CottonGen FAQ

Topics

About CottonGen

  1. What is CottonGen? last update 01/23/24 
  2. What data and information does CottonGen contain? last update 01/23/24 
  3. How is CottonGen supported? last update 01/23/24
  4. How is CottonGen structured?
  5. How do I cite CottonGen? last update 01/23/24
  6. How can I contact CottonGen?

Data Curation, Submission, and Download last update 01/31/24 

  1. Can I submit my data to CottonGen?
  2. Can I download data from CottonGen?
  3. Who should I contact if I think I have found a mistake in the database?
  4. Who contributes data and/or assistance to CottonGen?
  5. How can I find out what’s new in CottonGen?
  6. How do I know what’s coming next in CottonGen

CottonGen Data last update 01/24/24

  1. Do I need a CottonGen account to access data?
  2. What types of markers does CottonGen house? 
  3. Is there a tutorial or help section on how to find marker information?
  4. What types of maps does CottonGen house?
  5. Can I view a list of all the maps with detailed information, such as genome, population size, etc?
  6. Is there a tutorial or help section on how to use MapViewer?
  7. Is there a tutorial or help section on how to use the Genome Browser (JBrowse) viewer?
  8. What genome data is available on CottonGen GBrowse?

CottonGen BIMS (Breeding Information Management System) v2022

  1. What is BIMS?
  2. How do I use BIMS?
  3. BIMS FAQ

 

  About CottonGen

  • What is CottonGen?

CottonGen is the long-established cotton community's genomics, genetics, and breeding database.  It provides a comprehensive collection of data, various analysis tools, a Breeding Information Management System, and links to external resources of interest to cotton researchers.  The CottonGen database was released in 2012 based on the consolidation and expansion of the data from CottonDB (established in 1995) and the Cotton Marker Database (established in 2002) with enhanced tools for easy querying, visualization, and downloading of research data. CottonGen is built using the open-source Tripal database infrastructure. 

 

  • What data and information does CottonGen contain? 
The current major data components of CottonGen (*green are hyperlinks to data or data searches):
More information on searching these data types can be found in the CottonGen User Manual: Data Searches.  For details on data numbers, please see the Data Overview Page.
  •  How is CottonGen Supported?
The CottonGen project is funded by:
  •  How is CottonGen structured?
CottonGen uses Tripal, a toolkit for construction of online genomic and genetic databases.  Tripal provides a web-front end for the Generic Database schema Chado which houses biological data. Tripal also integrates with Drupal, a Content Management System (CMS) that enables non-technical users to provide content, provides user management and social capabilities, and provides site developers with an interface that facilitates easier construction of websites.
  •  How do I cite CottonGen?
If you use CottonGen data or tools in your research, please use the following citation to reference us (not the database URL):
Yu, J, Jung S, Cheng CH, Lee T, Zheng P, Buble K, Crabb J, Humann J, Hough H, Jones D, Campbell JT, Udall J, Main D (2021) CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research.  Plants 2021, 10(12), 2805
Yu J, Jung S, Cheng CH, Ficklin SP, Lee T, Zheng P, Jones D, Percy R, Main D (2014) CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic Acids Research 42(D1), D1229-D1236.
 
To cite original data sources, look for the "Publication" link in the left-hand menu of CottonGen feature pages.
  • How can I contact CottonGen?
    The CottonGen staff can be reached via this contact form, or by selecting "Contact Us" under Help in the header menu.

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Data Curation, Submission and Download

  • Can I submit my data to CottonGen?
We accept data that is peer-reviewed via manuscript submission. You can prepare your data by following our Data submission templates for the most common data such as markers, maps, QTLs, GWAS, etc., and then email them to us. If you have any questions please contact us using this contact form and we will work with you to input your data.  If you have an expression or genomic data, please contact us before attempting to submit it.
  • Can I download data from CottonGen?
Yes.  There are different ways to download data from CottonGen:
  • Via the Download page for genome annotations and other large static bulk data sets
  • CottonGen chado data can be downloaded through CottonGen-related search pages.  After completing a search you have the option to download the matching data (refer to the CottonGen User Manual: Data Searches for details).
  • CottonGen Map data can be downloaded via the Map Data Summary page: Click on the map name to go the map you want to download, then click on 'Map Loci' and 'Map QTL', then copy and paste to same the map data.
  • CottonGen genome alignment data and sequences under a specific chromosome and region can be downloaded via CottonGen JBrowse (refer to this JBrowse video tutorial for details). 
  • Who should I contact if I think I have found a mistake in the database?
Please contact us via this contact form, or by selecting "Contact Us" under Help in the header menu.
  • Who contributes data and/or assistance to CottonGen?
CottonGen has several collaborators and many contributors. See our Data Contributor page for details.  If you are looking for a specific individual, you can search using their name here.
  • How can I find what’s new in CottonGen?
You can find what has recently been accomplished on the Work Completed page, found under General in the header menu.
  • How do I know what’s coming next in CottonGen?
You can find work in progress at CottonGen through the Work in Progress page, found under General in the header menu.

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CottonGen Data

  • Do I need a CottonGen account to access data?
No, you do not need an account to view publicly available data.  CottonGen also houses private breeding data for which breeders need an account to access and transfer.
However, we encourage you to join the CottonGen.org Mailing List by sign-in [HERE], filling in the requested information and checking the box of 'CottonGen Mailing List' (and the box of 'ICGI Member' as you want), for reason that you can get more recent updates/news, short-training videos, newsletters, and for all types of communication about cotton genomics, genetics and breeding research: questions, concerns, community announcements, and employment, etc.)  
  • ​What types of markers does CottonGen house?
  • All current marker types are listed at the Marker Type Table. The majority of markers in this database are SNPs and SSRs. 
  • All marker types are searchable from the CottonGen Marker Search. 
  • The Data Overview page lists the number of each marker type.
  • Is there a tutorial or help section on how to find marker information?
Yes.  Please see the CottonGen User Manual: Markers.
  • What types of maps does CottonGen house?
CottonGen currently has over 123 maps total, including genetic (many with QTLs), bin, consensus, physical, association, and in silico maps. These can be viewed through Search Map page.
  • Can I view a list of all the maps with detailed information, such as genome, population size, etc?
Yes. The complete list of maps available on CottonGen, including map details, is available on the Map Data Summary page.
  • Is there a tutorial or help section on how to use the Map Viewer?
Yes.  please view a short training video on How to get started with MapViewer
More MapViewer's Video tutorial, User Manual, and more examples can be found from the session of  'Learn more about MapViewer' on CottonGen's MapViewer Page
  • Is there a tutorial or help section on how to use JBrowse?
Yes. Please see this JBrowse video tutorial.
  • What genome data is available on CottonGen JBrowse?
The page CottonGen JBrowse lists all current whole genome sequences. Click on the genome name from the list to learn about the details of the assembly.

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Breeding Information Management System (BIMS)

  • What is BIMS?
CottonGen BIMS (Breeding Information Management System) is a Tripal module being developed by Mainlab Bioinformatics which allows users to explore the publically available breeding data in CottonGen while also providing a data management solution for private breeding programs.
  • How do I use BIMS?
The BIMS user manual is available here.

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