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Nucleic Acids Research Database by Mind Map: Nucleic Acids Research Database
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Nucleic Acids Research Database

Numbers available :

1512 online databases sorted into 14 categories and 41 subcategories

88 new online databases

77 update articles on databases that have been previously featured in the NAR

Criteria for selection into NAR databases

Free accessible


Credible and Trustable

Significance and scientific excellence.


Novel development

Focus on various aspects of nucleic acids and proteins involved in nucleic acid metabolism interactions

Why we need to group these databases?

To provide a higher-order organization of large-scale data submitted by a single organization or a consortium, or relating to the same whole-genome assembly.

To track tools, databases, and methods in the field

So that information of the resources can be most effectively exploited

More systematic and manageable

Keyword tagging allows users to narrow down the resources that suit their needs

Why databases are created and shared?

To provide better integration and cross-referencing tools

Latest development can be kept up-to-date

To allow interaction between researchers

Everyone has the opportunity to help make the collection better and more meaningful

To store the massive information of research work

Allow multiple users to have access to data

Why some databases are no longer in the databases and dropped from it?

Deleted as they are found to be obsolete and non-responsive.

Commercialized and does not provide free version anymore

e.g: ExDom database of exon–intron structures of genes in seven eukaryotic genomes

Improved annotation of the human genome made some resources that covered specific areas of the genome no longer useful

Some are integrated into larger projects

e.g: segmental duplication database were merged with Database of Genomic Variants

e.g: NCBI’s Cancer Chromosomes database were merged into dbVar

Organisation of databases and its major grouping: (Categories list)

Nucleotide Sequence Databases

International Nucleotide Sequence Database Collaboration, DDBJ - DNA Data Bank of Japan, European Nucleotide Archive, GenBank

Coding and non-coding DNA, Dfam, SINEBase, UCNEbase, DoriC

Gene structure, introns and exons, splice sites, APPRIS, ChiTaRS, GeneTack, HEXEvent, SpliceAid-F, Spliceosome Database

Transcriptional regulator sites and transcription factors, ChIPBase, Factorbook, HOCOMOCO, TFClass

RNA sequence databases








Protein sequence databases

General sequence databases, UniProt

Protein properties, eProS, SwissSidechain, TOPPR

Protein localization and targeting, ValidNESs

Protein sequence motifs and active sites

Protein domain databases; protein classification, OrtholugeDB

Databases of individual protein families, Cyanolyase, DoBISCUIT, EENdb, KIDFamMap, UUCD

Structural Database

Small molecules

Carbohydrates, Glycan Fragment DB

Nucleic acid structure, MetalPDB, Voronoia4RNA

Protein structure, D2P2, Genome3D, SIFTS, 2P2Idb, NPIDB, PDBe, CATH, SCOP

Genomics Databases (non-vertebrate)

Genome annotation terms, ontologies and nomenclature, dcGO, DGA, BioGPS

Taxonomy and identification

General genomics databases

Viral genome databases, HBVdb, Papillomavirus Episteme

Prokaryotic genome databases, meta.MicrobesOnline, SecReT4, SEVA, MicroScope, EcoCyc, EcoGene, RegulonDB

Unicellular eukaryotes genome databases, PR2

Fungal genome databases, NetwoRx

Invertebrate genome databases, MonarchBase, WDDD, WormQTL, FlyAtlas

Metabolic and Signaling Pathways

Enzymes and enzyme nomenclature, EBI Enzyme Portal

Metabolic pathways, ClusterMine360, ECMDB, LAMP, MetaboLights, RNApathwaysDB, WholeCellKB

Protein-protein interactions, prePPI, PTMcode, SynSysNet, TissueNet

Signalling pathways, Quorumpeps

Human and other Vertebrate Genomes

Model organisms, comparative genomics, H2DB, NHPRTR, OikoBase, RhesusBase, ZInC, GenColors, Genomicus

Human genome databases, maps and viewers

Human ORFs

Human Genes and Diseases

General human genetics databases, NIH Genetic Testing Registry

General polymorphism databases, dbVar, DGVa, ClinVar

Cancer gene databases, CellLineNavigator, TSGene

Gene-, system- or disease-specific databases, LncRNADisease

Microarray Data and other Gene Expression Databases




Allen Brain Atlas


Gene Expression Omnibus


Stanford Microarray Database

Proteomics databases

Protein and peptide identifications and their associated supporting evidence

Details of post-translational modifications

e.g. MitoMiner

Other Molecular Biology databases

Drugs and drug design, BioLiP, G4LDB, GDSC, NPACT, StreptomeDB, SwissBioisostere


Organelle databases

Plant databases

General plant databases, PGDD, PIECE

Arabidopsis thaliana

Rice, OrysPSSP, RiceFREND

Other plants

Immunological databases


Cell biology



NCBI Bookshelf

Evolution of NAR database

Start April of 1991 (18 articles) & May of 1992 (19 artiles)

Nuleotide sequence database, GenBank, the EMBL Data Library, compilations of small RNA, tRNA, and 5S, 16S, and 23S rRNA sequences, DNA sequences from Escherichia coli and a human genome database (GDB)

Protein database, SWISS-PROT, PIR,, PROSITE, Restriction Enzyme Database (REBASE), Transcription Factors Database (TFD), Histone database

medical genetics database, Haemophilia B

July 1, 1993- First formal Database Issue (24 articles)

RNA and protein structure

ENZYME database

Prepared by Group 4: