Sumit Madan, Justyna Szostak, Ravikumar Komandur Elayavilli, Richard Tzong-Han Tsai, Mehdi Ali, Longhua Qian, Majid Rastegar-Mojarad, Julia Hoeng, Juliane Fluck

Database, Volume 2019, 2019, baz084, https://doi.org/10.1093/database/baz084

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DeepScreening: a deep learning-based screening web server for accelerating drug discovery

Zhihong Liu, Jiewen Du, Jiansong Fang, Yulong Yin, Guohuan Xu, Liwei Xie

Database, Volume 2019, 2019, baz104, https://doi.org/10.1093/database/baz104

‘One DB to rule them all’—the RING: a Regulatory INteraction Graph combining TFs, genes/proteins, SNPs, diseases and drugs

Gianfranco Politano, Stefano Di Carlo, Alfredo Benso

Database, Volume 2019, 2019, baz108, https://doi.org/10.1093/database/baz108

SCNBase: a genomics portal for the soybean cyst nematode (Heterodera glycines)

Rick Masonbrink, Tom R Maier, Arun S Seetharam, Parijat S Juvale, Levi Baber, Thomas J Baum, Andrew J Severin

Database, Volume 2019, 2019, baz111, https://doi.org/10.1093/database/baz111

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Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus

Marcin J Skwark, Pedro H M Torres, Liviu Copoiu, Bridget Bannerman, R Andres Floto, Tom L Blundell

Database, Volume 2019, 2019, baz113, https://doi.org/10.1093/database/baz113

RareLSD: a manually curated database of lysosomal enzymes associated with rare diseases

Sana Akhter, Harpreet Kaur, Piyush Agrawal, Gajendra P S Raghava

Database, Volume 2019, 2019, baz112, https://doi.org/10.1093/database/baz112

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FoodBase corpus: a new resource of annotated food entities

Gorjan Popovski, Barbara Koroušić Seljak, Tome Eftimov

Database, Volume 2019, 2019, baz121, https://doi.org/10.1093/database/baz121

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PCIR: a database of Plant Chloroplast Inverted Repeats

Rui Zhang, Fangfang Ge, Huayang Li, Yudong Chen, Ying Zhao, Ying Gao, Zhiguo Liu, Long Yang

Database, Volume 2019, 2019, baz127, https://doi.org/10.1093/database/baz127

Evaluation of an automatic article selection method for timelier updates of the Comet Core Outcome Set database

Christopher R Norman, Elizabeth Gargon, Mariska M G Leeflang, Aurélie Névéol, Paula R Williamson

Database, Volume 2019, 2019, baz109, https://doi.org/10.1093/database/baz109

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MIRKB: a myocardial infarction risk knowledge base

Chaoying Zhan, Manhong Shi, Rongrong Wu, Hongxin He, Xingyun Liu, Bairong Shen

Database, Volume 2019, 2019, baz125, https://doi.org/10.1093/database/baz125

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Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps

Katheryn Buble, Sook Jung, Jodi L Humann, Jing Yu, Chun-Huai Cheng, Taein Lee, Stephen P Ficklin, Heidi Hough, Bradford Condon, Margaret E Staton, Jill L Wegrzyn, Dorrie Main

Database, Volume 2019, 2019, baz100, https://doi.org/10.1093/database/baz100

Enabling semantic queries across federated bioinformatics databases

Ana Claudia Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, Christophe Dessimoz

Database, Volume 2019, 2019, baz106, https://doi.org/10.1093/database/baz106

RPGeNet v2.0: expanding the universe of retinal disease gene interactions network

Rodrigo Arenas-Galnares, Sergio Castillo-Lara, Vasileios Toulis, Daniel Boloc, Roser Gonzàlez-Duarte, Gemma Marfany, Josep F Abril

Database, Volume 2019, 2019, baz120, https://doi.org/10.1093/database/baz120

PMBD: a Comprehensive Plastics Microbial Biodegradation Database

Zhiqiang Gan, Houjin Zhang

Database, Volume 2019, 2019, baz119, https://doi.org/10.1093/database/baz119

The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation

Sickle Cell Disease Ontology Working Group

Database, Volume 2019, 2019, baz118, https://doi.org/10.1093/database/baz118

Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery

Jean-Philippe F Gourdine, Matthew H Brush, Nicole A Vasilevsky, Kent Shefchek, Sebastian Köhler, Nicolas Matentzoglu, Monica C Munoz-Torres, Julie A McMurry, Xingmin Aaron Zhang, Peter N Robinson, Melissa A Haendel

Database, Volume 2019, 2019, baz114, https://doi.org/10.1093/database/baz114

Identification of tRNA-derived ncRNAs in TCGA and NCI-60 panel cell lines and development of the public database tRFexplorer

Alessandro La Ferlita, Salvatore Alaimo, Dario Veneziano, Giovanni Nigita, Veronica Balatti, Carlo M Croce, Alfredo Ferro, Alfredo Pulvirenti

Database, Volume 2019, 2019, baz115, https://doi.org/10.1093/database/baz115

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A new unbiased and highly automated approach to find new prognostic markers in preclinical research

Martin Neidnicht, Daniela Mittermüller, Katharina Effenberger-Neidnicht

Database, Volume 2019, 2019, baz107, https://doi.org/10.1093/database/baz107

ODNA: a manually curated database of noncoding RNAs associated with orthopedics

Changcheng You, Kai Zhu, Qiuhua Zhang, Jnglong Yan, Yufu Wang, Jing Li

Database, Volume 2019, 2019, baz126, https://doi.org/10.1093/database/baz126

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Machine learning approach to literature mining for the genetics of complex diseases

Jessica Schuster, Michael Superdock, Anthony Agudelo, Paul Stey, James Padbury, Indra Neil Sarkar, Alper Uzun

Database, Volume 2019, 2019, baz124, https://doi.org/10.1093/database/baz124

Reactome and ORCID—fine-grained credit attribution for community curation

Guilherme Viteri, Lisa Matthews, Thawfeek Varusai, Marc Gillespie, Marija Milacic, Justin Cook, Joel Weiser, Solomon Shorser, Konstantinos Sidiropoulos, Antonio Fabregat, Robin Haw, Guanming Wu, Lincoln Stein, Peter D’Eustachio, Henning Hermjakob

Database, Volume 2019, 2019, baz123, https://doi.org/10.1093/database/baz123

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A general approach for improving deep learning-based medical relation extraction using a pre-trained model and fine-tuning

Tao Chen, Mingfen Wu, Hexi Li

Database, Volume 2019, 2019, baz116, https://doi.org/10.1093/database/baz116

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RAACBook: a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou’s five-step rule

Lei Zheng, Shenghui Huang, Nengjiang Mu, Haoyue Zhang, Jiayu Zhang, Yu Chang, Lei Yang, Yongchun Zuo

Database, Volume 2019, 2019, baz131, https://doi.org/10.1093/database/baz131

Plant Regulomics Portal (PRP): a comprehensive integrated regulatory information and analysis portal for plant genomes

Ganesh Panzade, Indu Gangwar, Supriya Awasthi, Nitesh Sharma, Ravi Shankar

Database, Volume 2019, 2019, baz130, https://doi.org/10.1093/database/baz130

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NeoPeptide: an immunoinformatic database of T-cell-defined neoantigens

Wei-Jun Zhou, Zhi Qu, Chao-Yang Song, Yang Sun, An-Li Lai, Ma-Yao Luo, Yu-Zhe Ying, Hu Meng, Zhao Liang, Yan-Jie He, Yu-Hua Li, Jian Liu

Database, Volume 2019, 2019, baz128, https://doi.org/10.1093/database/baz128

Improved standardization of transcribed digital specimen data

Quentin Groom, Mathias Dillen, Helen Hardy, Sarah Phillips, Luc Willemse, Zhengzhe Wu

Database, Volume 2019, 2019, baz129, https://doi.org/10.1093/database/baz129

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GenoSurf: metadata driven semantic search system for integrated genomic datasets

Arif Canakoglu, Anna Bernasconi, Andrea Colombo, Marco Masseroli, Stefano Ceri

Database, Volume 2019, 2019, baz132, https://doi.org/10.1093/database/baz132

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UPObase: an online database of unspecific peroxygenases

Muniba Faiza, Dongming Lan, Shengfeng Huang, Yonghua Wang

Database, Volume 2019, 2019, baz122, https://doi.org/10.1093/database/baz122

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AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences

Abhijeet Singh, Bettina Müller, Hans-Henrik Fuxelius, Anna Schnürer

Database, Volume 2019, 2019, baz142, https://doi.org/10.1093/database/baz142

The human DEPhOsphorylation Database DEPOD: 2019 update

Nikhil P Damle, Maja Köhn

Database, Volume 2019, 2019, baz133, https://doi.org/10.1093/database/baz133

Mesophotic.org: a repository for scientific information on mesophotic ecosystems

Pim Bongaerts, Gonzalo Perez-Rosales, Veronica Z Radice, Gal Eyal, Andrea Gori, Erika Gress, Nicholas M Hammerman, Alejandra Hernandez-Agreda, Jack Laverick, Paul Muir, Hudson Pinheiro, Richard L Pyle, Luiz Rocha, Joseph A Turner, Ryan Booker

Database, Volume 2019, 2019, baz140, https://doi.org/10.1093/database/baz140

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SGID: a comprehensive and interactive database of the silkworm

Zhenglin Zhu, Zhufen Guan, Gexin Liu, Yawang Wang, Ze Zhang

Database, Volume 2019, 2019, baz134, https://doi.org/10.1093/database/baz134

RHPCG: a database of the Regulation of the Hippo Pathway in Cancer Genome

Chengyu Wang, Fan Yang, Tingting Chen, Qi Dong, Zhangxiang Zhao, Yaoyao Liu, Bo Chen, Haihai Liang, Huike Yang, Yunyan Gu

Database, Volume 2019, 2019, baz135, https://doi.org/10.1093/database/baz135

The COMPARE Data Hubs

Clara Amid, Nima Pakseresht, Nicole Silvester, Suran Jayathilaka, Ole Lund, Lukasz D Dynovski, Bálint Á Pataki, Dávid Visontai, Basil Britto Xavier, Blaise T F Alako, Ariane Belka, Jose L B Cisneros, Matthew Cotten, George B Haringhuizen, Peter W Harrison, Dirk Höper, Sam Holt, Camilla Hundahl, Abdulrahman Hussein … Guy Cochrane

Database, Volume 2019, 2019, baz136, https://doi.org/10.1093/database/baz136

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Original Article

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Peter Brown, RELISH Consortium, Yaoqi Zhou

Database, Volume 2019, 2019, baz085, https://doi.org/10.1093/database/baz085

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NutriGenomeDB: a nutrigenomics exploratory and analytical platform

Roberto Martín-Hernández, Guillermo Reglero, José M Ordovás, Alberto Dávalos

Database, Volume 2019, 2019, baz097, https://doi.org/10.1093/database/baz097

ProtMiscuity: a database of promiscuous proteins

Ana Julia Velez Rueda, Nicolas Palopoli, Matías Zacarías, Leandro Matías Sommese, Gustavo Parisi

Database, Volume 2019, 2019, baz103, https://doi.org/10.1093/database/baz103

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Extraction of chemical–protein interactions from the literature using neural networks and narrow instance representation

Rui Antunes, Sérgio Matos

Database, Volume 2019, 2019, baz095, https://doi.org/10.1093/database/baz095

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RiceRelativesGD: a genomic database of rice relatives for rice research

Lingfeng Mao, Meihong Chen, Qinjie Chu, Lei Jia, Most Humaira Sultana, Dongya Wu, Xiangdong Kong, Jie Qiu, Chu-Yu Ye, Qian-Hao Zhu, Xi Chen, Longjiang Fan

Database, Volume 2019, 2019, baz110, https://doi.org/10.1093/database/baz110

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CDEK: Clinical Drug Experience Knowledgebase

Rebekah H Griesenauer, Constantino Schillebeeckx, Michael S Kinch

Database, Volume 2019, 2019, baz087, https://doi.org/10.1093/database/baz087

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PICEAdatabase: a web database for Picea omics and phenotypic information

Nan Lu, Tianqing Zhu, Fangqun Ouyang, Yan Xia, Qingfen Li, Zirui Jia, Jiwen Hu, Juanjuan Ling, Wenjun Ma, Guijuan Yang, Hanguo Zhang, Lisheng Kong, Junhui Wang

Database, Volume 2019, 2019, baz089, https://doi.org/10.1093/database/baz089

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SOCCOMAS: a FAIR web content management system that uses knowledge graphs and that is based on semantic programming

Lars Vogt, Roman Baum, Philipp Bhatty, Christian Köhler, Sandra Meid, Björn Quast, Peter Grobe

Database, Volume 2019, 2019, baz067, https://doi.org/10.1093/database/baz067

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An effective biomedical data migration tool from resource description framework to JSON

Jian Liu, Mo Yang, Lei Zhang, Weijun Zhou

Database, Volume 2019, 2019, baz088, https://doi.org/10.1093/database/baz088

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VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases

Chien-Yueh Lee, Amrita Chattopadhyay, Li-Mei Chiang, Jyh-Ming Jimmy Juang, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y Chuang

Database, Volume 2019, 2019, baz075, https://doi.org/10.1093/database/baz075

Combined alignments of sequences and domains characterize unknown proteins with remotely related protein search PSISearch2D

Minglei Yang, Wenliang Zhang, Guocai Yao, Haiyue Zhang, Weizhong Li

Database, Volume 2019, 2019, baz092, https://doi.org/10.1093/database/baz092

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Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases

Shawna Spoor, Chun-Huai Cheng, Lacey-Anne Sanderson, Bradford Condon, Abdullah Almsaeed, Ming Chen, Anthony Bretaudeau, Helena Rasche, Sook Jung, Dorrie Main, Kirstin Bett, Margaret Staton, Jill L Wegrzyn, F Alex Feltus, Stephen P Ficklin

Database, Volume 2019, 2019, baz077, https://doi.org/10.1093/database/baz077

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IRAM: virus capsid database and analysis resource

Iman Almansour, Mazen Alhagri, Rahaf Alfares, Manal Alshehri, Razan Bakhashwain, Ahmed Maarouf

Database, Volume 2019, 2019, baz079, https://doi.org/10.1093/database/baz079

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MycoResistance: a curated resource of drug resistance molecules in Mycobacteria

Enyu Dai, Hao Zhang, Xu Zhou, Qian Song, Di Li, Lei Luo, Xinyu Xu, Wei Jiang, Hong Ling

Database, Volume 2019, 2019, baz074, https://doi.org/10.1093/database/baz074

A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases

Susie S Y Huang, Fatima Al Ali, Sabri Boughorbel, Mohammed Toufiq, Damien Chaussabel, Mathieu Garand

Database, Volume 2019, 2019, baz066, https://doi.org/10.1093/database/baz066

Semalytics: a semantic analytics platform for the exploration of distributed and heterogeneous cancer data in translational research

Andrea Mignone, Alberto Grand, Alessandro Fiori, Enzo Medico, Andrea Bertotti

Database, Volume 2019, 2019, baz080, https://doi.org/10.1093/database/baz080

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Phytochelatin database: a resource for phytochelatin complexes of nutritional and environmental metals

Kristine K Dennis, Karan Uppal, Ken H Liu, Chunyu Ma, Bill Liang, Young-Mi Go, Dean P Jones

Database, Volume 2019, 2019, baz083, https://doi.org/10.1093/database/baz083

PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database

Rezarta Islamaj, W John Wilbur, Natalie Xie, Noreen R Gonzales, Narmada Thanki, Roxanne Yamashita, Chanjuan Zheng, Aron Marchler-Bauer, Zhiyong Lu

Database, Volume 2019, 2019, baz064, https://doi.org/10.1093/database/baz064

PTSD Biomarker Database: deep dive metadatabase for PTSD biomarkers, visualizations and analysis tools

Daniel Domingo-Fernández, Allison Provost, Alpha Tom Kodamullil, Josep Marín-Llaó, Heather Lasseter, Kristophe Diaz, Nikolaos P Daskalakis, Lee Lancashire, Martin Hofmann-Apitius, Magali Haas

Database, Volume 2019, 2019, baz081, https://doi.org/10.1093/database/baz081

Oomycete Gene Table: an online database for comparative genomic analyses of the oomycete microorganisms

Thidarat Rujirawat, Preecha Patumcharoenpol, Weerayuth Kittichotirat, Theerapong Krajaejun

Database, Volume 2019, 2019, baz082, https://doi.org/10.1093/database/baz082

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PRRDB 2.0: a comprehensive database of pattern-recognition receptors and their ligands

Dilraj Kaur, Sumeet Patiyal, Neelam Sharma, Salman Sadullah Usmani, Gajendra P S Raghava

Database, Volume 2019, 2019, baz076, https://doi.org/10.1093/database/baz076

MolMeDB: Molecules on Membranes Database

Jakub Juračka, Martin Šrejber, Michaela Melíková, Václav Bazgier, Karel Berka

Database, Volume 2019, 2019, baz078, https://doi.org/10.1093/database/baz078

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SeQuery: an interactive graph database for visualizing the GPCR superfamily

Geng-Ming Hu, M K Secario, Chi-Ming Chen

Database, Volume 2019, 2019, baz073, https://doi.org/10.1093/database/baz073

MepmiRDB: a medicinal plant microRNA database

Dongliang Yu, Jiangjie Lu, Weishan Shao, Xiaoxia Ma, Tian Xie, Hidetaka Ito, Tingzhang Wang, Min Xu, Huizhong Wang, Yijun Meng

Database, Volume 2019, 2019, baz070, https://doi.org/10.1093/database/baz070

Mr.Vc: a database of microarray and RNA-seq of Vibrio cholerae

Zhiyuan Zhang, Guozhong Chen, Jun Hu, Wajid Hussain, Fenxia Fan, Yalin Yang, Zhigang Zhou, Xiaodong Fang, Jun Zhu, Wei-Hua Chen, Zhi Liu

Database, Volume 2019, 2019, baz069, https://doi.org/10.1093/database/baz069

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AmyloWiki: an integrated database for Bacillus velezensis FZB42, the model strain for plant growth-promoting Bacilli

Ben Fan, Cong Wang, Xiaolei Ding, Bingyao Zhu, Xiaofeng Song, Rainer Borriss

Database, Volume 2019, 2019, baz071, https://doi.org/10.1093/database/baz071

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CCRDB: a cancer circRNAs-related database and its application in hepatocellular carcinoma-related circRNAs

Qingyu Liu, Yanning Cai, Haiquan Xiong, Yiyun Deng, Xianhua Dai

Database, Volume 2019, 2019, baz063, https://doi.org/10.1093/database/baz063

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Re-curation and rational enrichment of knowledge graphs in Biological Expression Language

Charles Tapley Hoyt, Daniel Domingo-Fernández, Rana Aldisi, Lingling Xu, Kristian Kolpeja, Sandra Spalek, Esther Wollert, John Bachman, Benjamin M Gyori, Patrick Greene, Martin Hofmann-Apitius

Database, Volume 2019, 2019, baz068, https://doi.org/10.1093/database/baz068

SpinachBase: a central portal for spinach genomics

Keeley Collins, Kun Zhao, Chen Jiao, Chenxi Xu, Xiaofeng Cai, Xiaoli Wang, Chenhui Ge, Shaojun Dai, Quanxi Wang, Quanhua Wang, Zhangjun Fei, Yi Zheng

Database, Volume 2019, 2019, baz072, https://doi.org/10.1093/database/baz072

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Endometriosis Knowledgebase: a gene-based resource on endometriosis

Shaini Joseph, Smita D Mahale

Database, Volume 2019, 2019, baz062, https://doi.org/10.1093/database/baz062

Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases

Marcos Martínez-Romero, Martin J O'Connor, Attila L Egyedi, Debra Willrett, Josef Hardi, John Graybeal, Mark A Musen

Database, Volume 2019, 2019, baz059, https://doi.org/10.1093/database/baz059

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Chickspress: a resource for chicken gene expression

Fiona M McCarthy, Ken Pendarvis, Amanda M Cooksey, Cathy R Gresham, Matt Bomhoff, Sean Davey, Eric Lyons, Tad S Sonstegard, Susan M Bridges, Shane C Burgess

Database, Volume 2019, 2019, baz058, https://doi.org/10.1093/database/baz058

LanceletDB: an integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species

Leiming You, Jiaqi Chi, Shengfeng Huang, Ting Yu, Guangrui Huang, Yuchao Feng, Xiaopu Sang, Xinhui Gao, Ting’an Li, Zirui Yue, Aijie Liu, Shangwu Chen, Anlong Xu

Database, Volume 2019, 2019, baz056, https://doi.org/10.1093/database/baz056

VigSatDB: genome-wide microsatellite DNA marker database of three species of Vigna for germplasm characterization and improvement

Rahul Singh Jasrotia, Pramod Kumar Yadav, Mir Asif Iquebal, S B Bhatt, Vasu Arora, U B Angadi, Rukam Singh Tomar, Sarika Jaiswal, Anil Rai, Dinesh Kumar

Database, Volume 2019, 2019, baz055, https://doi.org/10.1093/database/baz055

Chemical–protein interaction extraction via contextualized word representations and multihead attention

Yijia Zhang, Hongfei Lin, Zhihao Yang, Jian Wang, Yuanyuan Sun

Database, Volume 2019, 2019, baz054, https://doi.org/10.1093/database/baz054

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GIDB: a knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal cancer

Ying Wang, Yueqian Wang, Shuangkuai Wang, Yuantao Tong, Ling Jin, Hui Zong, Rongbin Zheng, Jinxuan Yang, Zeyu Zhang, En Ouyang, Mengyan Zhou, Xiaoyan Zhang

Database, Volume 2019, 2019, baz051, https://doi.org/10.1093/database/baz051

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The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups

Malo Le Boulch, Patrice Déhais, Sylvie Combes, Géraldine Pascal

Database, Volume 2019, 2019, baz049, https://doi.org/10.1093/database/baz049

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rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots

Jan Jelínek, David Hoksza, Jan Hajič, Jan Pešek, Jan Drozen, Tomáš Hladík, Michal Klimpera, Jiří Vohradský, Josef Pánek

Database, Volume 2019, 2019, baz047, https://doi.org/10.1093/database/baz047

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An effective biomedical document classification scheme in support of biocuration: addressing class imbalance

Xiangying Jiang, Martin Ringwald, Judith A Blake, Cecilia Arighi, Gongbo Zhang, Hagit Shatkay

Database, Volume 2019, 2019, baz045, https://doi.org/10.1093/database/baz045

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CANCROX: a cross-species cancer therapy database

Paulo Muniz de Ávila, Diego Cesar Valente e Silva, Paulo Cesar de Melo Bernardo, Ramon Gustavo Teodoro Marques da Silva, Ana Lúcia Fachin, Mozart Marins, Edilson Carlos Caritá

Database, Volume 2019, 2019, baz044, https://doi.org/10.1093/database/baz044

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ChlamBase: a curated model organism database for the Chlamydia research community

Tim Putman, Kevin Hybiske, Derek Jow, Cyrus Afrasiabi, Sebastien Lelong, Marco Alvarado Cano, Gregory S Stupp, Andra Waagmeester, Benjamin M Good, Chunlei Wu, Andrew I Su

Database, Volume 2019, 2019, baz041, https://doi.org/10.1093/database/baz041

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The Natural History Museum Data Portal

Ben Scott, Ed Baker, Matt Woodburn, Sarah Vincent, Helen Hardy, Vincent S Smith

Database, Volume 2019, 2019, baz038, https://doi.org/10.1093/database/baz038

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PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data

Oscar Franzén, Li-Ming Gan, Johan L M Björkegren

Database, Volume 2019, 2019, baz046, https://doi.org/10.1093/database/baz046

An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar

M L Famiglietti, A Estreicher, L Breuza, S Poux, N Redaschi, I Xenarios, A Bridge

Database, Volume 2019, 2019, baz040, https://doi.org/10.1093/database/baz040

A dimensional warehouse for integrating operational data from clinical trials

Michael A Farnum, Lalit Mohanty, Mathangi Ashok, Paul Konstant, Joseph Ciervo, Victor S Lobanov, Dimitris K Agrafiotis

Database, Volume 2019, 2019, baz039, https://doi.org/10.1093/database/baz039

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Quantitative phenotype analysis to identify, validate and compare rat disease models

Yiqing Zhao, Jennifer R Smith, Shur-Jen Wang, Melinda R Dwinell, Mary Shimoyama

Database, Volume 2019, 2019, baz037, https://doi.org/10.1093/database/baz037

Building deep learning models for evidence classification from the open access biomedical literature

Gully A Burns, Xiangci Li, Nanyun Peng

Database, Volume 2019, 2019, baz034, https://doi.org/10.1093/database/baz034

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AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution

Kevin Correia, Shi M Yu, Radhakrishnan Mahadevan

Database, Volume 2019, 2019, baz022, https://doi.org/10.1093/database/baz022

Curating gene sets: challenges and opportunities for integrative analysis

Jason Bubier, David Hill, Gaurab Mukherjee, Timothy Reynolds, Erich J Baker, Alexander Berger, Jake Emerson, Judith A Blake, Elissa J Chesler

Database, Volume 2019, 2019, baz036, https://doi.org/10.1093/database/baz036

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A late-binding, distributed, NoSQL warehouse for integrating patient data from clinical trials

Eric Yang, Jeremy D Scheff, Shih C Shen, Michael A Farnum, James Sefton, Victor S Lobanov, Dimitris K Agrafiotis

Database, Volume 2019, 2019, baz032, https://doi.org/10.1093/database/baz032

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MSGP: the first database of the protein components of the mammalian stress granules

Catarina Nunes, Isa Mestre, Adriana Marcelo, Rebekah Koppenol, Carlos A Matos, Clévio Nóbrega

Database, Volume 2019, 2019, baz031, https://doi.org/10.1093/database/baz031

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YESdb: integrative analysis of environmental stress in yeast

Evi Berchtold, Gergely Csaba, Ralf Zimmer

Database, Volume 2019, 2019, baz023, https://doi.org/10.1093/database/baz023

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Ontology based text mining of gene-phenotype associations: application to candidate gene prediction

Şenay Kafkas, Robert Hoehndorf

Database, Volume 2019, 2019, baz019, https://doi.org/10.1093/database/baz019

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Statistical principle-based approach for recognizing and normalizing microRNAs described in scientific literature

Hong-Jie Dai, Chen-Kai Wang, Nai-Wen Chang, Ming-Siang Huang, Jitendra Jonnagaddala, Feng-Duo Wang, Wen-Lian Hsu

Database, Volume 2019, 2019, baz030, https://doi.org/10.1093/database/baz030

Tetrahymena Comparative Genomics Database (TCGD): a community resource for Tetrahymena

Wentao Yang, Chuanqi Jiang, Ying Zhu, Kai Chen, Guangying Wang, Dongxia Yuan, Wei Miao, Jie Xiong

Database, Volume 2019, 2019, baz029, https://doi.org/10.1093/database/baz029

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PIRSitePredict for protein functional site prediction using position-specific rules

Chuming Chen, Qinghua Wang, Hongzhan Huang, Cholanayakanahalli R Vinayaka, John S Garavelli, Cecilia N Arighi, Darren A Natale, Cathy H Wu

Database, Volume 2019, 2019, baz026, https://doi.org/10.1093/database/baz026

PamulDB: a comprehensive genomic resource for the study of human- and animal-pathogenic Pasteurella multocida

Tian Li, Xiao-Fei Xu, Hui-Hui Du, Li Li, Neng-Zhang Li, Ze-Yang Zhou, Yuan-Yi Peng

Database, Volume 2019, 2019, baz025, https://doi.org/10.1093/database/baz025

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SuCComBase: a manually curated repository of plant sulfur-containing compounds

Sarahani Harun, Muhammad-Redha Abdullah-Zawawi, Mohd Rusman Arief A-Rahman, Nor Azlan Nor Muhammad, Zeti-Azura Mohamed-Hussein

Database, Volume 2019, 2019, baz021, https://doi.org/10.1093/database/baz021

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EnDisease: a manually curated database for enhancer-disease associations

Wanwen Zeng, Xu Min, Rui Jiang

Database, Volume 2019, 2019, baz020, https://doi.org/10.1093/database/baz020

FairBase: a comprehensive database of fungal A-to-I RNA editing

Jinding Liu, Dongbo Wang, Yinna Su, Kun Lang, Rongjing Duan, YuFeng Wu, Fei Ma, Shuiqing Huang

Database, Volume 2019, 2019, baz018, https://doi.org/10.1093/database/baz018

A cross-source, system-agnostic solution for clinical data review

Michael A Farnum, Mathangi Ashok, Daniel Kowalski, Fang Du, Lalit Mohanty, Paul Konstant, Joseph Ciervo, Victor S Lobanov, Dimitris K Agrafiotis

Database, Volume 2019, 2019, baz017, https://doi.org/10.1093/database/baz017

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RiceMetaSysB: a database of blast and bacterial blight responsive genes in rice and its utilization in identifying key blast-resistant WRKY genes

V Sureshkumar, Bipratip Dutta, Vishesh Kumar, G Prakash, Dwijesh C Mishra, K K Chaturvedi, Anil Rai, Amitha Mithra Sevanthi, Amolkumar U Solanke

Database, Volume 2019, 2019, baz015, https://doi.org/10.1093/database/baz015

Integrated curation and data mining for disease and phenotype models at the Rat Genome Database

Shur-Jen Wang, Stanley J F Laulederkind, Yiqing Zhao, G Thomas Hayman, Jennifer R Smith, Monika Tutaj, Jyothi Thota, Marek A Tutaj, Matthew J Hoffman, Elizabeth R Bolton, Jeffrey De Pons, Melinda R Dwinell, Mary Shimoyama

Database, Volume 2019, 2019, baz014, https://doi.org/10.1093/database/baz014

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A scalable, aggregated genotypic–phenotypic database for human disease variation

Ryan Barrett, Cynthia L Neben, Anjali D Zimmer, Gilad Mishne, Wendy McKennon, Alicia Y Zhou, Jeremy Ginsberg

Database, Volume 2019, 2019, baz013, https://doi.org/10.1093/database/baz013

Using deep learning to identify translational research in genomic medicine beyond bench to bedside

Yi-Yu Hsu, Mindy Clyne, Chih-Hsuan Wei, Muin J Khoury, Zhiyong Lu

Database, Volume 2019, 2019, baz010, https://doi.org/10.1093/database/baz010

The radish genome database (RadishGD): an integrated information resource for radish genomics

Hee-Ju Yu, Seunghoon Baek, Young-Joon Lee, Ara Cho, Jeong-Hwan Mun

Database, Volume 2019, 2019, baz009, https://doi.org/10.1093/database/baz009

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Integration of macromolecular complex data into the Saccharomyces Genome Database

Edith D Wong, Marek S Skrzypek, Shuai Weng, Gail Binkley, Birgit H M Meldal, Livia Perfetto, Sandra E Orchard, Stacia R Engel, J Michael Cherry, the SGD Project

Database, Volume 2019, 2019, baz008, https://doi.org/10.1093/database/baz008

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Annotation of gene product function from high-throughput studies using the Gene Ontology

Helen Attrill, Pascale Gaudet, Rachael P Huntley, Ruth C Lovering, Stacia R Engel, Sylvain Poux, Kimberly M Van Auken, George Georghiou, Marcus C Chibucos, Tanya Z Berardini, Valerie Wood, Harold Drabkin, Petra Fey, Penelope Garmiri, Midori A Harris, Tony Sawford, Leonore Reiser, Rebecca Tauber, Sabrina Toro, The Gene Ontology Consortium

Database, Volume 2019, 2019, baz007, https://doi.org/10.1093/database/baz007

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ZincBind—the database of zinc binding sites

Sam M Ireland, Andrew C R Martin

Database, Volume 2019, 2019, baz006, https://doi.org/10.1093/database/baz006

APID database: redefining protein–protein interaction experimental evidences and binary interactomes

Diego Alonso-López, Francisco J Campos-Laborie, Miguel A Gutiérrez, Luke Lambourne, Michael A Calderwood, Marc Vidal, Javier De Las Rivas

Database, Volume 2019, 2019, baz005, https://doi.org/10.1093/database/baz005

One tool to find them all: a case of data integration and querying in a distributed LIMS platform

Alberto Grand, Emanuele Geda, Andrea Mignone, Andrea Bertotti, Alessandro Fiori

Database, Volume 2019, 2019, baz004, https://doi.org/10.1093/database/baz004

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Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research

Gerhard Rambold, Pelin Yilmaz, Janno Harjes, Sabrina Klaster, Veronica Sanz, Anton Link, Frank Oliver Glöckner, Dagmar Triebel

Database, Volume 2019, 2019, baz002, https://doi.org/10.1093/database/baz002

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Automatic identification of relevant chemical compounds from patents

Saber A Akhondi, Hinnerk Rey, Markus Schwörer, Michael Maier, John Toomey, Heike Nau, Gabriele Ilchmann, Mark Sheehan, Matthias Irmer, Claudia Bobach, Marius Doornenbal, Michelle Gregory, Jan A Kors

Database, Volume 2019, 2019, baz001, https://doi.org/10.1093/database/baz001

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Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine

Rezarta Islamaj Doğan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altınel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang … Zhiyong Lu

Database, Volume 2019, 2019, bay147, https://doi.org/10.1093/database/bay147

Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase

Phani V Garapati, Jingyao Zhang, Alix J Rey, Steven J Marygold

Database, Volume 2019, 2019, bay144, https://doi.org/10.1093/database/bay144

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RRMdb—an evolutionary-oriented database of RNA recognition motif sequences

Martyna Nowacka, Pietro Boccaletto, Elzbieta Jankowska, Tomasz Jarzynka, Janusz M Bujnicki, Stanislaw Dunin-Horkawicz

Database, Volume 2019, 2019, bay148, https://doi.org/10.1093/database/bay148

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RAEdb: a database of enhancers identified by high-throughput reporter assays

Zena Cai, Ya Cui, Zhiying Tan, Gaihua Zhang, Zhongyang Tan, Xinlei Zhang, Yousong Peng

Database, Volume 2019, 2019, bay140, https://doi.org/10.1093/database/bay140

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Enhanced taxonomy annotation of antiviral activity data from ChEMBL

Anastasia A Nikitina, Alexey A Orlov, Liubov I Kozlovskaya, Vladimir A Palyulin, Dmitry I Osolodkin

Database, Volume 2019, 2019, bay139, https://doi.org/10.1093/database/bay139

Extracting chemical–protein interactions from literature using sentence structure analysis and feature engineering

Pei-Yau Lung, Zhe He, Tingting Zhao, Disa Yu, Jinfeng Zhang

Database, Volume 2019, 2019, bay138, https://doi.org/10.1093/database/bay138

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TogoGenome/TogoStanza: modularized Semantic Web genome database

Toshiaki Katayama, Shuichi Kawashima, Shinobu Okamoto, Yuki Moriya, Hirokazu Chiba, Yuki Naito, Takatomo Fujisawa, Hiroshi Mori, Toshihisa Takagi

Database, Volume 2019, 2019, bay132, https://doi.org/10.1093/database/bay132

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Combining relation extraction with function detection for BEL statement extraction

Suwen Liu, Wei Cheng, Longhua Qian, Guodong Zhou

Database, Volume 2019, 2019, bay133, https://doi.org/10.1093/database/bay133

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Database Update

Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms

Jochen T Bick, Shuqin Zeng, Mark D Robinson, Susanne E Ulbrich, Stefan Bauersachs

Database, Volume 2019, 2019, baz086, https://doi.org/10.1093/database/baz086

GrainGenes: centralized small grain resources and digital platform for geneticists and breeders

Victoria C Blake, Margaret R Woodhouse, Gerard R Lazo, Sarah G Odell, Charlene P Wight, Nicholas A Tinker, Yi Wang, Yong Q Gu, Clay L Birkett, Jean-Luc Jannink, Dave E Matthews, David L Hane, Steve L Michel, Eric Yao, Taner Z Sen

Database, Volume 2019, 2019, baz065, https://doi.org/10.1093/database/baz065

YeasTSS: an integrative web database of yeast transcription start sites

Jonathan McMillan, Zhaolian Lu, Judith S Rodriguez, Tae-Hyuk Ahn, Zhenguo Lin

Database, Volume 2019, 2019, baz048, https://doi.org/10.1093/database/baz048

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GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies

Meenakshi S Iyer, Kartik Bhargava, Murugavel Pavalam, Ramanathan Sowdhamini

Database, Volume 2019, 2019, baz042, https://doi.org/10.1093/database/baz042

Update on cpnDB: a reference database of chaperonin sequences

Sarah J Vancuren, Janet E Hill

Database, Volume 2019, 2019, baz033, https://doi.org/10.1093/database/baz033

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PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe

Pritha Ghosh, Teerna Bhattacharyya, Oommen K Mathew, Ramanathan Sowdhamini

Database, Volume 2019, 2019, baz028, https://doi.org/10.1093/database/baz028

Increased interactivity and improvements to the GigaScience database, GigaDB

Si Zhe Xiao, Chris Armit, Scott Edmunds, Laurie Goodman, Peter Li, Mary Ann Tuli, Christopher Ian Hunter

Database, Volume 2019, 2019, baz016, https://doi.org/10.1093/database/baz016

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ImmunoSPdb: an archive of immunosuppressive peptides

Salman Sadullah Usmani, Piyush Agrawal, Manika Sehgal, Pradeep Kumar Patel, Gajendra P S Raghava

Database, Volume 2019, 2019, baz012, https://doi.org/10.1093/database/baz012

LIVE: a manually curated encyclopedia of experimentally validated interactions of lncRNAs

Gaole An, Jiaqi Sun, Chao Ren, Zhangyi Ouyang, Lingyun Zhu, Xiaochen Bo, Shaoliang Peng, Wenjie Shu

Database, Volume 2019, 2019, baz011, https://doi.org/10.1093/database/baz011

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ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank

Piyush Agrawal, Sumeet Patiyal, Rajesh Kumar, Vinod Kumar, Harinder Singh, Pawan Kumar Raghav, Gajendra P S Raghava

Database, Volume 2019, 2019, bay142, https://doi.org/10.1093/database/bay142

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The integrated National NeuroAIDS Tissue Consortium database: a rich platform for neuroHIV research

Abigail J Heithoff, Steven A Totusek, Duc Le, Lucas Barwick, Gary Gensler, Donald R Franklin, Allison C Dye, Sanjit Pandey, Seth Sherman, Chittibabu Guda, Howard S Fox

Database, Volume 2019, 2019, bay134, https://doi.org/10.1093/database/bay134

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Database Tool

ApicoTFdb: the comprehensive web repository of apicomplexan transcription factors and transcription-associated co-factors

Rahila Sardar, Abhinav Kaushik, Rajan Pandey, Asif Mohmmed, Shakir Ali, Dinesh Gupta

Database, Volume 2019, 2019, baz094, https://doi.org/10.1093/database/baz094

CasPDB: an integrated and annotated database for Cas proteins from bacteria and archaea

Zhongjie Tang, ShaoQi Chen, Ang Chen, Bifang He, Yuwei Zhou, Guoshi Chai, FengBiao Guo, Jian Huang

Database, Volume 2019, 2019, baz093, https://doi.org/10.1093/database/baz093

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piRDisease v1.0: a manually curated database for piRNA associated diseases

Azhar Muhammad, Ramay Waheed, Nauman Ali Khan, Hong Jiang, Xiaoyuan Song

Database, Volume 2019, 2019, baz052, https://doi.org/10.1093/database/baz052

A web-based tool for the prediction of rice transcription factor function

Anil Kumar Nalini Chandran, Sunok Moon, Yo-Han Yoo, Yoon-Shil Gho, Peijian Cao, Rita Sharma, Manoj K Sharma, Pamela C Ronald, Ki-Hong Jung

Database, Volume 2019, 2019, baz061, https://doi.org/10.1093/database/baz061

ResMarkerDB: a database of biomarkers of response to antibody therapy in breast and colorectal cancer

Judith Pérez-Granado, Janet Piñero, Laura I Furlong

Database, Volume 2019, 2019, baz060, https://doi.org/10.1093/database/baz060

CropCircDB: a comprehensive circular RNA resource for crops in response to abiotic stress

Kai Wang, Chong Wang, Baohuan Guo, Kun Song, Chuanhong Shi, Xin Jiang, Keyi Wang, Yacong Tan, Lequn Wang, Lin Wang, Jiangjiao Li, Ying Li, Yu Cai, Hongwei Zhao, Xiaoyong Sun

Database, Volume 2019, 2019, baz053, https://doi.org/10.1093/database/baz053

PlantMP: a database for moonlighting plant proteins

Bo Su, Zhuang Qian, Tianshu Li, Yuwei Zhou, Aloysius Wong

Database, Volume 2019, 2019, baz050, https://doi.org/10.1093/database/baz050

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SELER: a database of super-enhancer-associated lncRNA- directed transcriptional regulation in human cancers

Zhi-Wei Guo, Chen Xie, Kun Li, Xiang-Ming Zhai, Geng-Xi Cai, Xue-Xi Yang, Ying-Song Wu

Database, Volume 2019, 2019, baz027, https://doi.org/10.1093/database/baz027

PKAD: a database of experimentally measured pKa values of ionizable groups in proteins

Swagata Pahari, Lexuan Sun, Emil Alexov

Database, Volume 2019, 2019, baz024, https://doi.org/10.1093/database/baz024

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CircFunBase: a database for functional circular RNAs

Xianwen Meng, Dahui Hu, Peijing Zhang, Qi Chen, Ming Chen

Database, Volume 2019, 2019, baz003, https://doi.org/10.1093/database/baz003

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Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis

Guocai Chen, Juan Camilo Ramírez, Nan Deng, Xing Qiu, Canglin Wu, W Jim Zheng, Hulin Wu

Database, Volume 2019, 2019, bay145, https://doi.org/10.1093/database/bay145

PubTerm: a web tool for organizing, annotating and curating genes, diseases, molecules and other concepts from PubMed records

José Garcia-Pelaez, David Rodriguez, Roberto Medina-Molina, Gerardo Garcia-Rivas, Carlos Jerjes-Sánchez, Victor Trevino

Database, Volume 2019, 2019, bay137, https://doi.org/10.1093/database/bay137

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TP53LNC-DB, the database of lncRNAs in the p53 signalling network

Muhammad Riaz Khan, Ihtisham Bukhari, Ranjha Khan, Hafiz Muhammad Jafar Hussain, Mian Wu, Rick Francis Thorne, Jinming Li, Guangzhi Liu

Database, Volume 2019, 2019, bay136, https://doi.org/10.1093/database/bay136

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AtFusionDB: a database of fusion transcripts in Arabidopsis thaliana

Ajeet Singh, Shafaque Zahra, Durdam Das, Shailesh Kumar

Database, Volume 2019, 2019, bay135, https://doi.org/10.1093/database/bay135

Perspective/Opinion

Involving community in genes and pathway curation

Sushma Naithani, Parul Gupta, Justin Preece, Priyanka Garg, Valerie Fraser, Lillian K Padgitt-Cobb, Matthew Martin, Kelly Vining, Pankaj Jaiswal

Database, Volume 2019, 2019, bay146, https://doi.org/10.1093/database/bay146

Technical Report

A manual corpus of annotated main findings of clinical case reports

Neil R Smalheiser, Mengqi Luo, Sidharth Addepalli, Xiaokai Cui

Database, Volume 2019, 2019, bay143, https://doi.org/10.1093/database/bay143

Corrigendum

ChlamBase: a curated model organism database for the Chlamydia research community

Tim Putman, Kevin Hybiske, Derek Jow, Cyrus Afrasiabi, Sebastien Lelong, Marco Alvarado Cano, Gregory S Stupp, Andra Waagmeester, Benjamin M Good, Chunlei Wu, Andrew I Su

Database, Volume 2019, 2019, baz091, https://doi.org/10.1093/database/baz091

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LncCeRBase: a database of experimentally validated human competing endogenous long non-coding RNAs

Cong Pian, Guangle Zhang, Tengfei Tu, Xiangyu Ma, Fei Li

Database, Volume 2019, 2019, baz090, https://doi.org/10.1093/database/baz090

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Volume 2019, 2019

Original Article

Database Update

Database Tool