Map Curation on GrainGenes Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson Biological...
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Transcript of Map Curation on GrainGenes Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson Biological...
![Page 1: Map Curation on GrainGenes Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson Biological Databases Curators Meeting October 2003.](https://reader035.fdocuments.in/reader035/viewer/2022062519/56649ce05503460f949aa8b8/html5/thumbnails/1.jpg)
Map Curation on GrainGenes
Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson
Biological Databases Curators Meeting
October 2003
![Page 2: Map Curation on GrainGenes Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson Biological Databases Curators Meeting October 2003.](https://reader035.fdocuments.in/reader035/viewer/2022062519/56649ce05503460f949aa8b8/html5/thumbnails/2.jpg)
![Page 3: Map Curation on GrainGenes Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson Biological Databases Curators Meeting October 2003.](https://reader035.fdocuments.in/reader035/viewer/2022062519/56649ce05503460f949aa8b8/html5/thumbnails/3.jpg)
The Maps and Map Data page has links to articles, raw data and line maps
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‘Map’ of CS x CheyenneDisomic Substitution
![Page 5: Map Curation on GrainGenes Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson Biological Databases Curators Meeting October 2003.](https://reader035.fdocuments.in/reader035/viewer/2022062519/56649ce05503460f949aa8b8/html5/thumbnails/5.jpg)
Raw Mapping data of CS x Cheyenne Disomic Substitution
![Page 6: Map Curation on GrainGenes Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson Biological Databases Curators Meeting October 2003.](https://reader035.fdocuments.in/reader035/viewer/2022062519/56649ce05503460f949aa8b8/html5/thumbnails/6.jpg)
The Maps and Map Data page has links to articles, raw data and line maps
![Page 7: Map Curation on GrainGenes Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson Biological Databases Curators Meeting October 2003.](https://reader035.fdocuments.in/reader035/viewer/2022062519/56649ce05503460f949aa8b8/html5/thumbnails/7.jpg)
Web Summary of Interactive Maps links to the GrainGenes database
![Page 8: Map Curation on GrainGenes Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson Biological Databases Curators Meeting October 2003.](https://reader035.fdocuments.in/reader035/viewer/2022062519/56649ce05503460f949aa8b8/html5/thumbnails/8.jpg)
Flavors of GrainGenes Maps
Genetic: Loci mapped byrecombination frequency inSynthetic x Opata
![Page 9: Map Curation on GrainGenes Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson Biological Databases Curators Meeting October 2003.](https://reader035.fdocuments.in/reader035/viewer/2022062519/56649ce05503460f949aa8b8/html5/thumbnails/9.jpg)
Flavors of GrainGenes Maps
Highlighted loci have bestBLAST hits.
Consensus: combined maps of hexaploid wheat by Sorrells et al.
![Page 10: Map Curation on GrainGenes Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson Biological Databases Curators Meeting October 2003.](https://reader035.fdocuments.in/reader035/viewer/2022062519/56649ce05503460f949aa8b8/html5/thumbnails/10.jpg)
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Wheat and Barley Public EST Resources
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Flavors of GrainGenes Maps
Physical: loci mapped byphysical placement ona chromosome.
This is a deletion map from the U.S. wheat genome project.
![Page 13: Map Curation on GrainGenes Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson Biological Databases Curators Meeting October 2003.](https://reader035.fdocuments.in/reader035/viewer/2022062519/56649ce05503460f949aa8b8/html5/thumbnails/13.jpg)
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Sequence Records from the NSF ESTs contain thesupporting data and linksto maps supported byother projects:
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QTL map from a barleymalting quality study
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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
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3. Convert locus names to GrainGenes standardized
nomenclature
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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.
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The Genome Browser (GBrowse) is a new mapviewing tool.
![Page 25: Map Curation on GrainGenes Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson Biological Databases Curators Meeting October 2003.](https://reader035.fdocuments.in/reader035/viewer/2022062519/56649ce05503460f949aa8b8/html5/thumbnails/25.jpg)
Click on a Bin bar to see all loci mapped to that region
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Click on a Probe ESTs link to access queryfeatures on wEST
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The CMAP viewer will allow users to compare maps.
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NCBI is importingGrainGenes records for the Entrez Map ViewTool.
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Maps forEducation
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In-Depth pages willprovide links to PubMedliterature searches, NCBI,GrainGenes, etc.
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