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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, Maria-Esther Vidal, Eric Haag, Louiqa Raschid, Andreas Thor
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, Xiaojing Ma, Rongjun Ban, Qianli Huang, Wenjie Wang, Jia Liu, Yongsheng Liu
Database, Volume 2015, 2015, bav002, https://doi.org/10.1093/database/bav002
LocSigDB: a database of protein localization signals
Simarjeet Negi, Sanjit Pandey, Satish M. Srinivasan, Akram Mohammed, Chittibabu Guda
Database, Volume 2015, 2015, bav003, https://doi.org/10.1093/database/bav003
MnTEdb, a collective resource for mulberry transposable elements
Bi Ma, Tian Li, Zhonghuai Xiang, Ningjia He
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, Sebastian Köhler, Sandra Doelken, Nigel Collier, Anika Oellrich, Damian Smedley, Francisco M Couto, Gareth Baynam, Andreas Zankl, Peter N. Robinson
Database, Volume 2015, 2015, bav005, https://doi.org/10.1093/database/bav005
PathCards: multi-source consolidation of human biological pathways
Frida Belinky, Noam Nativ, Gil Stelzer, Shahar Zimmerman, Tsippi Iny Stein, Marilyn Safran, Doron Lancet
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, Xiaoman Li, Haiyan Hu
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, Zhiming Dai, Xiaowei Xie, Xuyang Feng, Dan Liu, Zhou Songyang, Yuanyan Xiong
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, Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Jennifer R. Smith, Jeff De Pons, Melinda R. Dwinell, Mary Shimoyama
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, R. C. Jiménez, P. Porras, N. del-Toro, M. Duesbury, M. Dumousseau, S. Orchard, H. Choi, P. Ping, N. C. Zong, M. Askenazi, B. H. Habermann, Henning Hermjakob
Database, Volume 2015, 2015, bau131, https://doi.org/10.1093/database/bau131
The Listeria monocytogenes strain 10403S BioCyc database
Renato H. Orsi, Teresa M. Bergholz, Martin Wiedmann, Kathryn J. Boor
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, Hayley Dingerdissen, Yu Fan, Naila Gulzar, Yang Pan, Tsung-Jung Wu, Cheng Yan, Haichen Zhang, Raja Mazumder
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, Lynn M. Schriml, Qing-Rong Chen, Maureen Colbert, Daniel J. Crichton, Richard Finney, Ying Hu, Warren A. Kibbe, Heather Kincaid, Daoud Meerzaman, Elvira Mitraka, Yang Pan, Krista M. Smith, Sudhir Srivastava, Sari Ward, Cheng Yan, Raja Mazumder
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, Daniel González Peña, Gonzalo Gómez-López, David G. Pisano
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, Núria Queralt-Rosinach, Àlex Bravo, Jordi Deu-Pons, Anna Bauer-Mehren, Martin Baron, Ferran Sanz, Laura I. Furlong
Database, Volume 2015, 2015, bav028, https://doi.org/10.1093/database/bav028
ProtoBug: functional families from the complete proteomes of insects
Nadav Rappoport, Michal Linial
Database, Volume 2015, 2015, bau122, https://doi.org/10.1093/database/bau122
NeuroPep: a comprehensive resource of neuropeptides
Yan Wang, Mingxia Wang, Sanwen Yin, Richard Jang, Jian Wang, Zhidong Xue, Tao Xu
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, Kenneth Bryan, Fiona S. L. Brinkman, David J. Lynn
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, Kai C. Bader, Manuel Spannagl, Yu Wang, Eva Bauer, Chris-Carolin Schön, Klaus F. X. Mayer
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, Marilena M. Bourdakou, Emmanouil I. Athanasiadis, George M. Spyrou
Database, Volume 2015, 2015, bav048, https://doi.org/10.1093/database/bav048
HCSD: the human cancer secretome database
Amir Feizi, Amir Banaei-Esfahani, Jens Nielsen
Database, Volume 2015, 2015, bav051, https://doi.org/10.1093/database/bav051
Drug-Path: a database for drug-induced pathways
Hui Zeng, Chengxiang Qiu, Qinghua Cui
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, Yaseswini Neelamraju, Sarath Chandra Janga
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, Rosario Distefano, Hugo A. Wefer, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno
Database, Volume 2015, 2015, bav069, https://doi.org/10.1093/database/bav069
MESSI: metabolic engineering target selection and best strain identification tool
Kang Kang, Jun Li, Boon Leong Lim, Gianni Panagiotou
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, Aamir W. Khan, Mohan A. V. S. K Katta, Gaurav Agarwal, Mahendar Thudi, Pradeep Ruperao, David Edwards, Rajeev K. Varshney
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, A.N. Kondakova, Ph.V. Toukach
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, Jing Bai, Aiwei Wu, Yuan Wang, Jinwen Zhang, Zishan Wang, Yongsheng Li, Juan Xu, Xia Li
Database, Volume 2015, 2015, bav082, https://doi.org/10.1093/database/bav082
CRCDA—Comprehensive resources for cancer NGS data analysis
Manonanthini Thangam, 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, 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, Luiz M. R. Gadelha, Jr, Ronaldo Bastos Francini-Filho, Rodrigo Leão de Moura, Gilberto Menezes Amado-Filho, Alex Cardoso Bastos, Rodolfo Pinheiro da Rocha Paranhos, Carlos Eduardo Rezende, Jean Swings, Eduardo Siegle, Nils Edvin Asp Neto, Sigrid Neumann Leitão, Ricardo Coutinho, Marta Mattoso, Paulo S. Salomon, Rogério A.B. Valle, Renato Crespo Pereira, Ricardo Henrique Kruger, Cristiane Thompson, Fabiano L. Thompson
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, Sherman W. Jack, Halid Kirunda, Margaret L. Khaitsa, Mark L. Lawrence, Stephen Pruett, Daniel G. Peterson
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, Carlos Vargas-Chávez, Amparo Latorre, Andrés Moya
Database, Volume 2015, 2015, bav109, https://doi.org/10.1093/database/bav109
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics
Junyang Yue, Jian Liu, Rongjun Ban, Wei Tang, Lin Deng, Zhangjun Fei, Yongsheng Liu
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, Samuel Bosch, Lennert Tyberghein, Filip Waumans, Bart Vanhoorne, Francisco Hernandez, Olivier De Clerck, Jan Mees
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, Jie Feng, Tao Li, Feng Ge, Jindong Zhao
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, Stanley J. F. Laulederkind, G. Thomas Hayman, Victoria Petri, Weisong Liu, Jennifer R. Smith, Rajni Nigam, Melinda R. Dwinell, Mary Shimoyama
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, Ramona Walls, Jacob Parnell, Rachel Gallery, Jie Zheng, Susanna-Assunta Sansone, Alejandra Gonzalez-Beltran
Database, Volume 2015, 2015, bau132, https://doi.org/10.1093/database/bau132
EcoliNet: a database of cofunctional gene network for Escherichia coli
Hanhae Kim, Jung Eun Shim, Junha Shin, Insuk Lee
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, Olaf Wolkenhauer, Dagmar Waltemath
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, Erin McDonnell, Carol Nyaga, Min Wu, Sherry Wu, Hayda Almeida, Marie-Jean Meurs, Leila Kosseim, Justin Powlowski, Greg Butler, Adrian Tsang
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, Noreen R. Gonzales, Shennan Lu, Jane He, Gabriele H. Marchler, Zhouxi Wang, Aron Marchler-Bauer
Database, Volume 2015, 2015, bav012, https://doi.org/10.1093/database/bav012
Shared resources, shared costs—leveraging biocuration resources
Sandra Orchard, 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, Drew T. Erickson, Nikhil R. Podduturi, Laurence D. Rowe, Esther T. Chan, Jean M. Davidson, Benjamin C. Hitz, Marcus Ho, Brian T. Lee, Stuart Miyasato, Gregory R. Roe, Matt Simison, Cricket A. Sloan, J. Seth Strattan, Forrest Tanaka, W. James Kent, J. Michael Cherry, Eurie L. Hong
Database, Volume 2015, 2015, bav010, https://doi.org/10.1093/database/bav010
RNABP COGEST: a resource for investigating functional RNAs
Sohini Bhattacharya, Shriyaa Mittal, Swati Panigrahi, Purshotam Sharma, Preethi S. P., Rahul Paul, Sukanya Halder, Antarip Halder, Dhananjay Bhattacharyya, Abhijit Mitra
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, Isha Bhutani, Kamal Jain, Pawan Gupta, Debendra K. Sahoo, Raman Parkesh
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, Tanmoy Jana, Sudipto Saha
Database, Volume 2015, 2015, bav014, https://doi.org/10.1093/database/bav014
Scaling drug indication curation through crowdsourcing
Ritu Khare, John D. Burger, John S. Aberdeen, David W. Tresner-Kirsch, Theodore J. Corrales, Lynette Hirchman, Zhiyong Lu
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, Tao Ke, Sadia Tehrim, Fengming Sun, Boshou Liao, Wei Hua
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, Jingchun Sun, W. Jim Zheng, Junjie Chen, Hua Xu
Database, Volume 2015, 2015, bav015, https://doi.org/10.1093/database/bav015
Standard development at the Human Variome Project
Timothy D. Smith, Mauno Vihinen
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, Jiao Deng, Rebecca Njeri Damaris, Mei Yang, Liming Xu, Pingfang Yang
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, Sungyong You, Do Young Hyeon, Byeongsoo Kang, Hyerim Kim, Kyoung Mii Park, Byungwoo Han, Daehee Hwang, Sunghoon Kim
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, Karen E. Ross, Gang Li, K. Vijay-Shanker, Cathy H. Wu, Cecilia N. Arighi
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, Nishita Mohan, Tom L. Blundell
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, Wydemberg Araújo, Ana Isabela Lopes Sales, Alaine de Brito Guerra, Sinara Carla da Silva Araújo, Ana Tereza Ribeiro de Vasconcelos, Lucymara F. Agnez-Lima, Ana Teresa Freitas
Database, Volume 2015, 2015, bav033, https://doi.org/10.1093/database/bav033
dbPSP: a curated database for protein phosphorylation sites in prokaryotes
Zhicheng Pan, Bangshan Wang, Ying Zhang, Yongbo Wang, Shahid Ullah, Ren Jian, Zexian Liu, Yu Xue
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, Jieyi Zhao, Trevor Cohen, Cui Tao, Jingchun Sun, Hua Xu, Elmer V. Bernstam, Andrew Lawson, Jia Zeng, Amber M. Johnson, Vijaykumar Holla, Ann M. Bailey, Humberto Lara-Guerra, Beate Litzenburger, Funda Meric-Bernstam, W. Jim Zheng
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, Marja Talikka, Jurjen Willem Westra, William Hayes, Anselmo Di Fabio, Jennifer Park, Walter K. Schlage, Alain Sewer, Brett Fields, Sam Ansari, Florian Martin, Emilija Veljkovic, Renee Kenney, Manuel C. Peitsch, Julia Hoeng
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, Mohieddin Jafari, Shiva Kalantari
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, Bo Xu, Yifan Yang, Rongjun Ban, Furhan Iqbal, Howard J Cooke, Yuanwei Zhang, Qinghua Shi
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, Debasisa Mohanty
Database, Volume 2015, 2015, bav039, https://doi.org/10.1093/database/bav039
GBIS: the information system of the German Genebank
Markus Oppermann, Stephan Weise, Claudia Dittmann, Helmut Knüpffer
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, Gilbert S. Omenn, Yuanfang Guan
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, Marcus C. Chibucos, Pascale Gaudet, Michelle Giglio, Gemma L. Holliday, Hong Huang, Suzanna E. Lewis, Anne Niknejad, Sandra Orchard, Sylvain Poux, Nives Skunca, Marc Robinson-Rechavi
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, T. Alexander Dececchi, Nizar Ibrahim, Hilmar Lapp, Paula Mabee
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, Yi-Fan Chiang-Hsieh, Yi-An Chen, Chi-Nga Chow, Nai-Yun Wu, Ping-Fu Hou, Wen-Chi Chang
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, Huayan Gao, Sizhe Xiao, Jinyue Liao, Daxi Wang, Jiajie Tu, Owen M. Rennert, Wai-Yee Chan, Tin-Lap Lee
Database, Volume 2015, 2015, bav044, https://doi.org/10.1093/database/bav044
GraP: platform for functional genomics analysis of Gossypium raimondii
Liwei Zhang, Jinyan Guo, Qi You, Xin Yi, Yi Ling, Wenying Xu, Jinping Hua, Zhen Su
Database, Volume 2015, 2015, bav047, https://doi.org/10.1093/database/bav047
An Ebola virus-centered knowledge base
Maulik R. Kamdar, 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, Fabian Müller, Karl Nordström, Thomas Lengauer, Marcel H. Schulz
Database, Volume 2015, 2015, bav050, https://doi.org/10.1093/database/bav050
dbHiMo: a web-based epigenomics platform for histone-modifying enzymes
Jaeyoung Choi, Ki-Tae Kim, Aram Huh, Seomun Kwon, Changyoung Hong, Fred O. Asiegbu, Junhyun Jeon, Yong-Hwan Lee
Database, Volume 2015, 2015, bav052, https://doi.org/10.1093/database/bav052
kpath: integration of metabolic pathway linked data
Ismael Navas-Delgado, María Jesús García-Godoy, Esteban López-Camacho, Maciej Rybinski, Armando Reyes-Palomares, Miguel Ángel Medina, José F. Aldana-Montes
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, Ben W. Price, S. D. Rycroft, Jon Hill, Vincent S. Smith
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, Pururawa Mayank Chaubey, György Várady, Edit Szabó, Hajnalka Sarankó, Lia Hofstetter, Bernd Roschitzki, Bruno Stieger, Balázs Sarkadi
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, Sam Ansari, Sumit Madan, Juliane Fluck, Marja Talikka, Anita Iskandar, Hector De Leon, Martin Hofmann-Apitius, Manuel C. Peitsch, Julia Hoeng
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, Louis Cronje, Oliver Bezuidt, Oleg N. Reva
Database, Volume 2015, 2015, bav058, https://doi.org/10.1093/database/bav058
G4RNA: an RNA G-quadruplex database
Jean-Michel Garant, Mikael J. Luce, Michelle S. Scott, Jean-Pierre Perreault
Database, Volume 2015, 2015, bav059, https://doi.org/10.1093/database/bav059
CrisprGE: a central hub of CRISPR/Cas-based genome editing
Karambir Kaur, Himani Tandon, Amit Kumar Gupta, Manoj Kumar
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, Aaron Marc Saunders, Mads Albertsen, Marta Nierychlo, Bianca McIlroy, Aviaja Anna Hansen, Søren Michael Karst, Jeppe Lund Nielsen, Per Halkjær Nielsen
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, Xiaotian Lu, Ziding Zhang
Database, Volume 2015, 2015, bav064, https://doi.org/10.1093/database/bav064
SInCRe—structural interactome computational resource for Mycobacterium tuberculosis
Rahul Metri, Sridhar Hariharaputran, Gayatri Ramakrishnan, Praveen Anand, Upadhyayula S. Raghavender, Bernardo Ochoa-Montaño, Alicia P. Higueruelo, Ramanathan Sowdhamini, Nagasuma R. Chandra, Tom L. Blundell, Narayanaswamy Srinivasan
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, Matthew McKnight Croken, Kevin R. Shieh, Julie Sullivan, Gos Micklem, Kami Kim, Aaron Golden
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, Pierre M. Durand, Scott Hazelhurst
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, Andreas Lennartsson, Rezvan Ehsani, Ivan V. Kulakovskiy, Ilya E. Vorontsov, Pouda Panahandeh, Grigory Khimulya, Takeya Kasukawa, The FANTOM Consortium, Finn Drabløs
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, Pantelis G. Bagos, Amos Bairoch, Alex Bateman, Arnaud Chatonnet, Mark Jinan Chen, David J. Craik, Robert D. Finn, David Gloriam, Daniel H. Haft, Bernard Henrissat, Gemma L. Holliday, Vignir Isberg, Quentin Kaas, David Landsman, Nicolas Lenfant, Gerard Manning, Nozomi Nagano, Narayanaswamy Srinivasan … Gerrit Vriend
Database, Volume 2015, 2015, bav063, https://doi.org/10.1093/database/bav063
Human metabolic atlas: an online resource for human metabolism
Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen
Database, Volume 2015, 2015, bav068, https://doi.org/10.1093/database/bav068
SHIELD: an integrative gene expression database for inner ear research
Jun Shen, Déborah I. Scheffer, Kelvin Y. Kwan, David P. Corey
Database, Volume 2015, 2015, bav071, https://doi.org/10.1093/database/bav071
Curcumin Resource Database
Anil Kumar, Hasnahana Chetia, Swagata Sharma, Debajyoti Kabiraj, Narayan Chandra Talukdar, Utpal Bora
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, Sanjit Pandey, James J. Beaudoin, Lorena Baccaglini, Chittibabu Guda, Howard S. Fox
Database, Volume 2015, 2015, bav074, https://doi.org/10.1093/database/bav074
Phytochemica: a platform to explore phytochemicals of medicinal plants
Shivalika Pathania, Sai Mukund Ramakrishnan, Ganesh Bagler
Database, Volume 2015, 2015, bav075, https://doi.org/10.1093/database/bav075
MetazSecKB: the human and animal secretome and subcellular proteome knowledgebase
John Meinken, Gary Walker, Chester R. Cooper, Xiang Jia Min
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, Stéphane Audic, Loraine Brillet-Guéguen, Christophe Caron, Christian Jeanthon
Database, Volume 2015, 2015, bav080, https://doi.org/10.1093/database/bav080
FlyVar: a database for genetic variation in Drosophila melanogaster
Fei Wang, Lichun Jiang, Yong Chen, Nele A. Haelterman, Hugo J. Bellen, Rui Chen
Database, Volume 2015, 2015, bav079, https://doi.org/10.1093/database/bav079
DENdb: database of integrated human enhancers
Haitham Ashoor, Dimitrios Kleftogiannis, Aleksandar Radovanovic, Vladimir B. Bajic
Database, Volume 2015, 2015, bav085, https://doi.org/10.1093/database/bav085
LncReg: a reference resource for lncRNA-associated regulatory networks
Zhong Zhou, Yi Shen, Muhammad Riaz Khan, Ao Li
Database, Volume 2015, 2015, bav083, https://doi.org/10.1093/database/bav083
Deep Question Answering for protein annotation
Julien Gobeill, Arnaud Gaudinat, Emilie Pasche, Dina Vishnyakova, Pascale Gaudet, Amos Bairoch, Patrick Ruch
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, Jack Cheng, Chien-Hung Huang, Jeffrey J. P. Tsai, Yu-Hsuan Liu, Nilubon Kurubanjerdjit, Wen-Tsong Hsieh, Huey-Yi Chen, Ka-Lok Ng
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, Michael R. Berthold, Michael P. Hedrick, Michael K. Gilson
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, Annet Sollie, Anna Sijtsma, Dennis Hendriksen, Bart Charbon, Mark de Haan, Tommy de Boer, Fleur Kelpin, Jonathan Jetten, Joeri K. van der Velde, Nynke Smidt, Rolf Sijmons, Hans Hillege, Morris A. Swertz
Database, Volume 2015, 2015, bav089, https://doi.org/10.1093/database/bav089
Comprehensive comparative homeobox gene annotation in human and mouse
Laurens G. Wilming, Veronika Boychenko, Jennifer L. Harrow
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, Tilo Henning, Patrick Plitzner, Andreas Müller, Anton Güntsch, Ben C. Stöver, Kai F. Müller, Walter G. Berendsohn, Thomas Borsch
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, Canglin Wu, Hongyu Miao, Hulin Wu
Database, Volume 2015, 2015, bav095, https://doi.org/10.1093/database/bav095
MGDB: a comprehensive database of genes involved in melanoma
Di Zhang, Rongrong Zhu, Hanqian Zhang, Chun-Hou Zheng, Junfeng Xia
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, Hui Zhi, Yunpeng Zhang, Yue Liu, Jizhou Zhang, Yue Gao, Maoni Guo, Shangwei Ning, Xia Li
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, Alexandre Angers-Loustau, Peter Henriksson, Laura Bonfini, Alex Patak, Joachim Kreysa
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, Réka Haraszi, Csaba Maulis
Database, Volume 2015, 2015, bav100, https://doi.org/10.1093/database/bav100
NeuroTransDB : highly curated and structured transcriptomic metadata for neurodegenerative diseases
Shweta Bagewadi, Subash Adhikari, Anjani Dhrangadhariya, Afroza Khanam Irin, Christian Ebeling, Aishwarya Alex Namasivayam, Matthew Page, Martin Hofmann-Apitius, Philipp Senger
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, Chen Xie, Jian-Rong Yang, Jun-Hao Li, Jian-Hua Yang, Limin Zheng
Database, Volume 2015, 2015, bav102, https://doi.org/10.1093/database/bav102
Developing the eHistology Atlas
Lorna Richardson, Liz Graham, Julie Moss, Nick Burton, Yogmatee Roochun, Chris Armit, Richard A. Baldock
Database, Volume 2015, 2015, bav105, https://doi.org/10.1093/database/bav105
Differential ligand-signaling network of CCL19/CCL21-CCR7 system
Rajesh Raju, Sachin Gadakh, Priyanka Gopal, Bijesh George, Jayshree Advani, Sowmya Soman, T. S. K. Prasad, Reshmi Girijadevi
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, Tudor Groza, Damian Smedley, Peter N. Robinson, Anika Oellrich, Dietrich Rebholz-Schuhmann
Database, Volume 2015, 2015, bav104, https://doi.org/10.1093/database/bav104
MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins
Yuan Zhou, Shiping Yang, Tonglin Mao, Ziding Zhang
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, Isha Bhutani, Arun Kumar Somavarapu, Sahil Mahajan, Raman Parkesh, Pawan Gupta
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, Sarika Jaiswal, U.B. Angadi, Gaurav Sablok, Vasu Arora, Sunil Kumar, Anil Rai, Dinesh Kumar
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, 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, Eric R. Gamazon, Xu Zhang, Anuar Konkashbaev, Cong Liu, Keely L. Szilágyi, M. Eileen Dolan, Nancy J. Cox
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, Chunjie Liu, Wei Liu, Yuliang Wu, Zhaowu Ma, Hu Chen, An-Yuan Guo
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, G. V. Padma Raju, Suresh B. Mudunuri, Ratna Prabha, Dhananjaya P. Singh, Vesselin Baev, Galina Yahubyan, Peter J. Ralph, Nicola La Porta
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, Jian Wu, Jianli Liang, Feng Cheng, Xiaowu Wang
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, Kenta Nakai, Ashwini Patil
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, Oriol Vidal-Cortes, Oscar Gallardo, Joaquin Abian, Montserrat Carrascal
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, Hadriana Rodríguez, Diego Martínez, María Pardo, María Jesús Sobrido
Database, Volume 2015, 2015, bav107, https://doi.org/10.1093/database/bav107
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