
 
  
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Best regards,
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'''4.  Clearly state the FlyBase release (e.g. FB2020_06) used when referring to data obtained from FlyBase'''
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* Data are updated in FlyBase approximately every 2 months and so are subject to change
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* The FlyBase release number is found in the header and footer of every FlyBase page
  
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the FlyBase literature curators.
 
  
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[[Category:DONE]]
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'''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).'''
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* Gene-specific landmarks (e.g. transcription start, exon number) are subject to change
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* The current genome release is found in the header of [https://{{flybaseorg}}/jbrowse/?data=data%2Fjson%2Fdmel JBrowse] and in the [http://{{flybaseorg}}/cgi-bin/get_static_page.pl?file=release_notes.html&title=Release%20Notes Release Notes]
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* 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 [https://{{flybaseorg}}/downloads/archivedata archives] page 
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'''6.  When naming a gene for the first time, follow the guidelines in our [http://{{flybaseorg}}/wiki/FlyBase:Nomenclature nomenclature document] and/or [http://{{flybaseorg}}/contact/email contact us] *prior to publication* to check validity'''
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'''7.  Provide supplementary data files in tab separated value (.tsv), spreadsheet (.xls), bed, gff3 or wig (not pdf or image) formats.'''
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* These formats facilitate computational integration of large data sets
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* Provide a clear explanation of what each column represents
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* 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.
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'''8.  After publication, use the FlyBase [http://{{flybaseorg}}/submission/publication/ Fast-Track Your Paper] tool.'''
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* This accelerates getting the data from your paper into FlyBase
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* Shortly after being indexed in PubMed, the corresponding author should receive an email from FlyBase with a personalised hyperlink to the tool
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* If you do not receive an email, click the Fast-Track Your Paper icon on the FlyBase homepage.
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'''9.  Finally, please [http://{{flybaseorg}}/contact/email 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.'''
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[[Category:In Progress]]

Latest revision as of 16:03, 15 February 2024

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.

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