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Volume 2013
2013
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EISSN 1758-0463

Volume 2013, 2013

Original Articles

RefPrimeCouch—a reference gene primer CouchApp
Jascha Silbermann and others
Database, Volume 2013, 2013, bat081, https://doi.org/10.1093/database/bat081
A CTD–Pfizer collaboration: manual curation of 88 000 scientific articles text mined for drug–disease and drug–phenotype interactions
Allan Peter Davis and others
Database, Volume 2013, 2013, bat080, https://doi.org/10.1093/database/bat080
Chemical annotation of small and peptide-like molecules at the Protein Data Bank
Jasmine Y. Young and others
Database, Volume 2013, 2013, bat079, https://doi.org/10.1093/database/bat079
Addition of a breeding database in the Genome Database for Rosaceae
Kate Evans and others
Database, Volume 2013, 2013, bat078, https://doi.org/10.1093/database/bat078
CoIN: a network analysis for document triage
Yi-Yu Hsu and Hung-Yu Kao
Database, Volume 2013, 2013, bat076, https://doi.org/10.1093/database/bat076
HypoxiaDB: a database of hypoxia-regulated proteins
Pankaj Khurana and others
Database, Volume 2013, 2013, bat074, https://doi.org/10.1093/database/bat074
Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases
Lacey-Anne Sanderson and others
Database, Volume 2013, 2013, bat075, https://doi.org/10.1093/database/bat075
RAvariome: a genetic risk variants database for rheumatoid arthritis based on assessment of reproducibility between or within human populations
Yoko Nagai and Tadashi Imanishi
Database, Volume 2013, 2013, bat073, https://doi.org/10.1093/database/bat073
HTS-DB: an online resource to publish and query data from functional genomics high-throughput siRNA screening projects
Rebecca E. Saunders and others
Database, Volume 2013, 2013, bat072, https://doi.org/10.1093/database/bat072
Ureidoglycolate hydrolase, amidohydrolase, lyase: how errors in biological databases are incorporated in scientific papers and vice versa
Riccardo Percudani and others
Database, Volume 2013, 2013, bat071, https://doi.org/10.1093/database/bat071
yApoptosis: yeast apoptosis database
Kwanjeera Wanichthanarak and others
Database, Volume 2013, 2013, bat068, https://doi.org/10.1093/database/bat068
Capturing cooperative interactions with the PSI-MI format
Kim Van Roey and others
Database, Volume 2013, 2013, bat066, https://doi.org/10.1093/database/bat066
BioC: a minimalist approach to interoperability for biomedical text processing
Donald C. Comeau and others
Database, Volume 2013, 2013, bat064, https://doi.org/10.1093/database/bat064
Groups: knowledge spreadsheets for symbolic biocomputing
Michael Travers and others
Database, Volume 2013, 2013, bat061, https://doi.org/10.1093/database/bat061
IQdb: an intelligence quotient score-associated gene resource for human intelligence
Lei Kong and others
Database, Volume 2013, 2013, bat063, https://doi.org/10.1093/database/bat063
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort
Sushil Tripathi and others
Database, Volume 2013, 2013, bat062, https://doi.org/10.1093/database/bat062
metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research
Mike Lyne and others
Database, Volume 2013, 2013, bat060, https://doi.org/10.1093/database/bat060
BGDB: a database of bivalent genes
Qingyan Li and others
Database, Volume 2013, 2013, bat057, https://doi.org/10.1093/database/bat057
Rapid storage and retrieval of genomic intervals from a relational database system using nested containment lists
Laura K. Wiley and others
Database, Volume 2013, 2013, bat056, https://doi.org/10.1093/database/bat056
BmTEdb: a collective database of transposable elements in the silkworm genome
Hong-En Xu and others
Database, Volume 2013, 2013, bat055, https://doi.org/10.1093/database/bat055
JBioWH: an open-source Java framework for bioinformatics data integration
Roberto Vera and others
Database, Volume 2013, 2013, bat051, https://doi.org/10.1093/database/bat051
DoSA: Database of Structural Alignments
Swapnil Mahajan and others
Database, Volume 2013, 2013, bat048, https://doi.org/10.1093/database/bat048
lncRNome: a comprehensive knowledgebase of human long noncoding RNAs
Deeksha Bhartiya and others
Database, Volume 2013, 2013, bat034, https://doi.org/10.1093/database/bat034
A guide to best practices for Gene Ontology (GO) manual annotation
Rama Balakrishnan and others
Database, Volume 2013, 2013, bat054, https://doi.org/10.1093/database/bat054
DBATE: database of alternative transcripts expression
Valerio Bianchi and others
Database, Volume 2013, 2013, bat050, https://doi.org/10.1093/database/bat050
Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases
Julien Gobeill and others
Database, Volume 2013, 2013, bat041, https://doi.org/10.1093/database/bat041
Analysis of disease-associated objects at the Rat Genome Database
Shur-Jen Wang and others
Database, Volume 2013, 2013, bat046, https://doi.org/10.1093/database/bat046
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells
Huilei Xu and others
Database, Volume 2013, 2013, bat045, https://doi.org/10.1093/database/bat045
The CARLSBAD Database: A Confederated Database of Chemical Bioactivities
Stephen L. Mathias and others
Database, Volume 2013, 2013, bat044, https://doi.org/10.1093/database/bat044
Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint
Karen E. Ross and others
Database, Volume 2013, 2013, bat038, https://doi.org/10.1093/database/bat038
UMD-MLH1/MSH2/MSH6 databases: description and analysis of genetic variations in French Lynch syndrome families
Philippe Grandval and others
Database, Volume 2013, 2013, bat036, https://doi.org/10.1093/database/bat036
The non-obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes
Charles A. Steward and others
Database, Volume 2013, 2013, bat032, https://doi.org/10.1093/database/bat032
The Banana Genome Hub
Gaëtan Droc and others
Database, Volume 2013, 2013, bat035, https://doi.org/10.1093/database/bat035
Cataloging the biomedical world of pain through semi-automated curation of molecular interactions
Daniel G. Jamieson and others
Database, Volume 2013, 2013, bat033, https://doi.org/10.1093/database/bat033
From manual curation to visualization of gene families and networks across Solanaceae plant species
Anuradha Pujar and others
Database, Volume 2013, 2013, bat028, https://doi.org/10.1093/database/bat028
The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update
Ivan Sadowski and others
Database, Volume 2013, 2013, bat026, https://doi.org/10.1093/database/bat026
RiceSRTFDB: A database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis
Pushp Priya and Mukesh Jain
Database, Volume 2013, 2013, bat027, https://doi.org/10.1093/database/bat027
PhenoDigm: analyzing curated annotations to associate animal models with human diseases
Damian Smedley and others
Database, Volume 2013, 2013, bat025, https://doi.org/10.1093/database/bat025
PCorral—interactive mining of protein interactions from MEDLINE
Chen Li and others
Database, Volume 2013, 2013, bat030, https://doi.org/10.1093/database/bat030
The MetaboLights repository: curation challenges in metabolomics
Reza M. Salek and others
Database, Volume 2013, 2013, bat029, https://doi.org/10.1093/database/bat029
The Protein Model Portal—a comprehensive resource for protein structure and model information
Juergen Haas and others
Database, Volume 2013, 2013, bat031, https://doi.org/10.1093/database/bat031
The challenge of increasing Pfam coverage of the human proteome
Jaina Mistry and others
Database, Volume 2013, 2013, bat023, https://doi.org/10.1093/database/bat023
PhenoMiner: quantitative phenotype curation at the rat genome database
Stanley J F Laulederkind and others
Database, Volume 2013, 2013, bat015, https://doi.org/10.1093/database/bat015
Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts
Mariana Neves and others
Database, Volume 2013, 2013, bat020, https://doi.org/10.1093/database/bat020
Sequencing and comparative analysis of the gorilla MHC genomic sequence
Laurens G. Wilming and others
Database, Volume 2013, 2013, bat011, https://doi.org/10.1093/database/bat011
hLGDB: a database of human lysosomal genes and their regulation
Alessandro Brozzi and others
Database, Volume 2013, 2013, bat024, https://doi.org/10.1093/database/bat024
Identification and prioritization of novel uncharacterized peptidases for biochemical characterization
Neil D. Rawlings
Database, Volume 2013, 2013, bat022, https://doi.org/10.1093/database/bat022
A database for curating the associations between killer cell immunoglobulin-like receptors and diseases in worldwide populations
Louise Y. C. Takeshita and others
Database, Volume 2013, 2013, bat021, https://doi.org/10.1093/database/bat021
Annotating the biomedical literature for the human variome
Karin Verspoor and others
Database, Volume 2013, 2013, bat019, https://doi.org/10.1093/database/bat019
MalaCards: an integrated compendium for diseases and their annotation
Noa Rappaport and others
Database, Volume 2013, 2013, bat018, https://doi.org/10.1093/database/bat018
Towards the Collaborative Curation of the Registry underlying identifiers.org
Nick Juty and others
Database, Volume 2013, 2013, bat017, https://doi.org/10.1093/database/bat017
Biological Database of Images and Genomes: tools for community annotations linking image and genomic information
Andrew T Oberlin and others
Database, Volume 2013, 2013, bat016, https://doi.org/10.1093/database/bat016
curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome
Benjamin Frederick Ganzfried and others
Database, Volume 2013, 2013, bat013, https://doi.org/10.1093/database/bat013
The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database
Stacia R. Engel and J. Michael Cherry
Database, Volume 2013, 2013, bat012, https://doi.org/10.1093/database/bat012
Uncovering hidden duplicated content in public transcriptomics data
Marta Rosikiewicz and others
Database, Volume 2013, 2013, bat010, https://doi.org/10.1093/database/bat010
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary
Gerhard Mayer and others
Database, Volume 2013, 2013, bat009, https://doi.org/10.1093/database/bat009
YY1TargetDB: an integral information resource for Yin Yang 1 target loci
Andy M. Guo and others
Database, Volume 2013, 2013, bat007, https://doi.org/10.1093/database/bat007
T-HOD: a literature-based candidate gene database for hypertension, obesity and diabetes
Hong-Jie Dai and others
Database, Volume 2013, 2013, bas061, https://doi.org/10.1093/database/bas061
Using the OntoGene pipeline for the triage task of BioCreative 2012
Fabio Rinaldi and others
Database, Volume 2013, 2013, bas053, https://doi.org/10.1093/database/bas053
The YeastGenome app: the Saccharomyces Genome Database at your fingertips
Edith D. Wong and others
Database, Volume 2013, 2013, bat004, https://doi.org/10.1093/database/bat004
CrossTope: a curate repository of 3D structures of immunogenic peptide: MHC complexes
Marialva Sinigaglia and others
Database, Volume 2013, 2013, bat002, https://doi.org/10.1093/database/bat002
‘What’s in the NIDDK CDR?’—public query tools for the NIDDK central data repository
Huaqin Pan and others
Database, Volume 2013, 2013, bas058, https://doi.org/10.1093/database/bas058
Evidence classification of high-throughput protocols and confidence integration in RegulonDB
Verena Weiss and others
Database, Volume 2013, 2013, bas059, https://doi.org/10.1093/database/bas059
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans
Prudence Mutowo-Meullenet and others
Database, Volume 2013, 2013, bas062, https://doi.org/10.1093/database/bas062
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task
Cecilia N. Arighi and others
Database, Volume 2013, 2013, bas056, https://doi.org/10.1093/database/bas056
PPInterFinder—a mining tool for extracting causal relations on human proteins from literature
Kalpana Raja and others
Database, Volume 2013, 2013, bas052, https://doi.org/10.1093/database/bas052
The Xenbase literature curation process
Jeff B. Bowes and others
Database, Volume 2013, 2013, bas046, https://doi.org/10.1093/database/bas046
Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment
Matthew A. Bertone and others
Database, Volume 2013, 2013, bas057, https://doi.org/10.1093/database/bas057

Database Tool

Nencki Genomics Database—Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs
Izabella Krystkowiak and others
Database, Volume 2013, 2013, bat069, https://doi.org/10.1093/database/bat069
BBGRE: brain and body genetic resource exchange
Joo Wook Ahn and others
Database, Volume 2013, 2013, bat067, https://doi.org/10.1093/database/bat067
SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation
Damiano Piovesan and others
Database, Volume 2013, 2013, bat065, https://doi.org/10.1093/database/bat065
GnpIS: an information system to integrate genetic and genomic data from plants and fungi
Delphine Steinbach and others
Database, Volume 2013, 2013, bat058, https://doi.org/10.1093/database/bat058
CREDO: a structural interactomics database for drug discovery
Adrian M. Schreyer and Tom L. Blundell
Database, Volume 2013, 2013, bat049, https://doi.org/10.1093/database/bat049
MisPred: a resource for identification of erroneous protein sequences in public databases
Alinda Nagy and László Patthy
Database, Volume 2013, 2013, bat053, https://doi.org/10.1093/database/bat053
T2D@ZJU: a knowledgebase integrating heterogeneous connections associated with type 2 diabetes mellitus
Zhenzhong Yang and others
Database, Volume 2013, 2013, bat052, https://doi.org/10.1093/database/bat052
CHD@ZJU: a knowledgebase providing network-based research platform on coronary heart disease
Leihong Wu and others
Database, Volume 2013, 2013, bat047, https://doi.org/10.1093/database/bat047
GoSynthetic database tool to analyse natural and engineered molecular processes
Chunguang Liang and others
Database, Volume 2013, 2013, bat043, https://doi.org/10.1093/database/bat043
eFG: an electronic resource for Fusarium graminearum
Xiaoping Liu and others
Database, Volume 2013, 2013, bat042, https://doi.org/10.1093/database/bat042
FSRD: fungal stress response database
Zsolt Karányi and others
Database, Volume 2013, 2013, bat037, https://doi.org/10.1093/database/bat037
dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts
Jonathan Vincent and others
Database, Volume 2013, 2013, bat014, https://doi.org/10.1093/database/bat014
The Eimeria Transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria
Luiz Thibério Rangel and others
Database, Volume 2013, 2013, bat006, https://doi.org/10.1093/database/bat006
pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes
Wen-Ling Chan and others
Database, Volume 2013, 2013, bat001, https://doi.org/10.1093/database/bat001
PIPEMicroDB: microsatellite database and primer generation tool for pigeonpea genome
Sarika and others
Database, Volume 2013, 2013, bas054, https://doi.org/10.1093/database/bas054
bc-GenExMiner 3.0: new mining module computes breast cancer gene expression correlation analyses
Pascal Jézéquel and others
Database, Volume 2013, 2013, bas060, https://doi.org/10.1093/database/bas060

Database Update

Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content
Joseph A. Rothwell and others
Database, Volume 2013, 2013, bat070, https://doi.org/10.1093/database/bat070
Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance
Benjamin D. Heavner and others
Database, Volume 2013, 2013, bat059, https://doi.org/10.1093/database/bat059
TIMBAL v2: update of a database holding small molecules modulating protein–protein interactions
Alicia P. Higueruelo and others
Database, Volume 2013, 2013, bat039, https://doi.org/10.1093/database/bat039
TIARA genome database: update 2013
Dongwan Hong and others
Database, Volume 2013, 2013, bat003, https://doi.org/10.1093/database/bat003
Tetrahymena Functional Genomics Database (TetraFGD): an integrated resource for Tetrahymena functional genomics
Jie Xiong and others
Database, Volume 2013, 2013, bat008, https://doi.org/10.1093/database/bat008
The Annotation-enriched non-redundant patent sequence databases
Weizhong Li and others
Database, Volume 2013, 2013, bat005, https://doi.org/10.1093/database/bat005

Letter to the Editor

DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration
Pascale Gaudet and others
Database, Volume 2013, 2013, bat077, https://doi.org/10.1093/database/bat077

Corrigendum

The challenge of increasing Pfam coverage of the human proteome
Jaina Mistry and others
Database, Volume 2013, 2013, bat040, https://doi.org/10.1093/database/bat040
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