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Volume 2015
2015
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EISSN 1758-0463

Volume 2015, 2015

Determining similarity of scientific entities in annotation datasets
Guillermo Palma and others
Database, Volume 2015, 2015, bau123, https://doi.org/10.1093/database/bau123
FR database 1.0: a resource focused on fruit development and ripening
Junyang Yue and others
Database, Volume 2015, 2015, bav002, https://doi.org/10.1093/database/bav002
LocSigDB: a database of protein localization signals
Simarjeet Negi and others
Database, Volume 2015, 2015, bav003, https://doi.org/10.1093/database/bav003
MnTEdb, a collective resource for mulberry transposable elements
Bi Ma and others
Database, Volume 2015, 2015, bav004, https://doi.org/10.1093/database/bav004
Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora
Tudor Groza and others
Database, Volume 2015, 2015, bav005, https://doi.org/10.1093/database/bav005
PathCards: multi-source consolidation of human biological pathways
Frida Belinky and others
Database, Volume 2015, 2015, bav006, https://doi.org/10.1093/database/bav006
PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples
Yiyu Zheng and others
Database, Volume 2015, 2015, bav007, https://doi.org/10.1093/database/bav007
TeloPIN: a database of telomeric proteins interaction network in mammalian cells
Zhenhua Luo and others
Database, Volume 2015, 2015, bav018, https://doi.org/10.1093/database/bav018

Database Tool

OntoMate: a text-mining tool aiding curation at the Rat Genome Database
Weisong Liu and others
Database, Volume 2015, 2015, bau129, https://doi.org/10.1093/database/bau129
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study
J. M. Villaveces and others
Database, Volume 2015, 2015, bau131, https://doi.org/10.1093/database/bau131
The Listeria monocytogenes strain 10403S BioCyc database
Renato H. Orsi and others
Database, Volume 2015, 2015, bav027, https://doi.org/10.1093/database/bav027
BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis
Quan Wan and others
Database, Volume 2015, 2015, bav019, https://doi.org/10.1093/database/bav019
Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis
Tsung-Jung Wu and others
Database, Volume 2015, 2015, bav032, https://doi.org/10.1093/database/bav032
miRGate: a curated database of human, mouse and rat miRNA–mRNA targets
Eduardo Andrés-León and others
Database, Volume 2015, 2015, bav035, https://doi.org/10.1093/database/bav035
DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes
Janet Piñero and others
Database, Volume 2015, 2015, bav028, https://doi.org/10.1093/database/bav028
ProtoBug: functional families from the complete proteomes of insects
Nadav Rappoport and Michal Linial
Database, Volume 2015, 2015, bau122, https://doi.org/10.1093/database/bau122
NeuroPep: a comprehensive resource of neuropeptides
Yan Wang and others
Database, Volume 2015, 2015, bav038, https://doi.org/10.1093/database/bav038
CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization
Silvia Frias and others
Database, Volume 2015, 2015, bav041, https://doi.org/10.1093/database/bav041
DroughtDB: an expert-curated compilation of plant drought stress genes and their homologs in nine species
Svenja Alter and others
Database, Volume 2015, 2015, bav046, https://doi.org/10.1093/database/bav046
GeneStoryTeller: a mobile app for quick and comprehensive information retrieval of human genes
Stergiani V. Eleftheriou and others
Database, Volume 2015, 2015, bav048, https://doi.org/10.1093/database/bav048
HCSD: the human cancer secretome database
Amir Feizi and others
Database, Volume 2015, 2015, bav051, https://doi.org/10.1093/database/bav051
Drug-Path: a database for drug-induced pathways
Hui Zeng and others
Database, Volume 2015, 2015, bav061, https://doi.org/10.1093/database/bav061
Database of RNA binding protein expression and disease dynamics (READ DB)
Seyedsasan Hashemikhabir and others
Database, Volume 2015, 2015, bav072, https://doi.org/10.1093/database/bav072
OCDB: a database collecting genes, miRNAs and drugs for obsessive-compulsive disorder
Anna P. Privitera and others
Database, Volume 2015, 2015, bav069, https://doi.org/10.1093/database/bav069
MESSI: metabolic engineering target selection and best strain identification tool
Kang Kang and others
Database, Volume 2015, 2015, bav076, https://doi.org/10.1093/database/bav076
CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea
Dadakhalandar Doddamani and others
Database, Volume 2015, 2015, bav078, https://doi.org/10.1093/database/bav078
Carbohydrate Structure Database: tools for statistical analysis of bacterial, plant and fungal glycomes
K.S. Egorova and others
Database, Volume 2015, 2015, bav073, https://doi.org/10.1093/database/bav073
Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data
Zheng Zhao and others
Database, Volume 2015, 2015, bav082, https://doi.org/10.1093/database/bav082
CRCDA—Comprehensive resources for cancer NGS data analysis
Manonanthini Thangam and Ramesh Kumar Gopal
Database, Volume 2015, 2015, bav092, https://doi.org/10.1093/database/bav092
WaspAtlas: a Nasonia vitripennis gene database and analysis platform
Nathaniel J. Davies and Eran Tauber
Database, Volume 2015, 2015, bav103, https://doi.org/10.1093/database/bav103
BaMBa: towards the integrated management of Brazilian marine environmental data
Pedro Milet Meirelles and others
Database, Volume 2015, 2015, bav088, https://doi.org/10.1093/database/bav088
ERAIZDA: a model for holistic annotation of animal infectious and zoonotic diseases
Teresia M. Buza and others
Database, Volume 2015, 2015, bav110, https://doi.org/10.1093/database/bav110
SymbioGenomesDB: a database for the integration and access to knowledge on host–symbiont relationships
Mariana Reyes-Prieto and others
Database, Volume 2015, 2015, bav109, https://doi.org/10.1093/database/bav109
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics
Junyang Yue and others
Database, Volume 2015, 2015, bav113, https://doi.org/10.1093/database/bav113

Original Articles

Fishing for data and sorting the catch: assessing the data quality, completeness and fitness for use of data in marine biogeographic databases
Leen Vandepitte and others
Database, Volume 2015, 2015, bau125, https://doi.org/10.1093/database/bau125
CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002
Yaohua Yang and others
Database, Volume 2015, 2015, bau127, https://doi.org/10.1093/database/bau127
PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus . Application in hypertension and renal disease
Shur-Jen Wang and others
Database, Volume 2015, 2015, bau128, https://doi.org/10.1093/database/bau128
Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach
Philippe Rocca-Serra and others
Database, Volume 2015, 2015, bau132, https://doi.org/10.1093/database/bau132
EcoliNet: a database of cofunctional gene network for Escherichia coli
Hanhae Kim and others
Database, Volume 2015, 2015, bav001, https://doi.org/10.1093/database/bav001
Combining computational models, semantic annotations and simulation experiments in a graph database
Ron Henkel and others
Database, Volume 2015, 2015, bau130, https://doi.org/10.1093/database/bau130
mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support
Kimchi Strasser and others
Database, Volume 2015, 2015, bav008, https://doi.org/10.1093/database/bav008
Improving the consistency of domain annotation within the Conserved Domain Database
Myra K. Derbyshire and others
Database, Volume 2015, 2015, bav012, https://doi.org/10.1093/database/bav012
Shared resources, shared costs—leveraging biocuration resources
Sandra Orchard and Henning Hermjakob
Database, Volume 2015, 2015, bav009, https://doi.org/10.1093/database/bav009
Ontology application and use at the ENCODE DCC
Venkat S. Malladi and others
Database, Volume 2015, 2015, bav010, https://doi.org/10.1093/database/bav010
RNABP COGEST: a resource for investigating functional RNAs
Sohini Bhattacharya and others
Database, Volume 2015, 2015, bav011, https://doi.org/10.1093/database/bav011
EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape
Saurabh Loharch and others
Database, Volume 2015, 2015, bav013, https://doi.org/10.1093/database/bav013
LMPID: A manually curated database of linear motifs mediating protein–protein interactions
Debasree Sarkar and others
Database, Volume 2015, 2015, bav014, https://doi.org/10.1093/database/bav014
Scaling drug indication curation through crowdsourcing
Ritu Khare and others
Database, Volume 2015, 2015, bav016, https://doi.org/10.1093/database/bav016
PTGBase: an integrated database to study tandem duplicated genes in plants
Jingyin Yu and others
Database, Volume 2015, 2015, bav017, https://doi.org/10.1093/database/bav017
Colorectal cancer drug target prediction using ontology-based inference and network analysis
Cui Tao and others
Database, Volume 2015, 2015, bav015, https://doi.org/10.1093/database/bav015
Standard development at the Human Variome Project
Timothy D. Smith and others
Database, Volume 2015, 2015, bav024, https://doi.org/10.1093/database/bav024
LOTUS-DB: an integrative and interactive database for Nelumbo nucifera study
Kun Wang and others
Database, Volume 2015, 2015, bav023, https://doi.org/10.1093/database/bav023
Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer
Ji-Hyun Lee and others
Database, Volume 2015, 2015, bav022, https://doi.org/10.1093/database/bav022
Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system
Catalina O. Tudor and others
Database, Volume 2015, 2015, bav020, https://doi.org/10.1093/database/bav020
CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis
Bernardo Ochoa-Montaño and others
Database, Volume 2015, 2015, bav026, https://doi.org/10.1093/database/bav026
BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies
Jorge S. Oliveira and others
Database, Volume 2015, 2015, bav033, https://doi.org/10.1093/database/bav033
dbPSP: a curated database for protein phosphorylation sites in prokaryotes
Zhicheng Pan and others
Database, Volume 2015, 2015, bav031, https://doi.org/10.1093/database/bav031
Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature
Guocai Chen and others
Database, Volume 2015, 2015, bav034, https://doi.org/10.1093/database/bav034
Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems
Stéphanie Boué and others
Database, Volume 2015, 2015, bav030, https://doi.org/10.1093/database/bav030
PEIMAN 1.0: Post-translational modification Enrichment, Integration and Matching ANalysis
Payman Nickchi and others
Database, Volume 2015, 2015, bav037, https://doi.org/10.1093/database/bav037
Follicle Online: an integrated database of follicle assembly, development and ovulation
Juan Hua and others
Database, Volume 2015, 2015, bav036, https://doi.org/10.1093/database/bav036
novPTMenzy: a database for enzymes involved in novel post-translational modifications
Shradha Khater and Debasisa Mohanty
Database, Volume 2015, 2015, bav039, https://doi.org/10.1093/database/bav039
GBIS: the information system of the German Genebank
Markus Oppermann and others
Database, Volume 2015, 2015, bav021, https://doi.org/10.1093/database/bav021
MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse
Hong-Dong Li and others
Database, Volume 2015, 2015, bav045, https://doi.org/10.1093/database/bav045
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations
Frederic B. Bastian and others
Database, Volume 2015, 2015, bav043, https://doi.org/10.1093/database/bav043
Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy
Wasila Dahdul and others
Database, Volume 2015, 2015, bav040, https://doi.org/10.1093/database/bav040
AtmiRNET: a web-based resource for reconstructing regulatory networks of Arabidopsis microRNAs
Chia-Hung Chien and others
Database, Volume 2015, 2015, bav042, https://doi.org/10.1093/database/bav042
GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development
Alfred Chun-Shui Luk and others
Database, Volume 2015, 2015, bav044, https://doi.org/10.1093/database/bav044
GraP: platform for functional genomics analysis of Gossypium raimondii
Liwei Zhang and others
Database, Volume 2015, 2015, bav047, https://doi.org/10.1093/database/bav047
An Ebola virus-centered knowledge base
Maulik R. Kamdar and Michel Dumontier
Database, Volume 2015, 2015, bav049, https://doi.org/10.1093/database/bav049
A general concept for consistent documentation of computational analyses
Peter Ebert and others
Database, Volume 2015, 2015, bav050, https://doi.org/10.1093/database/bav050
dbHiMo: a web-based epigenomics platform for histone-modifying enzymes
Jaeyoung Choi and others
Database, Volume 2015, 2015, bav052, https://doi.org/10.1093/database/bav052
kpath: integration of metabolic pathway linked data
Ismael Navas-Delgado and others
Database, Volume 2015, 2015, bav053, https://doi.org/10.1093/database/bav053
BioAcoustica: a free and open repository and analysis platform for bioacoustics
Edward Baker and others
Database, Volume 2015, 2015, bav054, https://doi.org/10.1093/database/bav054
Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications
Tamás Hegedűs and others
Database, Volume 2015, 2015, bav056, https://doi.org/10.1093/database/bav056
Construction of biological networks from unstructured information based on a semi-automated curation workflow
Justyna Szostak and others
Database, Volume 2015, 2015, bav057, https://doi.org/10.1093/database/bav057
Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes
Rian Pierneef and others
Database, Volume 2015, 2015, bav058, https://doi.org/10.1093/database/bav058
G4RNA: an RNA G-quadruplex database
Jean-Michel Garant and others
Database, Volume 2015, 2015, bav059, https://doi.org/10.1093/database/bav059
CrisprGE: a central hub of CRISPR/Cas-based genome editing
Karambir Kaur and others
Database, Volume 2015, 2015, bav055, https://doi.org/10.1093/database/bav055
MiDAS: the field guide to the microbes of activated sludge
Simon Jon McIlroy and others
Database, Volume 2015, 2015, bav062, https://doi.org/10.1093/database/bav062
BEAN 2.0: an integrated web resource for the identification and functional analysis of type III secreted effectors
Xiaobao Dong and others
Database, Volume 2015, 2015, bav064, https://doi.org/10.1093/database/bav064
SInCRe—structural interactome computational resource for Mycobacterium tuberculosis
Rahul Metri and others
Database, Volume 2015, 2015, bav060, https://doi.org/10.1093/database/bav060
toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research
David B. Rhee and others
Database, Volume 2015, 2015, bav066, https://doi.org/10.1093/database/bav066
EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A
Andrew Ndhlovu and others
Database, Volume 2015, 2015, bav065, https://doi.org/10.1093/database/bav065
EpiFactors: a comprehensive database of human epigenetic factors and complexes
Yulia A. Medvedeva and others
Database, Volume 2015, 2015, bav067, https://doi.org/10.1093/database/bav067
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat
Patricia C. Babbitt and others
Database, Volume 2015, 2015, bav063, https://doi.org/10.1093/database/bav063
Human metabolic atlas: an online resource for human metabolism
Natapol Pornputtapong and others
Database, Volume 2015, 2015, bav068, https://doi.org/10.1093/database/bav068
SHIELD: an integrative gene expression database for inner ear research
Jun Shen and others
Database, Volume 2015, 2015, bav071, https://doi.org/10.1093/database/bav071
Curcumin Resource Database
Anil Kumar and others
Database, Volume 2015, 2015, bav070, https://doi.org/10.1093/database/bav070
The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies
Matyas F. Cserhati and others
Database, Volume 2015, 2015, bav074, https://doi.org/10.1093/database/bav074
Phytochemica: a platform to explore phytochemicals of medicinal plants
Shivalika Pathania and others
Database, Volume 2015, 2015, bav075, https://doi.org/10.1093/database/bav075
MetazSecKB: the human and animal secretome and subcellular proteome knowledgebase
John Meinken and others
Database, Volume 2015, 2015, bav077, https://doi.org/10.1093/database/bav077
MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution
Dominique Boeuf and others
Database, Volume 2015, 2015, bav080, https://doi.org/10.1093/database/bav080
FlyVar: a database for genetic variation in Drosophila melanogaster
Fei Wang and others
Database, Volume 2015, 2015, bav079, https://doi.org/10.1093/database/bav079
DENdb: database of integrated human enhancers
Haitham Ashoor and others
Database, Volume 2015, 2015, bav085, https://doi.org/10.1093/database/bav085
LncReg: a reference resource for lncRNA-associated regulatory networks
Zhong Zhou and others
Database, Volume 2015, 2015, bav083, https://doi.org/10.1093/database/bav083
Deep Question Answering for protein annotation
Julien Gobeill and others
Database, Volume 2015, 2015, bav081, https://doi.org/10.1093/database/bav081
FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events
Praveen Kumar Korla and others
Database, Volume 2015, 2015, bav086, https://doi.org/10.1093/database/bav086
Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME
George Nicola and others
Database, Volume 2015, 2015, bav087, https://doi.org/10.1093/database/bav087
SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data
Chao Pang and others
Database, Volume 2015, 2015, bav089, https://doi.org/10.1093/database/bav089
Comprehensive comparative homeobox gene annotation in human and mouse
Laurens G. Wilming and others
Database, Volume 2015, 2015, bav091, https://doi.org/10.1093/database/bav091
Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens
Norbert Kilian and others
Database, Volume 2015, 2015, bav094, https://doi.org/10.1093/database/bav094
RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse
Zhi-Ping Liu and others
Database, Volume 2015, 2015, bav095, https://doi.org/10.1093/database/bav095
MGDB: a comprehensive database of genes involved in melanoma
Di Zhang and others
Database, Volume 2015, 2015, bav097, https://doi.org/10.1093/database/bav097
miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs
Peng Wang and others
Database, Volume 2015, 2015, bav098, https://doi.org/10.1093/database/bav098
JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms
Mauro Petrillo and others
Database, Volume 2015, 2015, bav101, https://doi.org/10.1093/database/bav101
ProPepper: a curated database for identification and analysis of peptide and immune-responsive epitope composition of cereal grain protein families
Angéla Juhász and others
Database, Volume 2015, 2015, bav100, https://doi.org/10.1093/database/bav100
NeuroTransDB : highly curated and structured transcriptomic metadata for neurodegenerative diseases
Shweta Bagewadi and others
Database, Volume 2015, 2015, bav099, https://doi.org/10.1093/database/bav099
MtiBase: a database for decoding microRNA target sites located within CDS and 5′UTR regions from CLIP-Seq and expression profile datasets
Zhi-Wei Guo and others
Database, Volume 2015, 2015, bav102, https://doi.org/10.1093/database/bav102
Developing the eHistology Atlas
Lorna Richardson and others
Database, Volume 2015, 2015, bav105, https://doi.org/10.1093/database/bav105
Differential ligand-signaling network of CCL19/CCL21-CCR7 system
Rajesh Raju and others
Database, Volume 2015, 2015, bav106, https://doi.org/10.1093/database/bav106
PhenoMiner: from text to a database of phenotypes associated with OMIM diseases
Nigel Collier and others
Database, Volume 2015, 2015, bav104, https://doi.org/10.1093/database/bav104
MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins
Yuan Zhou and others
Database, Volume 2015, 2015, bav108, https://doi.org/10.1093/database/bav108
ONRLDB—manually curated database of experimentally validated ligands for orphan nuclear receptors: insights into new drug discovery
Ravikanth Nanduri and others
Database, Volume 2015, 2015, bav112, https://doi.org/10.1093/database/bav112
SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications
Mir Asif Iquebal and others
Database, Volume 2015, 2015, bav111, https://doi.org/10.1093/database/bav111
Biocuration with insufficient resources and fixed timelines
Raul Rodriguez-Esteban
Database, Volume 2015, 2015, bav116, https://doi.org/10.1093/database/bav116

Reviews

Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges
Saikat Chowdhury and Ram Rup Sarkar
Database, Volume 2015, 2015, bau126, https://doi.org/10.1093/database/bau126

Database Update

SCAN database: facilitating integrative analyses of cytosine modification and expression QTL
Wei Zhang and others
Database, Volume 2015, 2015, bav025, https://doi.org/10.1093/database/bav025
An update of miRNASNP database for better SNP selection by GWAS data, miRNA expression and online tools
Jing Gong and others
Database, Volume 2015, 2015, bav029, https://doi.org/10.1093/database/bav029
ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection
Gaurav Sablok and others
Database, Volume 2015, 2015, bav084, https://doi.org/10.1093/database/bav084
Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources
Xiaobo Wang and others
Database, Volume 2015, 2015, bav093, https://doi.org/10.1093/database/bav093
HitPredict version 4: comprehensive reliability scoring of physical protein–protein interactions from more than 100 species
Yosvany López and others
Database, Volume 2015, 2015, bav117, https://doi.org/10.1093/database/bav117
LymPHOS 2.0: an update of a phosphosite database of primary human T cells
Tien Dung Nguyen and others
Database, Volume 2015, 2015, bav115, https://doi.org/10.1093/database/bav115

Corrigendum

Automated semantic annotation of rare disease cases: a case study
Maria Taboada and others
Database, Volume 2015, 2015, bav107, https://doi.org/10.1093/database/bav107
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