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Volume 2017
2017
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EISSN 1758-0463

Volume 2017, 2017

Original Article

The BioC-BioGRID corpus: full text articles annotated for curation of protein–protein and genetic interactions
Rezarta Islamaj Doğan and others
Database, Volume 2017, 2017, baw147, https://doi.org/10.1093/database/baw147
BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences
K.E. Ravikumar and others
Database, Volume 2017, 2017, baw156, https://doi.org/10.1093/database/baw156
Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study
Qingyu Chen and others
Database, Volume 2017, 2017, baw163, https://doi.org/10.1093/database/baw163
FARME DB: a functional antibiotic resistance element database
James C. Wallace and others
Database, Volume 2017, 2017, baw165, https://doi.org/10.1093/database/baw165
Automatic query generation using word embeddings for retrieving passages describing experimental methods
Ferhat Aydın and others
Database, Volume 2017, 2017, baw166, https://doi.org/10.1093/database/baw166
RAIN: RNA–protein Association and Interaction Networks
Alexander Junge and others
Database, Volume 2017, 2017, baw167, https://doi.org/10.1093/database/baw167
KTCNlncDB—a first platform to investigate lncRNAs expressed in human keratoconus and non-keratoconus corneas
Michał W. Szcześniak and others
Database, Volume 2017, 2017, baw168, https://doi.org/10.1093/database/baw168
VerSeDa: vertebrate secretome database
Ana R. Cortazar and others
Database, Volume 2017, 2017, baw171, https://doi.org/10.1093/database/baw171
OCaPPI-Db: an oligonucleotide probe database for pathogen identification through hybridization capture
Cyrielle Gasc and others
Database, Volume 2017, 2017, baw172, https://doi.org/10.1093/database/baw172
SilkPathDB: a comprehensive resource for the study of silkworm pathogens
Tian Li and others
Database, Volume 2017, 2017, bax001, https://doi.org/10.1093/database/bax001
Outreach and online training services at the Saccharomyces Genome Database
Kevin A. MacPherson and others
Database, Volume 2017, 2017, bax002, https://doi.org/10.1093/database/bax002
Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects
Anton Güntsch and others
Database, Volume 2017, 2017, bax003, https://doi.org/10.1093/database/bax003
Carotenoids Database: structures, chemical fingerprints and distribution among organisms
Junko Yabuzaki
Database, Volume 2017, 2017, bax004, https://doi.org/10.1093/database/bax004
Biocuration in the structure–function linkage database: the anatomy of a superfamily
Gemma L. Holliday and others
Database, Volume 2017, 2017, bax006, https://doi.org/10.1093/database/bax006
Workflow and web application for annotating NCBI BioProject transcriptome data
Roberto Vera Alvarez and others
Database, Volume 2017, 2017, bax008, https://doi.org/10.1093/database/bax008
HopBase: a unified resource for Humulus genomics
Steven T. Hill and others
Database, Volume 2017, 2017, bax009, https://doi.org/10.1093/database/bax009
The ‘straight mouse’: defining anatomical axes in 3D embryo models
Chris Armit and others
Database, Volume 2017, 2017, bax010, https://doi.org/10.1093/database/bax010
Curated protein information in the Saccharomyces genome database
Sage T. Hellerstedt and others
Database, Volume 2017, 2017, bax011, https://doi.org/10.1093/database/bax011
Strategies towards digital and semi-automated curation in RegulonDB
Fabio Rinaldi and others
Database, Volume 2017, 2017, bax012, https://doi.org/10.1093/database/bax012
Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD)
Xiangying Jiang and others
Database, Volume 2017, 2017, bax017, https://doi.org/10.1093/database/bax017
AnnoSys—implementation of a generic annotation system for schema-based data using the example of biodiversity collection data
L. Suhrbier and others
Database, Volume 2017, 2017, bax018, https://doi.org/10.1093/database/bax018
Exploring convolutional neural networks for drug–drug interaction extraction
Víctor Suárez-Paniagua and others
Database, Volume 2017, 2017, bax019, https://doi.org/10.1093/database/bax019
Literature consistency of bioinformatics sequence databases is effective for assessing record quality
Mohamed Reda Bouadjenek and others
Database, Volume 2017, 2017, bax021, https://doi.org/10.1093/database/bax021
TMPL: a database of experimental and theoretical transmembrane protein models positioned in the lipid bilayer
Guillaume Postic and others
Database, Volume 2017, 2017, bax022, https://doi.org/10.1093/database/bax022
ABCMdb reloaded: updates on mutations in ATP binding cassette proteins
Hedvig Tordai and others
Database, Volume 2017, 2017, bax023, https://doi.org/10.1093/database/bax023
Chemical-induced disease relation extraction via convolutional neural network
Jinghang Gu and others
Database, Volume 2017, 2017, bax024, https://doi.org/10.1093/database/bax024
WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata
Tim E. Putman and others
Database, Volume 2017, 2017, bax025, https://doi.org/10.1093/database/bax025
NaviCom: a web application to create interactive molecular network portraits using multi-level omics data
Mathurin Dorel and others
Database, Volume 2017, 2017, bax026, https://doi.org/10.1093/database/bax026
Automated PDF highlighting to support faster curation of literature for Parkinson’s and Alzheimer’s disease
Honghan Wu and others
Database, Volume 2017, 2017, bax027, https://doi.org/10.1093/database/bax027
GeneHancer: genome-wide integration of enhancers and target genes in GeneCards
Simon Fishilevich and others
Database, Volume 2017, 2017, bax028, https://doi.org/10.1093/database/bax028
Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis
Yalbi Itzel Balderas-Martínez and others
Database, Volume 2017, 2017, bax030, https://doi.org/10.1093/database/bax030
Surveying the Maize community for their diversity and pedigree visualization needs to prioritize tool development and curation
Taner Z. Sen and others
Database, Volume 2017, 2017, bax031, https://doi.org/10.1093/database/bax031
Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community
Surya Saha and others
Database, Volume 2017, 2017, bax032, https://doi.org/10.1093/database/bax032
TriatoKey: a web and mobile tool for biodiversity identification of Brazilian triatomine species
Luciana Márcia de Oliveira and others
Database, Volume 2017, 2017, bax033, https://doi.org/10.1093/database/bax033
In silico characterization of tandem repeats in Trichophyton rubrum and related dermatophytes provides new insights into their role in pathogenesis
Matheus Eloy Franco and others
Database, Volume 2017, 2017, bax035, https://doi.org/10.1093/database/bax035
BioM2MetDisease: a manually curated database for associations between microRNAs, metabolites, small molecules and metabolic diseases
Yanjun Xu and others
Database, Volume 2017, 2017, bax037, https://doi.org/10.1093/database/bax037
Triage by ranking to support the curation of protein interactions
Luc Mottin and others
Database, Volume 2017, 2017, bax040, https://doi.org/10.1093/database/bax040
decodeRNA— predicting non-coding RNA functions using guilt-by-association
Steve Lefever and others
Database, Volume 2017, 2017, bax042, https://doi.org/10.1093/database/bax042
Text mining and expert curation to develop a database on psychiatric diseases and their genes
Alba Gutiérrez-Sacristán and others
Database, Volume 2017, 2017, bax043, https://doi.org/10.1093/database/bax043
PigVar: a database of pig variations and positive selection signatures
Zhong-Yin Zhou and others
Database, Volume 2017, 2017, bax048, https://doi.org/10.1093/database/bax048
Benchmarking distributed data warehouse solutions for storing genomic variant information
Marek S. Wiewiórka and others
Database, Volume 2017, 2017, bax049, https://doi.org/10.1093/database/bax049
CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network
Bülent Arman Aksoy and others
Database, Volume 2017, 2017, bax054, https://doi.org/10.1093/database/bax054
Elsevier’s approach to the bioCADDIE 2016 Dataset Retrieval Challenge
Antony Scerri and others
Database, Volume 2017, 2017, bax056, https://doi.org/10.1093/database/bax056
BioSearch: a semantic search engine for Bio2RDF
Wei Hu and others
Database, Volume 2017, 2017, bax059, https://doi.org/10.1093/database/bax059
A RESTful application programming interface for the PubMLST molecular typing and genome databases
Keith A. Jolley and others
Database, Volume 2017, 2017, bax060, https://doi.org/10.1093/database/bax060
A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge
Trevor Cohen and others
Database, Volume 2017, 2017, bax061, https://doi.org/10.1093/database/bax061
Multi-field query expansion is effective for biomedical dataset retrieval
Mohamed Reda Bouadjenek and Karin Verspoor
Database, Volume 2017, 2017, bax062, https://doi.org/10.1093/database/bax062
KiPho: malaria parasite kinome and phosphatome portal
Rajan Pandey and others
Database, Volume 2017, 2017, bax063, https://doi.org/10.1093/database/bax063
Impact of translation on named-entity recognition in radiology texts
Luís Campos and others
Database, Volume 2017, 2017, bax064, https://doi.org/10.1093/database/bax064
Query expansion using MeSH terms for dataset retrieval: OHSU at the bioCADDIE 2016 dataset retrieval challenge
Theodore B Wright and others
Database, Volume 2017, 2017, bax065, https://doi.org/10.1093/database/bax065
AllerBase: a comprehensive allergen knowledgebase
Kiran Kadam and others
Database, Volume 2017, 2017, bax066, https://doi.org/10.1093/database/bax066
RampDB: a web application and database for the exploration and prediction of receptor activity modifying protein interactions
Nadav Topaz and others
Database, Volume 2017, 2017, bax067, https://doi.org/10.1093/database/bax067
First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes
Carlos-Francisco Méndez-Cruz and others
Database, Volume 2017, 2017, bax070, https://doi.org/10.1093/database/bax070
Improving taxonomic accuracy for fungi in public sequence databases: applying ‘one name one species’ in well-defined genera with Trichoderma/Hypocrea as a test case
Barbara Robbertse and others
Database, Volume 2017, 2017, bax072, https://doi.org/10.1093/database/bax072
An online analytical processing multi-dimensional data warehouse for malaria data
S M Niaz Arifin and others
Database, Volume 2017, 2017, bax073, https://doi.org/10.1093/database/bax073
FishTrace: a genetic catalogue of European fishes
Antonella Zanzi and Jann Th Martinsohn
Database, Volume 2017, 2017, bax075, https://doi.org/10.1093/database/bax075
Database of resistance related metabolites in Wheat Fusarium head blight Disease (MWFD)
Anuradha Surendra and Miroslava Cuperlovic-Culf
Database, Volume 2017, 2017, bax076, https://doi.org/10.1093/database/bax076
In-Cardiome: integrated knowledgebase for coronary artery disease enabling translational research
Ankit Sharma and others
Database, Volume 2017, 2017, bax077, https://doi.org/10.1093/database/bax077
Proficiency of data interpretation: identification of signaling SNPs/specific loci for coronary artery disease
Asma N Cheema and others
Database, Volume 2017, 2017, bax078, https://doi.org/10.1093/database/bax078
eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality
Ruoyao Ding and others
Database, Volume 2017, 2017, bax081, https://doi.org/10.1093/database/bax081
Biomarker identification of hepatocellular carcinoma using a methodical literature mining strategy
Nai-Wen Chang and others
Database, Volume 2017, 2017, bax082, https://doi.org/10.1093/database/bax082
Improving average ranking precision in user searches for biomedical research datasets
Douglas Teodoro and others
Database, Volume 2017, 2017, bax083, https://doi.org/10.1093/database/bax083
DLREFD: a database providing associations of long non-coding RNAs, environmental factors and phenotypes
Ya-Zhou Sun and others
Database, Volume 2017, 2017, bax084, https://doi.org/10.1093/database/bax084
YGMD: a repository for yeast cooperative transcription factor sets and their target gene modules
Wei-Sheng Wu and others
Database, Volume 2017, 2017, bax085, https://doi.org/10.1093/database/bax085
Gold-standard ontology-based anatomical annotation in the CRAFT Corpus
Michael Bada and others
Database, Volume 2017, 2017, bax087, https://doi.org/10.1093/database/bax087
A semantic-based workflow for biomedical literature annotation
Pedro Sernadela and José Luís Oliveira
Database, Volume 2017, 2017, bax088, https://doi.org/10.1093/database/bax088
Collaborative relation annotation and quality analysis in Markyt environment
Martín Pérez-Pérez and others
Database, Volume 2017, 2017, bax090, https://doi.org/10.1093/database/bax090
Leveraging word embeddings and medical entity extraction for biomedical dataset retrieval using unstructured texts
Yanshan Wang and others
Database, Volume 2017, 2017, bax091, https://doi.org/10.1093/database/bax091
Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research
Tasnia Tahsin and others
Database, Volume 2017, 2017, bax093, https://doi.org/10.1093/database/bax093
HisgAtlas 1.0: a human immunosuppression gene database
Yuan Liu and others
Database, Volume 2017, 2017, bax094, https://doi.org/10.1093/database/bax094
GRONS: a comprehensive genetic resource of nicotine and smoking
Zhonghai Fang and others
Database, Volume 2017, 2017, bax097, https://doi.org/10.1093/database/bax097
PCOSBase: a manually curated database of polycystic ovarian syndrome
Nor Afiqah-Aleng and others
Database, Volume 2017, 2017, bax098, https://doi.org/10.1093/database/bax098

Technical Report

blend4php: a PHP API for galaxy
Connor Wytko and others
Database, Volume 2017, 2017, baw154, https://doi.org/10.1093/database/baw154
CHOmine: an integrated data warehouse for CHO systems biology and modeling
Matthias P. Gerstl and others
Database, Volume 2017, 2017, bax034, https://doi.org/10.1093/database/bax034
Edaphostat: interactive ecological analysis of soil organism occurrences and preferences from the Edaphobase data warehouse
Jonas Hausen and others
Database, Volume 2017, 2017, bax080, https://doi.org/10.1093/database/bax080

Database Tool

MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota
Aitor Blanco-Míguez and others
Database, Volume 2017, 2017, baw157, https://doi.org/10.1093/database/baw157
FirebrowseR: an R client to the Broad Institute’s Firehose Pipeline
Mario Deng and others
Database, Volume 2017, 2017, baw160, https://doi.org/10.1093/database/baw160
Boechera microsatellite website: an online portal for species identification and determination of hybrid parentage
Fay-Wei Li and others
Database, Volume 2017, 2017, baw169, https://doi.org/10.1093/database/baw169
PCPPI: a comprehensive database for the prediction of Penicillium–crop protein–protein interactions
Junyang Yue and others
Database, Volume 2017, 2017, baw170, https://doi.org/10.1093/database/baw170
The HIV oligonucleotide database (HIVoligoDB)
João Carneiro and others
Database, Volume 2017, 2017, bax005, https://doi.org/10.1093/database/bax005
GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii)
Zhenzhen Xu and others
Database, Volume 2017, 2017, bax013, https://doi.org/10.1093/database/bax013
miRnalyze: an interactive database linking tool to unlock intuitive microRNA regulation of cell signaling pathways
Sankha Subhra Das and others
Database, Volume 2017, 2017, bax015, https://doi.org/10.1093/database/bax015
GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species
Richard J. Challis and others
Database, Volume 2017, 2017, bax039, https://doi.org/10.1093/database/bax039
TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species
Sony Malhotra and others
Database, Volume 2017, 2017, bax041, https://doi.org/10.1093/database/bax041
NutriChem 2.0: exploring the effect of plant-based foods on human health and drug efficacy
Yueqiong Ni and others
Database, Volume 2017, 2017, bax044, https://doi.org/10.1093/database/bax044
MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data
Max Ruas and others
Database, Volume 2017, 2017, bax046, https://doi.org/10.1093/database/bax046
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis
Felipe Torres and others
Database, Volume 2017, 2017, bax047, https://doi.org/10.1093/database/bax047
The Grass Carp Genome Database (GCGD): an online platform for genome features and annotations
Yaxin Chen and others
Database, Volume 2017, 2017, bax051, https://doi.org/10.1093/database/bax051
New extension software modules to enhance searching and display of transcriptome data in Tripal databases
Ming Chen and others
Database, Volume 2017, 2017, bax052, https://doi.org/10.1093/database/bax052
Cancer Odor Database (COD): a critical databank for cancer diagnosis research
Sajjad Janfaza and others
Database, Volume 2017, 2017, bax055, https://doi.org/10.1093/database/bax055
NRDTD: a database for clinically or experimentally supported non-coding RNAs and drug targets associations
Xing Chen and others
Database, Volume 2017, 2017, bax057, https://doi.org/10.1093/database/bax057
RegulatorDB: a resource for the analysis of yeast transcriptional regulation
John A. Choi and John J. Wyrick
Database, Volume 2017, 2017, bax058, https://doi.org/10.1093/database/bax058
IsoPlot: a database for comparison of mRNA isoforms in fruit fly and mosquitoes
I-Man Ng and others
Database, Volume 2017, 2017, bax069, https://doi.org/10.1093/database/bax069
EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species
Leandro Costa Nascimento and others
Database, Volume 2017, 2017, bax079, https://doi.org/10.1093/database/bax079
PlantCircNet: a database for plant circRNA–miRNA–mRNA regulatory networks
Peijing Zhang and others
Database, Volume 2017, 2017, bax089, https://doi.org/10.1093/database/bax089
Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases
Sook Jung and others
Database, Volume 2017, 2017, bax092, https://doi.org/10.1093/database/bax092
PTS: a pharmaceutical target seeker
Peng Ding and others
Database, Volume 2017, 2017, bax095, https://doi.org/10.1093/database/bax095

Erratum

RAIN: RNA–protein Association and Interaction Networks
Database, Volume 2017, 2017, bax007, https://doi.org/10.1093/database/bax007
Strategies towards digital and semi-automated curation in RegulonDB
Fabio Rinaldi and others
Database, Volume 2017, 2017, bax012, https://doi.org/10.1093/database/bax029

Meeting Report

Better living through ontologies at the Immune Epitope Database
Randi Vita and others
Database, Volume 2017, 2017, bax014, https://doi.org/10.1093/database/bax014

Database Update

MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups
Simon Jon McIlroy and others
Database, Volume 2017, 2017, bax016, https://doi.org/10.1093/database/bax016
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation
Magali Ruffier and others
Database, Volume 2017, 2017, bax020, https://doi.org/10.1093/database/bax020
RetrogeneDB–a database of plant and animal retrocopies
Wojciech Rosikiewicz and others
Database, Volume 2017, 2017, bax038, https://doi.org/10.1093/database/bax038
MiRIAD update: using alternative polyadenylation, protein interaction network analysis and additional species to enhance exploration of the role of intragenic miRNAs and their host genes
Ludwig C. Hinske and others
Database, Volume 2017, 2017, bax053, https://doi.org/10.1093/database/bax053
SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets
Jin Li and others
Database, Volume 2017, 2017, bax071, https://doi.org/10.1093/database/bax071
Echinobase: an expanding resource for echinoderm genomic information
Parul Kudtarkar and R. Andrew Cameron
Database, Volume 2017, 2017, bax074, https://doi.org/10.1093/database/bax074
Update notifications for the BioCyc collection of databases
Suzanne Paley and Peter D Karp
Database, Volume 2017, 2017, bax086, https://doi.org/10.1093/database/bax086

Corrigendum

AnnoSys—implementation of a generic annotation system for schema-based data using the example of biodiversity collection data
L. Suhrbier and others
Database, Volume 2017, 2017, bax036, https://doi.org/10.1093/database/bax036
Biocuration in the structure–function linkage database: the anatomy of a superfamily
Gemma L. Holliday and others
Database, Volume 2017, 2017, bax045, https://doi.org/10.1093/database/bax045
MGFD: the maize gene families database
Lei Sheng and others
Database, Volume 2017, 2017, bax050, https://doi.org/10.1093/database/bax050

Perspective/Opinion

Information retrieval for biomedical datasets: the 2016 bioCADDIE dataset retrieval challenge
Kirk Roberts and others
Database, Volume 2017, 2017, bax068, https://doi.org/10.1093/database/bax068
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