Difference between revisions of "FlyBase:Author Guidelines"

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(Laura and I are working on this)
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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 make your paper more accessible to FlyBase curators. Following these steps will make it easier for FlyBase curators to correctly identify the genes and fly lines used in your paper. You’ll be helping FlyBase get it right, improving the service to all our users and helping the dissemination of your research.
  
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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. Unambiguously identify the existing genes or fly lines (alleles, deficiencies, transgenes, insertions) 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 Bloomington or the VDRC
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*The reference in which the line was first generated.
  
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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. Be explicit when you’ve generated a new fly line in your paper and provide details.'''
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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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* 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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* 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.  Clearly state the FlyBase release (e.g. FB2014_06) used when referring to data obtained from FlyBase'''
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* This is found in the header and footer of  every FlyBase page
  
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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. 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.'''
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* The current genome release is found in the header of [http://flybase.org/cgi-bin/gbrowse2/dmel/ GBrowse] or in the [http://flybase.org/static_pages/docs/release_notes.html Release Notes]
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*For those preferring a stable reference annotation set for their work, we recommend the NCBI RefSeq set (submitted annually by FlyBase).   
  
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the FlyBase literature curators.
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'''5.  When naming a gene for the first time, follow the guidelines in our [http://flybase.org/wiki/FlyBase:Nomenclature nomenclature document] and/or [http://flybase.org/cgi-bin/mailto-fbhelp.html contact us] *prior to publication* to check validity'''
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'''6.  After publication, use the [http://flybase.org/submission/publication/ Fast-Track Your Paper tool] to alert us.'''
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* 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 [http://flybase.org/submission/publication/ Fast-Track Your Paper (FTYP) tool]. If you do not receive an email, click the icon on the FlyBase homepage.
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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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* 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.  Finally, please [http://flybase.org/cgi-bin/mailto-fbhelp.html contact us] if you have any other queries relating to integration or display of your data.'''
  
 
[[Category:In Progress]]
 
[[Category:In Progress]]

Revision as of 08:36, 29 October 2014

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 make your paper more accessible to FlyBase curators. Following these steps will make it easier for FlyBase curators to correctly identify the genes and fly lines used in your paper. You’ll be helping FlyBase get it right, improving the service to all our users and helping 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.


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. 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.


7. 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.


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

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