Nucleic Acids Research Database

Get Started. It's Free
or sign up with your email address
Nucleic Acids Research Database by Mind Map: Nucleic Acids Research Database

1. Numbers available :

1.1. 1512 online databases sorted into 14 categories and 41 subcategories

1.1.1. 88 new online databases

1.1.2. 77 update articles on databases that have been previously featured in the NAR

2. Criteria for selection into NAR databases

2.1. Free accessible

2.2. Consistent

2.3. Credible and Trustable

2.4. Significance and scientific excellence.

2.5. Originality

2.6. Novel development

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

3. Why we need to group these databases?

3.1. 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.

3.2. To track tools, databases, and methods in the field

3.3. So that information of the resources can be most effectively exploited

3.4. More systematic and manageable

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

4. Why databases are created and shared?

4.1. To provide better integration and cross-referencing tools

4.2. Latest development can be kept up-to-date

4.3. To allow interaction between researchers

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

4.4. To store the massive information of research work

4.5. Allow multiple users to have access to data

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

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

5.2. Commercialized and does not provide free version anymore

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

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

5.4. Some are integrated into larger projects

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

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

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

6.1. Nucleotide Sequence Databases

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

6.1.2. Coding and non-coding DNA Dfam SINEBase UCNEbase DoriC

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

6.1.4. Transcriptional regulator sites and transcription factors ChIPBase Factorbook HOCOMOCO TFClass

6.2. RNA sequence databases

6.2.1. BSRD

6.2.2. DIANA-LncBase

6.2.3. Lncipedia

6.2.4. PlantRNA

6.2.5. SomamiR

6.2.6. YM500

6.2.7. DARNED

6.3. Protein sequence databases

6.3.1. General sequence databases UniProt

6.3.2. Protein properties eProS SwissSidechain TOPPR

6.3.3. Protein localization and targeting ValidNESs

6.3.4. Protein sequence motifs and active sites

6.3.5. Protein domain databases; protein classification OrtholugeDB

6.3.6. Databases of individual protein families Cyanolyase DoBISCUIT EENdb KIDFamMap UUCD

6.4. Structural Database

6.4.1. Small molecules

6.4.2. Carbohydrates Glycan Fragment DB

6.4.3. Nucleic acid structure MetalPDB Voronoia4RNA

6.4.4. Protein structure D2P2 Genome3D SIFTS 2P2Idb NPIDB PDBe CATH SCOP

6.5. Genomics Databases (non-vertebrate)

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

6.5.2. Taxonomy and identification

6.5.3. General genomics databases

6.5.4. Viral genome databases HBVdb Papillomavirus Episteme

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

6.5.6. Unicellular eukaryotes genome databases PR2

6.5.7. Fungal genome databases NetwoRx

6.5.8. Invertebrate genome databases MonarchBase WDDD WormQTL FlyAtlas

6.6. Metabolic and Signaling Pathways

6.6.1. Enzymes and enzyme nomenclature EBI Enzyme Portal

6.6.2. Metabolic pathways ClusterMine360 ECMDB LAMP MetaboLights RNApathwaysDB WholeCellKB

6.6.3. Protein-protein interactions prePPI PTMcode SynSysNet TissueNet

6.6.4. Signalling pathways Quorumpeps

6.7. Human and other Vertebrate Genomes

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

6.7.2. Human genome databases, maps and viewers

6.7.3. Human ORFs

6.8. Human Genes and Diseases

6.8.1. General human genetics databases NIH Genetic Testing Registry

6.8.2. General polymorphism databases dbVar DGVa ClinVar

6.8.3. Cancer gene databases CellLineNavigator TSGene

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

6.9. Microarray Data and other Gene Expression Databases

6.9.1. CircaDB

6.9.2. HemaExplorer

6.9.3. METscout

6.9.4. Allen Brain Atlas

6.9.5. ArrayExpress

6.9.6. Gene Expression Omnibus

6.9.7. GPX

6.9.8. Stanford Microarray Database

6.10. Proteomics databases

6.10.1. Protein and peptide identifications and their associated supporting evidence

6.10.2. Details of post-translational modifications

6.10.3. e.g. MitoMiner

6.11. Other Molecular Biology databases

6.11.1. Drugs and drug design BioLiP G4LDB GDSC NPACT StreptomeDB SwissBioisostere

6.11.2. TCMID

6.12. Organelle databases

6.13. Plant databases

6.13.1. General plant databases PGDD PIECE

6.13.2. Arabidopsis thaliana

6.13.3. Rice OrysPSSP RiceFREND

6.13.4. Other plants

6.14. Immunological databases

6.14.1. InnateDB

6.15. Cell biology

6.15.1. CloneDB

6.15.2. LUCApedia

6.15.3. NCBI Bookshelf

7. Evolution of NAR database

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

7.1.1. 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)

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

7.1.3. medical genetics database Haemophilia B

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

7.2.1. RNA and protein structure

7.2.2. ENZYME database

8. Prepared by Group 4: