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Map Curation on GrainGenes
Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson
Biological Databases Curators Meeting
October 2003
The Maps and Map Data page has links to articles, raw data and line maps
‘Map’ of CS x CheyenneDisomic Substitution
Raw Mapping data of CS x Cheyenne Disomic Substitution
The Maps and Map Data page has links to articles, raw data and line maps
Web Summary of Interactive Maps links to the GrainGenes database
Flavors of GrainGenes Maps
Genetic: Loci mapped byrecombination frequency inSynthetic x Opata
Flavors of GrainGenes Maps
Highlighted loci have bestBLAST hits.
Consensus: combined maps of hexaploid wheat by Sorrells et al.
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Wheat and Barley Public EST Resources
Flavors of GrainGenes Maps
Physical: loci mapped byphysical placement ona chromosome.
This is a deletion map from the U.S. wheat genome project.
Sequence Records from the NSF ESTs contain thesupporting data and linksto maps supported byother projects:
QTL map from a barleymalting quality study
Interactive Map Construction
1. Identify relevant maps from the literature, usually from Theoretical and Applied Genetics
find Reference Keyword=map* & Year=2002results in 186 objects
2. Contact authors to acquire raw data and a spreadsheet with loci and chromosome positions
3. Convert locus names to GrainGenes standardized
nomenclature
4. Check all loci to be sure a probe record exists
5. Create probe records for new loci involves going to references within the papercontact with authorscan be very time consuming!!!
6. Create other object records genes, germplasm, colleague, reference etc.
A map set takes ~ a week if all goes smoothly and authors cooperate.
The Genome Browser (GBrowse) is a new mapviewing tool.
Click on a Bin bar to see all loci mapped to that region
Click on a Probe ESTs link to access queryfeatures on wEST
The CMAP viewer will allow users to compare maps.
NCBI is importingGrainGenes records for the Entrez Map ViewTool.
Maps forEducation
In-Depth pages willprovide links to PubMedliterature searches, NCBI,GrainGenes, etc.
