GENica CMap Live Data Standards

1 Map set selection criteria
2 Map set information
3 Import file preparation
4 Locus naming conventions
5 Use of feature types
6 Revisions and exceptions
7 Links to related pages

Map set selection criteria

To be included in GENica CMap Live, a map set should be for a plant species of interest to MPBCRC participants, and:

be as published in a peer-reviewed journal, or
be as published on a curated website such as GrainGenes or Gramene, or
have been carefully updated or curated (e.g. composite maps generated by combining several maps, post-publication curation by the GRDC map curation project).

Map set information

For a map set to be included in GENica CMap Live, entries should be provided for the following fields, as outlined in the GENica instructions for map set information.

Map set name [required]

The map set name must be unique within GENica CMap Live, should be informative and, where possible, should reflect the name used for the map set in the source from which the map was derived. The use of "C", "C1", etc. is reserved for marking "combined maps".

Short name [required]

The short map set name must be unique within GENica CMap Live, should be informative and, where possible, should reflect the name used for the map set in the source from which the map was derived. The use of "C", "C1", etc. is reserved for marking "composite maps". The field is limited to 30 characters.

Species [required]

Because GENica CMap Live includes numerous versions of some wheat and barley map sets, it provides the additional "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 the "Species" categories "Wheat" and "Barley", which may contain other versions of these map sets.

Map type [required]

Reference(s) [required]

Complete reference information (if available), following the "instructions to authors" published by "Theoretical and Applied Genetics", or the full name and contact information of the main creator of the map set.

QTL [required, if applicable]

Notes [required]

If a map set is as published in a reference, this should be stated. If a map set has been edited after being published, or if no published information is available, full details should be provided on how the map set was generated (e.g. which component maps and what processes were used to generate consensus maps).

Record submitted by [required]

Full name and contact information of the person who has prepared the map set for import to CMap Live.

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Import file preparation

Map data are imported into GENica CMap in tab-delimited files formatted as specified by GMOD and prepared as described in the GENica instructions for preparing import files for CMap.

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Locus naming conventions

CMap can identify possible homologies in locus order and location between different genomes, but only when loci have identical entries under "feature name" or "aliases".
For a given map, feature names (that are displayed in the map viewer) should be chosen according to a consistent system.
Where possible, the following considerations should be taken into account when entering feature names and / or aliases:

"X" is not necessary in front of marker names (gwm197 instead of Xgwm197)
Chromosome locations are not required after marker names (gwm107 instead of gwm107-3B)
Numbers need not be preceded by leading zeros (wmc50 instead of wmc0050)
Marker names need not be written in italics
Marker names written in lower case (e.g. gwm107) or in mixed case (e.g. EBmac623) can be easier to read than if they are converted to all upper case (e.g. GWM107)
Letter suffixes are the preferred way of indicating multiple loci (gwm107b instead of gwm107.2)
For EST markers, entering the NCBI GenBank accession ID (e.g. EF212872) as a feature name and / or alias allows linking to the relevant GenBank entry
For AFLP markers, the preferred format is as in this example: P32/M50-138 (instead of E32M36d, E03M30-3, etc.)
QTLs:
1. A wheat QTL format was provided in the 1998 Wheat Gene Catalogue, section 6.2.2:
  "Locus symbols: The 'Q' should be followed by a trait designator, a period, a laboratory designator (see Section 5.6 [of the 1998 Wheat Gene Catalogue]), a hyphen (-) and the symbol for the chromosome in which the QTL is located. The trait designator should consist of no more than four and preferably three letters, the first of which is capitalized. Different QTLs for the same trait that are identified in one chromosome should be assigned the same symbol except for the addition of a period and an Arabic numeral after the chromosome designation. All characters in the locus symbol should be italicized. For example, QYld.psr-7B.1 and QYld.psr-7B.2 would designate two yield QTLs identified in chromosome 7B by the John Innes Centre. On a map of 7B, these could be abbreviated as QYld.psr.1 and QYld.psr.2."
2. GrainGenes povides a format for barley QTLs that may be useful for both barley and wheat:
  "The proposed name for the barley QTL, consisting of a "Q", a 2-4 letter acronym for the trait, a ".", a four letter string of the first two letters of the parents, a "-", and the "H" chromosome, e.g. QHD.StMo-2H. See the "Traits" worksheet in this workbook (i.e. the GrainGenes barley QTL workbook) for the current trait list."

(This list of considerations is based on the outcome of a GRDC-funded workshop led by Rudi Appels.)

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Use of feature types

A feature type should be indicated for each feature, see the CMap instructions how to enter this information in the map data import file.

If information on a "biological aspect" of a feature is available, then the corresponding 'biological' feature type (e.g. "Gene" or "Traitlocus") should be used, in preference to a feature type describing a 'technical aspect' of how the feature was detected (e.g. "SSR" or "RFLP").
For marker loci for which a biological feature type cannot be assigned, use the specific marker type (e.g. "RFLP" or "SSR").
If specific biological or technical information is not available, or if there is any doubt about the appropriate feature type, choose the generic feature type "Locus" (any feature that has been genetically mapped).

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