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Volume 2020, 2020

LeukmiR: a database for miRNAs and their targets in acute lymphoblastic leukemia

Abdul Rawoof, Guruprasadh Swaminathan, Shrish Tiwari, Rekha A Nair, Lekha Dinesh Kumar

Database, Volume 2020, 2020, baz151, https://doi.org/10.1093/database/baz151

Structured reviews for data and knowledge-driven research

Núria Queralt-Rosinach, Gregory S Stupp, Tong Shu Li, Michael Mayers, Maureen E Hoatlin, Matthew Might, Benjamin M Good, Andrew I Su

Database, Volume 2020, 2020, baaa015, https://doi.org/10.1093/database/baaa015

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An open-source GIS-enabled lookup service for Nagoya Protocol party information

Hendrikje Seifert, Marc Weber, Frank Oliver Glöckner, Ivaylo Kostadinov

Database, Volume 2020, 2020, baaa014, https://doi.org/10.1093/database/baaa014

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A structured model for immune exposures

Randi Vita, James A Overton, Patrick Dunn, Kei-Hoi Cheung, Steven H Kleinstein, Alessandro Sette, Bjoern Peters

Database, Volume 2020, 2020, baaa016, https://doi.org/10.1093/database/baaa016

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Strengthening of banana breeding through data digitalization

B Vignesh Kumar, S Backiyarani, A Chandrasekar, S Saranya, D Ramajayam, M S Saraswathi, P Durai, S Kalpana, S Uma

Database, Volume 2020, 2020, baz145, https://doi.org/10.1093/database/baz145

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UPCLASS: a deep learning-based classifier for UniProtKB entry publications

Douglas Teodoro, Julien Knafou, Nona Naderi, Emilie Pasche, Julien Gobeill, Cecilia N Arighi, Patrick Ruch

Database, Volume 2020, 2020, baaa026, https://doi.org/10.1093/database/baaa026

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HotSpotAnnotations—a database for hotspot mutations and annotations in cancer

Victor Trevino

Database, Volume 2020, 2020, baaa025, https://doi.org/10.1093/database/baaa025

MACSNVdb: a high-quality SNV database for interspecies genetic divergence investigation among macaques

Lianming Du, Tao Guo, Qin Liu, Xiuyue Zhang, Jinchuan Xing, Bisong Yue, Jing Li, Zhenxin Fan

Database, Volume 2020, 2020, baaa027, https://doi.org/10.1093/database/baaa027

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Why data citation isn't working, and what to do about it

Peter Buneman, Greig Christie, Jamie A Davies, Roza Dimitrellou, Simon D Harding, Adam J Pawson, Joanna L Sharman, Yinjun Wu

Database, Volume 2020, 2020, baaa022, https://doi.org/10.1093/databa/baaa022

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The Mnemiopsis Genome Project Portal: integrating new gene expression resources and improving data visualization

R Travis Moreland, Anh-Dao Nguyen, Joseph F Ryan, Andreas D Baxevanis

Database, Volume 2020, 2020, baaa029, https://doi.org/10.1093/database/baaa029

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A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function

Gemma L Holliday, Shoshana D Brown, David Mischel, Benjamin J Polacco, Patricia C Babbitt

Database, Volume 2020, 2020, baaa034, https://doi.org/10.1093/database/baaa034

MIPPIE: the mouse integrated protein–protein interaction reference

Gregorio Alanis-Lobato, Jannik S Möllmann, Martin H Schaefer, Miguel A Andrade-Navarro

Database, Volume 2020, 2020, baaa035, https://doi.org/10.1093/database/baaa035

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The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification

N Palopoli, J A Iserte, L B Chemes, C Marino-Buslje, G Parisi, T J Gibson, N E Davey

Database, Volume 2020, 2020, baaa040, https://doi.org/10.1093/database/baaa040

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Obtaining extremely large and accurate protein multiple sequence alignments from curated hierarchical alignments

Andrew F Neuwald, Christopher J Lanczycki, Theresa K Hodges, Aron Marchler-Bauer

Database, Volume 2020, 2020, baaa042, https://doi.org/10.1093/database/baaa042

RGPDB: database of root-associated genes and promoters in maize, soybean, and sorghum

Gleb Moisseyev, Kiyoul Park, Alix Cui, Daniel Freitas, Divith Rajagopal, Anji Reddy Konda, Madalayne Martin-Olenski, Mackenzie Mcham, Kan Liu, Qian Du, James C Schnable, Etsuko N Moriyama, Edgar B Cahoon, Chi Zhang

Database, Volume 2020, 2020, baaa038, https://doi.org/10.1093/database/baaa038

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GreenCircRNA: a database for plant circRNAs that act as miRNA decoys

Jingjing Zhang, Zhiqiang Hao, Shuwei Yin, Guanglin Li

Database, Volume 2020, 2020, baaa039, https://doi.org/10.1093/database/baaa039

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Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD)

Xiangying Jiang, Martin Ringwald, Judith Blake, Haggit Shatkay

Database, Volume 2020, 2020, baaa043, https://doi.org/10.1093/database/baaa043

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Identifying main finding sentences in clinical case reports

Mengqi Luo, Aaron M Cohen, Sidharth Addepalli, Neil R Smalheiser

Database, Volume 2020, 2020, baaa041, https://doi.org/10.1093/database/baaa041

ForageGrassBase: molecular resource for the forage grass meadow fescue (Festuca pratensis Huds.)

Jeevan Karloss Antony Samy, Odd Arne Rognli, Mallikarjuna Rao Kovi

Database, Volume 2020, 2020, baaa046, https://doi.org/10.1093/database/baaa046

FOBI: an ontology to represent food intake data and associate it with metabolomic data

Pol Castellano-Escuder, Raúl González-Domínguez, David S Wishart, Cristina Andrés-Lacueva, Alex Sánchez-Pla

Database, Volume 2020, 2020, baaa033, https://doi.org/10.1093/databa/baaa033

PvP01-DB: computational structural and functional characterization of soluble proteome of PvP01 strain of Plasmodium vivax

Ankita Singh, Rahul Kaushik, Dheeraj Kumar Chaurasia, Manpreet Singh, B Jayaram

Database, Volume 2020, 2020, baaa036, https://doi.org/10.1093/database/baaa036

Curation of cancer hallmark-based genes and pathways for in silico characterization of chemical carcinogenesis

Peir-In Liang, Chia-Chi Wang, Hsien-Jen Cheng, Shan-Shan Wang, Ying-Chi Lin, Pinpin Lin, Chun-Wei Tung

Database, Volume 2020, 2020, baaa045, https://doi.org/10.1093/database/baaa045

GTDB: an integrated resource for glycosyltransferase sequences and annotations

Chenfen Zhou, Qingwei Xu, Sheng He, Wei Ye, Ruifang Cao, Pengyu Wang, Yunchao Ling, Xing Yan, Qingzhong Wang, Guoqing Zhang

Database, Volume 2020, 2020, baaa047, https://doi.org/10.1093/database/baaa047

MaizeCUBIC: a comprehensive variation database for a maize synthetic population

Jingyun Luo, Chengcheng Wei, Haijun Liu, Shikun Cheng, Yingjie Xiao, Xiaqing Wang, Jianbing Yan, Jianxiao Liu

Database, Volume 2020, 2020, baaa044, https://doi.org/10.1093/database/baaa044

Automated generation of gene summaries at the Alliance of Genome Resources

Ranjana Kishore, Valerio Arnaboldi, Ceri E Van Slyke, Juancarlos Chan, Robert S Nash, Jose M Urbano, Mary E Dolan, Stacia R Engel, Mary Shimoyama, Paul W Sternberg, the Alliance of Genome Resources

Database, Volume 2020, 2020, baaa037, https://doi.org/10.1093/database/baaa037

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mAML: an automated machine learning pipeline with a microbiome repository for human disease classification

Fenglong Yang, Quan Zou

Database, Volume 2020, 2020, baaa050, https://doi.org/10.1093/database/baaa050

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RNAWRE: a resource of writers, readers and erasers of RNA modifications

Fulei Nie, Pengmian Feng, Xiaoming Song, Meng Wu, Qiang Tang, Wei Chen

Database, Volume 2020, 2020, baaa049, https://doi.org/10.1093/database/baaa049

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CHDGKB: a knowledgebase for systematic understanding of genetic variations associated with non-syndromic congenital heart disease

Lan Yang, Yang Yang, Xingyun Liu, Yongquan Chen, Yalan Chen, Yuxin Lin, Yan Sun, Bairong Shen

Database, Volume 2020, 2020, baaa048, https://doi.org/10.1093/database/baaa048

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SAGER: a database of Symbiodiniaceae and Algal Genomic Resource

Liying Yu, Tangcheng Li, Ling Li, Xin Lin, Hongfei Li, Chichi Liu, Chentao Guo, Senjie Lin

Database, Volume 2020, 2020, baaa051, https://doi.org/10.1093/database/baaa051

Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases

Shawna Spoor, Connor Wytko, Brian Soto, Ming Chen, Abdullah Almsaeed, Bradford Condon, Nic Herndon, Heidi Hough, Sook Jung, Meg Staton, Jill Wegrzyn, Dorrie Main, F Alex Feltus, Stephen P Ficklin

Database, Volume 2020, 2020, baaa032, https://doi.org/10.1093/database/baaa032

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Autophagy and Tumor Database: ATdb, a novel database connecting autophagy and tumor

Kelie Chen, Dexin Yang, Fan Zhao, Shengchao Wang, Yao Ye, Wenjie Sun, Haohua Lu, Zhi Ruan, Jinming Xu, Tianru Wang, Guang Lu, Liming Wang, Yu Shi, Honghe Zhang, Han Wu, Weiguo Lu, Han-Ming Shen, Dajing Xia, Yihua Wu

Database, Volume 2020, 2020, baaa052, https://doi.org/10.1093/database/baaa052

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

Peter Brown, RELISH Consortium, Yaoqi Zhou

Database, Volume 2020, 2020, baz138, https://doi.org/10.1093/database/baz138

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WellExplorer: an integrative resource linking hydraulic fracturing chemicals with hormonal pathways and geographic location

Owen Wetherbee, Jessica R Meeker, Caroline DeVoto, Trevor M Penning, Jason H Moore, Mary Regina Boland

Database, Volume 2020, 2020, baaa053, https://doi.org/10.1093/database/baaa053

CNSA: a data repository for archiving omics data

Xueqin Guo, Fengzhen Chen, Fei Gao, Ling Li, Ke Liu, Lijin You, Cong Hua, Fan Yang, Wanliang Liu, Chunhua Peng, Lina Wang, Xiaoxia Yang, Feiyu Zhou, Jiawei Tong, Jia Cai, Zhiyong Li, Bo Wan, Lei Zhang, Tao Yang … Xun Xu

Database, Volume 2020, 2020, baaa055, https://doi.org/10.1093/database/baaa055

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OPTIK: a database for understanding catchment areas to guide mobilization of cancer center assets

Dinesh Pal Mudaranthakam, Lisa M Harlan-Williams, Roy A Jensen, Hanluen Kuo, Vandita Garimella, Ronald C Chen, Matthew S Mayo, Hope Krebill

Database, Volume 2020, 2020, baaa054, https://doi.org/10.1093/database/baaa054

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Gliome database: a comprehensive web-based tool to access and analyze glia secretome data

Jong-Heon Kim, Su-Hyeong Park, Jin Han, Pan-Woo Ko, Dongseop Kwon, Kyoungho Suk

Database, Volume 2020, 2020, baaa057, https://doi.org/10.1093/database/baaa057

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FLUTE: Fast and reliable knowledge retrieval from biomedical literature

Emilee Holtzapple, Cheryl A Telmer, Natasa Miskov-Zivanov

Database, Volume 2020, 2020, baaa056, https://doi.org/10.1093/database/baaa056

CerealsDB—new tools for the analysis of the wheat genome: update 2020

Paul A Wilkinson, Alexandra M Allen, Simon Tyrrell, Luzie U Wingen, Xingdong Bian, Mark O Winfield, Amanda Burridge, Daniel S Shaw, Jan Zaucha, Simon Griffiths, Robert P Davey, Keith J Edwards, Gary L A Barker

Database, Volume 2020, 2020, baaa060, https://doi.org/10.1093/database/baaa060

ConoMode, a database for conopeptide binding modes

Xiao Li, Hao Liu, Chunxiao Gao, Yangyang Li, Dongning Jia, Yanbo Yang, Jinbo Yang, Zhiqiang Wei, Tao Jiang, Rilei Yu

Database, Volume 2020, 2020, baaa058, https://doi.org/10.1093/database/baaa058

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SPDB: a specialized database and web-based analysis platform for swine pathogens

Xiaoru Wang, Zongbao Liu, Xiaoying Li, Danwei Li, Jiayu Cai, He Yan

Database, Volume 2020, 2020, baaa063, https://doi.org/10.1093/database/baaa063

NCBI Taxonomy: a comprehensive update on curation, resources and tools

Conrad L Schoch, Stacy Ciufo, Mikhail Domrachev, Carol L Hotton, Sivakumar Kannan, Rogneda Khovanskaya, Detlef Leipe, Richard Mcveigh, Kathleen O’Neill, Barbara Robbertse, Shobha Sharma, Vladimir Soussov, John P Sullivan, Lu Sun, Seán Turner, Ilene Karsch-Mizrachi

Database, Volume 2020, 2020, baaa062, https://doi.org/10.1093/database/baaa062

FAIR digital objects in environmental and life sciences should comprise workflow operation design data and method information for repeatability of study setups and reproducibility of results

Janno Harjes, Anton Link, Tanja Weibulat, Dagmar Triebel, Gerhard Rambold

Database, Volume 2020, 2020, baaa059, https://doi.org/10.1093/database/baaa059

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LAMP2: a major update of the database linking antimicrobial peptides

Guizi Ye, Hongyu Wu, Jinjiang Huang, Wei Wang, Kuikui Ge, Guodong Li, Jiang Zhong, Qingshan Huang

Database, Volume 2020, 2020, baaa061, https://doi.org/10.1093/database/baaa061

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A content-based dataset recommendation system for researchers—a case study on Gene Expression Omnibus (GEO) repository

Braja Gopal Patra, Kirk Roberts, Hulin Wu

Database, Volume 2020, 2020, baaa064, https://doi.org/10.1093/database/baaa064

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A database resource and online analysis tools for coronaviruses on a historical and global scale

Zhenglin Zhu, Kaiwen Meng, Gexin Liu, Geng Meng

Database, Volume 2020, 2020, baaa070, https://doi.org/10.1093/database/baaa070

Color Data v2: a user-friendly, open-access database with hereditary cancer and hereditary cardiovascular conditions datasets

Mark J Berger, Hannah E Williams, Ryan Barrett, Anjali D Zimmer, Wendy McKennon, Huy Hong, Jeremy Ginsberg, Alicia Y Zhou, Cynthia L Neben

Database, Volume 2020, 2020, baaa083, https://doi.org/10.1093/database/baaa083

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A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain

Carlota Cardoso, Rita T Sousa, Sebastian Köhler, Catia Pesquita

Database, Volume 2020, 2020, baaa078, https://doi.org/10.1093/database/baaa078

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A checklist recipe: making species data open and FAIR

Lien Reyserhove, Peter Desmet, Damiano Oldoni, Tim Adriaens, Diederik Strubbe, Amy J S Davis, Sonia Vanderhoeven, Filip Verloove, Quentin Groom

Database, Volume 2020, 2020, baaa084, https://doi.org/10.1093/database/baaa084

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CircR2Cancer: a manually curated database of associations between circRNAs and cancers

Wei Lan, Mingrui Zhu, Qingfeng Chen, Baoshan Chen, Jin Liu, Min Li, Yi-Ping Phoebe Chen

Database, Volume 2020, 2020, baaa085, https://doi.org/10.1093/database/baaa085

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CitrusKB: a comprehensive knowledge base for transcriptome and interactome of Citrus spp. infected by Xanthomonas citri subsp. citri at different infection stages

Adriano Ferrasa, Mayara M Murata, Teresa D C G Cofre, Juliana S Cavallini, Gustavo Peron, Maria H M Julião, José Belasque, Henrique Ferreira, Maria Inês T Ferro, Rui P Leite, Jr, Helen A Penha, Flávia M S Carvalho, Alessandro M Varani, Roberto H Herai, Jesus A Ferro

Database, Volume 2020, 2020, baaa081, https://doi.org/10.1093/database/baaa081

WGVD: an integrated web-database for wheat genome variation and selective signatures

Jierong Wang, Weiwei Fu, Rui Wang, Dexiang Hu, Hong Cheng, Jing Zhao, Yu Jiang, Zhensheng Kang

Database, Volume 2020, 2020, baaa090, https://doi.org/10.1093/database/baaa090

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DPL: a comprehensive database on sequences, structures, sources and functions of peptide ligands

Fangyu Wang, Ning Li, Chunfeng Wang, Guangxu Xing, Shuai Cao, Qian Xu, Yunshang Zhang, Man Hu, Gaiping Zhang

Database, Volume 2020, 2020, baaa089, https://doi.org/10.1093/database/baaa089

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Exploring functionally annotated transcriptional consensus regulatory elements with CONREL

Davide Dalfovo, Samuel Valentini, Alessandro Romanel

Database, Volume 2020, 2020, baaa071, https://doi.org/10.1093/database/baaa071

YQFC: a web tool to compare quantitative biological features between two yeast gene lists

Wei-Sheng Wu, Lai-Ji Wang, Han-Chen Yen, Yan-Yuan Tseng

Database, Volume 2020, 2020, baaa076, https://doi.org/10.1093/database/baaa076

CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats

Alejandro Rubio, Pablo Mier, Miguel A Andrade-Navarro, Andrés Garzón, Juan Jiménez, Antonio J Pérez-Pulido

Database, Volume 2020, 2020, baaa088, https://doi.org/10.1093/database/baaa088

The IMEx coronavirus interactome: an evolving map of Coronaviridae–host molecular interactions

L Perfetto, C Pastrello, N del-Toro, M Duesbury, M Iannuccelli, M Kotlyar, L Licata, B Meldal, K Panneerselvam, S Panni, N Rahimzadeh, S Ricard-Blum, L Salwinski, A Shrivastava, G Cesareni, M Pellegrini, S Orchard, I Jurisica, H Hermjakob, P Porras

Database, Volume 2020, 2020, baaa096, https://doi.org/10.1093/database/baaa096

OCCAM: prediction of small ORFs in bacterial genomes by means of a target-decoy database approach and machine learning techniques

Fabio R. Cerqueira, Ana Tereza Ribeiro Vasconcelos

Database, Volume 2020, 2020, baaa067, https://doi.org/10.1093/database/baaa067

TopoDB: a novel multifunctional management system for laboratory animal colonies

Adam Renschen, Atsuko Matsunaga, Jorge R Oksenberg, Adam Santaniello, Alessandro Didonna

Database, Volume 2020, 2020, baaa098, https://doi.org/10.1093/database/baaa098

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STOREFISH 2.0: a database on the reproductive strategies of teleost fishes

Stéphane Teletchea, Fabrice Teletchea

Database, Volume 2020, 2020, baaa095, https://doi.org/10.1093/database/baaa095

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GPCR-PEnDB: a database of protein sequences and derived features to facilitate prediction and classification of G protein-coupled receptors

Khodeza Begum, Jonathon E Mohl, Fredrick Ayivor, Eder E Perez, Ming-Ying Leung

Database, Volume 2020, 2020, baaa087, https://doi.org/10.1093/database/baaa087

Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes

Hong Cui, Limin Zhang, Bruce Ford, Hsin-liang Chen, James A Macklin, Anton Reznicek, Julian Starr

Database, Volume 2020, 2020, baaa079, https://doi.org/10.1093/database/baaa079

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Predicted rat interactome database and gene set linkage analysis

Yu-Tian Tao, Xiao-Bao Ding, Jie Jin, Hai-Bo Zhang, Wen-Ping Guo, Li Ruan, Qiao-Lei Yang, Peng-Cheng Chen, Heng Yao, Xin Chen

Database, Volume 2020, 2020, baaa086, https://doi.org/10.1093/database/baaa086

EukRef-excavates: seven curated SSU ribosomal RNA gene databases

Martin Kolisko, Olga Flegontova, Anna Karnkowska, Gordon Lax, Julia M Maritz, Tomáš Pánek, Petr Táborský, Jane M Carlton, Ivan Čepička, Aleš Horák, Julius Lukeš, Alastair G B Simpson, Vera Tai

Database, Volume 2020, 2020, baaa080, https://doi.org/10.1093/database/baaa080

WCSdb: a database of wild Coffea species

Romain Guyot, Perla Hamon, Emmanuel Couturon, Nathalie Raharimalala, Jean-Jacques Rakotomalala, Sreenath Lakkanna, Sylvie Sabatier, Antoine Affouard, Pierre Bonnet

Database, Volume 2020, 2020, baaa069, https://doi.org/10.1093/database/baaa069

RecipeDB: a resource for exploring recipes

Devansh Batra, Nirav Diwan, Utkarsh Upadhyay, Jushaan Singh Kalra, Tript Sharma, Aman Kumar Sharma, Dheeraj Khanna, Jaspreet Singh Marwah, Srilakshmi Kalathil, Navjot Singh, Rudraksh Tuwani, Ganesh Bagler

Database, Volume 2020, 2020, baaa077, https://doi.org/10.1093/database/baaa077

Siberian sturgeon multi-tissue reference transcriptome database

Christophe Klopp, Cédric Cabau, Gonzalo Greif, André Lasalle, Santiago Di Landro, Denise Vizziano-Cantonnet

Database, Volume 2020, 2020, baaa082, https://doi.org/10.1093/database/baaa082

MetaTropismDB: a database of organ-specific metastasis induced by human cancer cell lines in mouse models

Matteo Giulietti, Marco Bastianoni, Monia Cecati, Annamaria Ruzzo, Massimo Bracci, Marco Malavolta, Francesco Piacenza, Robertina Giacconi, Francesco Piva

Database, Volume 2020, 2020, baaa100, https://doi.org/10.1093/database/baaa100

KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling

Hugo Mochão, Pedro Barahona, Rafael S Costa

Database, Volume 2020, 2020, baaa093, https://doi.org/10.1093/database/baaa093

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BarleyVarDB: a database of barley genomic variation

Cong Tan, Brett Chapman, Penghao Wang, Qisen Zhang, Gaofeng Zhou, Xiao-qi Zhang, Roberto A Barrero, Matthew I Bellgard, Chengdao Li

Database, Volume 2020, 2020, baaa091, https://doi.org/10.1093/database/baaa091

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A curated database reveals trends in single-cell transcriptomics

Valentine Svensson, Eduardo da Veiga Beltrame, Lior Pachter

Database, Volume 2020, 2020, baaa073, https://doi.org/10.1093/database/baaa073

OGDA: a comprehensive organelle genome database for algae

Tao Liu, Yutong Cui, Xuli Jia, Jing Zhang, Ruoran Li, Yahui Yu, Shangang Jia, Jiangyong Qu, Xumin Wang

Database, Volume 2020, 2020, baaa097, https://doi.org/10.1093/database/baaa097

An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries

Braja Gopal Patra, Babak Soltanalizadeh, Nan Deng, Leqing Wu, Vahed Maroufy, Canglin Wu, W Jim Zheng, Kirk Roberts, Hulin Wu, Ashraf Yaseen

Database, Volume 2020, 2020, baaa074, https://doi.org/10.1093/database/baaa074

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VarStack: a web tool for data retrieval to interpret somatic variants in cancer

Morgan Howard, Bruce Kane, Mary Lepry, Paul Stey, Ashok Ragavendran, Ece D Gamsiz Uzun

Database, Volume 2020, 2020, baaa092, https://doi.org/10.1093/database/baaa092

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ThRSDB: a database of Thai rice starch composition, molecular structure and functionality

Kwanjeera Wanichthanarak, Maysaya Thitisaksakul

Database, Volume 2020, 2020, baaa068, https://doi.org/10.1093/database/baaa068

RegulomePA: a database of transcriptional regulatory interactions in Pseudomonas aeruginosa PAO1

Edgardo Galán-Vásquez, Beatriz Carely Luna-Olivera, Marcelino Ramírez-Ibáñez, Agustino Martínez-Antonio

Database, Volume 2020, 2020, baaa106, https://doi.org/10.1093/database/baaa106

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A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing

Diana Sousa, Andre Lamurias, Francisco M Couto

Database, Volume 2020, 2020, baaa104, https://doi.org/10.1093/database/baaa104

ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls

Harry Biggs, Padmini Parthasarathy, Alexandra Gavryushkina, Paul P Gardner

Database, Volume 2020, 2020, baaa105, https://doi.org/10.1093/database/baaa105

HAHmiR.DB: a server platform for high-altitude human miRNA–gene coregulatory networks and associated regulatory circuits

Pankaj Khurana, Apoorv Gupta, Ragumani Sugadev, Yogendra Kumar Sharma, Bhuvnesh Kumar

Database, Volume 2020, 2020, baaa101, https://doi.org/10.1093/database/baaa101

Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties

Carlos-Francisco Méndez-Cruz, Antonio Blanchet, Alan Godínez, Ignacio Arroyo-Fernández, Socorro Gama-Castro, Sara Berenice Martínez-Luna, Cristian González-Colín, Julio Collado-Vides

Database, Volume 2020, 2020, baaa109, https://doi.org/10.1093/database/baaa109

Applying graph database technology for analyzing perturbed co-expression networks in cancer

Claire M Simpson, Florian Gnad

Database, Volume 2020, 2020, baaa110, https://doi.org/10.1093/database/baaa110

CEG 2.0: an updated database of clusters of essential genes including eukaryotic organisms

Shuo Liu, Shu-Xuan Wang, Wei Liu, Chen Wang, Fa-Zhan Zhang, Yuan-Nong Ye, Candy-S Wu, Wen-Xin Zheng, Nini Rao, Feng-Biao Guo

Database, Volume 2020, 2020, baaa112, https://doi.org/10.1093/database/baaa112

CamRegBase: a gene regulation database for the biofuel crop, Camelina sativa

Fabio Gomez-Cano, Lisa Carey, Kevin Lucas, Tatiana García Navarrete, Eric Mukundi, Steve Lundback, Danny Schnell, Erich Grotewold

Database, Volume 2020, 2020, baaa075, https://doi.org/10.1093/database/baaa075

NPBS database: a chemical data resource with relational data between natural products and biological sources

Tingjun Xu, Weiming Chen, Junhong Zhou, Jingfang Dai, Yingyong Li, Yingli Zhao

Database, Volume 2020, 2020, baaa102, https://doi.org/10.1093/database/baaa102

Novel methods included in SpolLineages tool for fast and precise prediction of Mycobacterium tuberculosis complex spoligotype families

David Couvin, Wilfried Segretier, Erick Stattner, Nalin Rastogi

Database, Volume 2020, 2020, baaa108, https://doi.org/10.1093/database/baaa108

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MuscleAtlasExplorer: a web service for studying gene expression in human skeletal muscle

Olof Asplund, Johan Rung, Leif Groop, Rashmi Prasad B, Ola Hansson

Database, Volume 2020, 2020, baaa111, https://doi.org/10.1093/database/baaa111

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HeartBioPortal2.0: new developments and updates for genetic ancestry and cardiometabolic quantitative traits in diverse human populations

Bohdan B Khomtchouk, Christopher S Nelson, Kasra A Vand, Salvator Palmisano, Robert L Grossman

Database, Volume 2020, 2020, baaa115, https://doi.org/10.1093/database/baaa115

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CorkOakDB—The Cork Oak Genome Database Portal

Cirenia Arias-Baldrich, Marta Contreiras Silva, Filippo Bergeretti, Inês Chaves, Célia Miguel, Nelson J M Saibo, Daniel Sobral, Daniel Faria, Pedro M Barros

Database, Volume 2020, 2020, baaa114, https://doi.org/10.1093/database/baaa114

Creating a Metabolic Syndrome Research Resource using the National Health and Nutrition Examination Survey

Willysha S Jenkins, Christian Richardson, Ariel Williams, PhD, Clarlynda R Williams-DeVane, PhD

Database, Volume 2020, 2020, baaa103, https://doi.org/10.1093/database/baaa103

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People are essential to linking biodiversity data

Quentin Groom, Anton Güntsch, Pieter Huybrechts, Nicole Kearney, Siobhan Leachman, Nicky Nicolson, Roderic D M Page, David P Shorthouse, Anne E Thessen, Elspeth Haston

Database, Volume 2020, 2020, baaa072, https://doi.org/10.1093/database/baaa072

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Original Articles

Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications

Antonia Lock, Midori A Harris, Kim Rutherford, Jacqueline Hayles, Valerie Wood

Database, Volume 2020, 2020, baaa028, https://doi.org/10.1093/database/baaa028

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RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis

Vidisha Singh, George D Kalliolias, Marek Ostaszewski, Maëva Veyssiere, Eleftherios Pilalis, Piotr Gawron, Alexander Mazein, Eric Bonnet, Elisabeth Petit-Teixeira, Anna Niarakis

Database, Volume 2020, 2020, baaa017, https://doi.org/10.1093/database/baaa017

Integrating image caption information into biomedical document classification in support of biocuration

Xiangying Jiang, Pengyuan Li, James Kadin, Judith A Blake, Martin Ringwald, Hagit Shatkay

Database, Volume 2020, 2020, baaa024, https://doi.org/10.1093/database/baaa024

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ASFVdb: an integrative resource for genomic and proteomic analyses of African swine fever virus

Zhenglin Zhu, Geng Meng

Database, Volume 2020, 2020, baaa023, https://doi.org/10.1093/database/baaa023

ctcRbase: the gene expression database of circulating tumor cells and microemboli

Lei Zhao, Xiaohong Wu, Tong Li, Jian Luo, Dong Dong

Database, Volume 2020, 2020, baaa020, https://doi.org/10.1093/database/baaa020

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Integrated querying and version control of context-specific biological networks

Tyler Cowman, Mustafa Coşkun, Ananth Grama, Mehmet Koyutürk

Database, Volume 2020, 2020, baaa018, https://doi.org/10.1093/database/baaa018

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FerrDb: a manually curated resource for regulators and markers of ferroptosis and ferroptosis-disease associations

Nan Zhou, Jinku Bao

Database, Volume 2020, 2020, baaa021, https://doi.org/10.1093/database/baaa021

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TeaMiD: a comprehensive database of simple sequence repeat markers of tea

Himanshu Dubey, Hukam C Rawal, Megha Rohilla, Urvashi Lama, P Mohan Kumar, Tanoy Bandyopadhyay, Madhurjya Gogoi, Nagendra Kumar Singh, Tapan Kumar Mondal

Database, Volume 2020, 2020, baaa013, https://doi.org/10.1093/database/baaa013

uORFlight: a vehicle toward uORF-mediated translational regulation mechanisms in eukaryotes

Ruixia Niu, Yulu Zhou, Yu Zhang, Rui Mou, Zhijuan Tang, Zhao Wang, Guilong Zhou, Sibin Guo, Meng Yuan, Guoyong Xu

Database, Volume 2020, 2020, baaa007, https://doi.org/10.1093/database/baaa007

KRGDB: the large-scale variant database of 1722 Koreans based on whole genome sequencing

Kwang Su Jung, Kyung-Won Hong, Hyun Youn Jo, Jongpill Choi, Hyo-Jeong Ban, Seong Beom Cho, Myungguen Chung

Database, Volume 2020, 2020, baz146, https://doi.org/10.1093/database/baz146

WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans

Basten L Snoek, Mark G Sterken, Margi Hartanto, Albert-Jan van Zuilichem, Jan E Kammenga, Dick de Ridder, Harm Nijveen

Database, Volume 2020, 2020, baz149, https://doi.org/10.1093/database/baz149

Building a pipeline to solicit expert knowledge from the community to aid gene summary curation

Giulia Antonazzo, Jose M Urbano, Steven J Marygold, Gillian H Millburn, Nicholas H Brown

Database, Volume 2020, 2020, baz152, https://doi.org/10.1093/database/baz152

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PCaLiStDB: a lifestyle database for precision prevention of prostate cancer

Yalan Chen, Xingyun Liu, Yijun Yu, Chunjiang Yu, Lan Yang, Yuxin Lin, Ting Xi, Ziyun Ye, Zhe Feng, Bairong Shen

Database, Volume 2020, 2020, baz154, https://doi.org/10.1093/database/baz154

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RESTful API for iPTMnet: a resource for protein post-translational modification network discovery

Sachin Gavali, Julie Cowart, Chuming Chen, Karen E Ross, Cecilia Arighi, Cathy H Wu

Database, Volume 2020, 2020, baz157, https://doi.org/10.1093/database/baz157

Phenotype–genotype network construction and characterization: a case study of cardiovascular diseases and associated non-coding RNAs

Rongrong Wu, Yuxin Lin, Xingyun Liu, Chaoying Zhan, Hongxin He, Manhong Shi, Zhi Jiang, Bairong Shen

Database, Volume 2020, 2020, baz147, https://doi.org/10.1093/database/baz147

ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them

Erik Czipa, Mátyás Schiller, Tibor Nagy, Levente Kontra, László Steiner, Júlia Koller, Orsolya Pálné-Szén, Endre Barta

Database, Volume 2020, 2020, baz141, https://doi.org/10.1093/database/baz141

Bio-AnswerFinder: a system to find answers to questions from biomedical texts

Ibrahim Burak Ozyurt, Anita Bandrowski, Jeffrey S Grethe

Database, Volume 2020, 2020, baz137, https://doi.org/10.1093/database/baz137

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Variation benchmark datasets: update, criteria, quality and applications

Anasua Sarkar, Yang Yang, Mauno Vihinen

Database, Volume 2020, 2020, baz117, https://doi.org/10.1093/database/baz117

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PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding

Elisa Banchi, Claudio G Ametrano, Samuele Greco, David Stanković, Lucia Muggia, Alberto Pallavicini

Database, Volume 2020, 2020, baz155, https://doi.org/10.1093/database/baz155

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Ewé: a web-based ethnobotanical database for storing and analysing data

Estevão do Nascimento Fernandes de Souza, Julie A Hawkins

Database, Volume 2020, 2020, baz144, https://doi.org/10.1093/database/baz144

GREG—studying transcriptional regulation using integrative graph databases

Songqing Mei, Xiaowei Huang, Chengshu Xie, Antonio Mora

Database, Volume 2020, 2020, baz162, https://doi.org/10.1093/database/baz162

HSPMdb: a computational repository of heat shock protein modulators

Prashant Singh, Breezy Unik, Anuradhika Puri, Gandharva Nagpal, Balvinder Singh, Ankur Gautam, Deepak Sharma

Database, Volume 2020, 2020, baaa003, https://doi.org/10.1093/database/baaa003

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NipahVR: a resource of multi-targeted putative therapeutics and epitopes for the Nipah virus

Amit Kumar Gupta, Archit Kumar, Akanksha Rajput, Karambir Kaur, Showkat Ahmed Dar, Anamika Thakur, Kirti Megha, Manoj Kumar

Database, Volume 2020, 2020, baz159, https://doi.org/10.1093/database/baz159

dbPepNeo: a manually curated database for human tumor neoantigen peptides

Xiaoxiu Tan, Daixi Li, Pengjie Huang, Xingxing Jian, Huihui Wan, Guangzhi Wang, Yuyu Li, Jian Ouyang, Yong Lin, Lu Xie

Database, Volume 2020, 2020, baaa004, https://doi.org/10.1093/database/baaa004

Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes

Xiao-Bao Ding, Jie Jin, Yu-Tian Tao, Wen-Ping Guo, Li Ruan, Qiao-lei Yang, Peng-Cheng Chen, Heng Yao, Hai-bo Zhang, Xin Chen

Database, Volume 2020, 2020, baaa005, https://doi.org/10.1093/database/baaa005

Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase

Valerio Arnaboldi, Daniela Raciti, Kimberly Van Auken, Juancarlos N Chan, Hans-Michael Müller, Paul W Sternberg

Database, Volume 2020, 2020, baaa006, https://doi.org/10.1093/database/baaa006

Database Updates

Incorporation of a unified protein abundance dataset into the Saccharomyces genome database

Robert S Nash, Shuai Weng, Kalpana Karra, Edith D Wong, Stacia R Engel, J Michael Cherry, SGD Project

Database, Volume 2020, 2020, baaa008, https://doi.org/10.1093/database/baaa008

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RNA CoSSMos 2.0: an improved searchable database of secondary structure motifs in RNA three-dimensional structures

Katherine E Richardson, Charles C Kirkpatrick, Brent M Znosko

Database, Volume 2020, 2020, baz153, https://doi.org/10.1093/database/baz153

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Annotation and curation of the causality information in LncRNADisease

Kaiwen Jia, Yuanxu Gao, Jiangcheng Shi, Yuan Zhou, Yong Zhou, Qinghua Cui

Database, Volume 2020, 2020, baz150, https://doi.org/10.1093/database/baz150

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An update on the Symbiotic Genomes Database (SymGenDB): a collection of metadata, genomic, genetic and protein sequences, orthologs and metabolic networks of symbiotic organisms

Mariana Reyes-Prieto, Carlos Vargas-Chávez, Mercè Llabrés, Pere Palmer, Amparo Latorre, Andrés Moya

Database, Volume 2020, 2020, baz160, https://doi.org/10.1093/database/baz160

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Database Tools

Revenant: a database of resurrected proteins

Matias Sebastian Carletti, Alexander Miguel Monzon, Emilio Garcia-Rios, Guillermo Benitez, Layla Hirsh, Maria Silvina Fornasari, Gustavo Parisi

Database, Volume 2020, 2020, baaa031, https://doi.org/10.1093/database/baaa031

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Prot2HG: a database of protein domains mapped to the human genome

David Stanek, Dana M Bis-Brewer, Cima Saghira, Matt C Danzi, Pavel Seeman, Petra Lassuthova, Stephan Zuchner

Database, Volume 2020, 2020, baz161, https://doi.org/10.1093/database/baz161

Circad: a comprehensive manually curated resource of circular RNA associated with diseases

Mercy Rophina, Disha Sharma, Mukta Poojary, Vinod Scaria

Database, Volume 2020, 2020, baaa019, https://doi.org/10.1093/database/baaa019

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CancerLivER: a database of liver cancer gene expression resources and biomarkers

Harpreet Kaur, Sherry Bhalla, Dilraj Kaur, Gajendra PS Raghava

Database, Volume 2020, 2020, baaa012, https://doi.org/10.1093/database/baaa012

MMHub, a database for the mulberry metabolome

Dong Li, Bi Ma, Xiaofei Xu, Guo Chen, Tian Li, Ningjia He

Database, Volume 2020, 2020, baaa011, https://doi.org/10.1093/database/baaa011

Human Breathomics Database

Tien-Chueh Kuo, Cheng-En Tan, San-Yuan Wang, Olivia A Lin, Bo-Han Su, Ming-Tsung Hsu, Jessica Lin, Yu-Yen Cheng, Ciao-Sin Chen, Yu-Chieh Yang, Kuo-Hsing Chen, Shu-Wen Lin, Chao-Chi Ho, Ching-Hua Kuo, Yufeng Jane Tseng

Database, Volume 2020, 2020, baz139, https://doi.org/10.1093/database/baz139