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[GL_RefAnnotTable] Initial microbes updates
- Included Ensembl versions in Updates section of DPPD document - Fixed formatting in reference table - Recreated annotation tables, fixed broken columns - Added locally created databases to reference table - Fixed R version in workflow document R installation instructions - Updated reference table directory in workflow document instructions step #3 - Microbes-related changes: Added microbes to reference table, updated changelog
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‎GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A.md

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## Updates from previous version
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- Updated R from version 4.13 to 4.4.0
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- Updated Bioconductor from 3.15.1 to 3.19.1
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- Added functionality to create an annotation database using AnnotationForge. This applies to organisms without a maintained annotation database package in Bioconductor (e.g. org.Hs.eg.db). This is currently in use for Bacillus subtilis, subsp. subtilis 168 (BACSU), Escherichia coli,str. K-12 substr. MG1655 (ECOLI), and Oryzias latipes (ORYLA).
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- Added support for BACSU, ECOLI, ORYLA
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Ensembl Releases:
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- Animals: Updated from release 107 to 112
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- Plants: Updated from release 54 to 59
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- Bacteria: Updated from release 54 to 59
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Added NCBI as a reference source for FASTA and GTF files for bacteria to improve annotations.
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Updated R version from 4.1.3 to 4.4.0.
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Updated Bioconductor version from 3.15.1 to 3.19.1.
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Added support for:
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- Bacillus subtilis, subsp. subtilis 168
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- Brachypodium distachyon
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- Escherichia coli,str. K-12 substr. MG1655
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- Oryzias latipes
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- Lactobacillus acidophilus NCFM
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- Mycobacterium marinum M
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- Oryza sativa Japonica
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- Pseudomonas aeruginosa UCBPP-PA14
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- Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
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- Serratia liquefaciens ATCC 27592
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- Staphylococcus aureus MRSA252
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- Streptococcus mutans UA159
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- Vibrio fischeri ES114
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Added functionality to create an annotation database using AnnotationForge. This applies to organisms without a maintained annotation database package in Bioconductor (e.g. org.Hs.eg.db). This is currently in use for the following organisms:
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- Bacillus subtilis, subsp. subtilis 168
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- Brachypodium distachyon
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- Escherichia coli, str. K-12 substr. MG1655
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- Oryzias latipes
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- Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
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‎GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv

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name,species,strain,ensemblVersion,ref_source,fasta,gtf,taxon,annotations,genelab_annots_link,genelab_annots_info_link
2-
ARABIDOPSIS,Arabidopsis thaliana,,59,ensembl_plants,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/gtf/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.59.gtf.gz,3702,org.At.tair.db,https://figshare.com/ndownloader/files/46762531,https://figshare.com/ndownloader/files/46762525
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BACSU,Bacillus subtilis,subsp. subtilis 168,59,ensembl_bacteria,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/fasta/bacteria_0_collection/bacillus_subtilis_subsp_subtilis_str_168_gca_000009045/dna/Bacillus_subtilis_subsp_subtilis_str_168_gca_000009045.ASM904v1.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/gtf/bacteria_0_collection/bacillus_subtilis_subsp_subtilis_str_168_gca_000009045/Bacillus_subtilis_subsp_subtilis_str_168_gca_000009045.ASM904v1.59.gtf.gz,224308,,https://figshare.com/ndownloader/files/46762528,https://figshare.com/ndownloader/files/46762534
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BRADI,Brachypodium distachyon,,59,ensembl_plants,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/fasta/brachypodium_distachyon/dna/Brachypodium_distachyon.Brachypodium_distachyon_v3.0.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/gtf/brachypodium_distachyon/Brachypodium_distachyon.Brachypodium_distachyon_v3.0.59.gtf.gz,15368,,,
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BRARP,Brassica rapa,,59,ensembl_plants,http://ftp.ensemblgenomes.org/pub/plants/release-59/fasta/brassica_rapa/dna/Brassica_rapa.Brapa_1.0.dna.toplevel.fa.gz,http://ftp.ensemblgenomes.org/pub/plants/release-59/gtf/brassica_rapa/Brassica_rapa.Brapa_1.0.59.gtf.gz,3711,,,
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WORM,Caenorhabditis elegans,,112,ensembl,https://ftp.ensembl.org/pub/release-112/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz,https://ftp.ensembl.org/pub/release-112/gtf/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.112.gtf.gz,6239,org.Ce.eg.db,https://figshare.com/ndownloader/files/46762537,https://figshare.com/ndownloader/files/46762540
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ZEBRAFISH,Danio rerio,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna.primary_assembly.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/danio_rerio/Danio_rerio.GRCz11.112.gtf.gz,7955,org.Dr.eg.db,https://figshare.com/ndownloader/files/46762546,https://figshare.com/ndownloader/files/46762543
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FLY,Drosophila melanogaster,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.46.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.46.112.gtf.gz,7227,org.Dm.eg.db,https://figshare.com/ndownloader/files/46762549,https://figshare.com/ndownloader/files/46762552
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ARABIDOPSIS,Arabidopsis thaliana,,59,ensembl_plants,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/gtf/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.59.gtf.gz,3702,org.At.tair.db,https://figshare.com/ndownloader/files/48166390,https://figshare.com/ndownloader/files/48166381
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BACSU,Bacillus subtilis,subsp. subtilis 168,59,ensembl_bacteria,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/fasta/bacteria_0_collection/bacillus_subtilis_subsp_subtilis_str_168_gca_000009045/dna/Bacillus_subtilis_subsp_subtilis_str_168_gca_000009045.ASM904v1.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/gtf/bacteria_0_collection/bacillus_subtilis_subsp_subtilis_str_168_gca_000009045/Bacillus_subtilis_subsp_subtilis_str_168_gca_000009045.ASM904v1.59.gtf.gz,224308,org.Bsubtilissubspsubtilis168.eg.db,https://figshare.com/ndownloader/files/48166384,https://figshare.com/ndownloader/files/48166387
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BRADI,Brachypodium distachyon,,59,ensembl_plants,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/fasta/brachypodium_distachyon/dna/Brachypodium_distachyon.Brachypodium_distachyon_v3.0.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/gtf/brachypodium_distachyon/Brachypodium_distachyon.Brachypodium_distachyon_v3.0.59.gtf.gz,15368,org.Bdistachyon.eg.db,https://figshare.com/ndownloader/files/48166399,https://figshare.com/ndownloader/files/48166393
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BRARP,Brassica rapa,,59,ensembl_plants,http://ftp.ensemblgenomes.org/pub/plants/release-59/fasta/brassica_rapa/dna/Brassica_rapa.Brapa_1.0.dna.toplevel.fa.gz,http://ftp.ensemblgenomes.org/pub/plants/release-59/gtf/brassica_rapa/Brassica_rapa.Brapa_1.0.59.gtf.gz,,,,
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WORM,Caenorhabditis elegans,,112,ensembl,https://ftp.ensembl.org/pub/release-112/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz,https://ftp.ensembl.org/pub/release-112/gtf/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.112.gtf.gz,6239,org.Ce.eg.db,https://figshare.com/ndownloader/files/48166402,https://figshare.com/ndownloader/files/48166396
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ZEBRAFISH,Danio rerio,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna.primary_assembly.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/danio_rerio/Danio_rerio.GRCz11.112.gtf.gz,7955,org.Dr.eg.db,https://figshare.com/ndownloader/files/48166414,https://figshare.com/ndownloader/files/48166405
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FLY,Drosophila melanogaster,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.46.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.46.112.gtf.gz,7227,org.Dm.eg.db,https://figshare.com/ndownloader/files/48166411,https://figshare.com/ndownloader/files/48166408
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ERCC,,,,ThermoFisher,https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip,https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip,,,,
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ECOLI,Escherichia coli,str. K-12 substr. MG1655,59,ensembl_bacteria,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/fasta/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655_gca_000005845/dna/Escherichia_coli_str_k_12_substr_mg1655_gca_000005845.ASM584v2.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/gtf/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655_gca_000005845/Escherichia_coli_str_k_12_substr_mg1655_gca_000005845.ASM584v2.59.gtf.gz,511145,,https://figshare.com/ndownloader/files/46762555,https://figshare.com/ndownloader/files/46762558
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HUMAN,Homo sapiens,,112,ensembl,https://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz,https://ftp.ensembl.org/pub/release-112/gtf/homo_sapiens/Homo_sapiens.GRCh38.112.gtf.gz,9606,org.Hs.eg.db,https://figshare.com/ndownloader/files/46762501,https://figshare.com/ndownloader/files/46762495
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MOUSE,Mus musculus,,112,ensembl,https://ftp.ensembl.org/pub/release-112/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz,https://ftp.ensembl.org/pub/release-112/gtf/mus_musculus/Mus_musculus.GRCm39.112.gtf.gz,10090,org.Mm.eg.db,https://figshare.com/ndownloader/files/46762504,https://figshare.com/ndownloader/files/46762498
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,Mycobacterium marinum,LHM4,59,ensembl_bacteria,coming soon,coming soon,,,,
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ORYSJ,Oryza sativa,Japonica,59,ensembl_plants,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/fasta/oryza_sativa/dna/Oryza_sativa.IRGSP-1.0.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/gtf/oryza_sativa/Oryza_sativa.IRGSP-1.0.59.gtf.gz,4530,BSgenome.Osativa.MSU.MSU7,,
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ORYLA,Oryzias latipes,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/oryzias_latipes/dna/Oryzias_latipes.ASM223467v1.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/oryzias_latipes/Oryzias_latipes.ASM223467v1.112.gtf.gz,8090,,https://figshare.com/ndownloader/files/46762510,https://figshare.com/ndownloader/files/46762507
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RAT,Rattus norvegicus,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/rattus_norvegicus/dna/Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/rattus_norvegicus/Rattus_norvegicus.mRatBN7.2.112.gtf.gz,10116,org.Rn.eg.db,https://figshare.com/ndownloader/files/46537834,https://figshare.com/ndownloader/files/46537867
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YEAST,Saccharomyces cerevisiae,S288C,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.112.gtf.gz,559292,org.Sc.sgd.db,https://figshare.com/ndownloader/files/46762516,https://figshare.com/ndownloader/files/46762522
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STAA8,Staphylococcus aureus,UAMS-1,59,ensembl_bacteria,coming soon,coming soon,,,,
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,Streptococcus mutans,UA159,59,ensembl_bacteria,,,,,,
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ECOLI,Escherichia coli,str. K-12 substr. MG1655,59,ensembl_bacteria,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/fasta/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655_gca_000005845/dna/Escherichia_coli_str_k_12_substr_mg1655_gca_000005845.ASM584v2.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/gtf/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655_gca_000005845/Escherichia_coli_str_k_12_substr_mg1655_gca_000005845.ASM584v2.59.gtf.gz,511145,org.EcolistrK12substrMG1655.eg.db,https://figshare.com/ndownloader/files/48166417,https://figshare.com/ndownloader/files/48166420
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HUMAN,Homo sapiens,,112,ensembl,https://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz,https://ftp.ensembl.org/pub/release-112/gtf/homo_sapiens/Homo_sapiens.GRCh38.112.gtf.gz,9606,org.Hs.eg.db,https://figshare.com/ndownloader/files/48166477,https://figshare.com/ndownloader/files/48166471
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NOENTRY_LA,Lactobacillus acidophilus,NCFM,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/985/GCF_000011985.1_ASM1198v1/GCF_000011985.1_ASM1198v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/985/GCF_000011985.1_ASM1198v1/GCF_000011985.1_ASM1198v1_genomic.gtf.gz,272621,,https://figshare.com/ndownloader/files/48166447,https://figshare.com/ndownloader/files/48166450
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MOUSE,Mus musculus,,112,ensembl,https://ftp.ensembl.org/pub/release-112/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz,https://ftp.ensembl.org/pub/release-112/gtf/mus_musculus/Mus_musculus.GRCm39.112.gtf.gz,10090,org.Mm.eg.db,https://figshare.com/ndownloader/files/48166483,https://figshare.com/ndownloader/files/48166474
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NOENTRY_MM,Mycobacterium marinum,M,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/018/345/GCF_000018345.1_ASM1834v1/GCF_000018345.1_ASM1834v1_genomic.gtf.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/018/345/GCF_000018345.1_ASM1834v1/GCF_000018345.1_ASM1834v1_genomic.gtf.gz,216594,,https://figshare.com/ndownloader/files/48166459,https://figshare.com/ndownloader/files/48166462
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ORYSJ,Oryza sativa,Japonica,59,ensembl_plants,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/fasta/oryza_sativa/dna/Oryza_sativa.IRGSP-1.0.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/gtf/oryza_sativa/Oryza_sativa.IRGSP-1.0.59.gtf.gz,39947,,https://figshare.com/ndownloader/files/48166480,https://figshare.com/ndownloader/files/48166486
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ORYLA,Oryzias latipes,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/oryzias_latipes/dna/Oryzias_latipes.ASM223467v1.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/oryzias_latipes/Oryzias_latipes.ASM223467v1.112.gtf.gz,8090,org.Olatipes.eg.db,https://figshare.com/ndownloader/files/48166492,https://figshare.com/ndownloader/files/48166489
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PSEAE,Pseudomonas aeruginosa,UCBPP-PA14,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/014/625/GCF_000014625.1_ASM1462v1/GCF_000014625.1_ASM1462v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/014/625/GCF_000014625.1_ASM1462v1/GCF_000014625.1_ASM1462v1_genomic.gtf.gz,208963,,https://figshare.com/ndownloader/files/48166453,https://figshare.com/ndownloader/files/48166456
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RAT,Rattus norvegicus,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/rattus_norvegicus/dna/Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/rattus_norvegicus/Rattus_norvegicus.mRatBN7.2.112.gtf.gz,10116,org.Rn.eg.db,https://figshare.com/ndownloader/files/48166501,https://figshare.com/ndownloader/files/48166495
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YEAST,Saccharomyces cerevisiae,S288C,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.112.gtf.gz,559292,org.Sc.sgd.db,https://figshare.com/ndownloader/files/48166498,https://figshare.com/ndownloader/files/48166504
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SALTY,Salmonella enterica,serovar Typhimurium str. LT2,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/945/GCF_000006945.2_ASM694v2/GCF_000006945.2_ASM694v2_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/945/GCF_000006945.2_ASM694v2/GCF_000006945.2_ASM694v2_genomic.gtf.gz,99287,org.SentericaserovarTyphimuriumstrLT2.eg.db,https://figshare.com/ndownloader/files/48166423,https://figshare.com/ndownloader/files/48166426
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NOENTRY_SL,Serratia liquefaciens,ATCC 27592,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/422/085/GCF_000422085.1_ASM42208v1/GCF_000422085.1_ASM42208v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/422/085/GCF_000422085.1_ASM42208v1/GCF_000422085.1_ASM42208v1_genomic.gtf.gz,1346614,,https://figshare.com/ndownloader/files/48166465,https://figshare.com/ndownloader/files/48166468
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NOENTRY_SA,Staphylococcus aureus,MRSA252,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/505/GCF_000011505.1_ASM1150v1/GCF_000011505.1_ASM1150v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/505/GCF_000011505.1_ASM1150v1/GCF_000011505.1_ASM1150v1_genomic.gtf.gz,282458,,https://figshare.com/ndownloader/files/48166435,https://figshare.com/ndownloader/files/48166438
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NOENTRY_SM,Streptococcus mutans,UA159,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/007/465/GCF_000007465.2_ASM746v2/GCF_000007465.2_ASM746v2_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/007/465/GCF_000007465.2_ASM746v2/GCF_000007465.2_ASM746v2_genomic.gtf.gz,210007,,https://figshare.com/ndownloader/files/48166429,https://figshare.com/ndownloader/files/48166432
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NOENTRY_VF,Vibrio fischeri,ES114,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/805/GCF_000011805.1_ASM1180v1/GCF_000011805.1_ASM1180v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/805/GCF_000011805.1_ASM1180v1/GCF_000011805.1_ASM1180v1_genomic.gtf.gz,312309,,https://figshare.com/ndownloader/files/48166441,https://figshare.com/ndownloader/files/48166444

‎GeneLab_Reference_Annotations/README.md

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2020
**Developed by:**
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Mike Lee
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**Maintained by:**
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Alexis Torres
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**Maintained by:**
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Alexis Torres
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Crystal Han

‎GeneLab_Reference_Annotations/Workflow_Documentation/GL_RefAnnotTable-A/CHANGELOG.md

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### Added
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- Added AnnotationForge helper script to create local annotations databases if not available on Bioconductor
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- Added support for BACSU, ECOLI, and ORYLA via install-annot-dbi.R
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- Added support for:
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- Bacillus subtilis, subsp. subtilis 168
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- Brachypodium distachyon
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- Escherichia coli,str. K-12 substr. MG1655
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- Oryzias latipes
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- Lactobacillus acidophilus NCFM
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- Mycobacterium marinum M
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- Oryza sativa Japonica
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- Pseudomonas aeruginosa UCBPP-PA14
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- Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
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- Serratia liquefaciens ATCC 27592
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- Staphylococcus aureus MRSA252
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- Streptococcus mutans UA159
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- Vibrio fischeri ES114
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- Added AnnotationForge helper script install-annot-dbi.R to create organism-specific annotation packages (org.*.eg.db) in R if not available on Bioconductor. Used for:
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- Bacillus subtilis, subsp. subtilis 168
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- Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
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- Escherichia coli,str. K-12 substr. MG1655
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- Oryzias latipes
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- Added NCBI as a source for GASTA and GTF files
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- Animals: Ensembl release 112
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- Plants: Ensembl plants release 59
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- Bacteria: Ensembl bacteria release 59
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- Removed org.EcK12.eg.db and replaced with local annotations database creation since it is no longer on Bioconductor
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- Removed org.EcK12.eg.db and replaced it with a locally created annotations database, as it is no longer available on Bioconductor
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## [1.0.0](https://github.com/nasa/GeneLab_Data_Processing/releases/tag/GL_RefAnnotTable_1.0.0)

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