The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection

Abstract

The 2016 Database Issue of Nucleic Acids Research starts with overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB). Also included are descriptions of 62 new databases and updates on 95 databases that have been previously featured in NAR plus 17 previously described elsewhere. A number of papers in this issue deal with resources on nucleic acids, including various kinds of non-coding RNAs and their interactions, molecular dynamics simulations of nucleic acid structure, and two databases of super-enhancers. The protein database section features important updates on the EBI's Pfam, PDBe and PRIDE databases, as well as a variety of resources on pathways, metabolomics and metabolic modeling. This issue also includes updates on popular metagenomics resources, such as MG-RAST, EBI Metagenomics, and probeBASE, as well as a newly compiled Human Pan-Microbe Communities database. A significant fraction of the new and updated databases are dedicated to the genetic basis of disease, primarily cancer, and various aspects of drug research, including resources for patented drugs, their side effects, withdrawn drugs, and potential drug targets. A further six papers present updated databases of various antimicrobial and anticancer peptides. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been updated with the addition of 88 new resources and removal of 23 obsolete websites, which brought the current listing to 1685 databases.

NEW AND UPDATED DATABASES

The 2016 Nucleic Acids Research Database Issue is the 23rd annual collection of descriptions of various molecular biology databases. It includes 178 papers, of which 62 describe newly created databases (Table 1), 95 papers provide updates on databases that have been described in the previous NAR Database Issues and 17 contain updates on databases whose descriptions have previously been published in other journals (Table 2).

Table 1. Descriptions of new online databases in the 2016 NAR Database issue.

Database name	URL	Brief description
AgingChart	http://www.agingchart.org/	Pathways of age-related processes
Assembly	http://www.ncbi.nlm.nih.gov/assembly	Status of whole-genome shotgun assemblies
BacWGSTdb	http://bacdb.org/BacWGSTdb/	Bacterial whole genome sequence typing database
BIGNASim	http://mmb.irbbarcelona.org/BIGNASim/	Molecular dynamics simulations of nucleic acids
BreCAN-DB	http://brecandb.igib.res.in/	Breakpoint profiles of cancer genomes
Cancer RNA-Seq Nexus	http://syslab4.nchu.edu.tw/CRN	Transcriptome profiling in cancer cells
CauloBrowser	http://www.caulobrowser.org	Biology of Caulobacter crescentus
ccmGDB	http://bioinfo.mc.vanderbilt.edu/ccmGDB/	Cancer cell metabolism gene database
CEGA	http://cega.ezlab.org/	Conserved elements from genomic alignments
CircNet	http://circnet.mbc.nctu.edu.tw	Tissue-specific expression profiles of circular RNA
Colorectal Cancer Atlas	http://www.colonatlas.org	Genes and proteins of colorectal cancer cells
CRISPRz	http://research.nhgri.nih.gov/crisprz	CRISPR single guide RNAs to zebrafish genes
CSDB	http://csdb.glycoscience.ru/database	Carbohydrate structure database
DASHR	http://lisanwanglab.org/DASHR	Database of human small non-coding RNA
dbMAE	http://mae.hms.harvard.edu	Database of monoallelic gene expression
dbSUPER	http://bioinfo.au.tsinghua.edu.cn/dbsuper/	A database of super-enhancers
DESM	http://www.cbrc.kaust.edu.sa/desm	Microbial knowledge exploration systems
DIDA	http://dida.ibsquare.be	DIgenic disease database
Digital Development Database	http://cell-lineage.org	C. elegans development and cell differentiation
DMDD	http://dmdd.org.uk	Deciphering the mechanisms of developmental disorder
EK3D	http://www.iith.ac.in/EK3D/	Capsular polysaccharide (K antigen) structures of various E. coli serotypes
ENCODE DCC	http://www.encodeproject.org	ENCODE (Encyclopedia of DNA Elements) consortium data portal
FLOR-ID	http://www.flor-id.org/	Flowering interactive database
GEneSTATION	http://www.genestation.org	Genes in gestation: genomics of pregnancy-related tissues
GlyTouCan	https://glytoucan.org	International glycan Structure Repository
GreeNC	http://greenc.sciencedesigners.com/	Green non-coding: plant lncRNAs
HGTree	http://hgtree.snu.ac.kr	Horizontally transferred genes identified by tree-based methods
HPMCD	http://www.hpmcd.org/	Human pan-microbial communities database
hPSCreg	http://hpscreg.eu	Human pluripotent stem cell registry
IC4R	http://ic4r.org	Information commons for rice
InsectBase	http://www.insect-genome.com/	Insect genomes and transcriptomes
InterRNA	http://mfrlab.org/interrna/	Base interactions in RNA structures
JuncDB	http://juncdb.carmelab.huji.ac.il/	Exon-exon junction database
Lnc2Cancer	http://www.bio-bigdata.com/lnc2cancer/	Human lncRNA and cancer associations
MERAV	http://merav.wi.mit.edu	Metabolic gene rapid visualizer
Metabolomics Workbench	http://www.metabolomicsworkbench.org/	Metabolomics data, standards and protocols
MitoAge	http://www.mitoage.org	Mitochondrial DNA properties and aging
MutationAligner	http://www.mutationaligner.org	Mutation hotspots in protein domains in cancer
NBDB	http://nbdb.bii.a-star.edu.sg	Nucleotide binding protein motifs
OpenTein	http://opentein.hgc.jp/	Open teratoma investigation: images
PCOSKB	http://pcoskb.bicnirrh.res.in/	Polycystic ovary syndrome knowledgebase
PDBflex	http://pdbflex.org	Flexibility in protein structures
PhytoPath	http://www.phytopathdb.org/	Genomics of fungal, oomycete and bacterial phytopathogens
piRNAclusterDB	http://www.smallrnagroup-mainz.de/piRNAclusterDB.html	Clusters of piRNAs
PlanMine	http://planmine.mpi-cbg.de/	Planarian genomics
PlantDHS	http://plantdhs.org	Plant DNase I- hypersensitive Sites
RBP-Var	http://www.rbp-var.biols.ac.cn/	Variation that can affect RNA-protein interactions
RMBase	http://mirlab.sysu.edu.cn/rmbase/	RNA modification database
RPFdb	http://sysbio.sysu.edu.cn/rpfdb/	Ribosome profiling database
SATPdb	http://crdd.osdd.net/raghava/satpdb/	Structurally annotated therapeutic peptides
SBR-Blood	http://sbrblood.nhgri.nih.gov	Systems biology repository for hematopoietic cells
SEA	http://sea.edbc.org	Super enhancer archive
SigMol	http://bioinfo.imtech.res.in/manojk/sigmol	Quorum sensing signalling molecules
SIGNOR	http://signor.uniroma2.it/	Signaling network open resource
sORFs	http://www.sorfs.org	Small ORFs identified by ribosome profiling
Start2Fold	http://start2fold.eu	Hydrogen/deuterium exchange data on protein folding and stability
SureChEMBL	https://www.surechembl.org/	Chemical compounds in patent documents
SynLethDB	http://histone.sce.ntu.edu.sg/SynLethDB/	Synthetic lethality gene pairs as potential anticancer drug targets
TCGA SpliceSeq	http://projects.insilico.us.com/TCGASpliceSeq	Alternative splicing patterns in cancer cells
UET	http://mammoth.bcm.tmc.edu/uet/	Universal evolutionary trace: protein motifs important for function
WeGET	http://coexpression.cmbi.umcn.nl/	Weighted gene co-expression tool
WITHDRAWN	http://cheminfo.charite.de/withdrawn/	Withdrawn and discontinued drugs

Table 2. Updated description of databases most recently published elsewhere.

Database name	URL	Brief description
ANISEED	http://www.aniseed.cnrs.fr	Ascidian network for in situ expression and embryological data
BiGG Models	http://bigg.ucsd.edu	Biochemically, genetically and genomically structured metabolic network models
CPPsite	http://crdd.osdd.net/raghava/cppsite/	Validated cell penetrating peptides
DBAASP	http://dbaasp.org	Database of antimicrobial activity and structure of peptides
DGIdb	http://dgidb.genome.wustl.edu	Drug-gene interaction database
iGNM	http://gnmdb.csb.pitt.edu/	Protein functional motions based on Gaussian network model
IIDa	http://ophid.utoronto.ca/iid	Integrated interactions database: tissue-specific protein-protein interactions
iPPI-DB	http://www.ippidb.cdithem.fr/	Inhibitors of protein-protein interactions
KLIFS	http://klifs.vu-compmedchem.nl	Kinase-ligand interaction fingerprints and structures
MG-RAST	http://metagenomics.anl.gov/	Data portal for processing, analyzing, sharing and disseminating metagenomic data sets
MitoCarta	http://www.broadinstitute.org/pubs/ MitoCarta	Mouse and human mitochondrial proteins
MNXref/MetaNetX	http://www.metanetx.org	Genome-scale metabolic networks
MouseNet	http://www.inetbio.org/mousenet/	Functional network of mouse genes
PlantPAN	http://PlantPAN2.itps.ncku.edu.tw	Plant promoter analysis navigator
SIDER	http://sideeffects.embl.de/	Side effect resource: adverse drug reactions
sRNATarBasea	http://ccb1.bmi.ac.cn/srnatarbase/	sRNA-target interactions in bacteria
SugarBindDB	http://sugarbind.expasy.org	Host-pathogen interactions mediated by glycans

^aIID and sRNATarBase have been previously listed in the NAR Database Collection as entries nos. 897 and 1832, respectively.

This year's issue is again divided into eight sections that deal with (i) nucleic acid sequence and structure; (ii) protein sequence and structure; (iii) metabolic and signaling pathways; (iv) viruses, bacteria, protozoa and fungi; (v) genomes of human and model organisms; (vi) human diseases and drugs; (vii) plants and (viii) other topics, including mitochondrial databases and databases of chemical compounds. It should be noted, however, that these general categories may only partly reflect the database scope, so we encourage the reader to browse the entire table of contents: a useful database might be found in a totally unexpected bin. As an example, a researcher interested in G-protein coupled receptors would obviously be drawn to the dedicated resource GPCRdb (1), but would also find value in the broader IUPHAR/BPS Guide to Pharmacology (2), the two databases assigned to different sections based on their slightly different foci. The Nucleic Acids Research online Molecular Biology Database Collection, which is available at http://www.oxfordjournals.org/nar/database/a/, retains the same 15 categories and 41 subcategories as it did before.

The current issue opens with brief overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI), and Swiss Institute for Bioinformatics (SIB). These papers cover the recent developments and ongoing efforts at these centers and provide a general introduction into their activities that should be useful for both experienced and novice users. One more introductory paper describes the web resources that are supported by ELIXIR, the European life-sciences infrastructure for biological information, and presents a listing of their providers. This ELIXIR Tools and Data Services Registry aims to be a comprehensive and consistent registry of information about (mostly) European bioinformatics databases and tools.

In addition to the annual papers from the International Nucleotide Sequence Database collaboration (INSDC), which comprises the DNA Data Bank of Japan, the European Nucleotide Archive, and GenBank, this issue introduces the NCBI's new Assembly database (http://www.ncbi.nlm.nih.gov/assembly/), which helps track the progress of the genome assembly data in GenBank as the genome sequence progresses from a set of unordered contigs to a draft genome assembly and finally to a complete genome that includes either a single chromosome or multiple chromosomes (3).

Among newly created nucleic acid sequence resources, it is worth noting the Conserved Elements from Genomic Alignments (CEGA) database, a collection of non-coding sequences that are poorly characterized but highly conserved within various groups of vertebrates and include potential promoters, enhancers, and other regulatory elements (4), and a database of exon-exon junction sequences, aptly named JuncDB (5). Two more new databases, dbSUPER and SEA (6,7), collect the sequences of super-enhancers, the recently discovered regulatory elements that consist of clusters of transcriptional enhancers and regulate gene expression in a cell- and tissue-specific fashion (8). Other noteworthy contributions include updates on Dfam, a database of human DNA repeat families; ARESite, a resource on AU-rich elements in vertebrate UTRs; NPIDB, a nuclear-protein interaction database which proposes a new classification of DNA-protein complexes, and such popular databases of transcriptional regulation as JASPAR, HOCOMOCO, ORegAnno and RegulonDB. A potentially important new contribution is the BIGNAsim database of DNA dynamics based on molecular dynamics simulations using the ParmBSC1 force field (9). A separate block of papers features various RNA databases, including resources on 5S rRNA, tRNA, piRNA, circular RNA, long non-coding RNA and their interactions.

The protein sequence section features, among others, updates on such popular protein families databases as Pfam, PANTHER, eggNOG, GPCRdb, Transporter Classification database (TCDB), and two databases of proteases and protease inhibitors, MEROPS, which is now in its 20th year, and Degradome. The Pfam update paper deserves a particularly careful reading because it provides a detailed description of the recent and upcoming changes in this popular database as it attempts to cope with the rapidly increasing amount of sequence data. The authors see the solution in transitioning Pfam from attempting to incorporate the entire UniProt sequence database to focusing instead on the UniProt reference proteomes (at least for seed alignments), a much smaller set of higher-quality protein sequences (10).

With respect to protein sequence motifs, there is an update on the Eukaryotic Linear Motif (ELM) database and two new resources: the Nucleotide Binding Database (NBDB) of nucleotide-binding motifs and the Universal Evolutionary Trace (UET) database of predicted protein functional sites (11–13). The proteomics databases are represented by sORF, a collection of small ORFs identified by ribosome profiling (14), and updates on the widely used databases on proteomic peptide identification (PRIDE) and post-translational modifications (dbPTM) (15,16).

The protein structure-related papers include an update from PDBe (17) reporting significant improvements to the value added to and accessibility of structure reports. A trio of papers cover different aspects of protein folding, flexibility and dynamics: Start2Fold collates experimental hydrogen/deuterium exchange data, PDBFlex provides statistics of and animations between pairs of homologous structures in the PDB, and iGNM offers improved computationally predicted flexibility information for most PDB entries (18–20). Two databases use CATH structural domain classifications to shed light on protein function, Gene3D by assigning domain annotations and associated function predictions to proteomes and FunTree by attempting to better understand the evolution of protein function in superfamiles. Finally, the biological and medicinal interest in kinases fully justifies the effort spent in updating KLIFS, a database dedicated to a detailed understanding of kinase-ligand interactions.

The next section includes updated resources on metabolic pathways, such as KEGG, MetaCyc, Reactome, WikiPathways and the Escherichia coli metabolism database (ECMDB), and databases of metabolic network modeling, such as BiGG Models and MNXref/MetaNetX. A new arrival here is the Metabolomics Workbench (21), which strives to be a one-stop repository for all kinds of metabolomics data, including metabolite standards, protocols, tutorials and analysis tools.

Coverage of organismal genome diversity is provided by the updated Ensembl Genomes and Bacterial Diversity (BacDive) databases (22,23), as well as specialized resources dedicated to Caulobacter, Pseudomonas and Bacillus subtilis (24–26). The current issue also includes updates on popular metagenomics resources, such as MG-RAST, EBI Metagenomics and probeBASE (27–29), as well as the newly compiled Human Pan-Microbe Communities database (30). Another new arrival, the bacterial whole-genome sequence typing database BacWGST, aims to simplify the important task of identifying the bacterial strains in samples isolated from infection (31).

As in previous years, this Database Issue includes a selection of genome resources for human and model organisms (Ensembl, RefSeq, UCSC Genome Browser, ENCODE portal), including yeast (SGD), C. elegans (WormBase), Drosophila (FlyBase), ants, bees and wasps (Hymenoptera Genome Database), cow and mouse. The new arrivals include a collection of insect genome resources and genome databases of planaria and ascidians (32–34). A very interesting Deciphering the Mechanisms of Developmental Disorders (DMDD) database collects phenotypic data of mouse mutant embryos (35). This section also includes the database of autosomal monoallelic gene expression (dbMAE, (36)), which has been chosen by the NAR editors as one of the two Breakthrough papers in this issue. dbMAE provides manually curated data on allele-specific expression of autosomal genes, whereby the transcriptional activity of two alleles is epigenetically controlled and maintained in a clonal cell lineage, resulting in diversification of cells within the same tissue (37). dbMAE promises to become a useful resource that will help researchers achieve a better understanding of this recently emerged epigenetic phenomenon.

A significant fraction of the databases profiled in this issue (including ClinVar, GWASdb, HaploReg and others) are dedicated to human genetic variation as it relates to disease, primarily cancer, and various aspects of drug research. These include resources on patented drugs, their side effects, withdrawn drugs, and potential drug targets (38–40). Six papers in this section present updated databases of various antimicrobial and anticancer peptides. An interesting work, also chosen by the NAR editors as a Breakthrough paper, describes the newly compiled Database of Digenic Diseases (DIDA), which collects data on such diseases as Bardet-Biedl and Kallmann syndromes that are caused by single nucleotide variants or small indels in specific pairs of genes (41).

This issue also presents updates on the widely used databases of small molecules, NCBI's PubChem and EBI's ChEBI, and introduces SureChEMBL, the recently created database of chemicals found in patent documents (42–44). Two new glycoinformatics resources, the Carbohydrate Structure Database (CSDB) and the International Glycan Structure Repository (GlyTouCan), collect knowledge and facilitate further research on these important but often-overlooked compounds (45,46). Ten papers describe various plant databases, including an update on the popular Plant Promoter Analysis Navigator (47) and Information Commons for Rice (IC4R), a compendium of Chinese databases on all aspects of rice research (48). Finally, there are three databases on mitochondrial research: MitoCarta and MitoMiner, two excellent databases of mitochondrial proteins, and MitoAge, a database of mitochondrial DNA properties from various organisms (49–51).

UPDATED NAR ONLINE MOLECULAR BIOLOGY DATABASE COLLECTION

This year's update of the NAR online Molecular Biology Database Collection (which is freely available at http://www.oxfordjournals.org/nar/database/c/) involved inclusion of 62 new databases (Table 1) and 15 databases that have been previously described elsewhere and were not part of this Collection (Table 2). In addition, the Collection has been expanded by including such databases as Integrative Cancer Genomics (IntOGen) and Disease Variant Store (DIVAS) (52,53). Our curation checks revealed 121 non-responsive databases, of which 23 obsolete entries have been removed from the Collection and the rest marked for potential removal next year. In addition, 26 entries in the Collection have been updated with respect to their URLs, descriptions, and/or author contact information.

We welcome suggestions for inclusion in the Collection of additional databases that have been published in other journals. Such suggestions should be addressed to XMFS at xose.m.fernandez@gmail.com and should include database summaries in plain text, organized in accordance with the http://www.oxfordjournals.org/nar/database/summary/1 template.

FUNDING

The NIH Intramural Research Program at the National Library of Medicine [to M.Y.G.]. The open access publication charge for this paper has been waived by Oxford University Press - NAR.

Conflict of interest statement. The authors’ opinions do not necessarily reflect the views of their respective institutions. XMFS is an employee of Thermo Fisher Scientific Inc.