from Dave Matthews, Dec 1993
updated May 1998
How to Create Locus and Map_Data Records for GrainGenes
In GrainGenes a map is made up of one Map_Data record, a Locus record
for each of the loci, and accessory records of various types: Reference
records for the references, Germplasm records for the parents of the
mapping population, Probe records for the probes used, etc.
Below is a description of the fields used in the Locus and Map_Data
records. To submit data, enter your values between the pairs of double-
quotes ("), as shown in the examples. For fields that have no data, such
as Associated_gene in the example Locus record, delete the entire line.
LOCUS RECORDS:
DATA ENTRY FORM
Locus : ""
Type ""
Associated_gene ""
Probe ""
Mapped_bands "" "" ""
Map ""
Position ""
Chromosome ""
Chromosome_arm ""
EXAMPLE SYNTAX NOTES
Locus : "psr177"
Type "RFLP"
Probe "PSR177"
Mapped_bands "EcoRV" 9.3 "Ace CItr13384" Omit "s for all numeric fields.
Mapped_bands "EcoRV" 8.4 "Baca CItr15891"
Map "Ta-Tsunewaki-7A"
Position 23.4
Chromosome "7A"
Chromosome_arm "7AS"
EXPLANATION
Column heading Sample Entry Description or List of Choices
-----------------------------------------------------------------------------
Locus psr177, XHis2 Name of locus
Type RFLP Gene,RFLP,RAPD,Microsatellite,QTL
Centromere
Associated_gene Adh-A1 (Triticum) If the locus is a gene, give the
gene Name here
Candidate_gene Adh-A1 (Triticum) If the locus was mapped with a
known-function probe but is not
known to be the locus of the gene
itself
Probe PSR177 Name of probe
Mapped_bands "EcoRV" 9.3 Restriction enzyme, band size in Kb,
"Ace CItr13384" parent's Germplasm ID.
Map Ta-Tsunewaki-7A Name of linkage group, of a
particular map of a particular
species, where the locus is. (Will
be assigned by GrainGenes staff.)
Position 23.4 Position on this linkage group,
in the map's units
Chromosome 7A Chromosome where the locus is
Chromosome_arm 7AS Chromosome arm (A value should
ALSO be given for Chromosome.)
MAP_DATA RECORDS:
DATA ENTRY FORM SYNTAX NOTES
Map_Data : "" For values that are longer than one line,
Species "" as in the Remarks field, end each line
Female_parent "" except the last with " \".
Male_parent ""
Map_units ""
Reference ""
Contact ""
Remarks ""
Locus "" ""
EXAMPLE:
Map_Data : "T.tauschii, Gill"
Species "Triticum tauschii"
Female_parent "Triticum tauschii TA1691"
Male_parent "Triticum tauschii TA1704"
Map_units "cM"
Reference "ITM-92-27"
Contact "Gill, Bikram S."
Remarks "Parents are D genome wheat diploids. F2 families from 60 \
selfed F1 individuals were scored for 196 markers. Map units are cM, \
Kosambi-corrected."
Locus XksuA1 "HBHHH HAHHB HBBHH HBBBB HBHAB B-HAB HABH- BBHB- ABHHA \
HHBBA -HHHB HHBBH"
Locus XksuA3 "AAAHA AHBHH HHHAH BABAH HHHAH H-HBA HHHH- AAHH- HHHHB \
HHAHA -HHHB AAHHA"
Locus XksuA6 "ABAAA HAHHA AAAHB AAABA HAAAA --H-A HAHAA B--AA HHHHH \
BHHHH BHHHH AB-HH"
...
EXPLANATION
Column heading Sample Entry Description or List of Choices
-----------------------------------------------------------------------------
Map_Data Wheat, Anderson Name will be based on the common
name of the organism and the lab or
person who made the map. (Assigned
by GrainGenes staff.)
Species Triticum aestivum Name of a Species. If map is
derived from an interspecies cross,
list both.
Female_parent NY6432-18 Name of a Germplasm
Male_parent Clark's Cream Name of a Germplasm
Map_units cM, Haldane What are the units for the map
positions given for the loci
Reference CRS-33-453 Reference ID for the reference (see
"Constructing reference IDs").
Include the entire reference as a
separate record.
Contact Anderson, James A. Name of a Colleague
Remarks 78 F5 RI lines... Description of the mapping
population, mapping software, number
of loci, etc.
Locus, Segregation Xpsr177 113133013.. For each locus in the map, give the
list of mapping-population scores.
If the scores are not available,
just list the loci. Locus names
should be "GrainGenes-names", as used
for the Locus records.
Wherever the word "Name" is used above, it refers to the unique
identifier of a GrainGenes data record. If the record already exists in
the database, the Name must match the existing Name exactly. For example
the database should be searched to determine that the correct formulation
of the Contact value in the Map_Data example is "Anderson, James A." as
shown above rather than "Anderson JA", "Anderson, James", etc.
The only exception to this requirement for matching existing Names is
in the Names of Locus records themselves. Locus records should be named
exactly as they were when published. If they have not been published yet,
name them according to the wheat or barley rules described in "Naming loci",
in this menu.
WHAT'S THE LEAST I CAN DO?
The question sometimes arises, what are the minimum requirements for a
map in GrainGenes? What's the next-most valuable thing to add? And so on.
Here's a rough guide.
Minimum:
- Picture of the map, with positions or interval distances indicated, on paper
- Names and/or accession numbers of the parents of the mapping population
- What species?
- Reference, if published
- Who should be listed as the "Contact" for the data, i.e. who gets the credit
- Address information for Contact (if not already in the database)
Very useful:
- Raw mapping data
- Description of the probes used (if not already in the database)
- Description of any genes on the map (if not already in the database)
- Description of the population type and mapping procedures
Extra nice:
- Picture of the map, with positions or interval distances indicated, on disk
- Table of positions or intervals, on disk
Optimal:
- Labeled images of gels/autoradiograms, showing which bands were mapped
- Numeric estimates of the band sizes
- Everything in ACEDB format, ready to load
- Everything cross-checked against the existing database for items (Germplasm,
Probe, Colleague etc.) that are already in it under a slightly different
name