Volume 2018

2018

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EISSN 1758-0463

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Volume 2018, 2018

Original Article

ConTEdb: a comprehensive database of transposable elements in conifers

Fei Yi, Juanjuan Ling, Yao Xiao, Hanguo Zhang, Fangqun Ouyang, Junhui Wang

Database, Volume 2018, 2018, bay131, https://doi.org/10.1093/database/bay131

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Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement

Ibrahim Burak Ozyurt, Jeffrey S Grethe

Database, Volume 2018, 2018, bay130, https://doi.org/10.1093/database/bay130

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Accelerating annotation of articles via automated approaches: evaluation of the neXtA₅ curation-support tool by neXtProt

Aurore Britan, Isabelle Cusin, Valérie Hinard, Luc Mottin, Emilie Pasche, Julien Gobeill, Valentine Rech de Laval, Anne Gleizes, Daniel Teixeira, Pierre-André Michel, Patrick Ruch, Pascale Gaudet

Database, Volume 2018, 2018, bay129, https://doi.org/10.1093/database/bay129

iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature

Jia Ren, Gang Li, Karen Ross, Cecilia Arighi, Peter McGarvey, Shruti Rao, Julie Cowart, Subha Madhavan, K Vijay-Shanker, Cathy H Wu

Database, Volume 2018, 2018, bay128, https://doi.org/10.1093/database/bay128

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Where differences resemble: sequence-feature analysis in curated databases of intrinsically disordered proteins

Marco Necci, Damiano Piovesan, Silvio C E Tosatto

Database, Volume 2018, 2018, bay127, https://doi.org/10.1093/database/bay127

BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language

Charles Tapley Hoyt, Daniel Domingo-Fernández, Martin Hofmann-Apitius

Database, Volume 2018, 2018, bay126, https://doi.org/10.1093/database/bay126

PhytoTypeDB: a database of plant protein inter-cultivar variability and function

Marco Necci, Damiano Piovesan, Diego Micheletti, Lisanna Paladin, Alessandro Cestaro, Silvio C E Tosatto

Database, Volume 2018, 2018, bay125, https://doi.org/10.1093/database/bay125

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Cloud-based relational database for multimodal animal data

Niklas Pallast, Frederique Wieters, Marieke Nill, Gereon R Fink, Markus Aswendt

Database, Volume 2018, 2018, bay124, https://doi.org/10.1093/database/bay124

NBDC RDF portal: a comprehensive repository for semantic data in life sciences

Shuichi Kawashima, Toshiaki Katayama, Hideki Hatanaka, Tatsuya Kushida, Toshihisa Takagi

Database, Volume 2018, 2018, bay123, https://doi.org/10.1093/database/bay123

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BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics

Qingyu Chen, Nagesh C Panyam, Aparna Elangovan, Karin Verspoor

Database, Volume 2018, 2018, bay122, https://doi.org/10.1093/database/bay122

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Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems

Wasila Dahdul, Prashanti Manda, Hong Cui, James P Balhoff, T Alexander Dececchi, Nizar Ibrahim, Hilmar Lapp, Todd Vision, Paula M Mabee

Database, Volume 2018, 2018, bay110, https://doi.org/10.1093/database/bay110

ANCO-GeneDB: annotations and comprehensive analysis of candidate genes for alcohol, nicotine, cocaine and opioid dependence

Ruifeng Hu, Yulin Dai, Peilin Jia, Zhongming Zhao

Database, Volume 2018, 2018, bay121, https://doi.org/10.1093/database/bay121

Potent pairing: ensemble of long short-term memory networks and support vector machine for chemical-protein relation extraction

Farrokh Mehryary, Jari Björne, Tapio Salakoski, Filip Ginter

Database, Volume 2018, 2018, bay120, https://doi.org/10.1093/database/bay120

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RTPDB: a database providing associations between genetic variation or expression and cancer prognosis with radiotherapy-based treatment

Cheng-Dong Zhang, Yuan Yang, Huan-Huan Chen, Ting Zhang, Qiang Wang, Yuan Liang, Liang Zhang, Yan Zhou

Database, Volume 2018, 2018, bay118, https://doi.org/10.1093/database/bay118

GCDB: a glaucomatous chemogenomics database for in silico drug discovery

Yu Wei, Jinlong Li, Baiqing Li, Chunfeng Ma, Xuanming Xu, Xu Wang, Aqin Liu, Tengfei Du, Zhonghua Wang, Zhangyong Hong, Jianping Lin

Database, Volume 2018, 2018, bay117, https://doi.org/10.1093/database/bay117

Gene ontology concept recognition using named concept: understanding the various presentations of the gene functions in biomedical literature

Chia-Jung Yang, Jung-Hsien Chiang

Database, Volume 2018, 2018, bay115, https://doi.org/10.1093/database/bay115

LPTK: a linguistic pattern-aware dependency tree kernel approach for the BioCreative VI CHEMPROT task

Neha Warikoo, Yung-Chun Chang, Wen-Lian Hsu

Database, Volume 2018, 2018, bay108, https://doi.org/10.1093/database/bay108

MGH: a genome hub for the medicinal plant maca (Lepidium meyenii)

Junhao Chen, Jiawei Zhang, Meigui Lin, Wei Dong, Xinyue Guo, Yang Dong, Zhengjia Wang, Liangsheng Zhang, Fei Chen

Database, Volume 2018, 2018, bay113, https://doi.org/10.1093/database/bay113

ZFLNC: a comprehensive and well-annotated database for zebrafish lncRNA

Xiang Hu, Wen Chen, Jing Li, Shulan Huang, Xuling Xu, Xuan Zhang, Shuanglin Xiang, Changning Liu

Database, Volume 2018, 2018, bay114, https://doi.org/10.1093/database/bay114

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Overview of the BioCreative VI text-mining services for Kinome Curation Track

Julien Gobeill, Pascale Gaudet, Daniel Dopp, Adam Morrone, Indika Kahanda, Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu, Patrick Ruch

Database, Volume 2018, 2018, bay104, https://doi.org/10.1093/database/bay104

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siAbasic: a comprehensive database for potent siRNA-6Ø sequences without off-target effects

Jongyeun Park, Seung Hyun Ahn, Kwang Moon Cho, Dowoon Gu, Eun-Sook Jang, Sung Wook Chi

Database, Volume 2018, 2018, bay109, https://doi.org/10.1093/database/bay109

Toward a service-based workflow for automated information extraction from herbarium specimens

Agnes Kirchhoff, Ulrich Bügel, Eduard Santamaria, Fabian Reimeier, Dominik Röpert, Alexander Tebbje, Anton Güntsch, Fernando Chaves, Karl-Heinz Steinke, Walter Berendsohn

Database, Volume 2018, 2018, bay103, https://doi.org/10.1093/database/bay103

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Extracting chemical–protein relations using attention-based neural networks

Sijia Liu, Feichen Shen, Ravikumar Komandur Elayavilli, Yanshan Wang, Majid Rastegar-Mojarad, Vipin Chaudhary, Hongfang Liu

Database, Volume 2018, 2018, bay102, https://doi.org/10.1093/database/bay102

AGD: Aneurysm Gene Database

Ruya Sun, Chunmei Cui, Yuan Zhou, Qinghua Cui

Database, Volume 2018, 2018, bay100, https://doi.org/10.1093/database/bay100

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Large-scale automated machine reading discovers new cancer-driving mechanisms

Marco A Valenzuela-Escárcega, Özgün Babur, Gus Hahn-Powell, Dane Bell, Thomas Hicks, Enrique Noriega-Atala, Xia Wang, Mihai Surdeanu, Emek Demir, Clayton T Morrison

Database, Volume 2018, 2018, bay098, https://doi.org/10.1093/database/bay098

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Document triage for identifying protein–protein interactions affected by mutations: a neural network ensemble approach

Ling Luo, Zhihao Yang, Hongfei Lin, Jian Wang

Database, Volume 2018, 2018, bay097, https://doi.org/10.1093/database/bay097

Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling

Suwisa Kaewphan, Kai Hakala, Niko Miekka, Tapio Salakoski, Filip Ginter

Database, Volume 2018, 2018, bay096, https://doi.org/10.1093/database/bay096

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PalmXplore: oil palm gene database

Nik Shazana Nik Mohd Sanusi, Rozana Rosli, Mohd Amin Ab Halim, Kuang-Lim Chan, Jayanthi Nagappan, Norazah Azizi, Nadzirah Amiruddin, Tatiana V Tatarinova, Eng-Ti Leslie Low

Database, Volume 2018, 2018, bay095, https://doi.org/10.1093/database/bay095

An end-to-end deep learning architecture for extracting protein–protein interactions affected by genetic mutations

Tung Tran, Ramakanth Kavuluru

Database, Volume 2018, 2018, Pages 1–13, https://doi.org/10.1093/database/bay092

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Assisting document triage for human kinome curation via machine learning

Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu

Database, Volume 2018, 2018, bay091, https://doi.org/10.1093/database/bay091

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THE-DB: a threading model database for comparative protein structure analysis of the E. coli K12 and human proteomes

Justin S Diamond, Yang Zhang

Database, Volume 2018, 2018, bay090, https://doi.org/10.1093/database/bay090

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AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Lisa Harper, Jacqueline Campbell, Ethalinda K S Cannon, Sook Jung, Monica Poelchau, Ramona Walls, Carson Andorf, Elizabeth Arnaud, Tanya Z Berardini, Clayton Birkett, Steve Cannon, James Carson, Bradford Condon, Laurel Cooper, Nathan Dunn, Christine G Elsik, Andrew Farmer, Stephen P Ficklin, David Grant … Doreen Main

Database, Volume 2018, 2018, bay088, https://doi.org/10.1093/database/bay088

lncSLdb: a resource for long non-coding RNA subcellular localization

Xiao Wen, Lin Gao, Xingli Guo, Xing Li, Xiaotai Huang, Ying Wang, Haifu Xu, Ruijie He, Chenglong Jia, Feixiang Liang

Database, Volume 2018, 2018, bay085, https://doi.org/10.1093/database/bay085

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Drug Target Commons 2.0: a community platform for systematic analysis of drug–target interaction profiles

ZiaurRehman Tanoli, Zaid Alam, Markus Vähä-Koskela, Balaguru Ravikumar, Alina Malyutina, Alok Jaiswal, Jing Tang, Krister Wennerberg, Tero Aittokallio

Database, Volume 2018, 2018, bay083, https://doi.org/10.1093/database/bay083

SMMDB: a web-accessible database for small molecule modulators and their targets involved in neurological diseases

Subodh Kumar Mishra, Neha Jain, Uma Shankar, Arpita Tawani, Amit Mishra, Amit Kumar

Database, Volume 2018, 2018, bay082, https://doi.org/10.1093/database/bay082

PlaNC-TE: a comprehensive knowledgebase of non-coding RNAs and transposable elements in plants

Daniel Longhi Fernandes Pedro, Alan Péricles Rodrigues Lorenzetti, Douglas Silva Domingues, Alexandre Rossi Paschoal

Database, Volume 2018, 2018, bay078, https://doi.org/10.1093/database/bay078

A probabilistic automated tagger to identify human-related publications

Aaron M Cohen, Zackary O Dunivin, Neil R Smalheiser

Database, Volume 2018, 2018, bay079, https://doi.org/10.1093/database/bay079

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Spfy: an integrated graph database for real-time prediction of bacterial phenotypes and downstream comparative analyses

Kevin K Le, Matthew D Whiteside, James E Hopkins, Victor P J Gannon, Chad R Laing

Database, Volume 2018, 2018, bay086, https://doi.org/10.1093/database/bay086

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MetaHCR: a web-enabled metagenome data management system for hydrocarbon resources

Peter C Marks, Marc Bigler, Eric B Alsop, Adrien Vigneron, Bart P Lomans, Renato De Paula, Brett Geissler, Nicolas Tsesmetzis

Database, Volume 2018, 2018, bay087, https://doi.org/10.1093/database/bay087

Hierarchical bi-directional attention-based RNNs for supporting document classification on protein–protein interactions affected by genetic mutations

Aris Fergadis, Christos Baziotis, Dimitris Pappas, Haris Papageorgiou, Alexandros Potamianos

Database, Volume 2018, 2018, bay076, https://doi.org/10.1093/database/bay076

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Extracting chemical–protein relations with ensembles of SVM and deep learning models

Yifan Peng, Anthony Rios, Ramakanth Kavuluru, Zhiyong Lu

Database, Volume 2018, 2018, bay073, https://doi.org/10.1093/database/bay073

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realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta)

Fei Chen, Jiawei Zhang, Junhao Chen, Xiaojiang Li, Wei Dong, Jian Hu, Meigui Lin, Yanhui Liu, Guowei Li, Zhengjia Wang, Liangsheng Zhang

Database, Volume 2018, 2018, bay072, https://doi.org/10.1093/database/bay072

Leveraging prior knowledge for protein–protein interaction extraction with memory network

Huiwei Zhou, Zhuang Liu, Shixian Ning, Yunlong Yang, Chengkun Lang, Yingyu Lin, Kun Ma

Database, Volume 2018, 2018, bay071, https://doi.org/10.1093/database/bay071

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Improving the learning of chemical-protein interactions from literature using transfer learning and specialized word embeddings

P Corbett, J Boyle

Database, Volume 2018, 2018, bay066, https://doi.org/10.1093/database/bay066

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A Field Sensor: computing the composition and intent of PubMed queries

Lana Yeganova, Won Kim, Donald C Comeau, W John Wilbur, Zhiyong Lu

Database, Volume 2018, 2018, bay052, https://doi.org/10.1093/database/bay052

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HRPDviewer: human ribosome profiling data viewer

Wei-Sheng Wu, Yu-Xuan Jiang, Jer-Wei Chang, Yu-Han Chu, Yi-Hao Chiu, Yi-Hong Tsao, Torbjörn E M Nordling, Yan-Yuan Tseng, Joseph T Tseng

Database, Volume 2018, 2018, bay074, https://doi.org/10.1093/database/bay074

A set of domain rules and a deep network for protein coreference resolution

Chen Li, Zhiqiang Rao, Qinghua Zheng, Xiangrong Zhang

Database, Volume 2018, 2018, bay065, https://doi.org/10.1093/database/bay065

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CeleryDB: a genomic database for celery

Kai Feng, Xi-Lin Hou, Meng-Yao Li, Qian Jiang, Zhi-Sheng Xu, Jie-Xia Liu, Ai-Sheng Xiong

Database, Volume 2018, 2018, bay070, https://doi.org/10.1093/database/bay070

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KM-express: an integrated online patient survival and gene expression analysis tool for the identification and functional characterization of prognostic markers in breast and prostate cancers

Xin Chen, Zhengqiang Miao, Mayur Divate, Zuxianglan Zhao, Edwin Cheung

Database, Volume 2018, 2018, bay069, https://doi.org/10.1093/database/bay069

Atlas of Schistosoma mansoni long non-coding RNAs and their expression correlation to protein-coding genes

Elton J R Vasconcelos, Vinícius C Mesel, Lucas F daSilva, David S Pires, Guilherme M Lavezzo, Adriana S A Pereira, Murilo S Amaral, Sergio Verjovski-Almeida

Database, Volume 2018, 2018, bay068, https://doi.org/10.1093/database/bay068

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Identifying frequent patterns in biochemical reaction networks: a workflow

Fabienne Lambusch, Dagmar Waltemath, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Ron Henkel

Database, Volume 2018, 2018, bay051, https://doi.org/10.1093/database/bay051

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A database of wild rice germplasm of Oryza rufipogon species complex from different agro-climatic zones of India

Kabita Tripathy, Balwant Singh, Nisha Singh, Vandna Rai, Gauri Misra, Nagendra Kumar Singh

Database, Volume 2018, 2018, bay058, https://doi.org/10.1093/database/bay058

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Improved biomedical term selection in pseudo relevance feedback

Muhammad Nabeel Asim, Muhammad Wasim, Muhammad Usman Ghani Khan, Waqar Mahmood

Database, Volume 2018, 2018, bay056, https://doi.org/10.1093/database/bay056

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dbLGL: an online leukemia gene and literature database for the retrospective comparison of adult and childhood leukemia genetics with literature evidence

Yining Liu, Mingyu Luo, Zhaochen Jin, Min Zhao, Hong Qu

Database, Volume 2018, 2018, bay062, https://doi.org/10.1093/database/bay062

Chemical–gene relation extraction using recursive neural network

Sangrak Lim, Jaewoo Kang

Database, Volume 2018, 2018, bay060, https://doi.org/10.1093/database/bay060

RBPMetaDB: a comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins

Jin Li, Su-Ping Deng, Jacob Vieira, James Thomas, Valerio Costa, Ching-San Tseng, Franjo Ivankovic, Alfredo Ciccodicola, Peng Yu

Database, Volume 2018, 2018, bay054, https://doi.org/10.1093/database/bay054

ILDgenDB: integrated genetic knowledge resource for interstitial lung diseases (ILDs)

Smriti Mishra, Mohammad I Shah, Malay Sarkar, Nimisha Asati, Chittaranjan Rout

Database, Volume 2018, 2018, bay053, https://doi.org/10.1093/database/bay053

A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities

Charles Tapley Hoyt, Daniel Domingo-Fernández, Nora Balzer, Anka Güldenpfennig, Martin Hofmann-Apitius

Database, Volume 2018, 2018, bay050, https://doi.org/10.1093/database/bay050

SPRENO: a BioC module for identifying organism terms in figure captions

Hong-Jie Dai, Onkar Singh

Database, Volume 2018, 2018, bay048, https://doi.org/10.1093/database/bay048

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dbCRSR: a manually curated database for regulation of cancer radiosensitivity

Pengbo Wen, Junfeng Xia, Xianbin Cao, Bin Chen, Yinping Tao, Lijun Wu, An Xu, Guoping Zhao

Database, Volume 2018, 2018, bay049, https://doi.org/10.1093/database/bay049

DEXTER: Disease-Expression Relation Extraction from Text

Samir Gupta, Hayley Dingerdissen, Karen E Ross, Yu Hu, Cathy H Wu, Raja Mazumder, K Vijay-Shanker

Database, Volume 2018, 2018, bay045, https://doi.org/10.1093/database/bay045

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases

Hartmut Foerster, Aureliano Bombarely, James N D Battey, Nicolas Sierro, Nikolai V Ivanov, Lukas A Mueller

Database, Volume 2018, 2018, bay035, https://doi.org/10.1093/database/bay035

CircR2Disease: a manually curated database for experimentally supported circular RNAs associated with various diseases

Chunyan Fan, Xiujuan Lei, Zengqiang Fang, Qinghua Jiang, Fang-Xiang Wu

Database, Volume 2018, 2018, bay044, https://doi.org/10.1093/database/bay044

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GEMiCCL: mining genotype and expression data of cancer cell lines with elaborate visualization

Inhae Jeong, Namhee Yu, Insu Jang, Yukyung Jun, Min-Seo Kim, Jinhyuk Choi, Byungwook Lee, Sanghyuk Lee

Database, Volume 2018, 2018, bay041, https://doi.org/10.1093/database/bay041

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AbDb: antibody structure database—a database of PDB-derived antibody structures

Saba Ferdous, Andrew C R Martin

Database, Volume 2018, 2018, bay040, https://doi.org/10.1093/database/bay040

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PVCbase: an integrated web resource for the PVC bacterial proteomes

Nicola Bordin, Juan Carlos González-Sánchez, Damien P Devos

Database, Volume 2018, 2018, bay042, https://doi.org/10.1093/database/bay042

StraPep: a structure database of bioactive peptides

Jian Wang, Tailang Yin, Xuwen Xiao, Dan He, Zhidong Xue, Xinnong Jiang, Yan Wang

Database, Volume 2018, 2018, bay038, https://doi.org/10.1093/database/bay038

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Signalling maps in cancer research: construction and data analysis

Maria Kondratova, Nicolas Sompairac, Emmanuel Barillot, Andrei Zinovyev, Inna Kuperstein

Database, Volume 2018, 2018, bay036, https://doi.org/10.1093/database/bay036

An entropy-reducing data representation approach for bioinformatic data

Alan F McCulloch, Ruy Jauregui, Paul H Maclean, Rachael L Ashby, Roger A Moraga, Aurelie Laugraud, Rudiger Brauning, Ken G Dodds, John C McEwan

Database, Volume 2018, 2018, bay029, https://doi.org/10.1093/database/bay029

Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation

Amel Bekkar, Anne Estreicher, Anne Niknejad, Cristina Casals-Casas, Alan Bridge, Ioannis Xenarios, Julien Dorier, Isaac Crespo

Database, Volume 2018, 2018, bay031, https://doi.org/10.1093/database/bay031

A tutorial of diverse genome analysis tools found in the CoGe web-platform using Plasmodium spp. as a model

Andreina I Castillo, Andrew D L Nelson, Asher K Haug-Baltzell, Eric Lyons

Database, Volume 2018, 2018, bay030, https://doi.org/10.1093/database/bay030

dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

Ling Liu, Yi Xiong, Hongyun Gao, Dong-Qing Wei, Julie C Mitchell, Xiaolei Zhu

Database, Volume 2018, 2018, bay034, https://doi.org/10.1093/database/bay034

Probabilistic and machine learning-based retrieval approaches for biomedical dataset retrieval

Payam Karisani, Zhaohui S Qin, Eugene Agichtein

Database, Volume 2018, 2018, bax104, https://doi.org/10.1093/database/bax104

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Improved ontology-based similarity calculations using a study-wise annotation model

Sebastian Köhler

Database, Volume 2018, 2018, bay026, https://doi.org/10.1093/database/bay026

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GEOMetaCuration: a web-based application for accurate manual curation of Gene Expression Omnibus metadata

Zhao Li, Jin Li, Peng Yu

Database, Volume 2018, 2018, bay019, https://doi.org/10.1093/database/bay019

CITGeneDB: a comprehensive database of human and mouse genes enhancing or suppressing cold-induced thermogenesis validated by perturbation experiments in mice

Jin Li, Su-Ping Deng, Gang Wei, Peng Yu

Database, Volume 2018, 2018, bay012, https://doi.org/10.1093/database/bay012

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Finding relevant biomedical datasets: the UC San Diego solution for the bioCADDIE Retrieval Challenge

Wei Wei, Zhanglong Ji, Yupeng He, Kai Zhang, Yuanchi Ha, Qi Li, Lucila Ohno-Machado

Database, Volume 2018, 2018, bay017, https://doi.org/10.1093/database/bay017

PvaxDB: a comprehensive structural repository of Plasmodium vivax proteome

Ankita Singh, Rahul Kaushik, Himani Kuntal, B Jayaram

Database, Volume 2018, 2018, bay021, https://doi.org/10.1093/database/bay021

Baseline and extensions approach to information retrieval of complex medical data: Poznan's approach to the bioCADDIE 2016

Artur Cieslewicz, Jakub Dutkiewicz, Czeslaw Jedrzejek

Database, Volume 2018, 2018, bax103, https://doi.org/10.1093/database/bax103

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SPTEdb: a database for transposable elements in salicaceous plants

Fei Yi, Zirui Jia, Yao Xiao, Wenjun Ma, Junhui Wang

Database, Volume 2018, 2018, bay024, https://doi.org/10.1093/database/bay024

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YummyData: providing high-quality open life science data

Yasunori Yamamoto, Atsuko Yamaguchi, Andrea Splendiani

Database, Volume 2018, 2018, bay022, https://doi.org/10.1093/database/bay022

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The SNPcurator: literature mining of enriched SNP-disease associations

Noha S Tawfik, Marco R Spruit

Database, Volume 2018, 2018, bay020, https://doi.org/10.1093/database/bay020

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NDDVD: an integrated and manually curated Neurodegenerative Diseases Variation Database

Yang Yang, Chen Xu, Xingyun Liu, Chao Xu, Yuanyuan Zhang, Li Shen, Mauno Vihinen, Bairong Shen

Database, Volume 2018, 2018, bay018, https://doi.org/10.1093/database/bay018

Micropublication: incentivizing community curation and placing unpublished data into the public domain

Daniela Raciti, Karen Yook, Todd W Harris, Tim Schedl, Paul W Sternberg

Database, Volume 2018, 2018, bay013, https://doi.org/10.1093/database/bay013

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miRwayDB: a database for experimentally validated microRNA-pathway associations in pathophysiological conditions

Sankha Subhra Das, Pritam Saha, Nishant Chakravorty

Database, Volume 2018, 2018, bay023, https://doi.org/10.1093/database/bay023

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Prevention of data duplication for high throughput sequencing repositories

Idan Gabdank, Esther T Chan, Jean M Davidson, Jason A Hilton, Carrie A Davis, Ulugbek K Baymuradov, Aditi Narayanan, Kathrina C Onate, Keenan Graham, Stuart R Miyasato, Timothy R Dreszer, J Seth Strattan, Otto Jolanki, Forrest Y Tanaka, Benjamin C Hitz, Cricket A Sloan, J Michael Cherry

Database, Volume 2018, 2018, bay008, https://doi.org/10.1093/database/bay008

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TransAtlasDB: an integrated database connecting expression data, metadata and variants

Modupeore O Adetunji, Susan J Lamont, Carl J Schmidt

Database, Volume 2018, 2018, bay014, https://doi.org/10.1093/database/bay014

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The NCBI BioCollections Database

Shobha Sharma, Stacy Ciufo, Elena Starchenko, Dakshesh Darji, Larry Chlumsky, Ilene Karsch-Mizrachi, Conrad L Schoch

Database, Volume 2018, 2018, bay006, https://doi.org/10.1093/database/bay006

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AllerGAtlas 1.0: a human allergy-related genes database

Jinying Liu, Yuan Liu, Dan Wang, Mengqi He, Lihong Diao, Zhongyang Liu, Yang Li, Li Tang, Fuchu He, Dong Li, Shuzhen Guo

Database, Volume 2018, 2018, bay010, https://doi.org/10.1093/database/bay010

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Identification of errors in the IEDB using ontologies

Randi Vita, James A Overton, Bjoern Peters

Database, Volume 2018, 2018, bay005, https://doi.org/10.1093/database/bay005

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability

Randi Vita, James A Overton, Christopher J Mungall, Alessandro Sette, Bjoern Peters

Database, Volume 2018, 2018, bax105, https://doi.org/10.1093/database/bax105

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Fungal Stress Database (FSD)––a repository of fungal stress physiological data

Erzsébet Orosz, Nathalie van de Wiele, Tamás Emri, Miaomiao Zhou, Vincent Robert, Ronald P de Vries, István Pócsi

Database, Volume 2018, 2018, bay009, https://doi.org/10.1093/database/bay009

OliveNet™: a comprehensive library of compounds from Olea europaea

Natalie P Bonvino, Julia Liang, Elizabeth D McCord, Elena Zafiris, Natalia Benetti, Nancy B Ray, Andrew Hung, Dimitrios Boskou, Tom C Karagiannis

Database, Volume 2018, 2018, bay016, https://doi.org/10.1093/database/bay016

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Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Jasmine Y Young, John D Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M Berrisford, G Jawahar Swaminathan, Thomas J Oldfield, Aleksandras Gutmanas, Reiko Igarashi, David R Armstrong, Kumaran Baskaran, Li Chen, Minyu Chen, Alice R Clark, Luigi Di Costanzo, Dimitris Dimitropoulos … Stephen K Burley

Database, Volume 2018, 2018, bay002, https://doi.org/10.1093/database/bay002

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FishTEDB: a collective database of transposable elements identified in the complete genomes of fish

Feng Shao, Jianrong Wang, Hongen Xu, Zuogang Peng

Database, Volume 2018, 2018, bax106, https://doi.org/10.1093/database/bax106

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A generic workflow for effective sampling of environmental vouchers with UUID assignment and image processing

Dagmar Triebel, Wolfgang Reichert, Simone Bosert, Martin Feulner, Daniel Osieko Okach, Abderachid Slimani, Gerhard Rambold

Database, Volume 2018, 2018, bax096, https://doi.org/10.1093/database/bax096

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YAAM: Yeast Amino Acid Modifications Database

Leonardo Ledesma, Eduardo Sandoval, Uriel Cruz-Martínez, Ana María Escalante, Selene Mejía, Paola Moreno-Álvarez, Emiliano Ávila, Erik García, Gerardo Coello, Francisco Torres-Quiroz

Database, Volume 2018, 2018, bax099, https://doi.org/10.1093/database/bax099

Database Update

Ensembl variation resources

Sarah E Hunt, William McLaren, Laurent Gil, Anja Thormann, Helen Schuilenburg, Dan Sheppard, Andrew Parton, Irina M Armean, Stephen J Trevanion, Paul Flicek, Fiona Cunningham

Database, Volume 2018, 2018, bay119, https://doi.org/10.1093/database/bay119

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Medicinal Materials DNA Barcode Database (MMDBD) version 1.5—one-stop solution for storage, BLAST, alignment and primer design

Tin-Hang Wong, Grace Wing-Chiu But, Hoi-Yan Wu, Stacey Shun-Kei Tsang, David Tai-Wai Lau, Pang-Chui Shaw

Database, Volume 2018, 2018, bay112, https://doi.org/10.1093/database/bay112

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AutismKB 2.0: a knowledgebase for the genetic evidence of autism spectrum disorder

Changhong Yang, Jiarui Li, Qixi Wu, Xiaoxu Yang, August Yue Huang, Jie Zhang, Adam Yongxin Ye, Yanmei Dou, Linlin Yan, Wei-zhen Zhou, Lei Kong, Meng Wang, Chen Ai, Dechang Yang, Liping Wei

Database, Volume 2018, 2018, bay106, https://doi.org/10.1093/database/bay106

Growing and cultivating the forest genomics database, TreeGenes

Taylor Falk, Nic Herndon, Emily Grau, Sean Buehler, Peter Richter, Sumaira Zaman, Eliza M Baker, Risharde Ramnath, Stephen Ficklin, Margaret Staton, Frank A Feltus, Sook Jung, Doreen Main, Jill L Wegrzyn

Database, Volume 2018, 2018, bay084, https://doi.org/10.1093/database/bay084

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ChemDIS 2: an update of chemical-disease inference system

Chun-Wei Tung, Shan-Shan Wang

Database, Volume 2018, 2018, bay077, https://doi.org/10.1093/database/bay077

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Biopanning data bank 2018: hugging next generation phage display

Bifang He, Lixu Jiang, Yaocong Duan, Guoshi Chai, Yewei Fang, Juanjuan Kang, Min Yu, Ning Li, Zhongjie Tang, Pengcheng Yao, Pengcheng Wu, Ratmir Derda, Jian Huang

Database, Volume 2018, 2018, bay032, https://doi.org/10.1093/database/bay032

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Updated regulation curation model at the Saccharomyces Genome Database

Stacia R Engel, Marek S Skrzypek, Sage T Hellerstedt, Edith D Wong, Robert S Nash, Shuai Weng, Gail Binkley, Travis K Sheppard, Kalpana Karra, J Michael Cherry

Database, Volume 2018, 2018, bay007, https://doi.org/10.1093/database/bay007

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dbDEPC 3.0: the database of differentially expressed proteins in human cancer with multi-level annotation and drug indication

Qingmin Yang, Yuqi Zhang, Hui Cui, Lanming Chen, Yong Zhao, Yong Lin, Menghuan Zhang, Lu Xie

Database, Volume 2018, 2018, bay015, https://doi.org/10.1093/database/bay015

TISSUES 2.0: an integrative web resource on mammalian tissue expression

Oana Palasca, Alberto Santos, Christian Stolte, Jan Gorodkin, Lars Juhl Jensen

Database, Volume 2018, 2018, bay003, https://doi.org/10.1093/database/bay003

HTT-DB: new features and updates

Bruno Reis Dotto, Evelise Leis Carvalho, Alexandre Freitas da Silva, Filipe Zimmer Dezordi, Paulo Marcos Pinto, Tulio de Lima Campos, Antonio Mauro Rezende, Gabriel da Luz Wallau

Database, Volume 2018, 2018, bax102, https://doi.org/10.1093/database/bax102

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Database Tool

YHMI: a web tool to identify histone modifications and histone/chromatin regulators from a gene list in yeast

Wei-Sheng Wu, Hao-Ping Tu, Yu-Han Chu, Torbjörn E M Nordling, Yan-Yuan Tseng, Hung-Jiun Liaw

Database, Volume 2018, 2018, bay116, https://doi.org/10.1093/database/bay116

VianniaTopes: a database of predicted immunogenic peptides for Leishmania (Viannia) species

Alejandro Llanes, Carlos Mario Restrepo, Ricardo Lleonart

Database, Volume 2018, 2018, bay111, https://doi.org/10.1093/database/bay111

GFDP: the gene family database in poplar

Hao Wang, Hanwei Yan, Huanlong Liu, Rui Liu, Jun Chen, Yan Xiang

Database, Volume 2018, 2018, bay107, https://doi.org/10.1093/database/bay107

PVsiRNAdb: a database for plant exclusive virus-derived small interfering RNAs

Nikita Gupta, Shafaque Zahra, Ajeet Singh, Shailesh Kumar

Database, Volume 2018, 2018, bay105, https://doi.org/10.1093/database/bay105

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Tripal Developer Toolkit

Bradford Condon, Abdullah Almsaeed, Ming Chen, Joe West, Margaret Staton

Database, Volume 2018, 2018, bay099, https://doi.org/10.1093/database/bay099

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PubMed Labs: an experimental system for improving biomedical literature search

Nicolas Fiorini, Kathi Canese, Rostyslav Bryzgunov, Ievgeniia Radetska, Asta Gindulyte, Martin Latterner, Vadim Miller, Maxim Osipov, Michael Kholodov, Grisha Starchenko, Evgeny Kireev, Zhiyong Lu

Database, Volume 2018, 2018, bay094, https://doi.org/10.1093/database/bay094

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ATD: a comprehensive bioinformatics resource for deciphering the association of autophagy and diseases

Wenjing Wang, Peng Zhang, Leijie Li, Zhaobin Chen, Weiyang Bai, Guiyou Liu, Liangcai Zhang, Haiyang Jia, Li Li, Yingcui Yu, Mingzhi Liao

Database, Volume 2018, 2018, bay093, https://doi.org/10.1093/database/bay093

WaspBase: a genomic resource for the interactions among parasitic wasps, insect hosts and plants

Longfei Chen, Kun Lang, Shoudong Bi, Jiapeng Luo, Feiling Liu, Xinhai Ye, Jiadan Xu, Kang He, Fei Li, Gongyin Ye, Xuexin Chen

Database, Volume 2018, 2018, bay081, https://doi.org/10.1093/database/bay081

SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes

Judith Mary Hariprakash, Shamsudheen Karuthedath Vellarikkal, Ankit Verma, Anop Singh Ranawat, Rijith Jayarajan, Rowmika Ravi, Anoop Kumar, Vishal Dixit, Ambily Sivadas, Atul Kumar Kashyap, Vigneshwar Senthivel, Paras Sehgal, Vijayalakshmi Mahadevan, Vinod Scaria, Sridhar Sivasubbu

Database, Volume 2018, 2018, bay080, https://doi.org/10.1093/database/bay080

HDncRNA: a comprehensive database of non-coding RNAs associated with heart diseases

Wen-Jing Wang, Yu-Mei Wang, Yi Hu, Qin Lin, Rou Chen, Huan Liu, Wen-Ze Cao, Hui-Fang Zhu, Chang Tong, Li Li, Lu-Ying Peng

Database, Volume 2018, 2018, bay067, https://doi.org/10.1093/database/bay067

mutTCPdb: a comprehensive database for genomic variants of a tropical country neglected disease—tropical calcific pancreatitis

Garima Singh, Basharat Bhat, M S K Jayadev, Ch Madhusudhan, Ashutosh Singh

Database, Volume 2018, 2018, bay043, https://doi.org/10.1093/database/bay043

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RabGTD: a comprehensive database of rabbit genome and transcriptome

Lu Zhou, Qingyu Xiao, Jie Bi, Zhen Wang, Yixue Li

Database, Volume 2018, 2018, bay075, https://doi.org/10.1093/database/bay075

SDADB: a functional annotation database of protein structural domains

Cheng Zeng, Weihua Zhan, Lei Deng

Database, Volume 2018, 2018, bay064, https://doi.org/10.1093/database/bay064

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IsopiRBank: a research resource for tracking piRNA isoforms

Huan Zhang, Asim Ali, Jianing Gao, Rongjun Ban, Xiaohua Jiang, Yuanwei Zhang, Qinghua Shi

Database, Volume 2018, 2018, bay059, https://doi.org/10.1093/database/bay059

PtRFdb: a database for plant transfer RNA-derived fragments

Nikita Gupta, Ajeet Singh, Shafaque Zahra, Shailesh Kumar

Database, Volume 2018, 2018, bay063, https://doi.org/10.1093/database/bay063

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 2018, 2018, bay061, https://doi.org/10.1093/database/bay061

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MPD: a pathogen genome and metagenome database

Tingting Zhang, Jiaojiao Miao, Na Han, Yujun Qiang, Wen Zhang

Database, Volume 2018, 2018, bay055, https://doi.org/10.1093/database/bay055

LeptoDB: an integrated database of genomics and proteomics resource of Leptospira

Shruti Beriwal, Nikhil Padhiyar, Deven Bhatt, Prabhakar D Pandit, Afzal Ansari, Kumari Snehkant Lata, Zuber M Saiyed, Vibhisha Vaghasia, Priyanka Sharma, Shivarudrappa B Bhairappanavar, Subhash Soni, Jayashankar Das

Database, Volume 2018, 2018, bay057, https://doi.org/10.1093/database/bay057

A comparative synteny analysis tool for target-gene SNP marker discovery: connecting genomics data to breeding in Solanaceae

Junkyoung Choe, Ji-Eun Kim, Bong-Woo Lee, Jeong Hee Lee, Moon Nam, Youn-Il Park, Sung-Hwan Jo

Database, Volume 2018, 2018, bay047, https://doi.org/10.1093/database/bay047

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CBD: a biomarker database for colorectal cancer

Xueli Zhang, Xiao-Feng Sun, Yang Cao, Benchen Ye, Qiliang Peng, Xingyun Liu, Bairong Shen, Hong Zhang

Database, Volume 2018, 2018, bay046, https://doi.org/10.1093/database/bay046

LnChrom: a resource of experimentally validated lncRNA–chromatin interactions in human and mouse

Fulong Yu, Guanxiong Zhang, Aiai Shi, Jing Hu, Feng Li, Xinxin Zhang, Yan Zhang, Jian Huang, Yun Xiao, Xia Li, Shujun Cheng

Database, Volume 2018, 2018, bay039, https://doi.org/10.1093/database/bay039

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SNPversity: a web-based tool for visualizing diversity

David A Schott, Abhinav G Vinnakota, John L Portwood, II, Carson M Andorf, Taner Z Sen

Database, Volume 2018, 2018, bay037, https://doi.org/10.1093/database/bay037

Maser: one-stop platform for NGS big data from analysis to visualization

Sonoko Kinjo, Norikazu Monma, Sadahiko Misu, Norikazu Kitamura, Junichi Imoto, Kazutoshi Yoshitake, Takashi Gojobori, Kazuho Ikeo

Database, Volume 2018, 2018, bay027, https://doi.org/10.1093/database/bay027

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BioDataome: a collection of uniformly preprocessed and automatically annotated datasets for data-driven biology

Kleanthi Lakiotaki, Nikolaos Vorniotakis, Michail Tsagris, Georgios Georgakopoulos, Ioannis Tsamardinos

Database, Volume 2018, 2018, bay011, https://doi.org/10.1093/database/bay011

AntiTbPdb: a knowledgebase of anti-tubercular peptides

Salman Sadullah Usmani, Rajesh Kumar, Vinod Kumar, Sandeep Singh, Gajendra P S Raghava

Database, Volume 2018, 2018, bay025, https://doi.org/10.1093/database/bay025

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GAN: a platform of genomics and genetics analysis and application in Nicotiana

Shuai Yang, Xingwei Zhang, Huayang Li, Yudong Chen, Long Yang

Database, Volume 2018, 2018, bay001, https://doi.org/10.1093/database/bay001

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miRToolsGallery: a tag-based and rankable microRNA bioinformatics resources database portal

Liang Chen, Liisa Heikkinen, ChangLiang Wang, Yang Yang, K Emily Knott, Garry Wong

Database, Volume 2018, 2018, bay004, https://doi.org/10.1093/database/bay004

CellExpress: a comprehensive microarray-based cancer cell line and clinical sample gene expression analysis online system

Yi-Fang Lee, Chien-Yueh Lee, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y Chuang

Database, Volume 2018, 2018, bax101, https://doi.org/10.1093/database/bax101

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Erratum

TISSUES 2.0: an integrative web resource on mammalian tissue expression

Oana Palasca, Alberto Santos, Christian Stolte, Jan Gorodkin, Lars Juhl Jensen

Database, Volume 2018, 2018, bay028, https://doi.org/10.1093/database/bay028

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Review

A survey of ontology learning techniques and applications

Muhammad Nabeel Asim, Muhammad Wasim, Muhammad Usman Ghani Khan, Waqar Mahmood, Hafiza Mahnoor Abbasi

Database, Volume 2018, 2018, bay101, https://doi.org/10.1093/database/bay101

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