Hans Ienasescu, Kang Li, Robin Andersson, Morana Vitezic, Sarah Rennie, Yun Chen, Kristoffer Vitting-Seerup, Emil Lagoni, Mette Boyd, Jette Bornholdt, Michiel J. L. de Hoon, Hideya Kawaji, Timo Lassmann, The FANTOM Consortium, Yoshihide Hayashizaki, Alistair R. R. Forrest, Piero Carninci, Albin Sandelin

Database, Volume 2016, 2016, baw144, https://doi.org/10.1093/database/baw144

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TBro: visualization and management of de novo transcriptomes

Markus J. Ankenbrand, Lorenz Weber, Dirk Becker, Frank Förster, Felix Bemm

Database, Volume 2016, 2016, baw146, https://doi.org/10.1093/database/baw146

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iMITEdb: the genome-wide landscape of miniature inverted-repeat transposable elements in insects

Min-Jin Han, Qiu-Zhong Zhou, Hua-Hao Zhang, Xiaoling Tong, Cheng Lu, Ze Zhang, Fangyin Dai

Database, Volume 2016, 2016, baw148, https://doi.org/10.1093/database/baw148

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Crowd-sourcing and author submission as alternatives to professional curation

Peter D. Karp

Database, Volume 2016, 2016, baw149, https://doi.org/10.1093/database/baw149

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Reefgenomics.Org - a repository for marine genomics data

Yi Jin Liew, Manuel Aranda, Christian R. Voolstra

Database, Volume 2016, 2016, baw152, https://doi.org/10.1093/database/baw152

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The importance of digitized biocollections as a source of trait data and a new VertNet resource

Robert P. Guralnick, Paula F. Zermoglio, John Wieczorek, Raphael LaFrance, David Bloom, Laura Russell

Database, Volume 2016, 2016, baw158, https://doi.org/10.1093/database/baw158

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HEDD: the human epigenetic drug database

Yunfeng Qi, Dadong Wang, Daying Wang, Taicheng Jin, Liping Yang, Hui Wu, Yaoyao Li, Jing Zhao, Fengping Du, Mingxia Song, Renjun Wang

Database, Volume 2016, 2016, baw159, https://doi.org/10.1093/database/baw159

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viruSITE—integrated database for viral genomics

Matej Stano, Gabor Beke, Lubos Klucar

Database, Volume 2016, 2016, baw162, https://doi.org/10.1093/database/baw162

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RiceATM: a platform for identifying the association between rice agronomic traits and miRNA expression

Wei-Ting Liu, Chia-Chun Yang, Rong-Kuen Chen, Woei-Shyuan Jwo, Chih-Wen Wu, Wen-Yen Ting, Dah-Pyng Shung, Chun-Chi Liu, Jeremy J.W. Chen

Database, Volume 2016, 2016, baw151, https://doi.org/10.1093/database/baw151

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Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes

Marc Feuermann, Pascale Gaudet, Huaiyu Mi, Suzanna E. Lewis, Paul D. Thomas

Database, Volume 2016, 2016, baw155, https://doi.org/10.1093/database/baw155

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Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges

Ayush Singhal, Robert Leaman, Natalie Catlett, Thomas Lemberger, Johanna McEntyre, Shawn Polson, Ioannis Xenarios, Cecilia Arighi, Zhiyong Lu

Database, Volume 2016, 2016, baw161, https://doi.org/10.1093/database/baw161

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Database Tool

OGDD ( Olive Genetic Diversity Database ): a microsatellite markers' genotypes database of worldwide olive trees for cultivar identification and virgin olive oil traceability

Rayda Ben Ayed, Hanen Ben Hassen, Karim Ennouri, Riadh Ben Marzoug, Ahmed Rebai

Database, Volume 2016, 2016, bav090, https://doi.org/10.1093/database/bav090

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DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions

Xingyan Kuang, Andi Dhroso, Jing Ginger Han, Chi-Ren Shyu, Dmitry Korkin

Database, Volume 2016, 2016, bav114, https://doi.org/10.1093/database/bav114

ChemProt-3.0: a global chemical biology diseases mapping

Jens Kringelum, Sonny Kim Kjaerulff, Søren Brunak, Ole Lund, Tudor I. Oprea, Olivier Taboureau

Database, Volume 2016, 2016, bav123, https://doi.org/10.1093/database/bav123

ncRNA orthologies in the vertebrate lineage

Miguel Pignatelli, Albert J. Vilella, Matthieu Muffato, Leo Gordon, Simon White, Paul Flicek, Javier Herrero

Database, Volume 2016, 2016, bav127, https://doi.org/10.1093/database/bav127

HerDing: herb recommendation system to treat diseases using genes and chemicals

Wonjun Choi, Chan-Hun Choi, Young Ran Kim, Seon-Jong Kim, Chang-Su Na, Hyunju Lee

Database, Volume 2016, 2016, baw011, https://doi.org/10.1093/database/baw011

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dbWGFP: a database and web server of human whole-genome single nucleotide variants and their functional predictions

Jiaxin Wu, Mengmeng Wu, Lianshuo Li, Zhuo Liu, Wanwen Zeng, Rui Jiang

Database, Volume 2016, 2016, baw024, https://doi.org/10.1093/database/baw024

myPhyloDB: a local web server for the storage and analysis of metagenomic data

Daniel K. Manter, Matthew Korsa, Caleb Tebbe, Jorge A. Delgado

Database, Volume 2016, 2016, baw037, https://doi.org/10.1093/database/baw037

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The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development

Meik Kunz, Chunguang Liang, Santosh Nilla, Alexander Cecil, Thomas Dandekar

Database, Volume 2016, 2016, baw041, https://doi.org/10.1093/database/baw041

PmiRExAt: plant miRNA expression atlas database and web applications

Anoop Kishor Singh Gurjar, Abhijeet Singh Panwar, Rajinder Gupta, Shrikant S. Mantri

Database, Volume 2016, 2016, baw060, https://doi.org/10.1093/database/baw060

CoReCG: a comprehensive database of genes associated with colon-rectal cancer

Rahul Agarwal, Binayak Kumar, Msk Jayadev, Dhwani Raghav, Ashutosh Singh

Database, Volume 2016, 2016, baw059, https://doi.org/10.1093/database/baw059

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A web resource for mining HLA associations with adverse drug reactions: HLA-ADR

Gurpreet S. Ghattaoraya, Yenal Dundar, Faviel F. González-Galarza, Maria Helena Thomaz Maia, Eduardo José Melo Santos, Andréa Luciana Soares da Silva, Antony McCabe, Derek Middleton, Ana Alfirevic, Rumona Dickson, Andrew R. Jones

Database, Volume 2016, 2016, baw069, https://doi.org/10.1093/database/baw069

‘RE:fine drugs’: an interactive dashboard to access drug repurposing opportunities

Soheil Moosavinasab, Jeremy Patterson, Robert Strouse, Majid Rastegar-Mojarad, Kelly Regan, Philip R. O. Payne, Yungui Huang, Simon M. Lin

Database, Volume 2016, 2016, baw083, https://doi.org/10.1093/database/baw083

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ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods

Patrice Baa-Puyoulet, Nicolas Parisot, Gérard Febvay, Jaime Huerta-Cepas, Augusto F. Vellozo, Toni Gabaldón, Federica Calevro, Hubert Charles, Stefano Colella

Database, Volume 2016, 2016, baw081, https://doi.org/10.1093/database/baw081

GESDB: a platform of simulation resources for genetic epidemiology studies

Po-Ju Yao, Ren-Hua Chung

Database, Volume 2016, 2016, baw082, https://doi.org/10.1093/database/baw082

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ANItools web: a web tool for fast genome comparison within multiple bacterial strains

Na Han, Yujun Qiang, Wen Zhang

Database, Volume 2016, 2016, baw084, https://doi.org/10.1093/database/baw084

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SinEx DB: a database for single exon coding sequences in mammalian genomes

Roddy Jorquera, Rodrigo Ortiz, F. Ossandon, Juan Pablo Cárdenas, Rene Sepúlveda, Carolina González, David S. Holmes

Database, Volume 2016, 2016, baw095, https://doi.org/10.1093/database/baw095

Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text

Àlex Bravo, Tong Shu Li, Andrew I. Su, Benjamin M. Good, Laura I. Furlong

Database, Volume 2016, 2016, baw094, https://doi.org/10.1093/database/baw094

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PvTFDB: a Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes

Bhawna, V.S. Bonthala, MNV Prasad Gajula

Database, Volume 2016, 2016, baw114, https://doi.org/10.1093/database/baw114

MODEM: multi-omics data envelopment and mining in maize

Haijun Liu, Fan Wang, Yingjie Xiao, Zonglin Tian, Weiwei Wen, Xuehai Zhang, Xi Chen, Nannan Liu, Wenqiang Li, Lei Liu, Jie Liu, Jianbing Yan, Jianxiao Liu

Database, Volume 2016, 2016, baw117, https://doi.org/10.1093/database/baw117

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Skeleton Genetics: a comprehensive database for genes and mutations related to genetic skeletal disorders

Chong Chen, Yi Jiang, Chenyang Xu, Xinting Liu, Lin Hu, Yanbao Xiang, Qingshuang Chen, Denghui Chen, Huanzheng Li, Xueqin Xu, Shaohua Tang

Database, Volume 2016, 2016, baw127, https://doi.org/10.1093/database/baw127

IRNdb: the database of immunologically relevant non-coding RNAs

Elena Denisenko, Daniel Ho, Ousman Tamgue, Mumin Ozturk, Harukazu Suzuki, Frank Brombacher, Reto Guler, Sebastian Schmeier

Database, Volume 2016, 2016, baw138, https://doi.org/10.1093/database/baw138

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ToxReporter: viewing the genome through the eyes of a toxicologist

Mark Gosink

Database, Volume 2016, 2016, baw141, https://doi.org/10.1093/database/baw141

Database Update

ScaleNet: a literature-based model of scale insect biology and systematics

Mayrolin García Morales, Barbara D. Denno, Douglass R. Miller, Gary L. Miller, Yair Ben-Dov, Nate B. Hardy

Database, Volume 2016, 2016, bav118, https://doi.org/10.1093/database/bav118

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Ensembl regulation resources

Daniel R. Zerbino, Nathan Johnson, Thomas Juetteman, Dan Sheppard, Steven P. Wilder, Ilias Lavidas, Michael Nuhn, Emily Perry, Quentin Raffaillac-Desfosses, Daniel Sobral, Damian Keefe, Stefan Gräf, Ikhlak Ahmed, Rhoda Kinsella, Bethan Pritchard, Simon Brent, Ridwan Amode, Anne Parker, Steven Trevanion … Paul Flicek

Database, Volume 2016, 2016, bav119, https://doi.org/10.1093/database/bav119

Ensembl comparative genomics resources

Javier Herrero, Matthieu Muffato, Kathryn Beal, Stephen Fitzgerald, Leo Gordon, Miguel Pignatelli, Albert J. Vilella, Stephen M. J. Searle, Ridwan Amode, Simon Brent, William Spooner, Eugene Kulesha, Andrew Yates, Paul Flicek

Database, Volume 2016, 2016, bav096, https://doi.org/10.1093/database/bav096

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MGFD: the maize gene families database

Lei Sheng, Haiyang Jiang, Hanwei Yan, Xiaoyu Li, Yongxiang Lin, Hui Ye, Beijiu Cheng

Database, Volume 2016, 2016, baw004, https://doi.org/10.1093/database/baw004

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2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein–protein interactions

Marie-Jeanne Basse, Stéphane Betzi, Xavier Morelli, Philippe Roche

Database, Volume 2016, 2016, baw007, https://doi.org/10.1093/database/baw007

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Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms

Naresh Sahebrao Nagpure, Ajey Kumar Pathak, Rameshwar Pati, Iliyas Rashid, Jyoti Sharma, Shri Prakash Singh, Mahender Singh, Uttam Kumar Sarkar, Basdeo Kushwaha, Ravindra Kumar, S. Murali

Database, Volume 2016, 2016, baw012, https://doi.org/10.1093/database/baw012

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PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins

Chen Li, Jeremy Nagel, Steve Androulakis, Jiangning Song, Ashley M. Buckle

Database, Volume 2016, 2016, baw021, https://doi.org/10.1093/database/baw021

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An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework

Yi-An Chen, Lokesh P. Tripathi, Kenji Mizuguchi

Database, Volume 2016, 2016, baw009, https://doi.org/10.1093/database/baw009

The Disease Portals, disease–gene annotation and the RGD disease ontology at the Rat Genome Database

G. Thomas Hayman, Stanley J. F. Laulederkind, Jennifer R. Smith, Shur-Jen Wang, Victoria Petri, Rajni Nigam, Marek Tutaj, Jeff De Pons, Melinda R. Dwinell, Mary Shimoyama

Database, Volume 2016, 2016, baw034, https://doi.org/10.1093/database/baw034

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CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state

Alexander Miguel Monzon, Cristian Oscar Rohr, María Silvina Fornasari, Gustavo Parisi

Database, Volume 2016, 2016, baw038, https://doi.org/10.1093/database/baw038

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NPInter v3.0: an upgraded database of noncoding RNA-associated interactions

Yajing Hao, Wei Wu, Hui Li, Jiao Yuan, Jianjun Luo, Yi Zhao, Runsheng Chen

Database, Volume 2016, 2016, baw057, https://doi.org/10.1093/database/baw057

From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF

Sefa Kılıç, Dinara M. Sagitova, Shoshannah Wolfish, Benoit Bely, Mélanie Courtot, Stacy Ciufo, Tatiana Tatusova, Claire O’Donovan, Marcus C. Chibucos, Maria J. Martin, Ivan Erill

Database, Volume 2016, 2016, baw055, https://doi.org/10.1093/database/baw055

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Integration of new alternative reference strain genome sequences into the Saccharomyces genome database

Giltae Song, Rama Balakrishnan, Gail Binkley, Maria C. Costanzo, Kyla Dalusag, Janos Demeter, Stacia Engel, Sage T. Hellerstedt, Kalpana Karra, Benjamin C. Hitz, Robert S. Nash, Kelley Paskov, Travis Sheppard, Marek Skrzypek, Shuai Weng, Edith Wong, J. Michael Cherry

Database, Volume 2016, 2016, baw074, https://doi.org/10.1093/database/baw074

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The Ensembl gene annotation system

Bronwen L. Aken, Sarah Ayling, Daniel Barrell, Laura Clarke, Valery Curwen, Susan Fairley, Julio Fernandez Banet, Konstantinos Billis, Carlos García Girón, Thibaut Hourlier, Kevin Howe, Andreas Kähäri, Felix Kokocinski, Fergal J. Martin, Daniel N. Murphy, Rishi Nag, Magali Ruffier, Michael Schuster, Y. Amy Tang … Stephen M. J. Searle

Database, Volume 2016, 2016, baw093, https://doi.org/10.1093/database/baw093

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HPIDB 2.0: a curated database for host–pathogen interactions

Mais G. Ammari, Cathy R. Gresham, Fiona M. McCarthy, Bindu Nanduri

Database, Volume 2016, 2016, baw103, https://doi.org/10.1093/database/baw103

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ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions

Luis Marenco, Rixin Wang, Robert McDougal, Tsviya Olender, Michal Twik, Elspeth Bruford, Xinyi Liu, Jian Zhang, Doron Lancet, Gordon Shepherd, Chiquito Crasto

Database, Volume 2016, 2016, baw132, https://doi.org/10.1093/database/baw132

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Original Articles

Cryptosporidium hominis gene catalog: a resource for the selection of novel Cryptosporidium vaccine candidates

Olukemi O. Ifeonu, Raphael Simon, Sharon M. Tennant, Abhineet S. Sheoran, Maria C. Daly, Victor Felix, Jessica C. Kissinger, Giovanni Widmer, Myron M. Levine, Saul Tzipori, Joana C. Silva

Database, Volume 2016, 2016, baw137, https://doi.org/10.1093/database/baw137

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Value, but high costs in post-deposition data curation

Petra ten Hoopen, Clara Amid, Pier Luigi Buttigieg, Evangelos Pafilis, Panos Bravakos, Ana M. Cerdeño-Tárraga, Richard Gibson, Tim Kahlke, Aglaia Legaki, Kada Narayana Murthy, Gabriella Papastefanou, Emiliano Pereira, Marc Rossello, Ana Luisa Toribio, Guy Cochrane

Database, Volume 2016, 2016, bav126, https://doi.org/10.1093/database/bav126

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Portal of medical data models: information infrastructure for medical research and healthcare

Martin Dugas, Philipp Neuhaus, Alexandra Meidt, Justin Doods, Michael Storck, Philipp Bruland, Julian Varghese

Database, Volume 2016, 2016, bav121, https://doi.org/10.1093/database/bav121

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The Corvids Literature Database—500 years of ornithological research from a crow’s perspective

Gabriele Droege, Till Töpfer

Database, Volume 2016, 2016, bav122, https://doi.org/10.1093/database/bav122

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CCSI: a database providing chromatin–chromatin spatial interaction information

Xiaowei Xie, Wenbin Ma, Zhou Songyang, Zhenhua Luo, Junfeng Huang, Zhiming Dai, Yuanyan Xiong

Database, Volume 2016, 2016, bav124, https://doi.org/10.1093/database/bav124

Regulators of Androgen Action Resource: a one-stop shop for the comprehensive study of androgen receptor action

Adam D. DePriest, Michael V. Fiandalo, Simon Schlanger, Frederike Heemers, James L. Mohler, Song Liu, Hannelore V. Heemers

Database, Volume 2016, 2016, bav125, https://doi.org/10.1093/database/bav125

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NALDB: nucleic acid ligand database for small molecules targeting nucleic acid

Subodh Kumar Mishra, Amit Kumar

Database, Volume 2016, 2016, baw002, https://doi.org/10.1093/database/baw002

EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation

Evangelos Pafilis, Pier Luigi Buttigieg, Barbra Ferrell, Emiliano Pereira, Julia Schnetzer, Christos Arvanitidis, Lars Juhl Jensen

Database, Volume 2016, 2016, baw005, https://doi.org/10.1093/database/baw005

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The UniProtKB guide to the human proteome

Lionel Breuza, Sylvain Poux, Anne Estreicher, Maria Livia Famiglietti, Michele Magrane, Michael Tognolli, Alan Bridge, Delphine Baratin, Nicole Redaschi, The UniProt Consortium

Database, Volume 2016, 2016, bav120, https://doi.org/10.1093/database/bav120

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dbPEC: a comprehensive literature-based database for preeclampsia related genes and phenotypes

Alper Uzun, Elizabeth W. Triche, Jessica Schuster, Andrew T. Dewan, James F. Padbury

Database, Volume 2016, 2016, baw006, https://doi.org/10.1093/database/baw006

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Principles of metadata organization at the ENCODE data coordination center

Eurie L. Hong, Cricket A. Sloan, Esther T. Chan, Jean M. Davidson, Venkat S. Malladi, J. Seth Strattan, Benjamin C. Hitz, Idan Gabdank, Aditi K. Narayanan, Marcus Ho, Brian T. Lee, Laurence D. Rowe, Timothy R. Dreszer, Greg R. Roe, Nikhil R. Podduturi, Forrest Tanaka, Jason A. Hilton, J. Michael Cherry

Database, Volume 2016, 2016, baw001, https://doi.org/10.1093/database/baw001

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Effect of database drift on network topology and enrichment analyses: a case study for RegulonDB

Moritz E. Beber, Georgi Muskhelishvili, Marc-Thorsten Hütt

Database, Volume 2016, 2016, baw003, https://doi.org/10.1093/database/baw003

DemaDb: an integrated dematiaceous fungal genomes database

Chee Sian Kuan, Su Mei Yew, Chai Ling Chan, Yue Fen Toh, Kok Wei Lee, Wei-Hien Cheong, Wai-Yan Yee, Chee-Choong Hoh, Soon-Joo Yap, Kee Peng Ng

Database, Volume 2016, 2016, baw008, https://doi.org/10.1093/database/baw008

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PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya

Graham L. Cromar, Anthony Zhao, Xuejian Xiong, Lakshmipuram S. Swapna, Noeleen Loughran, Hongyan Song, John Parkinson

Database, Volume 2016, 2016, baw013, https://doi.org/10.1093/database/baw013

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Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado

Sook Jung, Taein Lee, Stephen Ficklin, Jing Yu, Chun-Huai Cheng, Dorrie Main

Database, Volume 2016, 2016, baw010, https://doi.org/10.1093/database/baw010

HistoneDB 2.0: a histone database with variants—an integrated resource to explore histones and their variants

Eli J. Draizen, Alexey K. Shaytan, Leonardo Mariño-Ramírez, Paul B. Talbert, David Landsman, Anna R. Panchenko

Database, Volume 2016, 2016, baw014, https://doi.org/10.1093/database/baw014

Wikidata as a semantic framework for the Gene Wiki initiative

Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Elvira Mitraka, Julia Turner, Tim Putman, Justin Leong, Chinmay Naik, Paul Pavlidis, Lynn Schriml, Benjamin M Good, Andrew I Su

Database, Volume 2016, 2016, baw015, https://doi.org/10.1093/database/baw015

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R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring

Frédéric Rimet, Philippe Chaumeil, François Keck, Lenaïg Kermarrec, Valentin Vasselon, Maria Kahlert, Alain Franc, Agnès Bouchez

Database, Volume 2016, 2016, baw016, https://doi.org/10.1093/database/baw016

Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model

Leonore Reiser, Tanya Z. Berardini, Donghui Li, Robert Muller, Emily M. Strait, Qian Li, Yarik Mezheritsky, Andrey Vetushko, Eva Huala

Database, Volume 2016, 2016, baw018, https://doi.org/10.1093/database/baw018

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KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins

Chen Li, Steve Androulakis, Ashley M. Buckle, Jiangning Song

Database, Volume 2016, 2016, baw019, https://doi.org/10.1093/database/baw019

From one to many: expanding the Saccharomyces cerevisiae reference genome panel

Stacia R. Engel, Shuai Weng, Gail Binkley, Kelley Paskov, Giltae Song, J. Michael Cherry

Database, Volume 2016, 2016, baw020, https://doi.org/10.1093/database/baw020

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High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis

Vahan Simonyan, Konstantin Chumakov, Hayley Dingerdissen, William Faison, Scott Goldweber, Anton Golikov, Naila Gulzar, Konstantinos Karagiannis, Phuc Vinh Nguyen Lam, Thomas Maudru, Olesja Muravitskaja, Ekaterina Osipova, Yang Pan, Alexey Pschenichnov, Alexandre Rostovtsev, Luis Santana-Quintero, Krista Smith, Elaine E. Thompson, Valery Tkachenko … Raja Mazumder

Database, Volume 2016, 2016, baw022, https://doi.org/10.1093/database/baw022

CSCdb: a cancer stem cells portal for markers, related genes and functional information

Yi Shen, Heming Yao, Ao Li, Minghui Wang

Database, Volume 2016, 2016, baw023, https://doi.org/10.1093/database/baw023

GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations

Amaia Sangrador-Vegas, Alex L. Mitchell, Hsin-Yu Chang, Siew-Yit Yong, Robert D. Finn

Database, Volume 2016, 2016, baw027, https://doi.org/10.1093/database/baw027

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Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task

Chih-Hsuan Wei, Yifan Peng, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Jiao Li, Thomas C. Wiegers, Zhiyong Lu

Database, Volume 2016, 2016, baw032, https://doi.org/10.1093/database/baw032

HNdb: an integrated database of gene and protein information on head and neck squamous cell carcinoma

Tiago Henrique, Nelson José Freitas da Silveira, Arthur Henrique Cunha Volpato, Mayra Mataruco Mioto, Ana Carolina Buzzo Stefanini, Adil Bachir Fares, João Gustavo da Silva Castro Andrade, Carolina Masson, Rossana Verónica Mendoza López, Fabio Daumas Nunes, Luis Paulo Kowalski, Patricia Severino, Eloiza Helena Tajara

Database, Volume 2016, 2016, baw026, https://doi.org/10.1093/database/baw026

Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation

Chung-Chi Huang, Zhiyong Lu

Database, Volume 2016, 2016, baw025, https://doi.org/10.1093/database/baw025

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CCProf: exploring conformational change profile of proteins

Che-Wei Chang, Chai-Wei Chou, Darby Tien-Hao Chang

Database, Volume 2016, 2016, baw029, https://doi.org/10.1093/database/baw029

CD-REST: a system for extracting chemical-induced disease relation in literature

Jun Xu, Yonghui Wu, Yaoyun Zhang, Jingqi Wang, Hee-Jin Lee, Hua Xu

Database, Volume 2016, 2016, baw036, https://doi.org/10.1093/database/baw036

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Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes

Tim E. Putman, Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Chunlei Wu, Andrew I. Su, Benjamin M. Good

Database, Volume 2016, 2016, baw028, https://doi.org/10.1093/database/baw028

View article

RSIADB, a collective resource for genome and transcriptome analyses in Rhizoctonia solani AG1 IA

Lei Chen, Peng Ai, Jinfeng Zhang, Qiming Deng, Shiquan Wang, Shuangcheng Li, Jun Zhu, Ping Li, Aiping Zheng

Database, Volume 2016, 2016, baw031, https://doi.org/10.1093/database/baw031

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Genic insights from integrated human proteomics in GeneCards

Simon Fishilevich, Shahar Zimmerman, Asher Kohn, Tsippi Iny Stein, Tsviya Olender, Eugene Kolker, Marilyn Safran, Doron Lancet

Database, Volume 2016, 2016, baw030, https://doi.org/10.1093/database/baw030

Chemical-induced disease relation extraction with various linguistic features

Jinghang Gu, Longhua Qian, Guodong Zhou

Database, Volume 2016, 2016, baw042, https://doi.org/10.1093/database/baw042

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ICEPO: the ion channel electrophysiology ontology

V. Hinard, A. Britan, J.S. Rougier, A. Bairoch, H. Abriel, P. Gaudet

Database, Volume 2016, 2016, baw017, https://doi.org/10.1093/database/baw017

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ATtRACT—a database of RNA-binding proteins and associated motifs

Girolamo Giudice, Fátima Sánchez-Cabo, Carlos Torroja, Enrique Lara-Pezzi

Database, Volume 2016, 2016, baw035, https://doi.org/10.1093/database/baw035

RegenBase: a knowledge base of spinal cord injury biology for translational research

Alison Callahan, Saminda W. Abeyruwan, Hassan Al-Ali, Kunie Sakurai, Adam R. Ferguson, Phillip G. Popovich, Nigam H. Shah, Ubbo Visser, John L. Bixby, Vance P. Lemmon

Database, Volume 2016, 2016, baw040, https://doi.org/10.1093/database/baw040

Efficient chemical-disease identification and relationship extraction using Wikipedia to improve recall

Daniel M. Lowe, Noel M. O’Boyle, Roger A. Sayle

Database, Volume 2016, 2016, baw039, https://doi.org/10.1093/database/baw039

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BRONCO: Biomedical entity Relation ONcology COrpus for extracting gene-variant-disease-drug relations

Kyubum Lee, Sunwon Lee, Sungjoon Park, Sunkyu Kim, Suhkyung Kim, Kwanghun Choi, Aik Choon Tan, Jaewoo Kang

Database, Volume 2016, 2016, baw043, https://doi.org/10.1093/database/baw043

ToxDB: pathway-level interpretation of drug-treatment data

C. Hardt, M.E. Beber, A. Rasche, A. Kamburov, D.G. Hebels, J.C. Kleinjans, R. Herwig

Database, Volume 2016, 2016, baw052, https://doi.org/10.1093/database/baw052

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3CDB: a manually curated database of chromosome conformation capture data

Xiaoxiao Yun, Lili Xia, Bixia Tang, Hui Zhang, Feifei Li, Zhihua Zhang

Database, Volume 2016, 2016, baw044, https://doi.org/10.1093/database/baw044

Extraction of chemical-induced diseases using prior knowledge and textual information

Ewoud Pons, Benedikt F.H. Becker, Saber A. Akhondi, Zubair Afzal, Erik M. van Mulligen, Jan A. Kors

Database, Volume 2016, 2016, baw046, https://doi.org/10.1093/database/baw046

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Exploiting syntactic and semantics information for chemical–disease relation extraction

Huiwei Zhou, Huijie Deng, Long Chen, Yunlong Yang, Chen Jia, Degen Huang

Database, Volume 2016, 2016, baw048, https://doi.org/10.1093/database/baw048

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Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource

Megan Druce, Chantal Hulo, Patrick Masson, Paula Sommer, Ioannis Xenarios, Philippe Le Mercier, Tulio De Oliveira

Database, Volume 2016, 2016, baw045, https://doi.org/10.1093/database/baw045

Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning

Yaoyun Zhang, Jun Xu, Hui Chen, Jingqi Wang, Yonghui Wu, Manu Prakasam, Hua Xu

Database, Volume 2016, 2016, baw049, https://doi.org/10.1093/database/baw049

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A crowdsourcing workflow for extracting chemical-induced disease relations from free text

Tong Shu Li, Àlex Bravo, Laura I. Furlong, Benjamin M. Good, Andrew I. Su

Database, Volume 2016, 2016, baw051, https://doi.org/10.1093/database/baw051

PGP repository: a plant phenomics and genomics data publication infrastructure

Daniel Arend, Astrid Junker, Uwe Scholz, Danuta Schüler, Juliane Wylie, Matthias Lange

Database, Volume 2016, 2016, baw033, https://doi.org/10.1093/database/baw033

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Kalium: a database of potassium channel toxins from scorpion venom

Alexey I. Kuzmenkov, Nikolay A. Krylov, Anton O. Chugunov, Eugene V. Grishin, Alexander A. Vassilevski

Database, Volume 2016, 2016, baw056, https://doi.org/10.1093/database/baw056

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Integrated sequence and immunology filovirus database at Los Alamos

Karina Yusim, Hyejin Yoon, Brian Foley, Shihai Feng, Jennifer Macke, Mira Dimitrijevic, Werner Abfalterer, James Szinger, Will Fischer, Carla Kuiken, Bette Korber

Database, Volume 2016, 2016, baw047, https://doi.org/10.1093/database/baw047

UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation

Van-Nui Nguyen, Kai-Yao Huang, Julia Tzu-Ya Weng, K. Robert Lai, Tzong-Yi Lee

Database, Volume 2016, 2016, baw054, https://doi.org/10.1093/database/baw054

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Chemical entity recognition in patents by combining dictionary-based and statistical approaches

Saber A. Akhondi, Ewoud Pons, Zubair Afzal, Herman van Haagen, Benedikt F.H. Becker, Kristina M. Hettne, Erik M. van Mulligen, Jan A. Kors

Database, Volume 2016, 2016, baw061, https://doi.org/10.1093/database/baw061

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ToxEvaluator: an integrated computational platform to aid the interpretation of toxicology study-related findings

D. Pelletier, T. C. Wiegers, A. Enayetallah, C. Kibbey, M. Gosink, P. Koza-Taylor, C. J. Mattingly, M. Lawton

Database, Volume 2016, 2016, baw062, https://doi.org/10.1093/database/baw062

BioCreative V CDR task corpus: a resource for chemical disease relation extraction

Jiao Li, Yueping Sun, Robin J. Johnson, Daniela Sciaky, Chih-Hsuan Wei, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Thomas C. Wiegers, Zhiyong Lu

Database, Volume 2016, 2016, baw068, https://doi.org/10.1093/database/baw068

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BioC-compatible full-text passage detection for protein–protein interactions using extended dependency graph

Yifan Peng, Cecilia Arighi, Cathy H. Wu, K. Vijay-Shanker

Database, Volume 2016, 2016, baw072, https://doi.org/10.1093/database/baw072

BelSmile: a biomedical semantic role labeling approach for extracting biological expression language from text

Po-Ting Lai, Yu-Yan Lo, Ming-Siang Huang, Yu-Cheng Hsiao, Richard Tzong-Han Tsai

Database, Volume 2016, 2016, baw064, https://doi.org/10.1093/database/baw064

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Mining chemical patents with an ensemble of open systems

Robert Leaman, Chih-Hsuan Wei, Cherry Zou, Zhiyong Lu

Database, Volume 2016, 2016, baw065, https://doi.org/10.1093/database/baw065

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PepPSy: a web server to prioritize gene products in experimental and biocuration workflows

Olivier Sallou, Paula D. Duek, Thomas A. Darde, Olivier Collin, Lydie Lane, Frédéric Chalmel

Database, Volume 2016, 2016, baw070, https://doi.org/10.1093/database/baw070

The Chinchilla Research Resource Database: resource for an otolaryngology disease model

Mary Shimoyama, Jennifer R. Smith, Jeff De Pons, Marek Tutaj, Pawjai Khampang, Wenzhou Hong, Christy B. Erbe, Garth D. Ehrlich, Lauren O. Bakaletz, Joseph E. Kerschner

Database, Volume 2016, 2016, baw073, https://doi.org/10.1093/database/baw073

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DPTEdb, an integrative database of transposable elements in dioecious plants

Shu-Fen Li, Guo-Jun Zhang, Xue-Jin Zhang, Jin-Hong Yuan, Chuan-Liang Deng, Lian-Feng Gu, Wu-Jun Gao

Database, Volume 2016, 2016, baw078, https://doi.org/10.1093/database/baw078

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BELTracker: evidence sentence retrieval for BEL statements

Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Hongfang Liu

Database, Volume 2016, 2016, baw079, https://doi.org/10.1093/database/baw079

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Argo: enabling the development of bespoke workflows and services for disease annotation

Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou

Database, Volume 2016, 2016, baw066, https://doi.org/10.1093/database/baw066

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A knowledge-poor approach to chemical-disease relation extraction

Firoj Alam, Anna Corazza, Alberto Lavelli, Roberto Zanoli

Database, Volume 2016, 2016, baw071, https://doi.org/10.1093/database/baw071

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BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences

Peter McQuilton, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, Milo Thurston, Allyson Lister, Eamonn Maguire, Susanna-Assunta Sansone

Database, Volume 2016, 2016, baw075, https://doi.org/10.1093/database/baw075

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Predicting structured metadata from unstructured metadata

Lisa Posch, Maryam Panahiazar, Michel Dumontier, Olivier Gevaert

Database, Volume 2016, 2016, baw080, https://doi.org/10.1093/database/baw080

URS DataBase: universe of RNA structures and their motifs

Eugene Baulin, Victor Yacovlev, Denis Khachko, Sergei Spirin, Mikhail Roytberg

Database, Volume 2016, 2016, baw085, https://doi.org/10.1093/database/baw085

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gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes

So Nakagawa, Mahoko Ueda Takahashi

Database, Volume 2016, 2016, baw087, https://doi.org/10.1093/database/baw087

Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria

Miguel A. Ibarra-Arellano, Adrián I. Campos-González, Luis G. Treviño-Quintanilla, Andreas Tauch, Julio A. Freyre-González

Database, Volume 2016, 2016, baw089, https://doi.org/10.1093/database/baw089

MET network in PubMed: a text-mined network visualization and curation system

Hong-Jie Dai, Chu-Hsien Su, Po-Ting Lai, Ming-Siang Huang, Jitendra Jonnagaddala, Toni Rose Jue, Shruti Rao, Hui-Jou Chou, Marija Milacic, Onkar Singh, Shabbir Syed-Abdul, Wen-Lian Hsu

Database, Volume 2016, 2016, baw090, https://doi.org/10.1093/database/baw090

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CoopTFD: a repository for predicted yeast cooperative transcription factor pairs

Wei-Sheng Wu, Fu-Jou Lai, Bor-Wen Tu, Darby Tien-Hao Chang

Database, Volume 2016, 2016, baw092, https://doi.org/10.1093/database/baw092

HITSZ_CDR: an end-to-end chemical and disease relation extraction system for BioCreative V

Haodi Li, Buzhou Tang, Qingcai Chen, Kai Chen, Xiaolong Wang, Baohua Wang, Zhe Wang

Database, Volume 2016, 2016, baw077, https://doi.org/10.1093/database/baw077

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Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

Sushil Tripathi, Steven Vercruysse, Konika Chawla, Karen R. Christie, Judith A. Blake, Rachael P. Huntley, Sandra Orchard, Henning Hermjakob, Liv Thommesen, Astrid Lægreid, Martin Kuiper

Database, Volume 2016, 2016, baw088, https://doi.org/10.1093/database/baw088

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AuDis: an automatic CRF-enhanced disease normalization in biomedical text

Hsin-Chun Lee, Yi-Yu Hsu, Hung-Yu Kao

Database, Volume 2016, 2016, baw091, https://doi.org/10.1093/database/baw091

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Mining clinical attributes of genomic variants through assisted literature curation in Egas

Sérgio Matos, David Campos, Renato Pinho, Raquel M. Silva, Matthew Mort, David N. Cooper, José Luís Oliveira

Database, Volume 2016, 2016, baw096, https://doi.org/10.1093/database/baw096

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SorghumFDB: sorghum functional genomics database with multidimensional network analysis

Tian Tian, Qi You, Liwei Zhang, Xin Yi, Hengyu Yan, Wenying Xu, Zhen Su

Database, Volume 2016, 2016, baw099, https://doi.org/10.1093/database/baw099

Coreference resolution improves extraction of Biological Expression Language statements from texts

Miji Choi, Haibin Liu, William Baumgartner, Justin Zobel, Karin Verspoor

Database, Volume 2016, 2016, baw076, https://doi.org/10.1093/database/baw076

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neXtA ₅ : accelerating annotation of articles via automated approaches in neXtProt

Luc Mottin, Julien Gobeill, Emilie Pasche, Pierre-André Michel, Isabelle Cusin, Pascale Gaudet, Patrick Ruch

Database, Volume 2016, 2016, baw098, https://doi.org/10.1093/database/baw098

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The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

Andrew D. Rouillard, Gregory W. Gundersen, Nicolas F. Fernandez, Zichen Wang, Caroline D. Monteiro, Michael G. McDermott, Avi Ma’ayan

Database, Volume 2016, 2016, baw100, https://doi.org/10.1093/database/baw100

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BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language

Fabio Rinaldi, Tilia Renate Ellendorff, Sumit Madan, Simon Clematide, Adrian van der Lek, Theo Mevissen, Juliane Fluck

Database, Volume 2016, 2016, baw067, https://doi.org/10.1093/database/baw067

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TMC-SNPdb: an Indian germline variant database derived from whole exome sequences

Pawan Upadhyay, Nilesh Gardi, Sanket Desai, Bikram Sahoo, Ankita Singh, Trupti Togar, Prajish Iyer, Ratnam Prasad, Pratik Chandrani, Sudeep Gupta, Amit Dutt

Database, Volume 2016, 2016, baw104, https://doi.org/10.1093/database/baw104

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki

Imad Abugessaisa, Hisashi Shimoji, Serkan Sahin, Atsushi Kondo, Jayson Harshbarger, Marina Lizio, Yoshihide Hayashizaki, Piero Carninci, The FANTOM consortium, Alistair Forrest, Takeya Kasukawa, Hideya Kawaji

Database, Volume 2016, 2016, baw105, https://doi.org/10.1093/database/baw105

Sieve-based coreference resolution enhances semi-supervised learning model for chemical-induced disease relation extraction

Hoang-Quynh Le, Mai-Vu Tran, Thanh Hai Dang, Quang-Thuy Ha, Nigel Collier

Database, Volume 2016, 2016, baw102, https://doi.org/10.1093/database/baw102

Establishment of Kawasaki disease database based on metadata standard

Yu Rang Park, Jae-Jung Kim, Young Jo Yoon, Young-Kwang Yoon, Ha Yeong Koo, Young Mi Hong, Gi Young Jang, Soo-Yong Shin, Jong-Keuk Lee, on behalf of the Korean Kawasaki Disease Genetics Consortium

Database, Volume 2016, 2016, baw109, https://doi.org/10.1093/database/baw109

NTTMUNSW BioC modules for recognizing and normalizing species and gene/protein mentions

Hong-Jie Dai, Onkar Singh, Jitendra Jonnagaddala, Emily Chia-Yu Su

Database, Volume 2016, 2016, baw111, https://doi.org/10.1093/database/baw111

How much does curation cost?

Peter D. Karp

Database, Volume 2016, 2016, baw110, https://doi.org/10.1093/database/baw110

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Improving the dictionary lookup approach for disease normalization using enhanced dictionary and query expansion

Jitendra Jonnagaddala, Toni Rose Jue, Nai-Wen Chang, Hong-Jie Dai

Database, Volume 2016, 2016, baw112, https://doi.org/10.1093/database/baw112

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Crowdsourcing and curation: perspectives from biology and natural language processing

Lynette Hirschman, Karën Fort, Stéphanie Boué, Nikos Kyrpides, Rezarta Islamaj Doğan, Kevin Bretonnel Cohen

Database, Volume 2016, 2016, baw115, https://doi.org/10.1093/database/baw115

BioC viewer: a web-based tool for displaying and merging annotations in BioC

Soo-Yong Shin, Sun Kim, W. John Wilbur, Dongseop Kwon

Database, Volume 2016, 2016, baw106, https://doi.org/10.1093/database/baw106

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Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data

J. D. Edwards, A. M. Baldo, L. A. Mueller

Database, Volume 2016, 2016, baw107, https://doi.org/10.1093/database/baw107

Onco-Regulon: an integrated database and software suite for site specific targeting of transcription factors of cancer genes

Navneet Tomar, Akhilesh Mishra, Nirotpal Mrinal, B. Jayaram

Database, Volume 2016, 2016, baw116, https://doi.org/10.1093/database/baw116

PIPE: a protein–protein interaction passage extraction module for BioCreative challenge

Yung-Chun Chang, Chun-Han Chu, Yu-Chen Su, Chien Chin Chen, Wen-Lian Hsu

Database, Volume 2016, 2016, baw101, https://doi.org/10.1093/database/baw101

The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge

Martin Pérez-Pérez, Gael Pérez-Rodríguez, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, Florentino Fdez-Riverola, Alfonso Valencia, Martin Krallinger, Anália Lourenço

Database, Volume 2016, 2016, baw120, https://doi.org/10.1093/database/baw120

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Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL)

Juliane Fluck, Sumit Madan, Sam Ansari, Alpha T. Kodamullil, Reagon Karki, Majid Rastegar-Mojarad, Natalie L. Catlett, William Hayes, Justyna Szostak, Julia Hoeng, Manuel Peitsch

Database, Volume 2016, 2016, baw113, https://doi.org/10.1093/database/baw113

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DDRprot: a database of DNA damage response-related proteins

Eduardo Andrés-León, Ildefonso Cases, Aida Arcas, Ana M. Rojas

Database, Volume 2016, 2016, baw123, https://doi.org/10.1093/database/baw123

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Automated detection of discourse segment and experimental types from the text of cancer pathway results sections

Gully A.P.C. Burns, Pradeep Dasigi, Anita de Waard, Eduard H. Hovy

Database, Volume 2016, 2016, baw122, https://doi.org/10.1093/database/baw122

Overview of the interactive task in BioCreative V

Qinghua Wang, Shabbir S. Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai, Barbra Ferrell, Juliane Fluck, Socorro Gama-Castro, Nancy George, Georgios Gkoutos, Afroza K. Irin, Lars J. Jensen … Cecilia N. Arighi

Database, Volume 2016, 2016, baw119, https://doi.org/10.1093/database/baw119

Discrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population

Matsuyuki Shirota, Kengo Kinoshita

Database, Volume 2016, 2016, baw124, https://doi.org/10.1093/database/baw124

Modeling biochemical pathways in the gene ontology

David P. Hill, Peter D’Eustachio, Tanya Z. Berardini, Christopher J. Mungall, Nikolai Renedo, Judith A. Blake

Database, Volume 2016, 2016, baw126, https://doi.org/10.1093/database/baw126

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