Genomics Proteomics Bioinformatics 13 (2015) 55–63

H O S T E D BY

Genomics Proteomics Bioinformatics

www.elsevier.com/locate/gpb
www.sciencedirect.com

RESOURCE REVIEW

Biological Databases for Human Research

#,a #,b *,c, *,d
Dong Zou , Lina Ma , Jun Yu Zhang Zhang

CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences,
Beijing 100101, China

Received 1 January 2015; revised 16 January 2015; accepted 16 January 2015

Available online 21 February 2015

Handled by Ge Gao

KEYWORDS Abstract The completion of the Human Genome Project lays a foundation for systematically
Human; studying the human genome from evolutionary history to precision medicine against diseases.
Database; With the explosive growth of biological data, there is an increasing number of biological databases
Big data; that have been developed in aid of human-related research. Here we present a collection of human-
Database category; related biological databases and provide a mini-review by classifying them into different categories
Curation according to their data types. As human-related databases continue to grow not only in count but
also in volume, challenges are ahead in big data storage, processing, exchange and curation.

Introduction from various database resources in an automated manner.

Therefore, developing databases to deal with gigantic volumes
of biological data is a fundamentally essential task in bioinfor-
As biological data accumulate at larger scales and increase at
matics. To be short, biological databases integrate enormous
exponential paces, thanks principally to higher-throughput
amounts of omics data, serving as crucially important
and lower-cost DNA sequencing technologies, the number of
resources and becoming increasingly indispensable for scien-
biological databases that have been developed to manage such
tists from wet-lab biologists to in silico bioinformaticians.
data deluge is growing at ever-faster rates. The major objec-
According to a report of 2014 Molecular Biology Database
tives of biological databases are not only to store, organize
Collection in the journal Nucleic Acids Research, there are a
and share data in a structured and searchable manner with
sum of 1552 databases that are publicly accessible online [1].
the aim to facilitate data retrieval and visualization for
It should be noted, however, that such count of publicly
humans, but also to provide web application programming
accessible databases is conservative. In fact, there are some
interfaces (APIs) for computers to exchange and integrate data
databases providing online services without publication in
* Corresponding authors. peer-reviewed journal (e.g., The RNA Modification Database
E-mail: [email protected] (Yu J), [email protected] (Zhang Z). at http://mods.rna.albany.edu) or being developed by commer-
#
Equal contribution. cial companies (e.g., Ingenuity Pathway Analysis at http://
a
ORCID: 0000-0002-7169-4965. www.ingenuity.com/products/ipa), making them under-
b
ORCID: 0000-0001-6390-6289. represented in the scientific community. Considering the con-
c
ORCID: 0000-0002-2702-055X. tinuously proliferating number of biological databases, it
d
ORCID: 0000-0001-6603-5060. becomes increasingly daunting and time-consuming to navi-
Peer review under responsibility of Beijing Institute of Genomics, gate in the huge volume of databases of interest. The
Chinese Academy of Sciences and Genetics Society of China.
http://dx.doi.org/10.1016/j.gpb.2015.01.006
1672-0229 ª 2015 The Authors. Production and hosting by Elsevier B.V. on behalf of Beijing Institute of Genomics, Chinese Academy of Sciences and
Genetics Society of China.
This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
56 Genomics Proteomics Bioinformatics 13 (2015) 55–63

completion of the Human Genome Project in 2003 holds sig- Human-related databases
nificant benefits for many fields from human evolution to per-
sonalized healthcare and precision medicine. In this report, we
Decoding the human genome bears great significance in, from a
present a collection of biological databases relevant to human
theoretical view, unveiling human evolutionary history, and
research and provide a mini-review by classifying them into
different categories. from an application view, exploring personalized medicine
against diverse diseases. Considering the heterogeneity in data
type, scope and curation, biological databases can be classified
Database classification into multiple categories under different criteria as presented
above, making it easier for people to effectively characterize
Biological databases are developed for diverse purposes, databases and identify the database(s) of interest. However,
encompass various types of data at heterogeneous coverage some databases are inaccessible over time or poorly main-
and are curated at different levels with different methods, so tained/updated or even never used [12]. In this study, therefore,
that there are accordingly several different criteria applicable we assemble a collection of human-related databases that are
to database classification. widely used and currently accessible via the Internet (Table 1).
As database classification based on data type is informative
Scope of data coverage and straightforward, we assign one major category to each data-
base, albeit one database may correspond to multiple categories.
According to the scope of data coverage, biological databases In what follows, we focus on databases categorized in DNA,
can be classified as comprehensive and specialized databases. RNA, protein, expression, pathway and disease, respectively.
Comprehensive databases cover different types of data from
numerous species and typical examples are GenBank [2], DNA databases
European Molecular Biology Laboratory (EMBL) [3], and
DNA Data Bank of Japan (DDBJ) [4]. These three databases A DNA database centers on managing DNA data from many
were established as the International Nucleotide Sequence or some specific species. The primary function of human DNA
Database Collaboration in 1988 to collect and disseminate databases includes establishment of the reference genome (e.g.,
DNA and RNA sequences. On the other hand, specialized NCBI RefSeq [8]), profiling of human genetic variation (e.g.,
databases contain specific types of data or data from specific dbSNP [13]), association of genotype with phenotype (e.g.,
organisms. For example, WormBase [5] is for nematode biol- EGA [14]), and identification of human microbiome metagen-
ogy and genomics and RiceWiki [6] is for community curation omes (e.g., IMG/HMP [15]). A representative example of
of rice genes. DNA database is GenBank [2], a collection of all publicly-
available DNA sequences (http://www.ncbi.nlm.nih.gov/gen-
Level of biocuration bank). Since its inception in 1982, GenBank grows at an extra-
ordinary pace and as of December 2014, contains over 184
According to level of data curation, biological databases can billion nucleotide bases in more than 179 million sequences
roughly fall into primary and secondary or derivative data- (http://www.ncbi.nlm.nih.gov/genbank/statistics).
bases. Primary databases contain raw data as archival reposi-
tory such as the NCBI Sequence Read Archive (SRA) [7], RNA databases
whereas secondary or derivative databases contain curated
information as added value, e.g., NCBI RefSeq [8]. It is well acknowledged that only a tiny proportion of the
human genome is transcribed into mRNAs, whereas the vast
Method of biocuration majority of the genome is transcribed into ‘‘dark matter’’––
non-coding RNAs (ncRNAs) that do not encode proteins
As a consequence of the explosive growth of data, curation [16], including microRNAs (miRNAs), small nucleolar RNAs
increasingly requires collective intelligence for collaborative (snoRNAs), piwiRNAs (piRNAs), and long non-coding
data integration and annotation. Therefore, biological data- RNA (lncRNA). Therefore, an increasing number of human
bases can also be classified as (1) expert-curated databases, RNA databases have been built for deciphering ncRNAs
e.g., RefSeq [8] and TAIR, [9] and (2) community-curated (e.g., GENCODE [17]), in particular lncRNAs that attract
databases, which are curated in a collective and collaborative the rising interest (e.g., LncRNAWiki [10]), and characterizing
manner by a number of researchers, e.g., LncRNAWiki [10] their functions and interactions (e.g., RNAcentral [18]). A
and GeneWiki [11]. representative example of RNA database is RNAcentral [18].
It provides unified access to the ncRNA sequence data supplied
Type of data managed by multiple databases including Rfam [19], lncRNAdb [20], and
miRBase [21] (http://rnacentral.org).
According to the types of data managed in different databases,
Protein databases
biological databases can roughly fall into the following cate-
gories: (1) DNA, (2) RNA, (3) protein, (4) expression, (5) path-
way, (6) disease, (7) nomenclature, (8) literature, and (9) The purpose of constructing protein databases includes collec-
standard and ontology. tion of universal proteins (e.g., UniProt [22]), identification of
 Zou D et al / Human-related Biological Databases 57

Table 1 Human-related biological databases*

Name Link Brief description Refs. Category#
1000 Genomes http://www.1000genomes.org A deep catalog of human genetic variation [17] DNA
AFND http://www.allelefrequencies.net Allele Frequency Net Database [37]
dbSNP http://www.ncbi.nlm.nih.gov/snp Database of single nucleotide polymorphisms [13]
DEG http://www.essentialgene.org Database of Essential Genes [38]
EGA http://www.ebi.ac.uk/ega European Genome–phenome Archive [14]
Ensembl http://www.ensembl.org Ensembl genome browser [39]
euGenes http://eugenes.org Genomic information for eukaryotic organisms [40]
GeneCards http://www.genecards.org Integrated database of human genes [41]
IMG/HMP https://img.jgi.doe.gov/imgm_hmp Human Microbiome MetaGenomes [15]
JASPAR http://jaspar.genereg.net Transcription factor binding profile database [42]
JGA http://trace.ddbj.nig.ac.jp/jga Japanese Genotype–phenotype Archive [43]
KEGG http://www.genome.jp/kegg Kyoto Encyclopedia of Genes and Genomes [44]
MITOMAP http://www.mitomap.org Human mitochondrial genome database [45]
NCBI RefSeq http://www.ncbi.nlm.nih.gov/refseq NCBI Reference Sequence Database [8]
PolymiRTS http://compbio.uthsc.edu/miRSNP Polymorphism in miRNAs and their Target Sites [46]
UCSC Genome http://genome.ucsc.edu UCSC Genome Browser database [47]
Browser
ChIPBase http://deepbase.sysu.edu.cn/chipbase Database of transcriptional regulation of lncRNA [48] RNA
and miRNA genes
DARNED http://darned.ucc.ie DAtabase of RNa EDiting in humans [49]
DIANA-LncBase http://diana.imis.athena-innovation.gr/ miRNA targets on lncRNAs [50]
DianaTools/index.php?r=lncBase/index
GENCODE http://www.gencodegenes.org Encyclopedia of genes and gene variants [17]
H-DBAS http://www.h-invitational.jp/h-dbas Human-transcriptome DataBase for Alternative [51]
Splicing
HEXEvent http://hexevent.mmg.uci.edu Database of Human EXon splicing Events [52]
LNCipedia http://www.lncipedia.org Annotated human lncRNA sequences [53]
LncRNA2Target http://www.lncrna2target.org Database of differentially-expressed genes after [54]
lncRNA knockdown or overexpression
lncRNAdb http://www.lncrnadb.org lncRNA Database [20]
lncRNASNP http://bioinfo.life.hust.edu.cn/ Database of SNPs in lncRNAs [55]
lncRNASNP
LncRNAWiki http://lncrna.big.ac.cn Human lncRNA Wiki [10]
miRBase http://www.mirbase.org miRNA Database [21]
miRTarBase http://mirtarbase.mbc.nctu.edu.tw Experimentally-validated miRNA–target [56]
interactions
miRWalk http://mirwalk.uni-hd.de Database of miRNA–target interactions [57]
NONCODE http://www.noncode.org Database of ncRNA genes [58]
NPInter http://www.bioinfo.org/NPInter Database of ncRNA interactions [59]
RADAR http://RNAedit.com Rigorously Annotated Database of A-to-I RNA [60]
editing
piRNABank http://pirnabank.ibab.ac.in Database of piwi-interacting RNAs [61]
RBPDB http://rbpdb.ccbr.utoronto.ca Database of RNA-binding specificities [62]
RDB http://ndbserver.rutgers.edu The nucleic acid database [63]
Rfam http://rfam.xfam.org Database of ncRNA families [19]
RNAcentral http://rnacentral.org International database of ncRNA sequences [18]
snoRNABase https://www-snorna.biotoul.fr Database of human H/ACA and C/D box [64]
snoRNAs
starBase http://starbase.sysu.edu.cn Database of ncRNA interaction networks [65]
TarBase http://diana.imis.athena-innovation.gr/ Experimentally-validated miRNA:gene [66]
DianaTools/index.php?r=tarbase/index interactions
TargetScan http://www.targetscan.org Predicted miRNA targets in mammals [67]
CATH http://cath.biochem.ucl.ac.uk Protein structure classification [68] Protein
CPLM http://cplm.biocuckoo.org Compendium of Protein Lysine Modifications [69]
DIP http://dip.doe-mbi.ucla.edu Database of Interacting Proteins [70]
EKPD http://ekpd.biocuckoo.org Eukaryotic Kinase and Phosphatase Database [71]
HPRD http://www.hprd.org Human Protein Reference Database [72]
hUbiquitome http://bioinfo.bjmu.edu.cn/hubi/ Ubiquitination sites and cascades [73]
InterPro http://www.ebi.ac.uk/interpro Protein sequence analysis and classification [74]
MEROPS http://merops.sanger.ac.uk Database of proteolytic enzymes, their substrates, [75]
and inhibitors
MINT http://mint.bio.uniroma2.it/mint Molecular INTeraction Database [76]
(continued)
58 Genomics Proteomics Bioinformatics 13 (2015) 55–63

Table 1 (continued)
Name Link Brief description Refs. Category#
ModBase http://salilab.org/modbase Database of comparative protein structure models [77]
mUbiSiDa http://reprod.njmu.edu.cn/mUbiSiDa Mammalian Ubiquitination Site Database [78]
PANTHER http://www.pantherdb.org Protein ANalysis THrough Evolutionary [79]
Relationships
PDB http://www.rcsb.org/pdb Protein Data Bank for 3D structures of biological [25]
macromolecules
PDBe http://www.ebi.ac.uk/pdbe Protein Data Bank in Europe [80]
Pfam http://pfam.xfam.org Database of conserved protein families and [23]
domains
PhosSNP http://phossnp.biocuckoo.org Genetic polymorphisms that influence protein [81]
phosphorylation
PIR http://pir.georgetown.edu Protein Information Resource [82]
PROSITE http://www.expasy.org/prosite Database of protein domains, families and [83]
functional sites
SysPTM http://lifecenter.sgst.cn/SysPTM Post-translational modifications [84]
TreeFam http://www.treefam.org Database of phylogenetic trees of animal species [24]
UniPROBE http://thebrain.bwh.harvard.edu/ Universal PBM Resource for Oligonucleotide [85]
uniprobe Binding Evaluation
UniProt http://www.uniprot.org Universal protein resource [22]
UUCD http://uucd.biocuckoo.org Ubiquitin and Ubiquitin-like Conjugation [86]
Database
ArrayExpress http://www.ebi.ac.uk/arrayexpress Database of functional genomics experiments [87] Expression
BioGPS http://biogps.org Portal for querying and organizing gene [88]
annotation resources
Expression Atlas http://www.ebi.ac.uk/gxa Differential and baseline expression [27]
Human Protein http://www.proteinatlas.org Tissue-based map of the human proteome [29]
Atlas
MOPED https://www.proteinspire.org Multi-Omics Profiling Expression Database [89]
NCBI GEO http://www.ncbi.nlm.nih.gov/geo Gene Expression Omnibus [26]
NRED http://nred.matticklab.com Database of lncRNA expression [90]
ONCOMINE https://www.oncomine.org Cancer microarray database [91]
PrimerBank http://pga.mgh.harvard.edu/primerbank Public resource for PCR primers [92]
PRIDE http://www.ebi.ac.uk/pride PRoteomics IDEntifications [93]
TiGER http://bioinfo.wilmer.jhu.edu/tiger Tissue-specific Gene Expression and Regulation [28]
WikiCell http://www.wikicell.org Unified resource for Human transcriptomics [94]
research
CPDB http://consensuspathdb.org Database of human interaction networks [95] Pathway
HMDB http://www.hmdb.ca Human Metabolome Database [96]
KEGG http://www.genome.jp/kegg/pathway. KEGG pathway maps [30]
PATHWAY html
MetaCyc http://metacyc.org Metabolic pathway database [97]
Pathway http://www.pathwaycommons.org Pathway commons [98]
Commons
PID http://pid.nci.nih.gov Pathway Interaction Database [99]
Reactome http://www.reactome.org Curated and peer-reviewed pathway database [100]
UniPathway http://www.grenoble.prabi.fr/ Universal Pathway [101]
obiwarehouse/unipathway
AlzBase http://alz.big.ac.cn/alzBase Database for gene dysregulation in Alzheimer’s [102] Disease
disease
CADgene http://www.bioguo.org/CADgene Coronary Artery Disease gene database [103]
COSMIC http://cancer.sanger.ac.uk Catalog Of Somatic Mutations In Cancer [104]
DiseaseMeth http://bioinfo.hrbmu.edu.cn/diseasemeth Human disease methylation database [105]
DisGeNET http://www.disgenet.org/web/ Gene–disease associations [106]
DisGeNET/v2.1
GOBO http://co.bmc.lu.se/gobo Gene expression-based Outcome for Breast cancer [107]
Online
GWAS Central http://www.gwascentral.org A comprehensive resource for the comparison and [108]
interrogation of genome-wide association studies
GWASdb http://jjwanglab.org/gwasdb Human genetic variants identified by genome- [109]
wide association studies
HbVar http://globin.cse.psu.edu/hbvar Hemoglobin variants and thalassemias [110]
HGMD http://www.hgmd.org Human Gene Mutation Database [111]
 Zou D et al / Human-related Biological Databases 59

Table 1 (continued)
Name Link Brief description Refs. Category#
ICGC http://icgc.org International Cancer Genome Consortium [33]
IDbases http://structure.bmc.lu.se/idbase Immunodeficiency-causing variations [112]
LncRNADisease http://cmbi.bjmu.edu.cn/lncrnadisease lncRNA and disease database [113]
LOVD http://www.lovd.nl Leiden open (source) Variation Database [114]
MalaCards http://www.malacards.org Human maladies and their annotations [115]
MethHC http://methhc.mbc.nctu.edu.tw Database of DNA methylation and gene [116]
expression in human cancer
MethyCancer http://methycancer.psych.ac.cn Database of human DNA Methylation and cancer [117]
miR2Disease http://www.miR2Disease.org Database for miRNA deregulation in human [118]
disease
MITOMAP http://www.mitomap.org/MITOMAP Polymorphisms and mutations in human [119]
mitochondrial DNA
NHGRI GWAS http://www.genome.gov/gwastudies Curated resource of SNP-trait associations [120]
Catalog
OMIM http://omim.org Online Mendelian Inheritance in Man [121]
T2D@ZJU http://tcm.zju.edu.cn/t2d Connections associated with type 2 diabetes [122]
TCGA http://cancergenome.nih.gov The Cancer Genome Atlas [32]
Universal http://www.umd.be/ Locus-specific database [123]
Mutation
Database
ViRBase http://www.rna-society.org/virbase Virus–host ncRNA associated interactions [124]
GO http://geneontology.org Gene ontology [125] Standard and ontology
HGNC http://www.genenames.org Database of human gene names [126]
Europe PMC http://europepmc.org Literature database in Europe [127] Literature
PubMed http://www.ncbi.nlm.nih.gov/pubmed Database of biomedical literature from [128]
MEDLINE
PubMed Central http://www.ncbi.nlm.nih.gov/pmc Free full-text literature archive [129]
Note: *This collection, however, by no means pictures the whole range of human-related databases that are currently available. Primary databases
(DDBJ/EMBL/GenBank) are not shown, as they contain raw data. #A database may correspond to multiple categories and only one major
category is shown here.

protein families and domains (e.g., Pfam [23]), reconstruction exploring tissue-specific gene expression and regulation (e.g.,
of phylogenetic trees (e.g., TreeFam [24]), and profiling of pro- TiGER [28]), and profiling expression information based on
tein structures (e.g., PDB [25]). A representative example of both RNA and protein data (e.g., Human Protein Atlas [29]).
protein database is PDB, the main primary database for 3D A representative case of expression database is Human
structures of biological macromolecules determined by X-ray Protein Atlas. As of 30 December 2014, it encompasses expres-
crystallography and NMR. Established in 1971, PDB contains sion profiles for a large majority of human protein-coding genes
105,465 biological macromolecular structures as of 30 based on both RNA (transcriptome analysis based on 213 tis-
December 2014, in which 27,393 entries belong to human sue and cell line samples) and protein data (proteome analysis
(http://www.rcsb.org/pdb). Another example is the Universal based on 24,028 antibodies) (http://www.proteinatlas.org).
Protein Resource (UniProt). As a collaborative project
between EMBL-EBI, Swiss Institute of Bioinformatics (SIB), Pathway databases
and Protein Information Resource (PIR), UniProt provides a
comprehensive, high-quality, and freely-accessible resource of Pathway databases contain biological pathways for metabolic,
protein sequence and functional information. Currently, signaling, and regulatory pathway analysis. A representative
UniProt includes three member databases: UniProt example is KEGG PATHWAY [30], a curated biological path-
Knowledgebase (UniProtKB), UniProt Reference Clusters way resource on the molecular interaction and reaction net-
(UniRef), and UniProt Archive (UniParc). In addition, works. As the core of KEGG, KEGG PATHWAY integrates
UniProtKB consists of two sections: Swiss-Prot (containing a many entities that are stored in KEGG sibling databases, includ-
collection of 547,357 manually-annotated and -reviewed ing genes, proteins, RNAs, chemical compounds, and chemical
proteins as of January 2015) and TrEMBL (containing a reactions (http://www.genome.jp/kegg/pathway.html).
collection of 89,451,166 un-reviewed proteins as of January
2015) (http://www.uniprot.org). Disease databases

Expression databases There are at least 200 forms of cancer in the world, causing
14.6% of all human deaths (http://en.wikipedia.org/wiki/
Expression databases can be used for various purposes, includ- Cancer). Thus, obtaining complete cancer genomes and
ing archiving expression data (e.g., GEO [26]), detecting dif- identifying molecular mutations and abnormal genes can pro-
ferential and baseline expression (e.g., Expression Atlas [27]), vide new insights for cancer prevention, detection, and
60 Genomics Proteomics Bioinformatics 13 (2015) 55–63

eventually, personalized treatment [31]. Toward this end, there (863 Program; Grant No. 2012AA020409) by the Ministry of
are two well-known cancer projects, viz., The Cancer Genome Science and Technology of China awarded to ZZ.
Atlas (TCGA) [32] and International Cancer Genome
Consortium (ICGC) [33]. TCGA, founded in 2006 by the
National Cancer Institute and National Human Genome
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