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GENica CMap General Map Set Information

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General map set information required in CMap Live

  • Beside the actual map set import file, entries for the fields listed here have to be available before a map can be transferred to CMap Live. When choosing entries for these fields, please take the CMap Live conventions and the currently available options into account, as described on this page. Click on the name of a field to jump to the relevant section.
  • If using GENica CMap Staging to prepare a map set for transfer to CMap Live, this information can be entered with the CMap Staging admin tools before advising GENica CMap curator that a map is ready to be transferred to CMap Live.
  • If you do not have access to GENica CMap Staging, please provide GENica CMap curator with entries for these fields in a message accompanying the CMap import file for your map.


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Choosing a "map set name" and "short name"

  • The map set name and abbreviated name are the only available information when selecting maps through the CMap "Maps" menu option. They should therefore be chosen to be short, yet as informative as possible.
  • Please consider these guidelines when deciding on a map set name:
  1. The name and the short name are both unique within CMap Live. Please check the CMap Live map set info webpages for map set names already in use.
  2. The "map set name" can be up to 64 characters long, the "short name" is limited to 30 characters.
  1. A map set's name should whenever possible follow the following format:
    <Descriptive Name> - <Map Author> - <Date of Publication>
    Example: Steptoe x Morex - Stein - 2006
    1. Descriptive Name:
      • If a map has been sourced from the literature or an on-line resource: The name is as close as possible to the map's pre-existing name.
      • If a map set was generated by analysing a population derived from a 2-parent cross, this should be indicated by giving the female parent's name first, separated with " x " (space-x-space) from the male parent's name (e.g. Igri x Franka).
      • The abbreviation "GG" can be used in a descriptive name to mark maps that were transferred from "GrainGenes", e.g. "Consensus GG".
      • The abbreviations "C", "C1", etc. are reserved for marking different versions of "composite maps", e.g. "Clipper x Sahara C", "Clipper x Sahara C1".
      • Abbreviated germplasm names should be avoided in the full-length descriptive name, if possible, but are preferred when choosing the short name for a map set.
        • "GrainGenes" does not provide an extensive list of germplasm abbreviations, however, you can check if an abbreviation is recorded for a given variety by searching the GrainGenes "Germplasm" browser. If an abbreviation exists, it will be listed next to "Synonym" (see e.g. the Germplasm Report for "Chinese Spring").
        • Inversely, you can search if an abbreviation you want to use is already recorded for another variety in GrainGenes (Find out how...).
    2. Map Author:
      • Where available and when space permits, the surname of the person who generated the map or who is first author of a publication presenting the map should be inserted after the descriptive name, separated by " - " (space-dash-space) from the map's descriptive name.
    3. Date of Publication:
      • Where available and when space permits, the year (or even month and year, as seems appropriate) when a map was generated or published should be provided after the author name, separated by " - " (space-dash-space) from the author's name.

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Choosing a "species"

  • Please refer to the Species Info webpage to see a list of "Species" currently existing in GENica CMap Live.
  • Because GENica CMap Live includes numerous versions of some wheat and barley map sets, it provides the "Species" categories "Wheat Curated" and "Barley Curated", to be used only for the most recent or best-quality versions of wheat and barley map sets, in addition to "Species" categories "Wheat" and "Barley", which may contain other versions of these map sets.
  • When adding an updated version of one of your map sets to CMap Live, please point this out to the GENica CMap curator, so the "Species" entry of the previously posted map sets can be changed accordingly, e.g. from "Wheat Curated" to "Wheat" (if applicable).

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Choosing a "map type"

  • Please inform the GENica CMap curator whether your map set's type is "Physical (Kb)", "Relational (bp)" or "Genetic (cM)", or if another "map type" has to be created.

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Providing "Reference(s)"

  1. Wherever possible, a reference to a printed or online publication in a peer-reviewed journal should be provided.
  2. If no published reference is available which meets the above criteria:
    1. If the map is derived from an online source (e.g. GrainGenes, a research group's personal webpage, ...):
      • Please provide the name of the database, its URL, and give the date when information was cited / downloaded. The URL can alternatively be provided as an aptly named link in the "Cross Reference" field, see the section below.
      • If the GENica CMap Live name for a map is different from the name used in its online source, provide the original map name as given online. Ideally, copy / paste a map name into this section to prevent typing errors.
    2. If the map is published in a thesis:
      • Aside from the notation "Ph.D. Thesis", "M.A. Thesis" or the like, theses are treated like a book reference, with the department from which the degree was earned used as the publisher (e.g.: Appels R (1972) Ph.D. Thesis. The biochemistry of cellular control mechanisms: the characterisation of chromatin from avian erythroid cells. University of Adelaide, Department of Biochemistry, Adelaide, p 29).
    3. If it is not possible to provide a reference to a journal, book, thesis or online publication of a map:
      • Please enter the full name of the map's main creator and contact information, followed by "unpublished results". Contact information should be sufficiently detailed to enable anyone visiting the webpage to reach the map's creator (e.g. "Matthew Hayden, Plant Genomics Centre, University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia, http://www.adelaide.edu.au/, unpublished results"). Alternatively, a link to a web page with contact information can also be provided as a "Cross Reference", see the section below.

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Providing "QTL" information

 Instructions for what information should be provided on QTLs in a map set are yet to be decided on by the GENica CMap leader.
 Julia Brueggemann, 13 April 2007

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Further relevant information

  • The "Notes" section is used to provide any further pertinent information on a map set. If, however, there is a need for another special category, an accordingly named "map set attribute" can be created, please contact the GENica CMap curator.
  • If a map is exactly as published in the reference(s) provided, please state this here.
  • If no published or online reference can be provided for a map set, or if a map set was edited after being published in print or online, provide full details on how the map set was generated, and / or which other map sets were used to generate it (e.g. in the case of "composite maps"). If space is insufficient to provide this information, please provide your contact details and / or a webaddress where further details can be found. A link to a webpage with supplementary information can equally be placed into the "Cross Reference" field, see below.

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Providing "Cross Reference(s)"

  • If information on a map is available online, you can provide the URL, plus a "Name" (optional) for the link to be displayed in CMAP.
  • If more than one cross reference is required, please indicate which URL and name belong together, and in which order to display the cross references.
  • Example: (Compare these "URL" and "Name" details to the CMAP Cross References shown below.)
  • What you provide: 
  URL1: http://wheat.pw.usda.gov/cgi-bin/graingenes/report.cgi?class=mapdata&name=Barley,+BinMap+2005 
  Name1: Link to GrainGenes Map Data Report for "Barley, BinMap 2005"
  URL2: http://barleygenomics.wsu.edu/
  Name2: Link to information on Andris Kleinhofs' work on the WSU Barley Genomics website
  URL3: http://www.genica.net.au/cmap/crcmpb-live/
  • How these cross references are displayed in CMap Live:
Link to GrainGenes Map Data Report for "Barley, BinMap 2005"
Link to information on Andris Kleinhofs' work on the WSU Barley Genomics website
http://www.genica.net.au/cmap/crcmpb-live/

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The "Record submitted by" entry

  • If questions about a map set arise (e.g. to ask if a particular map is of continuing interest when a more recent version has become available), the GENica CMap curator may choose to refer these to the person who prepared the data for CMap Live. This is why a contact name should be provided.
  • The person who has submitted the record need not be identical to the person who has created the map.
  • If no name is provided, the name of the person requesting that a map is transferred to CMap Live is entered here.

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Links to related pages

Data standards and instructions:

Go to the actual CMap installations:


This information has been prepared according to the "GENica CMap Live Data Standards", version 1, and the "GENica CMAP Contributors' Roles" description, version 2.
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