Nucleic Acids Research, 2021, Vol. 49, Database issue D1–D9
doi: 10.1093/nar/gkaa1216
The 2021 Nucleic Acids Research database issue and
the online molecular biology database collection
Daniel J. Rigden1,*
and Xos´e M. Fern´andez2
1
Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
and 2
Institut Curie, 25 rue d’Ulm, 75005 Paris, France
ABSTRACT
The 2021 Nucleic Acids Research database Issue
contains 189 papers spanning a wide range of biological
fields and investigation. It includes 89 papers
reporting on new databases and 90 covering
recent changes to resources previously published
in the Issue. A further ten are updates on
databases most recently published elsewhere. Seven
new databases focus on COVID-19 and SARS-CoV-
2 and many others offer resources for studying
the virus. Major returning nucleic acid databases
include NONCODE, Rfam and RNAcentral. Protein
family and domain databases include COG, Pfam,
SMART and Panther. Protein structures are covered
by RCSB PDB and dispersed proteins by PED
and MobiDB. In metabolism and signalling, STRING,
KEGG and WikiPathways are featured, along with returning
KLIFS and new DKK and KinaseMD, all focused
on kinases. IMG/M and IMG/VR update in the
microbial and viral genome resources section, while
human and model organism genomics resources include
Flybase, Ensembl and UCSC Genome Browser.
Cancer studies are covered by updates from canSAR
and PINA, as well as newcomers CNCdatabase and
Oncovar for cancer drivers. Plant comparative genomics
is catered for by updates from Gramene
and GreenPhylDB. The entire Database Issue is
freely available online on the Nucleic Acids Research
website (https://academic.oup.com/nar). The
NAR online Molecular Biology Database Collection
has been substantially updated, revisiting nearly
1000 entries, adding 90 new resources and eliminating
86 obsolete databases, bringing the current total
to 1641 databases. It is available at https://www.
oxfordjournals.org/nar/database/c/.
NEW AND UPDATED DATABASES
The 28th annual Nucleic Acids Research Database Issue
contains 189 papers spanning, as usual, a wide range of biology.
Unsurprisingly, COVID-19 casts a long shadow over
the Issue. Seven new databases specifically address the pandemic
and the SARS-CoV-2 virus responsible (Table 1) but
new and returning databases in all areas have rushed to support
research into the viral pandemic: the reader will find
reference to it throughout the Issue, sometimes in quite unexpected
places. The Issue contains a further 82 papers (Table
2) on new databases as well as 90 update papers on
databases previously published in NAR. To complete the
Issue, resources previously published elsewhere update in a
further 10 papers (Table 3).
As is customary, the Issue starts with reports from the
major database providers at the U.S. National Center for
Biotechnology Information (NCBI), the European Bioinformatics
Institute (EBI) and the National Genomics Data
Center (NGDC) in China (1–3). Thereafter, the usual categorisation
applies: (i) nucleic acid sequence and structure,
transcriptional regulation; (ii) protein sequence and structure;
(iii) metabolic and signaling pathways, enzymes and
networks; (iv) genomics of viruses, bacteria, protozoa and
fungi; (v) genomics of human and model organisms plus
comparative genomics; (vi) human genomic variation, diseases
and drugs; (vii) plants and (viii) other topics, such
as proteomics databases. Many resources are not easily
pigeon-holed so browsing of the whole Issue is strongly en-
couraged.
The COVID-19 papers span a number of sections clearly
indicating the multidisciplinary nature of the huge scientific
response to the pandemic. Navigating the deluge of
COVID-19 papers is a significant challenge in its own right
and one addressed by the NCBI’s LitCovid database (4)
which features manual curation supported by sophisticated
machine-learning assistance. SARS-CoV-2 nucleic acid sequence
data and associated curated metadata can be conveniently
obtained from the ViruSurf database (5) which
also covers other human pathogenic viruses. SARS-Cov-
2 comparative genomics is covered by the GESS database
(6) where temporal and geographical patterns of SNVs can
be analysed. SARS-Cov-2 protein structures – alone and in
complex with antibodies, receptors, and small molecules –
are collected at the CoV3D database (7) and made available
with a variety of bespoke analyses of sequential and
conformational diversity. Obviously, drug and vaccine de*To
whom correspondence should be addressed. Tel: +44 151 795 4467; Email: nardatabase@gmail.com
C The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which
permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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D2 Nucleic Acids Research, 2021, Vol. 49, Database issue
Table 1. Descriptions of new databases related to COVID-19 in the 2021 NAR database Issue
Database name URL Short description
CoV3D https://cov3d.ibbr.umd.edu/ Experimental coronavirus protein structures
COVID19 Drug Repository http://covid19.md.biu.ac.il/ Curated papers on COVID-19 drugs and drug
repurposing
DockCoV2 https://covirus.cc/drugs/ In silico drug docking against SARS-CoV2 targets
GESS https://wan-bioinfo.shinyapps.io/GESS/ Global Evaluation of SARS-CoV2 Sequences
LitCovid https://www.ncbi.nlm.nih.gov/research/coronavirus/ Curated COVID-19 literature
PAGER-COV http://discovery.informatics.uab.edu/PAGER-COV/ Pathways and gene lists related to COVID-19
ViruSurf http://gmql.eu/virusurf/ Portal to SARS-CoV2 sequences and variants
velopment are the primary drivers of SARS-Cov-2 protein
structure determination. Supporting these efforts is the
COVID19 Drugs Repository (8) which curates and integrates
experimental findings from the literature with information
from well-established small molecule databases to
support drug repurposing. In a similar vein, DockCoV2 (9)
contains in silico docking results for already approved drugs
against putative drug targets in the SARS-Cov-2 proteome.
Finally, recognising the therapeutic importance of an understanding
of the host response, PAGER-CoV (10) covers
pathways and gene lists relating to the viral infection and its
consequences.
In the ‘Nucleic acid databases’ section, two significant
returning databases focus on ncRNAs. The major news
from the NONCODE database (11) is the inclusion of
plant lncRNAs from 23 species, including their gene expression,
function annotation and sequence conservation
between species. NONCODE also reports new efforts to
document associations between mammalian lncRNAs and
cancers. MNDR (12) reports progress on a number of
fronts––including the addition of circRNA-disease associations
and ncRNA subcellular localization––resulting in a
quadrupling of database entries. Rfam (13) reaches version
14 with new RNA families, some community-derived (including
from masters students the paper reports) using a
new Rfam Cloud platform, and including coronavirus and
flavivirus entries. Integration with RNAcentral, also updating
here (14), is evident in a new sequence search and work
to make miRNA families more consistent with fellow member
miRBase (15). RNAcentral continues to grow impressively,
now encompassing 44 member ncRNA databases.
Resources added since the last publication expand content
in different directions, adding new classes of ncRNA such
as snoRNAs, new links to diseases and new organism cov-
erage.
Elsewhere, a number of databases focus on the structure,
at small or large scale, of nucleic acids. The new TBDB
(16) focuses on T-box riboswitch:tRNA pairs, where secondary
structure modelling is required to predict functionality,
while RASP (17) collects experimental data reporting
on RNA secondary structure from a variety of sources including
SARS-CoV-2. A major new arrival is the Nucleome
Data Bank (18), which brings together a repository of
experimental structural genomic data, computational tools
for the modelling of structures, and visualisation of structures
in the context of sequential data. They also introduce,
by analogy with PDB files, an NDB file format. In the same
area, 3DIV (19) reports an update focusing largely on 3D
cancer genomes and commenting on the consequences for
chromatin structure of the DNA structural variations associated
with some cancers. Finally, DNAmoreDB (20) collects
data on catalytic DNA molecules or DNAzymes, already
demonstrated to catalyse 20 different reactions with
that number sure to grow as research on their practical applications
continues.
In the section on protein sequence and structure
databases, users of protein family and domain databases
are particularly well-served. COG (21) returns to report
well over 200 new protein families and a similar number of
families updated to reflect recent experimental characterisation.
The current COG includes almost 5000 COGs and
annotates genomes of over 1200 microbes. Similarly popular
resources Pfam, SMART and Panther also report updates.
Pfam (22) adds over 350 new families, including entries
for previously unmatched SARS-CoV-2 proteins, and
improves the consistency of its content with the specialist
RepeatsDB resource, also updating here (23). A major
strategic decision reintroduces the automatically generated
Pfam-B supplement of non-curated sequence clusters calculated
using more efficient computational methods. SMART
(24), in contrast, does not aim for complete proteome coverage
and the most recent targeted focus has been mobile genetic
elements in bacteria and archaebacteria. The Panther
update (25) reports an interesting new facility for assigning
a function to a new sequence using tree grafting whereby
Gene Ontology terms are attached to a protein according
to the position at which it is best accommodated in the tree.
In the area of protein structure, the RCSB Protein Data
Bank (26) reminds us that this venerable database turns 50
in 2021, having grown from just seven entries then (27), and
distribution via magnetic tape, to ∼170 000 now. Its increasingly
comprehensive analytical and visualisation features
are exemplified using SARS-CoV-2 structures in the update
paper. Another database with a long history, ProThermDB,
covering thermodynamic parameters relating to protein
stability, returns revitalised and near-doubled in size after
15 years (28). Two new databases ThermoMutDB (29)
and FireProtDB (30) offer competition in the same area.
For proteins without regular stable structures, the Issue offers
a trio of databases. The main innovations at the returning
database MobiDB (31) cover functional annotations relating
to disordered regions; regions undergoing a disorder
to order transition on binding, predicted linear interaction
motifs, post-translational modifications and regions implicated
in phase separation. PED (32), also publishing an update,
covers experimentally characterized structural ensembles
of disordered regions and proteins. These are joined
by the newcomer MemMoRF (33) which covers features
within disordered regions that can interact with biological
membranes. Finally the Gene Ontology (34), a cornerstone
resource across all sections, contributes an update describing
how collaborations with expert groups and databases
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Nucleic Acids Research, 2021, Vol. 49, Database issue D3
Table 2. Descriptions of new databases in the 2021 NAR database Issue not specifically related to COVID-19
Database name URL Short description
Aging Atlas https://bigd.big.ac.cn/aging Aging related omics data
Animal-APAdb http://gong lab.hzau.edu.cn/Animal-APAdb/ Alternative polyadenylation in animals
AcrDB http://bcb.unl.edu/AcrDB/ Anti-CRISPR operons
AcrHub http://pacrispr.erc.monash.edu/AcrHub Anti-CRISPR proteins
ATACdb http://www.licpathway.net/ATACdb Human Assay-for-Transposase-Accessible Chromatin
data
AtMAD http://www.megabionet.org/atmad Arabidopsis thaliana Multi-omics Association
Database
BastionHub http://bastionhub.erc.monash.edu/ Substrates of Gram-negative secretion systems
BiG-FAM https://bigfam.bioinformatics.nl Biosynthetic gene cluster families
CancerImmunityQTL http://www.cancerimmunityqtl-hust.com/ ImmunQTLs across multiple cancer types
Chewie-NS https://chewbbaca.online/ Gene-by-gene schemas for microbial strain
identification
CMNPD https://www.cmnpd.org/ Comprehensive Marine Natural Product Database
CNCDatabase https://cncdatabase.med.cornell.edu/ Cancer drivers at non-coding regions
cncRNAdb http://www.rna-society.org/cncrnadb/ Coding and non-coding RNA
ConjuPepDB http://conjupepdb.ttk.hu/ Drug-peptide conjugates
CovInDB http://cadd.zju.edu.cn/cidb/ Covalent Inhibitor DataBase
crisprSQL http://www.crisprsql.com/ CRISPR/Cas9 Off-Target Cleavage Assays
CRISPR-view http://crispviewdatabase.weililab.org/ Functional genetic screens
CSEA-DB https://bioinfo.uth.edu/CSEADB/ Cell type specificity of genetic traits
CSVS http://csvs.babelomics.org/ Spanish genomes and exomes
Cyanorak http://www.sb-roscoff.fr/cyanorak Comparative genomics of cyanobacteria
Datanator https://datanator.info/ Molecular data for modeling biochemical networks
dbCAN-PUL http://bcb.unl.edu/dbCAN PUL/home Experimentally characterized CAZyme gene clusters
dbGuide https://sgrnascorer.cancer.gov/dbguide Manually curated and functionally validated guide
RNAs
DescribePROT http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/ Residue level prediction of structure and function
across proteomes
DKK https://darkkinome.org/ Dark Kinome Knowledgebase
DIGGER https://exbio.wzw.tum.de/digger Alternative splicing and protein-protein interactions
DNAmoreDB http://www.genesilico.pl/DNAmoreDB DNAzymes, i.e. DNA molecules with catalytic activity
DrugSpaceX https://drugspacex.simm.ac.cn/ 100 million compounds for virtual screening
DualSeqDB http://www.tartaglialab.com/dualseq/ Dual RNA-seq host-pathogen sequencing
FireProtDB https://loschmidt.chemi.muni.cz/fireprotdb Protein stability data
gcType http://gctype.wdcm.org/ WDCM 10K sequencing projects
GIMICA https://idrblab.org/gimica/ Host Genetic and Immune Factors Shaping Human
Microbiota
GlycoPOST https://glycopost.glycosmos.org/ Raw Mass Spectrometry glycomics data
GRNdb http://www.grndb.com/ TF-target relationships inferred from single cell and
bulk RNA-seq datasets
GSRS https://gsrs.ncats.nih.gov/app/substances Global Substance Registration System
HeRA https://hanlab.uth.edu/HeRA/ Human enhancer RNA Atlas
HERB http://herb.ac.cn/ High-throughput Experiment- and Reference-guided
dataBase of TCM
Housekeeping Transcript
Atlas
http://www.housekeeping.unicamp.br/ Human and mouse housekeeping genes
HumanMetagenomeDB https://webapp.ufz.de/hmgdb/ Curated and standardized metadata for human
metagenomes
iCSDB http://www.kobic.re.kr/icsdb integrated CRISPR Screens DataBase
IDDB http://mdl.shsmu.edu.cn/IDDB Infertility Disease DataBase
iModulonDB https://imodulondb.org/ ‘iModulons’, groups of independently-modulated
genes
IndiGenomes http://clingen.igib.res.in/indigen/ Genetic variation in 1000 Indian individuals
INTEDE https://idrblab.org/intede/ Interactome of Drug-Metabolizing Enzymes
KinaseMD https://bioinfo.uth.edu/kmd/ Kinase Mutations and Drug responses
LnCeCell http://bio-bigdata.hrbmu.edu.cn/LnCeCell/ lncRNA-associated ceRNA networks
LncExpDB https://bigd.big.ac.cn/lncexpdb Human lncRNA expression database
LncSEA http://bio.liclab.net/LncSEA/ Reference human lncRNA sets
m6A-Atlas http://www.xjtlu.edu.cn/biologicalsciences/atlas The N6-methyladenosine (m6A) epitranscriptome
including base-resolution data
markerDB http://www.markerdb.ca/ Biomarkers: chemical, protein, chromosomal and
genetic
MASI http://www.aiddlab.com/MASI/ Microbiota – Active Substance Interactions database
MeDAS https://das.chenlulab.com Alternative splicing during development in 20 species
MemMoRF http://memmorf.hegelab.org Membrane-binding Molecular Recognition Features
mMGE http://mgedb.comp-sysbio.org/ Human metagenomic extrachromosomal mobile
genetic elements
MolluscDB http://mgb.biocloud.net/home Comparative genomics of molluscs
Nucleome Data Bank https://ndb.rice.edu/ 3D genome structures and simulations
OncoVar https://oncovar.org/ Driver mutations, genes and pathways in cancer
Open Targets Genetics https://genetics.opentargets.org/ Drug targets prioritised from genetic data
PCAT http://pedtranscriptome.org Pediatric cancer transcriptome explorer
Peryton https://dianalab.e-ce.uth.gr/peryton Microbe–disease associations
PheLiGe https://phelige.com/ Genotype–phenotype associations
PhycoCosm http://phycocosm.jgi.doe.gov/ Comparative genomics of algae
PK-DB https://pk-db.com/ Pharmacokinetics data from clinical trials and
pre-clinical research
Planet Microbe https://www.planetmicrobe.org/ Oceanographic omics datasets linked to environmental
metadata
Plant-ImputeDB http://gong lab.hzau.edu.cn/Plant imputeDB Reference panels and imputation methods for plant
genomes
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Table 2. Continued
Database name URL Short description
PROTAC-DB http://cadd.zju.edu.cn/protacdb/ Proteolysis-targeting chimeras (PROTACs)
RASP http://rasp.zhanglab.net/ RNA secondary structure probing data
RBP2GO https://rbp2go.dkfz.de RNA-binding proteins across species
RJunBase www.RJunBase.org RNA splice junctions
RMDisease http://www.xjtlu.edu.cn/biologicalsciences/rmd Genetic variants that affect RNA modifications vs
disease
RMVar http://rmvar.renlab.org Genetic variants that affect RNA modifications vs
disease
SC2disease http://easybioai.com/sc2disease/ Single cell transcriptomics data and disease
SilencerDB http://health.tsinghua.edu.cn/silencerdb or
http://bioinfo.au.tsinghua.edu.cn/silencerdb/
Human silencers, validated or predicted
STAB http://stab.comp-sysbio.org/ Spatio-Temporal Cell Atlas of the Human Brain
TBDB https://tbdb.io Structurally annotated T-box riboswitch: tRNA pairs
TCRdb http://bioinfo.life.hust.edu.cn/TCRdb T-cell receptor (TCR) sequences
ThermoMutDB http://biosig.unimelb.edu.au/thermomutdb Protein Mutation Thermodynamics Database
TISCH http://tisch.comp-genomics.org/ Uniformly processed tumor (and microenvironment)
scRNA-seq data
TransCirc https://www.biosino.org/transcirc/ Protein coding potential of circRNAs
tRFtarget http://trftarget.net Targets of tRNA-derived fragments
tsRBase http://tsrbase.org/ tRNA-derived small RNA expression and function
VARAdb http://www.licpathway.net/VARAdb/ Variants and regulatory information
Table 3. Updated descriptions of databases most recently published elsewhere
Database name URL Short description
Bgee https://bgee.org/ Curated wild-type animal gene expression data
CellMinerCDB https://discover.nci.nih.gov/cellminercdb/ Cell line-based pharmacogenomics datasets
GeneLab https://genelab.nasa.gov/ Omics data relating to space biology and ionising
radiation
HMPDACC https://portal.hmpdacc.org/ Human Microbiome Project Data Coordination
Center
miRNASNP http://bioinfo.life.hust.edu.cn/miRNASNP/ miRNA-related SNPs and mutations
MitImpact https://mitimpact.css-mendel.it/ Precomputed pathogenicity predictions for human
mitochondrial genome mutations
ModelSEED Biochemistry https://modelseed.org/biochem Biochemical reactions
PLncDB http://plncdb.tobaccodb.org/ Plant long non-coding RNA
Project Score https://score.depmap.sanger.ac.uk/ CRISPR–Cas9 screens to identify cancer
dependencies
TREND-DB http://shiny.imbei.uni-mainz.de:3838/trend-db/ Conditional alternative polyadenylation
are being used to enrich, expand and improve the accuracy
of the ontology.
In the metabolic and signalling section, the hugely popular
STRING database of functional associations (35) offers
an update that describes improvements to the functional
enrichment tests available when users upload lists
of proteins. STRING also now allows users to visualise
and score all functional associations, as previously, or to
limit visualisation and scoring to only physical interactions.
The equally influential KEGG returns (36) with
improved treatments of viruses and new visualisations, a
more dynamic and interactive pathway map viewer and
global map display with more flexible and informative
colouring. A number of papers cover metabolic pathways.
WikiPathways (37) reports increased numbers of
pathways, metabolites and––importantly, given its modus
operandi––contributors. Distinct portals with their own
URLs support communities focused on topics as diverse as
COVID-19, rare diseases and lipid metabolism. The popular
ModelSEED Biochemistry database (38), publishing
here for the first time, reports a doubling of content since
its first iteration. Quantitative pathway modelling requires
easy access to relevant data. The new database Datanator
(39) steps in here to collect highly diverse data from a
wide range of relevant resources and present it in a normalised
and integrated fashion. Kinases are particularly
well covered this year with KLIFS, the database for kinase–
inhibitor interactions, reporting an update (40) that extends
coverage to atypical kinases and provides an API
for easy access. It is joined by two new resources, DKK
(41) focussing on the ‘Dark Kinome’ and collecting information
on substrates, inhibitor and tissue expression; and
KinaseMD (42) which provides a detailed analysis of the
impact of mutations on kinase structures and their consequences
for drug binding. Finally, two new databases feature
gene clusters. BiG-FAM (43), from the developers of
the well known antiSMASH database (44), contains families
of Biosynthetic Gene Clusters and enables a better understanding
(and exploitation) of the full range of microbial
natural product synthetic capacity. dbCAN-PUL (45) also
builds on and complements an earlier database, in this case
dbCAN-seq (46), and offers an online repository of experimentally
characterised Polysaccharide Utilization Loci.
The microbial genomics section begins with a pair of
databases devoted to anti-CRISPR (Acr) proteins. AcrHub
(47) brings together over 300 experimentally characterised
Acr proteins, 70 000 predicted Acr proteins and a variety
of modules for characterising potential Acrs in useruploaded
sequences. AcrDB (48) detects and presents operons
containing Acr-coding genes and nearby Aca regulatory
proteins and uses machine learning to score them further.
For comparative genomics, sister resources from the
JGI, IMG/M and IMG/VR report updates. IMG/M (49)
contains billions of genes from genomes and metagenomes
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and allows flexible mining and comparison between selected
groups of sequences. IMG/VR (50) has near-tripled in size
since its last update paper, its content dominated by 15 000
metagenomes that map across all continents and oceans.
Also focused on viruses, VIPERdb (51), the database of viral
capsids returns after a decade with new features including
structure-based sequence alignments that allow identification
of significantly conserved positions. Elsewhere
metagenomics, and the human microbiome in particular,
are a strong focus. Access to human metagenomes will be
facilitated by the new curated metadata resource HumanMetagenomeDB
(52) while another newcomer GIMICA
(53) focuses on human genetic and immune factors that influence
the human microbiota. The HMPDACC (54), published
here for the first time, takes a multi-omics view of the
human microbiome in health and disease, and encompasses
20 different data types. Finally, Planet Microbe (55) offers a
home for oceanographic omics datasets, linking them to as
much associated environmental context as possible.
In the next section, model organisms feature strongly.
Flybase returns (56) to report many new features including
Pathway Reports for major signalling pathways, better
annotation of enzymes and flagging of proteins whose orthology
to characterised human proteins renders them potentially
relevant to disease. The Mouse Genome Database
(57) also strongly emphasises the relevance to health and
disease of comparisons with human proteins, and has a dedicated
portal containing mouse research relevant to SARSCoV-2.
The ZFIN database (58) for zebrafish showcases
newly designed pages driven by community feedback and
describes the exchange of data with the Alliance of Genome
Resources (59). Elsewhere two groups of organisms, arguably
unfairly neglected hitherto, gain their own dedicated
comparative genomics databases. MolluscDB (60) caters to
members of the second largest animal phylum and includes
not only 20 diverse and high-quality mollusc genomes, but
also an array of functional genomic and even paleobiological
data. Phycocosm (61) harbours genome (nuclear and
plastid) and other omics data for the comparative study of
algae. The UCSC Genome Browser (62) is a popular choice
for interactive retrieval and display of genomes and associated
tracks at its own site or embedded in other databases.
Its response to the COVID-19 pandemic included rapidly
making the SARS-CoV-2 sequence available with a variety
of annotations, but also annotating human genome tracks
with SNPs relevant to disease susceptibility and severity. Finally,
the section also includes a trio of databases regarding
ncRNA expression. The popular deepBase updates with a
paper (63) describing a huge increase in expression datasets
incorporated plus new and strong foci on ncRNA expression
in cancer and exosomes. The new resource LncExpDB
(64) intensively covers human lncRNA expression, including
subcellular compartments and coexpression with potentially
interacting mRNA molecules. Finally, LncSEA (65),
also for human lncRNAs, supports research into lncRNA
function by deriving reference sets of lncRNAs. Users can
submit lncRNA lists for annotation and enrichment analy-
ses.
The section on human genomic variation, diseases and
drugs is again the largest in the Issue. Two new databases
report on genetic variability in national populations. CSVS
(66) reports on 2000 Spanish genomes and exomes and
is notable for the crowd-sourcing from local projects behind
its data, while IndiGenomes (67) covers 1000 Indian
genomes from the country’s notably diverse population.The
GVM (68) collects genetic variation information
from 41 species and contributes an update reporting a doubling
in size and an analysis of thousands of SARS-CoV-
2 variants. The new VARAdb database (69) comprehensively
annotates human variants with a welcome emphasis
on non-coding changes. Other databases link SNPs to
specific molecular phenomena. Thus, RMDisease (70) and
RMVar (71) each link genetic variants to RNA modifications
and consider their potential impacts on disease. miRNASNP
plays a similar role for SNPs that affect miRNAs
or their targets and this update (72) reports a dramatic
expansion and a strong focus on disease-related variants.
Linking genotypes to phenotypes is the focus of two new
databases PheLiGe (73) and Open Target Genetics (74).
The latter’s sister resource, the Open Targets Platform (75)
for linking drug targets to diseases, contributes an update
describing new scoring of drug targets from an increased
range of contributing datasets. These new sources include
Open Targets Genetics and Project Score, which includes
results from CRISPR knockout screens of cancer models
and which also features in this Issue (76). Other cancer
databases include two new resources specifically focusing
on cancer drivers, CNCdatabase (77) for non-coding
cancer drivers and Oncovar (78) which complements experimental
data with bioinformatically predicted drivers.
canSAR, the multi-faceted oncology database reports new
data, interface and query options (79). The paper guides the
reader through the database, from the notably clear target
synopsis pages to further information that would support
a researcher in validating a target in a particular cancer.
Among resources relevant to drug candidates, PubChem
(80) is the major returning database, reporting over 100 new
data sources enabling, for example, better links to literature,
patents, material properties and toxicological data. Finally,
given the explosion of interest in PROTACs for the targeted
degradation of disease-related proteins, it’s worth mentioning
PROTAC-DB (81) which collects information on PROTACs’
structures, biological activities and drug-like proper-
ties.
Crops are, as usual, a major focus in the plant database
section. SoyBase (82) returns with an update including new
features for visualisation of gene expression and soya pangenomes.
The family is covered more broadly at LegumeIP
(83) which now includes 17 legume genomes. A key focus is
enabling translation of knowledge on agriculturally desirable
traits from model genomes such as soybean to other
species. A new database, Plant-ImputeDB (84), will also
support crop breeding efforts by providing reference panels
for 12 commercially important crops, thereby enabling
better interpretation of genome variation. Two returning
databases facilitate comparative plant genomics work.
GreenPhylDB (85) adopts the concept of the pangenome
in order to facilitate exploration of evolutionary scenarios
within and between species. Gramene contributes a comprehensive
update (86) covering expanded content across
genomes, pathways and gene expression. It concludes with
an interesting view of the number of collaborations of the
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enterprise with other databases, including the Alliance of
Genome Resources (59). A multi-omics perspective of the
model plant Arabidopsis is offered by the new resource
AtMAD (87) which integrates genotypes, transcriptomes,
methylomes and phenotypes for 620 accessions.
As ever, the final section contains a fascinating variety of
databases that do not comfortably sit elsewhere. A single paper
covers both ArrayExpress and Biostudies (88) and describes
the migration of content from the former, that long
outgrew its genesis (89) as a repository for microarray data,
in favour of the more flexible and general possibilities of
the latter. Glycans are covered by the returning GlyTouCan
database (90) for glycan structures which brings improved
submission and validation, and by the new GlycoPOST (91)
which focuses on mass spectrometry of glycans and glycoproteins.
Elsewhere NASA GeneLab (92) publishes in NAR
for the first time and covers omics data obtained in space or
simulated space conditions. Finally, MitoCarta, the popular
focused resource for the mammalian mitochondrial proteome
updates with curated sub-organelle localization and
assignment of proteins to a set of 149 ‘MitoPathways’ (93).
NAR ONLINE MOLECULAR BIOLOGY DATABASE
COLLECTION
The ongoing COVID-19 crisis has shown the resilience of
the scientific community: resources were rapidly reallocated
as a response to the pandemic and enabled sequencing thousands
of strains, tracking infection rates as the virus spread
across the globe, structural biology etc. Making the most
of the data generated through various streams naturally involves
databases and their efforts are somehow reflected in
our database with the seven new COVID-specific databases
mentioned above but this is but a small fraction of the
international effort fueling the number of publications on
SARS-CoV-2 and coronavirus-related research (94).
The new normal reduced our travel schedules providing
additional time for a major revamp of our NAR online
Molecular Database Collection (accessible at https:
//www.oxfordjournals.org/nar/database/c/). In addition to
the customary removal of obsolete databases, hundreds
of entries were updated, corrected or expanded bringing
the total collection to 1641 databases. We thank the authors
for their support for our ongoing effort monitoring
the listed resources. Among the hundreds of entries
updated, many were due to direct communication with
xose.m.fernandez@gmail.com providing a plain text file
as defined in https://www.oxfordjournals.org/nar/database/
summary/1.
ACKNOWLEDGEMENTS
We thank Dr Martine Bernardes-Silva, especially, and the
rest of the Oxford University Press team led by Joanna Ventikos
for their help in compiling this Issue.
FUNDING
Funding for open access charge: Oxford University Press.
Conflict of interest statement. The authors’ opinions do not
necessarily reflect the views of their respective institutions.
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