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This is the Wiki site for the GRG project.

Organisms

The organisms that will be included in GRG are the following:

1. Zea mays subsp. mays (NCBI tax-id: 381124)

Go here for the main site for the Zea mays genomic data.

There are at least two different files to take into account for importing the data from this genome:

1. Main GFF file: ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v8.0/Zmays/annotation/Zmays_181_gene_exons.gff3.gz
2. The Chromosome-related data: http://ftp.maizesequence.org/current/filtered-set/ZmB73_5b_FGS_info.txt
3. Maizegenome GFF file: http://ftp.maizesequence.org/current/filtered-set/ZmB73_5b_FGS.gff.gz

2. Oryza sativa Japonica Group (NCBI tax-id: 39947)

1. Main GFF file: ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v8.0/Osativa/annotation/Osativa_193_gene_exons.gff3.gz

3. Sorghum bicolor (NCBI tax-id: 4558)

1. Main GFF file: ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v8.0/Sbicolor/annotation/Sbicolor_79_gene_exons.gff3.gz

4. Brachypodium distachyon (NCBI tax-id: 15368)

1. Main GFF file: ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v8.0/Bdistachyon/annotation/Bdistachyon_192_gene_exons.gff3.gz

5. Arabidopsis thaliana Columbia (NCBI tax-id: 3702)

1. Main GFF file: ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v8.0/Athaliana/annotation/Athaliana_167_gene_exons.gff3.gz

6. Arabidopsis lyrata lyrata MN47 (NCBI tax-id: 81972)

1. Main GFF file: ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v8.0/Alyrata/annotation/Alyrata_107_gene_exons.gff3.gz

Entities modeled as nodes (not included already in Bio4j)

• ProteinFamily
• ProteinFamilyGroup
• Chromosome
• GRGGene
• CISElement
• Promoter
• Intron
• Exon
• GRGCDS
• GRGMRNA
• FivePrimeUTR
• ThreePrimeUTR
• ChipSeqExperiment
• ChipChipExperiment
• RnaSeqExperiment
• GRGIntergenicRegion
• TFomeElement
• GRGProtein