Construction and content of the DBPR
Classification of Plant databases
The numbers of databases are growing at a very high speed due to the ongoing research and technology in all the research fields(24), some of the omics databases are available on the “National Center for Biotechnology Information (NCBI) (9) in different research area. for more easy access we have collected Plant databases and divided them into many classes, which are given below.
Plant DNA database
Database of plant DNA is a database in which genomic details of different plants are available in various databases such as PLAZA(21), Planteome (22), AtGDB (23), etc. It's tough to get the knowledge you need regarding plant genomes because reported research is scattered through a large range of publications and the majority are undisclosed, Database brings together information from smaller databases and literature (25). And we've compiled the strongest information on plant genomes to make the work simpler for the researcher.
Plant RNA database
The Plant RNA database and web-site incorporate knowledge from numerous independent computer-assisted searches and databases such as PsnoRNA database(15), PceRBase database(16) and CSRDB(17), etc. The RNA database was used to classify different plant species, and such sequences are used in the database as alignments. The database ultimately establishes a unifying nomenclature for all other RNAs i.e Small nucleolar RNAs, processing and modification of other RNAs, such as ribosomal and small nuclear spliceosomal RNAs, SnoRNAs are a large family of relatively well characterized non-coding RNAs (ncRNAs)(26).
Plant protein database
Plant protein databases have become an important part of contemporary biology. For plant protein structures, functions, and especially sequences, enormous amounts of data are generated. In the study of a new protein, database queries are always the first step. Comparison between proteins or between groups of proteins offers knowledge about the interaction between proteins inside or through genomes or across species, and therefore provides much greater knowledge than can be gained from researching a single protein alone(27). In a fact, there are also commonly accessible secondary sources originating from sample datasets. Such repositories restructure and annotate the data or offer predictions. Using several repositories can also help researchers consider a protein's structure and work, although certain plant protein databases are well recognized such as MPIM database(13), P3DB(14), etc. they are far from being completely used in the field of protein sciences. our database gives readers a starting point for discovering the value of online plant protein repositories.
Plant expression database
Plant expression database is a publicly accessible co-expressed gene sets database that will be a powerful resource for a broad spectrum of experimental projects, including targeting genes for functional detection of regulatory work e.g, SoyNet database(28), BarleyBase(29). Here we report the construction of the Arabidopsis thaliana trans-factor and cis-element prediction database (ATTED-II) that provides co-regulated, co-expressed gene relationships, On co-expressed genes resulting from microarray data and the cis elements expected(30).
Plant pathway database
The Plant Pathway database or Reactome database is a database of biochemical pathways for metabolic, signaling, reaction and regulation(19). Such as (MetaCrop(31), PathoPlant(32), PLaMoMdb (20)).These data bases also provide bioinformatics tools for the researchers to anticipate and analyze biological and biochemical pathways. Examples of biological pathways in Reactome include classical intermediary metabolism, signaling, transcriptional regulation, apoptosis and disease. The plant pathways databases accommodate the distinct type of reactions that is available for computational analysis.
Statistics of the DBPR
With the rapid growth of plant databases, we tried to gather all online plant databases to one database and give easy access to all plant researchers, therefore, we have provided access to 225 redundant databases (Tab-S1). We have collected all category-wide and year-wise database and have classified into 5 categories which shown in the Fig-2A. further, the category-wise growth of the plant databases shows the big difference of each and every category from the last decade of the plant research Fig-2B. while the year-wise growth gives clear figures of the improvement of plant database research with the passage of time Fig: 2C.
Usages of the DBPR Database
To provide useful and updated plant research the DBPR is developed in an easy and friendly searching way. For past search our database gives 3 options to accesses the data, user can click by the categories name or can direct click by the image expression (Fig 3A), which will lead to the clicked category’s table (Fig 3B), by further clicking users can get their needed information, or direct can type the name of the required database in the given search bar on the top of the database, (Fig 3C), which are we given and highlighted MMP database as an example.