TABLE 4.
Omics tools and databases.
| Database name | Omics | Description | URL |
| RiceGE | Genomics | It is a rice functional genomics express database | http://signal.salk.edu/cgi-bin/RiceGE |
| Oryza sativa genome Database | Genomics | It provides a sequence-centered genome view for Oryza sativa (ssp. japonica), | http://www.plantgdb.org/OsGDB/ |
| MSU-RGAP | Genomics | It provides sequence and annotation data for the rice genome (Nipponbare subspecies) | http://rice.uga.edu/ |
| RAP-DB | Genomics | It facilitates the analysis of genome structure and function of rice on the basis of the annotation. | https://rapdb.dna.affrc.go.jp/ |
| Gramene | Comparative Genomics | It is an open-source data resource for comparative functional genomics in crops and model plants | http://www.gramene.org/ |
| Oryzabase | Genomics | It is a comprehensive rice database providing information of classical rice genetics to recent genomics | https://shigen.nig.ac.jp/rice/oryzabase/ |
| OryGenesDB | Genomics | It displays sequence information such as the T-DNA and Ds flanking sequence tags (FSTs) | https://orygenesdb.cirad.fr/index.html |
| TIGR rice genome annotation DB | Genomics | It is a group of databases for searching with the BLAST programs blastn, blastx, tblastn, or tblastx. | http://blast.jcvi.org/euk-blast/index.cgi?project=osa1 |
| MOsDB | Genomics | It is a resource for publicly available sequences of the rice | https://pgsb.helmholtz-muenchen.de/plant/rice/index.jsp |
| Rice mutant DB | Genomics | It contains the information of approximate 129,000 rice T-DNA insertion (enhancer trap) lines generated by an enhancer trap system. | http://rmd.ncpgr.cn/ |
| Information Commons for Rice (IC4R) | Genomics | It is a database contributing to rice genome sequences, updating rice gene annotations and integrating multiple omics data | http://www.ic4r.org/ |
| RiceVarMap | Genomics | It is a database for rice genomic variation and its functional annotation. | http://ricevarmap.ncpgr.cn/ |
| RiceFrend | Genomics | It is a gene coexpression database in rice | https://ricefrend.dna.affrc.go.jp/ |
| Rice Transcription Factor Phylogenomics DB | Genomics | It combines various data types present in public databases encircling the structural features, orthologous relationships, availability of mutants and gene expression patterns for TF families | http://ricephylogenomics-khu.org/tf/home.php |
| Rice transporter database | Genomics | It contains information for all putative rice transporters | https://ricephylogenomics.ucdavis.edu/transporter/genInfo.shtml |
| The Rice Information GateWay (RIGW) | Genomics | It provides the sequenced genomes and related information in systematic and graphical ways | https://rice.hzau.edu.cn/rice_rs3/ |
| Rice Pan-genome Browser | Genomics | It provides sequences and gene annotations for the rice pan-genome and Gene presence-absence variations (PAVs) of rice accessions | https://cgm.sjtu.edu.cn/3kricedb/ |
| SNP-Seek | Genomics | Provides information related to rice SNPs | https://snp-seek.irri.org/ |
| Ricebase | Genomics | It is a rice breeding and genetics platform integrating molecular markers, pedigrees, and whole-genome data | https://www.ricebase.org/ |
| Rice imputation server | Genomics | It utilizes genetically and geographically diverse accessions to impute rice datasets out to 5.2M SNPs using the IMPUTE2 software. | http://rice-impute.biotech.cornell.edu/ |
| Ensemble_rice | Comparative Genomics | It is used for genome assembly, comparative genomics, and gene annotation | http://plants.ensembl.org/Oryza_sativa/Info/Index |
| Rice Diversity: GWAS Viewer | Genomics | Comprehensively view GWAS data | http://rs-bt-mccouch4.biotech.cornell.edu/GWAS_Viewer/plot/ |
| PLAZA | Comparative Genomics | It is an access point for plant comparative genomics centralizing genomic data produced by different genome sequencing programs. | https://bioinformatics.psb.ugent.be/plaza/versions/plaza_v4_monocots/ |
| PlantGDB | Comparative Genomics | It is used for sequence assemblies and annotation | http://www.plantgdb.org/ |
| Phytozome | Comparative Genomics | It is used for accessing, visualizing and analyzing sequenced plant genomes, as well as selected genomes and datasets | https://phytozome.jgi.doe.gov/pz/portal.html |
| ROAD | Genomics | It is a rice oligonucleotide array database | http://ricephylogenomics-khu.org/road/home.php |
| FIT-DB | Transcriptomics | It provides result of statistical modeling of transcriptomic dynamics in the field condition | https://fitdb.dna.affrc.go.jp/ |
| EXPath 2.0 | Transcriptomics | It is a database that collects and uses expression profiles derived from microarray under various conditions to infer metabolic pathways | http://expath.itps.ncku.edu.tw/ |
| Rice eFP | Transcriptomics | One of the major functions of Rice eFP is gene expression analysis | http://bar.utoronto.ca/efprice/cgi-bin/efpWeb.cgi |
| RiceXPro | Transcriptomics | It is a repository of gene expression profiles derived from microarray analysis of tissues/organs | https://ricexpro.dna.affrc.go.jp/ |
| RED | Transcriptomics | It is a repository of gene expression profiles derived from RNA-Seq data on rice tissues | http://expression.ic4r.org/ |
| TENOR | Transcriptomics | It is the transcriptome encyclopedia of rice | https://tenor.dna.affrc.go.jp/ |
| OryzaExpress | Transcriptomics | It is a sub-platform of PlantExpress for a single-species GEN analysis in rice. | http://plantomics.mind.meiji.ac.jp/OryzaExpress/ |
| UniVIO | Transcriptomics | It provides a data set of hormonome and transcriptome analyses in 14 organs of rice at the reproductive stage and in gibberellin-related mutants. | http://univio.psc.riken.jp/ |
| Genevestigator | Transcriptomics | It helps in analysis of deeply curated bulk tissue and single-cell transcriptomic data from public repositories with visualization tools | https://genevestigator.com/ |
| Expression Atlas | Transcriptomics | It helps to deduce gene expression across species and biological conditions | https://www.ebi.ac.uk/gxa/experiments?organism=Oryza+sativa+Japonica+Group |
| PLACE | Transcriptomics | It is a database of motifs found in plant cis-acting regulatory DNA elements | https://www.dna.affrc.go.jp/PLACE/?action=newplace |
| PlantCARE | Transcriptomics | It is a database for promoter analysis | http://bioinformatics.psb.ugent.be/webtools/plantcare/html/ |
| PPDB | Transcriptomics | It is a database for promoter analysis | http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/index.cgi |
| PlantPAN_V2 | Transcriptomics | It is an informative resource for detecting transcription factor binding sites | http://plantpan2.itps.ncku.edu.tw/index.html |
| NetMiner | Transcriptomics | An ensemble pipeline for high-quality RNA-seq-based gene co-expression network inference | https://github.com/czllab/NetMiner |
| PlantArrayNet | Transcriptomics | It generates co-expression information between genes based on correlation coefficients from accumulated microarray data of rice | http://bioinfo.mju.ac.kr/arraynet/ |
| COP DB | Transcriptomics | It is a database management system for understanding plant gene function by associating between co-expressed genes and biological processes | http://webs2.kazusa.or.jp/kagiana/cop0911/ |
| PODC | Transcriptomics | It is a database providing the information of gene networks (GENs) and knowledge-based functional annotations | http://plantomics.mind.meiji.ac.jp/podc/ |
| Plant rDNA database | Transcriptomics | It is an online resource providing information on numbers and positions of ribosomal DNA signals and their structures | https://www.plantrdnadatabase.com/ |
| PlantcircBase | Transcriptomics | It is a repository of publicly available back-splice junction sequences and their full-length sequences of circRNAs | http://ibi.zju.edu.cn/plantcircbase/ |
| PceRBase | Transcriptomics | It is a plant competing endogenous database | http://bis.zju.edu.cn/pcernadb/index.jsp |
| miRBase | Transcriptomics | the microRNA database | http://www.mirbase.org/ |
| IsomiR Bank | Transcriptomics | Database for microRNA isoforms. It is an integrative resource that contains the sequence and expression of isomers | https://mcg.ustc.edu.cn/bsc/isomir/ |
| PNRD | Transcriptomics | It is a plant non-coding RNA database | http://structuralbiology.cau.edu.cn/PNRD/index.php |
| CSRDB | Transcriptomics | It is a cereal small RNAs database | http://sundarlab.ucdavis.edu/smrnas/ |
| PlantRNA | Transcriptomics | The PlantRNA database contains tRNA gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. | http://plantrna.ibmp.cnrs.fr/plantrna/ |
| Rice Interactions Viewer | Proteomics | It is a database for protein-protein rice interaction | http://bar.utoronto.ca/interactions/cgi-bin/rice_interactions_viewer.cgi |
| STRING | Proteomics | It is used to study protein-protein interaction and functional enrichment analysis | https://string-db.org/ |
| PRIN | Proteomics | It is used to predict rice interactome network | http://bis.zju.edu.cn/prin/ |
| RiceNet | Proteomics | It is an improved network prioritization web server for rice | https://www.inetbio.org/ricenet/ |
| MCDRP | Proteomics | It is a manually curated database for rice proteins | http://www.genomeindia.org/biocuration/whatsnewver6.php |
| OryzaPG-DB | Proteomics | It is a rice proteogenomics database | https://github.com/MoHelmy/oryza-PG/ |
| Plant-PrAS | Proteomics | Database for physicochemical and structural properties | http://plant-pras.riken.jp/ |
| OMA browser | Proteomics | It is used for ortholog analysis | https://omabrowser.org/oma/home/ |
| POGsDB | Proteomics | It facilitates cross-species inferences about gene functions | http://pogs.uoregon.edu/#/ |
| InParanoid8 | Proteomics | To study ortholog groups with inparalogs | https://inparanoid.sbc.su.se/cgi-bin/index.cgi |
| GreenPhyl v4 | Proteomics | It is a database for species, genomes and pan-genomes | https://www.greenphyl.org/cgi-bin/index.cgi |
| Panther | Proteomics | It is used to perform Protein ANalysis THrough Evolutionary Relationships | http://www.pantherdb.org/ |
| PhosphoRice | Proteomics | It is a meta-predictor of rice-specific phosphorylation site | https://github.com/PEHGP/PhosphoRice |
| MassBank | Metabolomics | Metabolite annotation and MS-MS database | https://massbank.eu/MassBank/ |
| METLIN | Metabolomics | It is a collection of MS/MS data and incorporates the NIST MS/MS library and search software | https://www.sisweb.com/software/ms/wiley-metlin.htm |
| KNApSAcK | Metabolomics | Comprehensive Species Metabolite Relationship Database | http://www.knapsackfamily.com/KNApSAcK/ |
| MetaboLights | Metabolomics | It is a database for metabolomics experiments and derived information | https://www.ebi.ac.uk/metabolights/ |
| Plant Reactome | Metabolomics | Used to find reactions and pathways | https://plantreactome.gramene.org/index.php?lang=en |
| OryzaCYC | Metabolomics | To study plant metabolic network | https://plantcyc.org/databases/oryzacyc/6.0 |
| KEGG_rice | Metabolomics | To decipher pathway maps | https://www.genome.jp/kegg-bin/show_organism?menu_type=pathway_maps&org=dosa |
| RICECYC | Metabolomics | It is a catalog of known and/or predicted biochemical pathways from rice | http://pathway.gramene.org/gramene/ricecyc.shtml |
| MapMan | Metabolomics | It is used in pathway analysis | https://mapman.gabipd.org/home |
| Plant GSEA | Metabolomics | It is used for gene set enrichment analysis | http://structuralbiology.cau.edu.cn/PlantGSEA/index.php |
| AgriGo | Metabolomics | It is an ontology analysis tool | http://bioinfo.cau.edu.cn/agriGO/ |
| KEGG Mapper | Metabolomics | It is a tool for KEGG pathway mapping | https://www.genome.jp/kegg/mapper.html |
| MetaboAnalyst 5.0 | Metabolomics | It is a comprehensive platform dedicated for metabolomics data analysis | https://www.metaboanalyst.ca/ |