Databases and Bioinformatics Tools for Rice Research

Current Plant Biology 7–8 (2016) 39–52

Contents lists available at ScienceDirect

Current Plant Biology

jo urnal homepage: www.elsevier.com/locate/cpb

ଝ

Databases and bioinformatics tools for rice research

∗

Priyanka Garg, Pankaj Jaiswal

Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331, USA

a r t i c l e i n f o a b s t r a c t

Keywords: Rice is one of the most important agricultural crop in the world and widely studied model plant. The

Biological database

completion of whole genome sequence of rice (Oryza sativa) and high-throughput experimental plat-

Rice

forms have led to the generation of the tremendous amount of data, and development of the specialized

Gene expression

databases and bioinformatics tools for data processing, efﬁcient organization, analysis, and visualiza-

Biocuration

tion. In this article, we discuss a collection of biological databases that host genomics data on sequence,

Ontology

Pathways gene expression, genetic variation, gene-interactomes, and pathways, and facilitate data analysis and

visualization.

(http://creativecommons.org/licenses/by/4.0/).

1. Introduction organisms including rice. In contrast community-speciﬁc databases

cater to the need of a speciﬁc research community such as plant

Over the last decades, an increasing amount of genome-scale databases, e.g. PlantGDB [8], ENSEMBL Plants [9], Gramene [10],

experimental data sets became available and several online and PLEXdb [11], Gene Expression Atlas [12], Planteome [13], etc. The

open source, biology databases have emerged. For instance, cur- species-speciﬁc databases for the model and non-model organisms,

rently, ∼1685 publicly available, online databases are listed at NAR for example, RAPdb [14], Beijing Genomics Institute-Rice Informa-

online Molecular Biology Database Collection [1]. These databases tion System [15] and Rice SNP-Seek Database [16,17] provide in

can be categorized on the basis of data type, data curation methods, depth coverage of the data sets and are more speciﬁcally tuned to

the scope of data coverage and accessibility of the database. Many the need of a specialized small community of researchers Table 2.

such publicly funded resources host data (raw, annotated, ana- Furthermore, each database can be assigned to one or more cate-

lyzed) for various species including crops, model and non-model gories on the basis of their content, for example, gene expression

plants, whereas, others are dedicated to a group of species from a databases, molecular interaction databases, genome annotation,

taxonomic clade and may contain a certain type of data. In addition, nucleotide or protein databases, smallRNA databases, genomic

an array of tools and web applications are available that facilitate variation, phenome and pathway databases.

formatting, analysis and visualization of various types of genomic Rice is an important crop and serves as a model for monocotyle-

data. don family. Recent advances in rice genome biology have generated

Data coverage decides the target user community for a database. tremendous amount of data including fully sequenced high qual-

These large-scale public repositories or international archives, ity reference genomes [9,10], low coverage sequencing data from

usually developed and maintained by national and international 3010 rice accessions of the rice germplasm core collection with

projects, provide genomic data from several species. Table 1 lists an average sequencing depth of 14× [16–19], genetic variation,

some of the generic large-scale public repositories or archives, and transcriptomes, proteomes, metabolomes, etc. which necessitates

databases, for example, GenBank [2], EMBL [3], INSDC [4], and development of bioinformatics resources and databases for storage,

DDBJ [5] for sequences and annotation, PDB [6] for protein struc- processing, organization, analysis, and visualization of such data at

tures and UniProt [7] for protein information. These are long-term systems level.

sustainable repositories for archiving valuable data from several For the beneﬁt of rice researchers, we are providing a compre-

hensive list of such generic and specialized genomic databases,

resources, web applications and analysis tools (Tables 1 and 2).

ଝ Some of the information provided here is also useful to the commu-

This article is part of a special issue entitled “Genomic resources and databases”,

nity of plant researchers who may not be engaged in rice research. It

published in the journal Current Plant Biology 7–8, 2016.

∗ is possible that we may have missed some resources and we expect

Corresponding author.

E-mail address: [email protected] (P. Jaiswal). this list to grow in future.

http://dx.doi.org/10.1016/j.cpb.2016.12.006

40 P. Garg, P. Jaiswal / Current Plant Biology 7–8 (2016) 39–52

2. Resources for genes, genomes, genetic variations project) and their consequences on the gene function and struc-

ture, descriptions of phenotypic traits and plant pathway databases

The rice genome assembly, annotation, and associated infor- developed using the BioCyc platform such as RiceCyc [27], and the

mation is mainly provided by the MSU Rice Genome Annotation Reactome platform-based Plant Reactome that provides pathways

Project [20,21], the International rice genome sequencing project’s from the reference rice and gene homology-based projections to all

(IRGSP) rice RAPdb [14,22] and the Oryza Genome Evolution (OGE) Oryza species with sequenced genome or transcriptome [28]. The

project (http://oge.gramene.org). Gramene uses annotated rice features and data available at the genome portal of Gramene and

genes and genome assemblies of O. sativa ssp. japonica cv Nippon- their collaborator Ensembl Plants [9] are similar.

bare from IRGSP [14,22], O. sativa ssp. indica cv 93-11 and several In addition to Gramene, a number of databases provide genetic

wild Oryza species sequenced by the OGE and the Internatioanl variation data (SNPs and indels) including PmiRKB [29], Rice Varia-

Oryza Map Alignment Project (I-OMAP) (http://oge.gramene.org) tion Database [30], RiceVarMap [31], SNP haplotype database [32],

[23–26]. These genomes are presented by building an integrated and Rice SNP-Seek Database [16,17]. The largest data set (∼29

web resource for rice that includes rice species-speciﬁc genome million SNPs) for rice genetic variants come from the 3000 rice

browser, whole genome alignment, synteny, genetic and physi- genome sequencing project that is now being hosted at IRIC, a Rice

cal maps with genes, gene trees, ESTs and QTL locations, genetic SNP-Seek Database together with phenotype and variety informa-

diversity data including SNPs (from the 3000 rice genome sequence tion/passport data [16,17].

Table 1

Generic genomic databases and bioinformatics tools. The description may be copied from the original source [2,5–7,9–11,29,30,33,34,38,39,49,50–52,58,63–91].

Data Types

te/pr els, els, ng i li nd

tation

ud Database Name etc.)

no and latest Description Species URL es on release date (incl otein) cti Others on mutants, i Expression Expression , all RNA types RNA all Genetic/genomic Genetic/genomic wild speci wild variati Genome an Genome Gene/gene products products Gene/gene SNP including proteins and and proteins including Pathway/network/intera (transcript/metabo An open source, data resource

O. sativa and

Gramene for comparative functional

other plant h ttp://www.gramene.org Y Y Y Y Y Y

Nov 2016 genomics in cereals and other

species

plant spe cies [10].

It provides, information on

metab olic pathways inferred from

EXPath O. sativa and 2

microarr ay-based transcriptomic http://expath.itps.ncku.edu.tw Y Y Y

Oct 21, 201 2 plant species

data, gene annotati on and

orthologous genes[38].

PLANEX (PLAnt Contains pub licly available O. sativa and 7

co-Expression) GeneChip data obtained from the http://planex.plantbioinformatics.org Y Y Y

plan t species

database Gene Express ion Omnibus [63].

Provides informati on on co-

expre ssion gene-networks

ATT ED-II Oryza and 8

sup ported by microarray and http://atted.jp Y Y Y

Sep 1, 2015 plant species

RNA seq uencing-based transcriptomic data. [64]. PODC (Plant

A repository of annotated gene

Omics Data O. sativa and 7

expre ssion data and omics data http://bioinf.mind.meiji.ac.jp/podc Y Y Y Y

Center) plant species

analysis too ls [65].

Mar 16, 2016

A plan t miRNA data repositories

con taining .associated

PMRD (Plant information on sequence,

O. sativa and

MicroRN A secondary structure, target

120 pl ant http://bioinformatics.cau.edu.cn/PMRD Y Y Y Y

Datab ase) genes, expression profiles of

species

Nov 17, 2014 miRNAs and their mappi ng to the

spe cies-specific genome browser

[66].

NIAS GBdb

(National Institute A database containing

O. sativa and

of Agrobiological information on simple sequence

other plant h ttp://www.gene.affrc.go.jp/databases_en.php Y Y Y

Sciences repeat (SSR) polymorphisms in

species

planttfdb plant genomes [67].

database)

A databa se for rice reverse O. sativa ssp.

geneti cs, build with flanking indica and

OryGenesDB seq uence tags of various japonica, and 2 http://orygenesdb.cirad.fr/index.html Y Y Y

mutag ens and functional other plant

genomics da ta [68] species

P. Garg, P. Jaiswal / Current Plant Biology 7–8 (2016) 39–52 41

Table 1 (Continued)

All ows the user to retrieve data

related conserved structural-

O. sativa and 7

FamNe t functional domains within http://www.gene2function.de/famnet.html Y Y Y

plan t species

proteins from one or more plant

spe cies [69]

A comparative hub for annotated

plant genome and gene family

data. Provides a vi ew of the O. sativa and

Phytozome evolution ary history of every 64 other plant

h ttp://www.phytozome.net Y Y Y Oct 16,2015 plant gene at the level of and algae

sequence, gene structure, gene species

famil y and genome organization [70]. A relational database that

integrates data from rice,

POG s (Putative

Arabidop sis, and maize into

orthologous

'putative orthologous groups' O. sativa and 3

Groups 2) h ttp://pogs.uoregon.edu Y Y Y

(POGs) and allow comparisons plant species Datab ase

among orthologs and

2014

extrapolati on of annotations

among species [71].

The database con tains a

O. sativa and

GreenPhylDB catalogue of gene families

other plant h ttp://www.greenphyl.org/cgi-bin/index.cgi Y Y Y

Sep 4, 2015 covering a broad taxon omy of

species

green plants [72].

Provides informati on on

ppdb (plant transcription start sites (TSSs),

promoter core promoter structure (TATA Oryza and 4

h ttp://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/index.cgi Y Y Y

database) boxes, Initiators, Y Patches, GA plant species

Jun 5, 2013 and CA elements) and regulatory

element groups (REGs) [73].

Consisting o f large-scale

CSRDB (Cereal datasets of maize and rice

O. sativa and

Sma ll RNA smRNA sequences generated by http://sundarlab.ucdavis.edu/smrnas Y Y

maize

Datab ase) high-throughput pyrosequencing

[74].

Compiles transfer RNA (tRNA)

gene seque nces retrieved from O. sativa and

PlantRNA

full y annotated plant nuclear, 10 plant http://plantrna.ibmp.cnrs.fr Y Y Sep 6, 2012 plastid and mitochondrial species

genomes [75].

A Cen tral resource for annotated

proteins consisting of two

O. sativa and

UniProtKB secti ons: UniProtKB/Swiss-Prot

other organism h ttp://www.uniprot.org Y Y

Nov 2016 for manually annotated entries,

species

and UniProtKB /TrEMBL for

computer-annotated entries [7].

GenBank NIH genetic sequ ence database, O. sativa and

Updated on daily a repository of publicly available other organism http://www.ncbi.nlm.nih.gov Y Y basis DNA seq uences [2]. species

DDBJ O. sativa and

A public repo sitory of nucleotide

Updated on dail y other organism http://www.ddbj.nig.ac.jp Y Y

seq uence data [5].

bases species

Comprehen sive collection of

O. sativa and

EMBL nucleoti de sequences and

other organism h ttp://www.ebi.ac.uk/about Y Y

Dec 7, 2016 annotation from available pu blic

species

sou rces [76] . Provides Genome brow ser for

O. sativa and

Ensembl Plants several plant species various

other organism h ttp://plants.ensembl.org/index.html Y Y

Dec 2016 genomic data sets, and tools for

species analysis and visuali zation of

42 P. Garg, P. Jaiswal / Current Plant Biology 7–8 (2016) 39–52

Table 1 (Continued)

genome-scale large da ta sets in

the context o f genome [9]

O. sativa ssp.

Manuall y curated genes that are japonica cv. DroughtDB involved in drought stress http://pgsb.helmholtz-muenchen.de/droughtdb Y Y Nipponbare and

response [77]. 8 plant spe cies

A collection of biotic and abiotic stress responsive genes with options to identify probable

Transcription Factor Binding Sites in their promoters. An STIFDB2 (Stress integrated biocuration and O. sativa ssp. Responsive genomic data mining approach japonica and Transcription http://caps.ncbs.res.in/stifdb2 Y Y Y

have been employed to Indica and

Factor Database)

cha racterize the data set of Arabidopsis

Oct 2012

transcription factors and

con sensus binding sites from

literature and stress-responsive

genes from the Gene Expression

Omnibus [78].

Composed of a coll ection of

databases that relate to the

GR ASSIUS

con trol of gene expression in the (Grass Reg ulatory

grasses, and their relationship O. sativa and 3

Information www.grassius.org Y Y Y

with agronomic traits. Include s plant species

Services) transcription factors, promoters,

Aug 25, 2014

co-regulators and transcription

factor-ORF clone s [79].

Integ rated database for co-

expre ssed genes and

CoP database O. sativa and 7

biological processes in plants http://webs2.kazusa.or.jp/kagiana/cop0911 Y Y

Nov 11, 2009 plant species derived from microarray da ta

[39].

First integrative resource that

O. sativa and 7

IsomiR Bank con tains the sequence and http://mcg.ustc.edu.cn/bsc/isomir Y Y

organisms

expre ssion of isomiRs [80].

Provides informati on on the

Plant MPSS

expre ssion level of genes, and O. sativa ssp.

(mass ively

potential novel transcripts indica and

parall el signature http://mpss.udel.edu Y Y

(antisense transc ripts, alternative japonica and 3

seque ncing)

sp lice isoforms, and regulatory plant species

databases

intergenic tran scripts) [81].

Provides information on co-

PlantArr ayNet expresssed genes using O. sativa and 2

h ttp://arraynet.mju.ac.kr/arraynet Y Y

Jan 10 , 2011 microarray-based transcriptomic plant species data [82].

A unified gene expression

resource for plants and plant

pathogen s. It is a genotype to

pheno type, hypothesis building Oryza and 12

PLEXdb

information wa rehouse, other plant http://www.plexdb.org Y Y

Jun 2013

leveraging highly parallel species

expre ssion data with seamless

portals to related genetic,

physical, and pathway data [11].

P. Garg, P. Jaiswal / Current Plant Biology 7–8 (2016) 39–52 43

Table 1 (Continued)

BAR (Bio- Several plant

Analytical Provides interactive interfaces for

species

Resource for the exploratory visuali zation of http://bar.utoronto.ca Y Y

including O. plant biology) gene expre ssion data [83, 84] sativa. Jun 2, 2015

PmiRKB (Plant Provides four major functional

miRNA 21 O. sativa

modules-"SNPs", "Pri-miRNAs", http://bis.zju.edu.cn/pmirkb Y Y Knowled ge Base) and Arabidopsis "MiR—Tar", and "Self-reg"[29]. Jun 5, 2010 A web interface to access large sets of transcription factors of several plant species. O. sativa ssp.

Information including protein

PlnTFDB (plant indica and

seq uences, coding regions,

transcripti on japonica and http://plntfdb.bio.uni-potsdam.de/v3.0 Y Y

genomic sequences , expressed

factor da tabase) other plant seq uence tags (ESTs), domain species architecture and scientific

literature is provided for each

famil y [85].

PlantDHS (plant Integ rates histone modification,

O. sativa ssp.

DNase I RNA seq uencing, nucleosome japonica cv. hypersensitive positioning/ occupancy, http://plantdhs.org Y Y

Nipponbare and

site database) transcription factor binding sites,

2 plant spe cies

Feb 23,201 6 and genomic sequence [86].

Plant Homolog 16 plant sp.

A databa se composed of plant

Datab ase Including 10 http://phd.big.ac.cn Y Y

homologous gene s [30].

May 9 , 2015 Oryza species

Simple yet robust and extensible

PO (Plant con trolled vocabularies that O. sativa and

Ontology) acc urately reflect the biology of other plant www.plantontology.org Y Y Sep 2016 plant structures and species

developmental stages [58]

Plant-PrAS (Plan t Database of physicochemical

Protein and structural properties, and O. sativa and 5

h ttp://plant-pras.riken.jp Y Y

Annotation Suite) novel fun ctional region in plant plant species

database proteo mes [87].

PDB (Protein Worldwide archive of structural O. sativa and

Data Bank) data o f biological other organism http://www.rcsb.org/pdb Y Y Dec 6, 2016 macromolecules [6]. species MPIC

O. sativa and

(Mitochondrial Searchable information on the

23 othe r http://www.plantenergy.uwa.edu.au/applications/m

Protein Import protein import apparatus of pl ant Y Y

organism pic

Components) and non-plant mitochondria [88].

species

database

A databa se of molecular O. sativa and

PlantGDB

seq uence data from several plant other plant http://www.plantgdb.org Y

Jul 23, 2012

spe cies [89]. species

A web server for query,

visua lization, and analysis of

PlantAPA

poly(A) sites in plants , which can

(Alternative O. sativa and 3

profil e heterogeneous cleavage http://bmi.xmu.edu.cn/plantapa Y Y polyadenylation) plant species

sites and quantify expression

Aug 30, 2016

pa ttern of poly(A) sites across

di fferent conditions [90].

A resource for co mmon

referen ce ontologies for plants

Oryza and plant

Planteome and species-specific crop h ttp://www.planteome.org Y Y

species

ontologies. Also provides

ontology-ba sed annotation of rice

44 P. Garg, P. Jaiswal / Current Plant Biology 7–8 (2016) 39–52

Table 1 (Continued)

genes, QTLs, phenotypes, germplasms [49].

Functional annotation of plant Oryza and 2

Mercator pipeline h ttp://mapman.gabipd.org/web/guest/app/Mercator Y Y

'omics ' data [91]. plant species

Provides li fe scientists with

powe rful computational

CyVerse (former

infrastructure to handle huge Plants, animals,

iPlant http://www.cyverse.org Y Y Y datasets and complex analysis, and microbes

Collaborative) thus enabli ng data-driven

discovery [50].

A softwa re system that allows

experimentali sts without

informati cs or programming

Galaxy h ttp://galaxyproject.org Y Y expertise to perform complex

large-scale analysis with just a

Web brow ser [51, 52]

Database of allergenic proteins

MoCh A gained by bioinformatics tools or

(Molecular evidence of IgE binding. It has

Oryza and 3 h ttp://lilab.life.sjtu.edu.cn:8080/mocha/main-7.9-

Characteristi cs collected genome, transcriptome, Y Y

plan t species 2.html

database for proteo me data of reliable All ergens) experiments and molecular

features.

A we b-based tool for accessing

the diurnal and circadian

genome-wide expre ssion results

Diurnal Plant spe cies http://diurnal.mocklerlab.org Y Y

of genes from several array

experiments conducted on

common model plants [33].

Provides pow erful tools to

O.sativa and 16

explore gen e expression across

Genevestigator organism h ttps://genevestigator.com/gv Y Y a wide variety of biolog ical

species

con texts [34].

3. Resources for gene expression datasets, kegg-bin/show organism?menu type=pathway maps&org=dosa)

gene-interactomes, pathways and ontologies and the Plant Reactome [28], host pathway databases for metabolic,

regulatory, developmental and signaling pathway analysis.

The gene expression databases play a vital role in extracting, Table 1 also includes a number of publicly available molecu-

organizing and interpreting the information regarding the expres- lar interaction databases. The databases such as CoP [39] provides

sion proﬁle of a gene and genomes under a speciﬁc developmental information on the co-expressed genes based on transcriptome

stage or in response to a particular treatment to build a connec- analysis for 8 plant species including rice. DIPOS [40] is a database

tion between the genotype and phenotype of an organism. The of interacting proteins in Oryza sativa, while PRIN [41] is based on

transcriptomic data can be obtained using various experimental the interologs of six model organisms, where large-scale protein-

platforms, such as real-time PCR, microarray, and RNA-seq. The protein interaction experiments have been applied. RiceNet [42],

Diurnal [33], GENEVESTIGATOR [34] and EMBL-EBI Gene Expres- provides an updated network prioritization server for Oryza sativa

sion Atlas [12] are popular resources that host gene expression data. ssp. japonica.

EMBL-EBI Gene Expression Atlas provides information on the base- The use of ontologies such as the Gene Ontology (GO) [43]

line expression of the gene or a set of genes in a given sample from and the Plant Ontology (PO) [44] are instrumental in providing

the RNA-seq based experiments as well as their differential expres- high quality and consistency in the annotation of genes and gene

sion data from both the RNA-seq and microarray experiments. This products for molecular function, role in biological processes and

resource also updates expression data frequently by aligning it location in the cellular components (all sub classes of GO). The

against the most recent version of the genome assembly and anno- PO-based annotations include observations or samples isolated

tation available from the Plant Ensembl and Gramene database. The for expression and phenotype associations to plant structure and

rice-speciﬁc expression data is also hosted by resources like IC4R the plant growth and developmental stage, the two subclasses

[30], RiceFREND [35], RiceXPro [36]. of PO. The Plant Trait Ontology (TO) and the ontology- entity-

MCDRP [37] resource hosts manually curated annotation of rice quality attribute-based phenotype annotations are being promoted

proteins based on published datasets. EXPath [38] database pro- for mutant phenotype and QTL trait annotations [45–48]. These

vides information on metabolic pathways for several plant species annotations are often provided by the individual species speciﬁc

based on the analysis of the microarray-based gene expression databases. The Planteome is a new database (www.planteome.org)

data. Other databases such as RiceCyc [27], and OryzaCyc (http:// [49] that provided the reference set of ontologies for integration in

www.plantcyc.org/databases/oryzacyc/) host metabolic pathway the genome, expression and phenome projects. It also provides a

network for rice. Whereas, KEGG rice (http://www.genome.jp/ collection of ontology-based annotation of about 85 plant species

P. Garg, P. Jaiswal / Current Plant Biology 7–8 (2016) 39–52 45

including the various rice reference O. sativa subspecies japonica [54] tool provided by the Ensembl and Gramene, Pathway enrich-

and indica and the wild Oryza species. ment and comparison tools by Plant Reactome [28].

4. Web applications and bioinformatics analysis tools 5. Fundability, accessibility, and interoperability of

genomic data and resources

Web based tools provide an excellent platform to analyze

huge data sets and, thus enabling data-driven discoveries. For The primary aim of many plant genomic databases has been

example, CyVerse [50] and Galaxy [51,52] are two widely used to acquire, organize, represent, and help navigate and retrieve the

cyber infrastructure platforms for data storage, dissemination, and information of interest. In accordance with data collection tech-

high-throughput bioinformatics analysis. They provide access to niques, biological databases are classiﬁed into either Primary and

popular bioinformatics tools, access to computing infrastructure Secondary or both. Primary databases rely upon direct archiv-

and options to run user tools. CoGe [53] is another “platform ing of the experimental results as a data source such as NCBI

for performing Comparative Genomics research. It provides an Sequence Read Archive (SRA) [55], INSDC and its collaborator

open-ended network of interconnected tools to manage, ana- archives [4], Rice RAPdb [22]. The secondary databases are pop-

lyze, and visualize next-gen sequencing data” (Source: https:// ulated with processed and analyzed data of primary data-sets, e.g.

genomevolution.org/coge/). Besides the infrastructure platforms, NCBI RefSeq [56], EMBL-EBI’s Gene Expression Atlas [12]. However,

many of the databases listed in Tables 1 and 2 provide local data resources like Gramene [10,57], Plant Ontology [44,58], Planteome

analysis options. For example. the Variant Effect Predictor (VEP) [13], Ensembl Plants [9] and Plant Reactome [28] provide both the

Table 2

Rice speciﬁc databases. The description may be copied from the original source [20–22,12,14–17,30–32,35–37,41–42,48,68,92–113].

Data Types

ng on indels, , ncludi i

Database Name nteractions

and latest Description Species URL release date RNA types all nd Others Expression d species etc.) d species il w Genome annotation Genetic/genomic variati Genetic/genomic proteins a proteins

Pathway/network

(transcript/metabolite/protein) Gene/gene products (including SNP, mutants

Annotation datab ase for rice

comparative genomics and O. brachyantha,

RGKbase (Rice evolution ary biology, which O. glaberrima,

Genome includes ge nome sequence O. sativa ssp.

Knowled gebase) assemblies, transcriptomic and japonica cv. http://rgkbase.big.ac.cn/RGKbase Y Y Y Y Y Y

Jun 28, 2012 epigenomic data, genetic Nipponbare,

variations, quan titative trait loci ssp. Indica 93-

(QTLs) and the relevant literature 11, and PA64s

[92]. MCDR P Gene expression database for

(Manually O. sativa ssp.

rice proteins including metabolic

Curated Da tabase indica and http://www.genomeindia.org/biocuration Y Y Y Y Y

pathways and protein interaction

of Rice Proteins) japonica from publishe d articles [37].

Nov 30, 2016

Functional genomi cs database

linking annotation, sub-cellular

Rice DB O. sativa and

location, function , expression, http://ricedb.plantenergy.uwa.edu.au Y Y Y Y

Oct 23, 201 3 Arabidopsis

regulati on, and evolutionary

information [93].

Represents transcriptiona l

activity on the rice genome at the

nucleoti de level based on the

RNA-seq data un der 140

TENOR environmen tal stresses and plant O. sativa ssp. (Transcriptome

hormone treated conditions. japonica cv. http://tenor.dna.affrc.go.jp Y Y Y Y

ENcyclopedia Of

Expression profil es, information Nipponbare

Rice)

of cis-regu latory elements in

promoter regions and co-

expre ssed transcript are provided

for each transc ript [94].

Sub-pla tform of PlantExpress for

a single-species gene expre ssion

OryzaExpress analysis in O. sativa . Consists of

O. sativa http://plantomics.mind.meiji.ac.jp/OryzaExpress Y Y Y

Apr 22, 201 4 gene expression networks and

omics an notations derived from

microarr ay data [95].

Accommodates rice reference

Rice Expression

genome with standa rdized and

Datab ase Oryza spp http://expression.ic4r.org Y Y Y

acc urate gene annotations

Aug 2016 derived from RNA-seq data [30 ].

46 P. Garg, P. Jaiswal / Current Plant Biology 7–8 (2016) 39–52

Table 2 (Continued)

cDNA resource with

comprehensive information for

functiona l analysis of indica ssp.

O. sativa ssp.

and comparative genomics

RICD (Rice Indica indica Guang-

including sequ ences, protein http://www.ncgr.ac.cn/ricd Y Y Y Y

cDNA Database) lu-ai 4 and

domain ann otations, similarity Minghui 63 search results, SNPs and InDels information, and hyperlinks to gene annotation [96].

A database for rice reverse

geneti cs, build with FSTs O. sativa ssp. (flanking sequence tags) of indica and

OryGenesDB various mutagens and functional japonica, and 2 http://orygenesdb.cirad.fr/index.html Y Y Y

genomics da ta, collected from other plant

both international insertion species

co llections and the literature [68].

An integrative

genomic database for rice with an emphasis on combining

datasets in a way that maintains

Ricebase key li nks between the past and

O. sativa http://ricebase.org Y Y Y

Aug 10, 2016 current gen etic studies. Includes DNA sequence data, gene annotations, nucleotide variation

data and molecular marker

fragment size data [97]. Displays hormone-metabolome (hormonome) and transcriptome

data in a single formatted

UniVIO (uniformed) heat map.

(Uniformed Hormonome and transc riptome O. sativa ssp.

Vi ewer for data obtained from 14 organ japonica cv. http://univio.psc.riken.jp Y Y Y Y

Integrated Omics) parts of rice plants at the Nipponbare

Oct 22, 201 2 reproductive stage and seedling

sho ots of three gibberellin

signa ling mutants are included in

the database .[98].

Rice proteome databa se based

on sho tgun proteogenomics,

OryzaPG-DB con tains proteome of rice

(Oryza undi fferentiated cultured cells,

ProteoGenomic corresponding cDNA, transcript O. sativa http://oryzapg.iab.keio.ac.jp Y Y Y

Datab ase) and genome sequences, novel

Jan 30 , 2012 proteogenomics features and tupdated gene models annotation [99].

Q-TARO (QTL

Displays the co-localization of O. sativa ssp.

Annotation Rice

QTLs and distributi on of QTL indica and http://qtaro.abr.affrc.go.jp Y Y Y

Online Da tabase )

clusters on rice genome [100]. japonica

March 31, 2012

A resource for pu blicly available

MosDB

seq uences of the rice (Oryza http://pgsb.helmholtz- Updated on daily O. sativa Y Y

sativa L.) genome. Sub-platform muenchen.de/plant/rice/index.jsp

basis

of Plantdb [101].

Displays sequence and

annotation data for the rice

MSU Rice

genome . Includes genome

Genome O. sativa ssp.

brow ser, motifs/domains within

Annotation japonica cv. h ttp://rice.plantbiology.msu.edu Y Y the predicted gen es, a rice

Project Nipponbare

repeat database, identifi ed

Feb 7, 2012

related sequences in other plant

spe cies [20, 21].

P. Garg, P. Jaiswal / Current Plant Biology 7–8 (2016) 39–52 47

Table 2 (Continued)

RAP-DB (Rice Genomics database provides O. sativa ssp. Annotation

gene annotations for the genome japonica cv. http://rapdb.dna.affrc.go.jp Y Y

Project DataBase)

seq uence of rice [14, 22]. Nipponbare Aug 5, 2016 Provides access to the most updated version of the Oryza genome evolution (OGE) project and the International Oryza Map Several species OGE Gramene alignment (I_OMAP) project. http://oge.gramene.org Y Y of Oryza Includes, genome assembly, annotation, synteny, gene trees, SNPs and interspecific genome alignments. A wiki-based, publicly editable and open-content platform for RiceWiki Oryza http://wiki.ic4r.org/index.php/Main_Page Y Y community curation of rice genes

[102].

A coll ection of databases for six large gene famili es in rice,

including those for

glycosyltransferases, glyc oside

hydrolases, kinases, transcription factors, transporters , and

Rice

cytochrome P450

Phylogenomic O. sativa http://ricephylogenomics.ucdavis.edu/index.shtml Y Y Y

monooxy genases viz. Rice Database

Kinase Database, Rice GT Jun 2015 database, Rice GH database,

Rice TF database, Rice

transporter databa se, Rice

Cytochrome P450 database [103].

DIPOS (database

Provides comprehensive

of interacting

information of interacting proteins O. sativa http://www.riceresearch.info Y Y

proteins in Oryza

in rice [40].

sativa)

Metab olic network of rice.

Provides metabolic pa thways,

reactions, metabolites and

RiceCyc O. sativa ssp h ttp://pathway.gramene.org/RICE/organism-

ass ociated gene entities. The Y

Dec 2016 japonica su mmary?

analysis too ls provide pathway

comparison , and gene

expre ssion analysis.

Provides metabolic an d

h ttp://www.genome.jp/kegg-

regulatory pa thways, enzymes,

KEGG rice bin/show_ organism?menu_type=pathway_maps& Y

reactions, metabolites and

org=dosa

ass ociated gene entities.

Experimentall y determined gene- http://www.ebi.ac.uk/ebisearch/search.ebi?db=inta

IntAct rice O. sativa Y gene interaction da ta ct-experiments&t=Oryza+sativa

An updated network prioritization

server for Oryza sativa ssp.

Jap onica. Gene prioritization

RiceNe t O. sativa ssp.

allow s users to predict new http://www.inetbio.org/ricenet Y Y

Dec 29,201 4 japonica

can didate genes for a phenotype

or biological pathways by prioritizi ng rice genes [42].

48 P. Garg, P. Jaiswal / Current Plant Biology 7–8 (2016) 39–52

Table 2 (Continued)

Rice knowledgeb ase- expression profil es derived from RNA-seq IC4R (Information

data, genomic variations, plant

Commons for

homologs, post-translational Oryza http://ic4r.org Y Y

Rice)

modifications, literature as well

May 5 , 2015

as community-con tributed annotations [30]. A rice genome automated Rice GAAS (Rice annotation system, which Genome integrates programs for Automated O. sativa http://RiceGAAS.dna.affrc.go.jp Y Y prediction and analysis of Annotation protein-coding gene structure System) [104].

An open public repository of EMBL-EBI Gene gene expre ssion pattern data Expression Atlas under different biological O. sativa https://www.ebi.ac.uk/gxa/home Y Y Dec 2, 2016 conditions using both microarray and RNA-seq data [12]. Gene coexpression database O. sativa ssp. RiceFREND derived from Microarray data japonica cv. http://ricefrend.dna.affrc.go.jp Y Y Sep 13, 2012 [35]. Nipponbare

Repository of gene expression

profil es derived from microarray

analysis of tissues/organs RiceXPro (Rice encompassing the entire growth

O. sativa ssp.

EXpression of the rice plant under natural

japonica http://ricexpro.dna.affrc.go.jp Y Y

Profil e Database) field conditions, rice seedlings

2013 trea ted with various

phytohormones, and specific cell

type s/tissues isolated by laser

microdissection (LMD) [36 ].

ROAD (Rice A public resource for gene

O. sativa ssp.

O ligonucleotide expression and coexpression indica and http://www.ricearray.org Y Y

Array Database) analysis in rice derived from

japonica

Mar 28, 2012 microarr ay data [105].

A databa se of Arabidopsis

mutant lines overexpressing rice

full-length cDN A that contains a

RiceFOX O. sativa http://ricefox.psc.riken.jp Y Y Y

wide range of trai t information to

facilitate an alysis of gene

function [106 ].

Protein-protein interaction data of

PRIN are ba sed on the interologs

PRIN (predicted

of six model organisms where

rice interactome O. sativa http://bis.zju.edu.cn/prin Y Y

large-scale protein-protein netwo rk)

interaction experiments have

been applied [41].

Provides Genotype , Phenotype,

and Variety Information for rice

and SNP geno typing data. It

allow s quick retrieving of SNP

Rice SNP-Seek all eles for all varieties in a given O. sativa ssp.

Datab ase genome region, finding different japonica cv. http://www.oryzasnp.org/iric-portal Y Y

Feb 16, 2015 alleles from predefined varieties Nipponbare

and querying ba sic passport and

morph ological phenotypic

information abou t sequenced rice

line s [16, 17].

Rice Variation An atlas of re-sequen cing-based

Oryza varieties http://variation.ic4r.org Y Y

Datab ase rice genomic variations [30].

P. Garg, P. Jaiswal / Current Plant Biology 7–8 (2016) 39–52 49

Table 2 (Continued)

Database of rice genomic

variation. Contains SNPs and RiceVarMap INDELs identified from

O. sativa http:/ricevarmap.ncpgr.cn Y Y

Oct 7, 2015 seq uencing data of two sets of

rice ge rmplasms of cultivated

spe cies [31]. O. sativa An archive for collecting, ssp. Japonica RMD (Rice managing and searching cv. Zhonghua

Mutant Database) information of the T-DNA http://rmd.ncpgr.cn Y Y 11 , Zhong hua

Mar 1, 2012 insertion mutants generated by

15 and

an enhan cer trap system [107].

Nipponbare

Represents transcription factors

with comprehe nsive expression,

cis-regulatory element and

RiceSRTFDB mutant information derived from O. sativa http://www.nipgr.res.in/RiceSRTFDB.html Y Y

Microarr ay data of a curated set of 456 Affymetrix GeneChip Rice

Genome arrays [108]. A coll ection of abiotic stress

responsive quantitative trait loci

Q licRice (QTLs) in rice and their O. sativa http://nabg.iasri.res.in:8080/qlic-rice Y Y corresponding sequenced gene loci [109].

An integrated information

resource and comparative analysis wo rkbench for rice

BGI-RIS V2

genomes including detail ed

(Beiji ng Genomics

annotation data , including O. sativa ssp.

Institute-Rice

genetic markers, Bacterial indica and h ttp://rice.genomics.org.cn/rice/index2.jsp Y

Information

Artificial Ch romosome (BAC) end japonica

System)

seq uences, gene contents,

Oct 28, 200 8

cDNAs, oligos, tiling arrays,

repetitive elements , and genomic

polymorphisms [15]. O. rufipogon , O.

longistaminata,

Subplatf orm of Oryzabase. O. sativa ssp.

Provides geno me sequence japonica cv.

OryzaGeno me information for 21 wild Oryza Nipponbare,

h ttp://viewer.shigen.info/oryzagenome Y

Jun 19 , 2015 species together with several Nongken-58,

cultivated strain reference and Aus-type

seq uences [110]. Kasalath and indica,

Guangluai-4 Contains informati on about rice

Oryza sp.

development and anatomy, rice

Oryzabase (different h ttp://www.shigen.nig.ac.jp/rice/oryzabase/top/top.j

mutan ts, and genetic resources, Y Y

2016 species of sp

especia lly for wild varieties of rice

oryza) [48 , 111]. aus, indica,

tropical

HapRice SNP haplotype database [32]. japonica and http://qtaro.abr.affrc.go.jp/index.html Y temperate japonica

50 P. Garg, P. Jaiswal / Current Plant Biology 7–8 (2016) 39–52

Table 2 (Continued)

Genus Oryza

RiTE Da tabase A genus-wide collection of

and the closely-

(Rice TE transposable elements and h ttp://www.genome.arizona.edu/cgi-

related out- Y

database) Aug repeated sequences across 11 bin/rite/index.cgi

group Leersia

31, 201 5 diploid species [112].

perrieri.

A research organ ization involved

in serving, und erstanding,

sha ring, and using rice genetic

diversity, breeding and deli vering

IRRI (International

new varieties, developing and

Rice research Oryza http://irri.org Y

sha ring improved crop and

institute)

environmen tal management

practices, and facili tating the

large-scale adoption of

technologies.

The (r ice) Provides access restricted

h ttp://fiehnlab.ucdavis.edu/projects/rice_metabolo

metabolomics access to metabolomics data for Oryza sativa Y me

data rice [113].

collected data from external sources, but add their own quality data exchange, which makes it difﬁcult to integrate them in one

annotation in addition to serving as community access to primary place. In an ideal situation, there should be a single platform for

data for which there are no known archives. all the databases on a single domain of interest, where a user can

Almost all the resources provide some form of biocuration of search all the respective databases with a single query using APIs

data and metadata required for integration and proper interpre- and ontologies and compare the results. AraPort [62] and Gramene

tation of the experiments from which data sets originate. The [10]. Are such examples. Some databases are already integrating

collection methods, annotation and statistical signiﬁcance of this the links to other databases of similar data types to increase the

primary data affect the credibility and reliability of a resource. The credibility of their data, which is the ﬁrst step in providing a uniﬁed

source of data is simply a physical access to the data and data platform. It maximizes the use of data available in current resources

location or a live data accessed via an application programming and may help in avoiding redundancy. It provides better visibility to

interface (APIs) and semantic web. small databases and can collectively provide a bigger picture since

Depending on the data type, such as genome assembly, gene small databases generally focus on one speciﬁc aspect and present

calls, functional annotation, gene expression, QTL and phenotypes, detailed information.

genetic markers, genetic diversity data in the form of SNPs, SSRs,

indels, genotyping and germplasm collections, biocuration and bio- Acknowledgements

logical databases greatly differ in their data curation practices.

The processes may include, fully automated, semi-automated, only

PJ greatly appreciates the funding provided by the NSF funded

manual curation or a combination of all. Therefore, accessing data

Gramene project (NSF IOS 1127112) and the Planteome project

and comparing the datasets across two or more resources poses

(NSF IOS 1340112) which supported this work and PG. PG and PJ

a major challenge. The accessibility of the data sets is further

wrote the manuscript. Funding agencies had no role in the study

compromised due to the restrictions on the data download. Due

design, data analysis, or preparation of the manuscript.

to emerging need for data integration, its reuse and re-analysis,

semantic concepts based on ontologies and application program-

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