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A peer-reviewed article of this preprint also exists.
Database name | NCBI | DRA | ENA | GSA | IBDC | AGDR † | DRYAD ¥ | Zenodo ‡, ¥ | FigShare |
Genome sequence data | + | + | + | + | + | + | + | + | + |
WGS annotations | + | ? | ? | ? | ? | ? | ? | ? | + |
Genotyping data | + | ? | ? | ? | ? | ? | ? | ? | + |
Transcriptome sequence data | + | + | + | ? | ? | ? | + | + | + |
fq.gz | + | + | + | + | + | + | + | + | + |
BAM | + | + | + | + | + | + | + | + | + |
SFF | + | + | + | + | + | - | + | + | + |
HDF | + | + | + | + | + | - | + | + | + |
VCF | + | + | + | ? | ? | ? | + | + | + |
INSDC-Source | + | + | + | a | b | c | d | e | f |
Species/Crop | Database | Database URL |
---|---|---|
Arabidopsis | TAIR | https://www.arabidopsis.org/ |
Cassava | CassavaBase | https://www.cassavabase.org/ |
Citrus | Citrus Genome Database | https://www.citrusgenomedb.org/ |
Citrus/Diaphorina citri/Ca. Liberibacter asiaticus | Citrus Greening | https://www.citrusgreening.org/ |
Cotton | CottonGen | https://www.cottongen.org/ |
Cucurbit | Cucurbit Genomics | http://cucurbitgenomics.org/ |
Forest trees | TreeGenes | https://treegenesdb.org |
Hardwood Genomics | http://www.hardwoodgenomics.org/ | |
Grains | GrainGenes | https://wheat.pw.usda.gov |
Gramene | https://www.gramene.org/ | |
SorghumBase | https://www.sorghumbase.org/ | |
Triticeae toolbox, T3 | https://wheat.triticeaetoolbox.org/ | |
WheatIS | https://wheatis.org | |
KitBase | http://kitbase.ucdavis.edu/ | |
Legumes | KnowPulse | https://knowpulse.usask.ca/ |
Legume Information System | https://www.legumeinfo.org/ | |
PeanutBase | https://peanutbase.org | |
Pulses | Pulse Crop Database | https://www.pulsedb.org/ |
Soybase | https://www.soybase.org/ | |
Maize | MaizeGDB | https://maizegdb.org/ |
Musa | MusaBase | https://www.musabase.org/ |
Rosaceae | Genome Database for Rosaceae | https://www.rosaceae.org/ |
Solanaceae | Sol Genomics | https://solgenomics.net/ |
Sweet Potato | SweetPotatoBase | https://www.sweetpotatobase.org/ |
Vaccinium | Genome Database for Vaccinium | https://www.vaccinium.org/ |
Yam | YamBase | https://www.yambase.org/ |
Comparative genomic database used by multiple communities | ||
A comparative genomic database for ~300 plant species | Phytozome | https://phytozome-next.jgi.doe.gov/ |
A comparative genomic databasehosting 118 genomesfrom models, crops,fruits, vegetables, etc. | Gramene | https://www.gramene.org/ |
Others | AgBase | https://agbase.arizona.edu/ |
Bio-Analytic Resource | https://bar.utoronto.ca/ |
Category | Databases | URLs |
---|---|---|
Species-specific mutant collections |
Database of image and genome (MaizeDIG) |
https://maizedig.maizegdb.org/ |
Mutant Variety Database | https://nucleus.iaea.org/sites/mvd/SitePages/Home.aspx | |
Plant Genome Editing Database | http://plantcrispr.org/cgi-bin/crispr/index.cgi | |
RIKEN Arabidopsis Genome Encyclopedia (RARGE) |
http://rarge-v2.psc.riken.jp/line | |
TOMATOMA | https://tomatoma.nbrp.jp/index.jsp | |
Plant Editosome | https://ngdc.cncb.ac.cn/ped/ | |
Traits and QTL | Gramene QTL | https://archive.gramene.org/qtl/ |
Wheatqtl | http://www.wheatqtldb.net/ | |
GLOPNET | http://bio.mq.edu.au/~iwright/glopian.htm | |
TRY database | https://www.try-db.org/TryWeb/Home.php | |
Ecological Flora of the Britain and Ireland |
http://ecoflora.org.uk/ | |
BIOPOP | http://www.landeco.uni-oldenburg.de/Projects/biopop/main.htm | |
FloraWeb | https://www.floraweb.de/ | |
USDA GRIN | https://www.ars-grin.gov/ | |
BiolFlor | https://wiki.ufz.de/biolflor/index.jsp | |
LEDA | https://uol.de/en/landeco/research/leda | |
USDA PLANTS | https://plants.usda.gov/home | |
BROT | https://www.uv.es/jgpausas/brot.htm | |
AusTraits | https://austraits.org/ | |
Community Databases in Table 2 and Supplementary Table S3 |
||
Phenomics | GnpIS | https://urgi.versailles.inra.fr/gnpis |
PGP Repository | https://edal-pgp.ipk-gatersleben.de/ | |
Cartograplant | https://cartograplant.org/ | |
AgData commons Plants & Crops: |
https://data.nal.usda.gov/ag-data-commons-hierarchy/plants-crops | |
PathoPlant | http://www.pathoplant.de/ | |
PncStress | http://bis.zju.edu.cn/pncstress/ | |
Indian Crop Phenome DB (ICPD) | https://ibdc.rcb.res.in/icpd/ | |
Gene Expression | Ozone Stress Responsive Gene Database |
https://www.osrgd.com |
EBI-Plant Expression Atlas | https://www.ebi.ac.uk/gxa/plant/experiments | |
CoNeKT | https://conekt.sbs.ntu.edu.sg/ | |
Protein, peptides and proteomes |
Expath | http://expath.itps.ncku.edu.tw/ |
Proteome Xchange | https://www.proteomexchange.org | |
Plant Proteome Database | http://ppdb.tc.cornell.edu/ | |
PlantMWpIDB | https://plantmwpidb.com/ | |
Heat Shock Proteins database | http://hsfdb.bio2db.com/ | |
WallProtDB | https://www.polebio.lrsv.ups-tlse.fr/WallProtDB/ | |
Aramemnon | http://aramemnon.botanik.uni-koeln.de/ | |
PhosPhAt | https://phosphat.uni-hohenheim.de/db.html | |
Database of Phospho-sites in Plants |
http://dbppt.biocuckoo.org/browse.php | |
Plant Protein Phosphorylation Database |
https://www.p3db.org/home | |
qPTMplants | http://qptmplants.omicsbio.info/ | |
Plant PTM viewer | https://www.psb.ugent.be/webtools/ptm-viewer/ | |
PlaPPISite | http://zzdlab.com/plappisite/index.ph | |
M. truncatula Small Secreted Peptide Database |
https://mtsspdb.zhaolab.org/database | |
PlantPepDB | http://14.139.61.8/PlantPepDB/index.php | |
Arabidopsis PeptideAtlas | http://www.peptideatlas.org/builds/arabidopsis/ | |
Indian Structural Data Archive | https://isda.rcb.ac.in/ | |
Metabolites, biochemical, and small chemical entities |
Antimicrobial plant peptides (PhytAMP) |
http://phytamp.pfba-lab-tun.org/main.php |
PubChem | https://pubchem.ncbi.nlm.nih.gov | |
ChEBI | https://www.ebi.ac.uk/chebi | |
Metabolomics Workbench | https://www.metabolomicsworkbench.org | |
Secondary Knowledgebase |
MetaboLights | https://www.ebi.ac.uk/metabolights/index |
PoDP | https://pairedomicsdata.bioinformatics.nl/ | |
Plant Reactome pathway knowledgebase |
https://plantreactome.gramene.org | |
MetaCyc | https://metacyc.org | |
PMN | https://plantcyc.org/data | |
KEGG pathways | https://www.genome.jp/kegg/pathway.html | |
PlantPathMarks (PPMdb) | http://ppmdb.easyomics.org/ | |
The Bio-Analytic Resource (BAR) | https://bar.utoronto.ca | |
The protein-protein interaction database for Maize (PPIM) |
https://mai.fudan.edu.cn/ppim/ |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
supplementary.xlsx (103.05KB )
Submitted:
14 June 2023
Posted:
14 June 2023
You are already at the latest version
A peer-reviewed article of this preprint also exists.
supplementary.xlsx (103.05KB )
Submitted:
14 June 2023
Posted:
14 June 2023
You are already at the latest version
Database name | NCBI | DRA | ENA | GSA | IBDC | AGDR † | DRYAD ¥ | Zenodo ‡, ¥ | FigShare |
Genome sequence data | + | + | + | + | + | + | + | + | + |
WGS annotations | + | ? | ? | ? | ? | ? | ? | ? | + |
Genotyping data | + | ? | ? | ? | ? | ? | ? | ? | + |
Transcriptome sequence data | + | + | + | ? | ? | ? | + | + | + |
fq.gz | + | + | + | + | + | + | + | + | + |
BAM | + | + | + | + | + | + | + | + | + |
SFF | + | + | + | + | + | - | + | + | + |
HDF | + | + | + | + | + | - | + | + | + |
VCF | + | + | + | ? | ? | ? | + | + | + |
INSDC-Source | + | + | + | a | b | c | d | e | f |
Species/Crop | Database | Database URL |
---|---|---|
Arabidopsis | TAIR | https://www.arabidopsis.org/ |
Cassava | CassavaBase | https://www.cassavabase.org/ |
Citrus | Citrus Genome Database | https://www.citrusgenomedb.org/ |
Citrus/Diaphorina citri/Ca. Liberibacter asiaticus | Citrus Greening | https://www.citrusgreening.org/ |
Cotton | CottonGen | https://www.cottongen.org/ |
Cucurbit | Cucurbit Genomics | http://cucurbitgenomics.org/ |
Forest trees | TreeGenes | https://treegenesdb.org |
Hardwood Genomics | http://www.hardwoodgenomics.org/ | |
Grains | GrainGenes | https://wheat.pw.usda.gov |
Gramene | https://www.gramene.org/ | |
SorghumBase | https://www.sorghumbase.org/ | |
Triticeae toolbox, T3 | https://wheat.triticeaetoolbox.org/ | |
WheatIS | https://wheatis.org | |
KitBase | http://kitbase.ucdavis.edu/ | |
Legumes | KnowPulse | https://knowpulse.usask.ca/ |
Legume Information System | https://www.legumeinfo.org/ | |
PeanutBase | https://peanutbase.org | |
Pulses | Pulse Crop Database | https://www.pulsedb.org/ |
Soybase | https://www.soybase.org/ | |
Maize | MaizeGDB | https://maizegdb.org/ |
Musa | MusaBase | https://www.musabase.org/ |
Rosaceae | Genome Database for Rosaceae | https://www.rosaceae.org/ |
Solanaceae | Sol Genomics | https://solgenomics.net/ |
Sweet Potato | SweetPotatoBase | https://www.sweetpotatobase.org/ |
Vaccinium | Genome Database for Vaccinium | https://www.vaccinium.org/ |
Yam | YamBase | https://www.yambase.org/ |
Comparative genomic database used by multiple communities | ||
A comparative genomic database for ~300 plant species | Phytozome | https://phytozome-next.jgi.doe.gov/ |
A comparative genomic databasehosting 118 genomesfrom models, crops,fruits, vegetables, etc. | Gramene | https://www.gramene.org/ |
Others | AgBase | https://agbase.arizona.edu/ |
Bio-Analytic Resource | https://bar.utoronto.ca/ |
Category | Databases | URLs |
---|---|---|
Species-specific mutant collections |
Database of image and genome (MaizeDIG) |
https://maizedig.maizegdb.org/ |
Mutant Variety Database | https://nucleus.iaea.org/sites/mvd/SitePages/Home.aspx | |
Plant Genome Editing Database | http://plantcrispr.org/cgi-bin/crispr/index.cgi | |
RIKEN Arabidopsis Genome Encyclopedia (RARGE) |
http://rarge-v2.psc.riken.jp/line | |
TOMATOMA | https://tomatoma.nbrp.jp/index.jsp | |
Plant Editosome | https://ngdc.cncb.ac.cn/ped/ | |
Traits and QTL | Gramene QTL | https://archive.gramene.org/qtl/ |
Wheatqtl | http://www.wheatqtldb.net/ | |
GLOPNET | http://bio.mq.edu.au/~iwright/glopian.htm | |
TRY database | https://www.try-db.org/TryWeb/Home.php | |
Ecological Flora of the Britain and Ireland |
http://ecoflora.org.uk/ | |
BIOPOP | http://www.landeco.uni-oldenburg.de/Projects/biopop/main.htm | |
FloraWeb | https://www.floraweb.de/ | |
USDA GRIN | https://www.ars-grin.gov/ | |
BiolFlor | https://wiki.ufz.de/biolflor/index.jsp | |
LEDA | https://uol.de/en/landeco/research/leda | |
USDA PLANTS | https://plants.usda.gov/home | |
BROT | https://www.uv.es/jgpausas/brot.htm | |
AusTraits | https://austraits.org/ | |
Community Databases in Table 2 and Supplementary Table S3 |
||
Phenomics | GnpIS | https://urgi.versailles.inra.fr/gnpis |
PGP Repository | https://edal-pgp.ipk-gatersleben.de/ | |
Cartograplant | https://cartograplant.org/ | |
AgData commons Plants & Crops: |
https://data.nal.usda.gov/ag-data-commons-hierarchy/plants-crops | |
PathoPlant | http://www.pathoplant.de/ | |
PncStress | http://bis.zju.edu.cn/pncstress/ | |
Indian Crop Phenome DB (ICPD) | https://ibdc.rcb.res.in/icpd/ | |
Gene Expression | Ozone Stress Responsive Gene Database |
https://www.osrgd.com |
EBI-Plant Expression Atlas | https://www.ebi.ac.uk/gxa/plant/experiments | |
CoNeKT | https://conekt.sbs.ntu.edu.sg/ | |
Protein, peptides and proteomes |
Expath | http://expath.itps.ncku.edu.tw/ |
Proteome Xchange | https://www.proteomexchange.org | |
Plant Proteome Database | http://ppdb.tc.cornell.edu/ | |
PlantMWpIDB | https://plantmwpidb.com/ | |
Heat Shock Proteins database | http://hsfdb.bio2db.com/ | |
WallProtDB | https://www.polebio.lrsv.ups-tlse.fr/WallProtDB/ | |
Aramemnon | http://aramemnon.botanik.uni-koeln.de/ | |
PhosPhAt | https://phosphat.uni-hohenheim.de/db.html | |
Database of Phospho-sites in Plants |
http://dbppt.biocuckoo.org/browse.php | |
Plant Protein Phosphorylation Database |
https://www.p3db.org/home | |
qPTMplants | http://qptmplants.omicsbio.info/ | |
Plant PTM viewer | https://www.psb.ugent.be/webtools/ptm-viewer/ | |
PlaPPISite | http://zzdlab.com/plappisite/index.ph | |
M. truncatula Small Secreted Peptide Database |
https://mtsspdb.zhaolab.org/database | |
PlantPepDB | http://14.139.61.8/PlantPepDB/index.php | |
Arabidopsis PeptideAtlas | http://www.peptideatlas.org/builds/arabidopsis/ | |
Indian Structural Data Archive | https://isda.rcb.ac.in/ | |
Metabolites, biochemical, and small chemical entities |
Antimicrobial plant peptides (PhytAMP) |
http://phytamp.pfba-lab-tun.org/main.php |
PubChem | https://pubchem.ncbi.nlm.nih.gov | |
ChEBI | https://www.ebi.ac.uk/chebi | |
Metabolomics Workbench | https://www.metabolomicsworkbench.org | |
Secondary Knowledgebase |
MetaboLights | https://www.ebi.ac.uk/metabolights/index |
PoDP | https://pairedomicsdata.bioinformatics.nl/ | |
Plant Reactome pathway knowledgebase |
https://plantreactome.gramene.org | |
MetaCyc | https://metacyc.org | |
PMN | https://plantcyc.org/data | |
KEGG pathways | https://www.genome.jp/kegg/pathway.html | |
PlantPathMarks (PPMdb) | http://ppmdb.easyomics.org/ | |
The Bio-Analytic Resource (BAR) | https://bar.utoronto.ca | |
The protein-protein interaction database for Maize (PPIM) |
https://mai.fudan.edu.cn/ppim/ |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
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2022
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