Volume 2021

2021

EISSN 1758-0463

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Volume 2021, 2021

HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis

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

Database, Volume 2021, 2021, baab009, https://doi.org/10.1093/database/baab009

UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase–substrate interactions

Zhongyan Li, Siyu Chen, Jhih-Hua Jhong, Yuxuan Pang, Kai-Yao Huang, Shangfu Li, Tzong-Yi Lee

Database, Volume 2021, 2021, baab010, https://doi.org/10.1093/database/baab010

Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database

Florian Malard, Eugenia Wulff-Fuentes, Rex R Berendt, Guillaume Didier, Stephanie Olivier-Van Stichelen

Database, Volume 2021, 2021, baab039, https://doi.org/10.1093/database/baab039

Web tools to perform long non-coding RNAs analysis in oncology research

Shixing Gu, Guangjie Zhang, Qin Si, Jiawen Dai, Zhen Song, Yingshuang Wang

Database, Volume 2021, 2021, baab047, https://doi.org/10.1093/database/baab047

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circExp database: an online transcriptome platform for human circRNA expressions in cancers

Min Zhao, Yining Liu, Hong Qu

Database, Volume 2021, 2021, baab045, https://doi.org/10.1093/database/baab045

A nomenclature for echinoderm genes

Thomas R Beatman, Katherine M Buckley, Gregory A Cary, Veronica F Hinman, Charles A Ettensohn

Database, Volume 2021, 2021, baab052, https://doi.org/10.1093/database/baab052

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Nabe: an energetic database of amino acid mutations in protein–nucleic acid binding interfaces

Junyi Liu, Siyu Liu, Chenzhe Liu, Yaping Zhang, Yuliang Pan, Zixiang Wang, Jiacheng Wang, Ting Wen, Lei Deng

Database, Volume 2021, 2021, baab050, https://doi.org/10.1093/database/baab050

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A PostgreSQL Tripal solution for large-scale genotypic and phenotypic data

Lacey-Anne Sanderson, Carolyn T Caron, Reynold L Tan, Kirstin E Bett

Database, Volume 2021, 2021, baab051, https://doi.org/10.1093/database/baab051

lncExplore: a database of pan-cancer analysis and systematic functional annotation for lncRNAs from RNA-sequencing data

Yi-Wei Lee, Ming Chen, I-Fang Chung, Ting-Yu Chang

Database, Volume 2021, 2021, baab053, https://doi.org/10.1093/database/baab053

Peptipedia: a user-friendly web application and a comprehensive database for peptide research supported by Machine Learning approach

Cristofer Quiroz, Yasna Barrera Saavedra, Benjamín Armijo-Galdames, Juan Amado-Hinojosa, Álvaro Olivera-Nappa, Anamaria Sanchez-Daza, David Medina-Ortiz

Database, Volume 2021, 2021, baab055, https://doi.org/10.1093/database/baab055

Food Enzyme Database (FEDA): a web application gathering information about food enzyme preparations available on the European market

Marie Deckers, Julien Van Braeckel, Kevin Vanneste, Dieter Deforce, Marie-Alice Fraiture, Nancy h.c Roosens

Database, Volume 2021, 2021, baab060, https://doi.org/10.1093/database/baab060

HBFP: a new repository for human body fluid proteome

Dan Shao, Lan Huang, Yan Wang, Xueteng Cui, Yufei Li, Yao Wang, Qin Ma, Wei Du, Juan Cui

Database, Volume 2021, 2021, baab065, https://doi.org/10.1093/database/baab065

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The World Spider Trait database: a centralized global open repository for curated data on spider traits

Stano Pekár, Jonas O Wolff, Ľudmila Černecká, Klaus Birkhofer, Stefano Mammola, Elizabeth C Lowe, Caroline S Fukushima, Marie E Herberstein, Adam Kučera, Bruno A Buzatto, El Aziz Djoudi, Marc Domenech, Alison Vanesa Enciso, Yolanda M G Piñanez Espejo, Sara Febles, Luis F García, Thiago Gonçalves-Souza, Marco Isaia, Denis Lafage … Pedro Cardoso

Database, Volume 2021, 2021, baab064, https://doi.org/10.1093/database/baab064

https://botryosphaeriales.org/, an online platform for up-to-date classification and account of taxa of Botryosphaeriales

N a Wu, Asha J Dissanayake, Ishara S Manawasinghe, Achala R Rathnayaka, Jian-Kui Liu, Alan j.l Phillips, Itthayakorn Promputtha, Kevin D Hyde

Database, Volume 2021, 2021, baab061, https://doi.org/10.1093/database/baab061

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Mining drug–target and drug–adverse drug reaction databases to identify target–adverse drug reaction relationships

Cristiano Galletti, Patricia Mirela Bota, Baldo Oliva, Narcis Fernandez-Fuentes

Database, Volume 2021, 2021, baab068, https://doi.org/10.1093/database/baab068

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MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses

Taimoor Khan, Abbas Khan, Dong-Qing Wei

Database, Volume 2021, 2021, baab063, https://doi.org/10.1093/database/baab063

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies

Rebecca Jackson, Nicolas Matentzoglu, James A Overton, Randi Vita, James P Balhoff, Pier Luigi Buttigieg, Seth Carbon, Melanie Courtot, Alexander D Diehl, Damion M Dooley, William D Duncan, Nomi L Harris, Melissa A Haendel, Suzanna E Lewis, Darren A Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M Schriml, Barry Smith … Bjoern Peters

Database, Volume 2021, 2021, baab069, https://doi.org/10.1093/database/baab069

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Gene Ontology curation of the blood–brain barrier to improve the analysis of Alzheimer’s and other neurological diseases

Shirin C C Saverimuttu, Barbara Kramarz, Milagros Rodríguez-López, Penelope Garmiri, Helen Attrill, Katherine E Thurlow, Marios Makris, Sandra de Miranda Pinheiro, Sandra Orchard, Ruth C Lovering

Database, Volume 2021, 2021, baab067, https://doi.org/10.1093/database/baab067

JAMIR-eQTL: Japanese genome-wide identification of microRNA expression quantitative trait loci across dementia types

Shintaro Akiyama, Sayuri Higaki, Takahiro Ochiya, Kouichi Ozaki, Shumpei Niida, Daichi Shigemizu

Database, Volume 2021, 2021, baab072, https://doi.org/10.1093/database/baab072

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At-C-RNA database, a one-stop source for information on circRNAs in Arabidopsis thaliana in a unified format

Katarzyna Nowis, Paulina Jackowiak, Marek Figlerowicz, Anna Philips

Database, Volume 2021, 2021, baab074, https://doi.org/10.1093/database/baab074

Prototheca-ID: a web-based application for molecular identification of Prototheca species

Mikołaj Dziurzyński, Przemyslaw Decewicz, Mateusz Iskra, Zofia Bakuła, Tomasz Jagielski

Database, Volume 2021, 2021, baab073, https://doi.org/10.1093/database/baab073

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HFIP: an integrated multi-omics data and knowledge platform for the precision medicine of heart failure

Jing Wu, Min Zhao, Tao Li, Jinxiu Sun, Qi Chen, Chengliang Yin, Zhilong Jia, Chenghui Zhao, Gui Lin, Yuan Ni, Guotong Xie, Jinlong Shi, Kunlun He

Database, Volume 2021, 2021, baab076, https://doi.org/10.1093/database/baab076

DCMP: database of cancer mutant protein domains

Isaac Arnold Emerson, Kiran Kumar Chitluri

Database, Volume 2021, 2021, baab066, https://doi.org/10.1093/database/baab066

Corrigendum to: the SNPcurator: literature mining of enriched SNP-disease associations

Noha S Tawfik, Marco R Spruit

Database, Volume 2021, 2021, baab070, https://doi.org/10.1093/database/baab070

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Corrigendum to: QSDB—a graphical Quorum Sensing Database

Karsten Klein, Dimitar Garkov, Sina Rütschlin, Thomas Böttcher, Falk Schreiber

Database, Volume 2021, 2021, baab071, https://doi.org/10.1093/database/baab071

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iCAV: an integrative database of cancer-associated viruses

Bo Liu, Qingfeng Zhang, Jingou Wang, Shumin Cao, Zhiyuan Zhou, Ze-Xian Liu, Han Cheng

Database, Volume 2021, 2021, baab079, https://doi.org/10.1093/database/baab079

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The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine

Tavis K Anderson, Blake Inderski, Diego G Diel, Benjamin M Hause, Elizabeth G Porter, Travis Clement, Eric A Nelson, Jianfa Bai, Jane Christopher-Hennings, Phillip C Gauger, Jianqiang Zhang, Karen M Harmon, Rodger Main, Kelly M Lager, Kay S Faaberg

Database, Volume 2021, 2021, baab078, https://doi.org/10.1093/database/baab078

https://www.fungiofpakistan.com: a continuously updated online database of fungi in Pakistan

Mubashar Raza, Lei Cai, Muhammad Waseem Abbasi, Marium Tariq, Nalin N Wijayawardene

Database, Volume 2021, 2021, baab080, https://doi.org/10.1093/database/baab080

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The first comprehensive database of germline pathogenic variants in East Asian cancer patients

Xiaoshun Shi, Ruidong Li, Jianxue Zhai, Allen Menglin Chen, Kailing Huang, Zhouxia Zheng, Zhuona Chen, Xiaoyin Dong, Xiguang Liu, Di Lu, Siyang Feng, Dingwei Diao, Pengfei Ren, Zhaoguo Liu, Grant Morahan, Kaican Cai

Database, Volume 2021, 2021, baab075, https://doi.org/10.1093/database/baab075

Original Articles

HGFDB: a collective database of helmeted guinea fowl genomics

Xuzhen Li, Zhi Li, Quankuan Shen, Yunbin Pan, Xiao Dong, Zetan Xu, Shengchang Duan, Yunfei Li, Yuan Du, Shanshan Chen, Zhaocheng Ma, Yang Dong

Database, Volume 2021, 2021, baaa116, https://doi.org/10.1093/database/baaa116

Large-scale regulatory and signaling network assembly through linked open data

M Lefebvre, A Gaignard, M Folschette, J Bourdon, C Guziolowski

Database, Volume 2021, 2021, baaa113, https://doi.org/10.1093/database/baaa113

Converting disease maps into heavyweight ontologies: general methodology and application to Alzheimer’s disease

Vincent Henry, Ivan Moszer, Olivier Dameron, Laura Vila Xicota, Bruno Dubois, Marie-Claude Potier, Martin Hofmann-Apitius, Olivier Colliot, INSIGHT-preAD Study Group

Database, Volume 2021, 2021, baab004, https://doi.org/10.1093/database/baab004

Extraction of causal relations based on SBEL and BERT model

Yifan Shao, Haoru Li, Jinghang Gu, Longhua Qian, Guodong Zhou

Database, Volume 2021, 2021, baab005, https://doi.org/10.1093/database/baab005

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Curation of over 10 000 transcriptomic studies to enable data reuse

Nathaniel Lim, Stepan Tesar, Manuel Belmadani, Guillaume Poirier-Morency, Burak Ogan Mancarci, Jordan Sicherman, Matthew Jacobson, Justin Leong, Patrick Tan, Paul Pavlidis

Database, Volume 2021, 2021, baab006, https://doi.org/10.1093/database/baab006

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CMBD: a manually curated cancer metabolic biomarker knowledge database

Jing Chen, Xingyun Liu, Li Shen, Yuxin Lin, Bairong Shen

Database, Volume 2021, 2021, baaa094, https://doi.org/10.1093/database/baaa094

Development of a biomarker database toward performing disease classification and finding disease interrelations

Shaikh Farhad Hossain, Ming Huang, Naoaki Ono, Aki Morita, Shigehiko Kanaya, Md Altaf-Ul-Amin

Database, Volume 2021, 2021, baab011, https://doi.org/10.1093/database/baab011

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An immunologically friendly classification of non-peptidic ligands

Lindy Edwards, Rebecca Jackson, James A Overton, Randi Vita, Nina Blazeska, Bjoern Peters, Alessandro Sette

Database, Volume 2021, 2021, baab014, https://doi.org/10.1093/database/baab014

Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning

Eryk Kropiwnicki, John E Evangelista, Daniel J Stein, Daniel J B Clarke, Alexander Lachmann, Maxim V Kuleshov, Minji Jeon, Kathleen M Jagodnik, Avi Ma’ayan

Database, Volume 2021, 2021, baab017, https://doi.org/10.1093/database/baab017

Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature

Valerio Arnaboldi, Jaehyoung Cho, Paul W Sternberg

Database, Volume 2021, 2021, baab015, https://doi.org/10.1093/database/baab015

APICURON: a database to credit and acknowledge the work of biocurators

András Hatos, Federica Quaglia, Damiano Piovesan, Silvio C E Tosatto

Database, Volume 2021, 2021, baab019, https://doi.org/10.1093/database/baab019

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Tripal MegaSearch: a tool for interactive and customizable query and download of big data

Sook Jung, Chun-Huai Cheng, Katheryn Buble, Taein Lee, Jodi Humann, Jing Yu, James Crabb, Heidi Hough, Dorrie Main

Database, Volume 2021, 2021, baab023, https://doi.org/10.1093/database/baab023

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Increasing metadata coverage of SRA BioSample entries using deep learning–based named entity recognition

Adam Klie, Brian Y Tsui, Shamim Mollah, Dylan Skola, Michelle Dow, Chun-Nan Hsu, Hannah Carter

Database, Volume 2021, 2021, baab021, https://doi.org/10.1093/database/baab021

CANNUSE, a database of traditional Cannabis uses—an opportunity for new research

Manica Balant, Airy Gras, Francisco Gálvez, Teresa Garnatje, Joan Vallès, Daniel Vitales

Database, Volume 2021, 2021, baab024, https://doi.org/10.1093/database/baab024

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Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans

Tzu-Hsien Yang, Chung-Yu Wang, Hsiu-Chun Tsai, Cheng-Tse Liu

Database, Volume 2021, 2021, baab025, https://doi.org/10.1093/database/baab025

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COVIDOUTCOME—estimating COVID severity based on mutation signatures in the SARS-CoV-2 genome

Ádám Nagy, Balázs Ligeti, János Szebeni, Sándor Pongor, Balázs Győrffy

Database, Volume 2021, 2021, baab020, https://doi.org/10.1093/database/baab020

covid19census: U.S. and Italy COVID-19 metrics and other epidemiological data

Claudio Zanettini, Mohamed Omar, Wikum Dinalankara, Eddie Luidy Imada, Elizabeth Colantuoni, Giovanni Parmigiani, Luigi Marchionni

Database, Volume 2021, 2021, baab027, https://doi.org/10.1093/database/baab027

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Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies

Liliana Andrés-Hernández, Razlin Azman Halimi, Ramil Mauleon, Sean Mayes, Abdul Baten, Graham J King

Database, Volume 2021, 2021, baab028, https://doi.org/10.1093/database/baab028

Application of beta and gamma carbonic anhydrase sequences as tools for identification of bacterial contamination in the whole genome sequence of inbred Wuzhishan minipig (Sus scrofa) annotated in databases

Reza Zolfaghari Emameh, Seyed Nezamedin Hosseini, Seppo Parkkila

Database, Volume 2021, 2021, baab029, https://doi.org/10.1093/database/baab029

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emiRIT: a text-mining-based resource for microRNA information

Debarati Roychowdhury, Samir Gupta, Xihan Qin, Cecilia N Arighi, K Vijay-Shanker

Database, Volume 2021, 2021, baab031, https://doi.org/10.1093/database/baab031

BENviewer: a gene interaction network visualization server based on graph embedding model

Yunqing Liu, Yunchi Zhu, Chunpeng He, Zuhong Lu

Database, Volume 2021, 2021, baab033, https://doi.org/10.1093/database/baab033

dbGENVOC: database of GENomic Variants of Oral Cancer, with special reference to India

Sanchari Pradhan, Subrata Das, Animesh K Singh, Chitrarpita Das, Analabha Basu, Partha P Majumder, Nidhan K Biswas

Database, Volume 2021, 2021, baab034, https://doi.org/10.1093/database/baab034

ReMeDy: a platform for integrating and sharing published stem cell research data with a focus on iPSC trials

Kirill Borziak, Irena Parvanova, Joseph Finkelstein

Database, Volume 2021, 2021, baab038, https://doi.org/10.1093/database/baab038

Which methods are the most effective in enabling novice users to participate in ontology creation? A usability study

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

Database, Volume 2021, 2021, baab035, https://doi.org/10.1093/database/baab035

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MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses

Sebastien A Choteau, Audrey Wagner, Philippe Pierre, Lionel Spinelli, Christine Brun

Database, Volume 2021, 2021, baab032, https://doi.org/10.1093/database/baab032

KMDATA: a curated database of reconstructed individual patient-level data from 153 oncology clinical trials

Geoffrey Fell, Robert A Redd, Alyssa M Vanderbeek, Rifaquat Rahman, Bill Louv, Jon McDunn, Andrea Arfè, Brian M Alexander, Steffen Ventz, Lorenzo Trippa

Database, Volume 2021, 2021, baab037, https://doi.org/10.1093/database/baab037

TIDB: a comprehensive database of trained immunity

Yang Cao, Qingyang Dong, Dan Wang, Ying Liu, Pengcheng Zhang, Xiaobo Yu, Chao Niu

Database, Volume 2021, 2021, baab041, https://doi.org/10.1093/database/baab041

CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer

Amrita Chattopadhyay, Zi Han Teoh, Chi-Yun Wu, Jyh-Ming Jimmy Juang, Liang-Chuan Lai, Mong-Hsun Tsai, Chia-Hsin Wu, Tzu-Pin Lu, Eric Y Chuang

Database, Volume 2021, 2021, baab044, https://doi.org/10.1093/database/baab044

MUSTARD—a comprehensive resource of mutation-specific therapies in cancer

Gauri Mittal, Anu R I, Aastha Vatsyayan, Kavita Pandhare, Vinod Scaria

Database, Volume 2021, 2021, baab042, https://doi.org/10.1093/database/baab042

Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students

Paula Duek, Camille Mary, Monique Zahn-Zabal, Amos Bairoch, Lydie Lane

Database, Volume 2021, 2021, baab046, https://doi.org/10.1093/database/baab046

Male Infertility Knowledgebase: decoding the genetic and disease landscape

Shaini Joseph, Smita D Mahale

Database, Volume 2021, 2021, baab049, https://doi.org/10.1093/database/baab049

The Breeding Information Management System (BIMS): an online resource for crop breeding

Sook Jung, Taein Lee, Ksenija Gasic, B. Todd Campbell, Jing Yu, Jodi Humann, Sushan Ru, Daniel Edge-Garza, Heidi Hough, Dorrie Main

Database, Volume 2021, 2021, baab054, https://doi.org/10.1093/database/baab054

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MODB: a comprehensive mitochondrial genome database for Mollusca

Jiangyong Qu, Yanran Xu, Yutong Cui, Sen Wu, Lijun Wang, Xiumei Liu, Zhikai Xing, Xiaoyu Guo, Shanshan Wang, Ruoran Li, Xiaoyue Sun, Xiang Li, Xiyue Wang, Tao Liu, Xumin Wang

Database, Volume 2021, 2021, baab056, https://doi.org/10.1093/database/baab056

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QSDB—a graphical Quorum Sensing Database

Karsten Klein, Dimitar Garkov, Sina Rütschlin, Thomas Böttcher, Falk Schreiber

Database, Volume 2021, 2021, baab058, https://doi.org/10.1093/database/baab058

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COVIDium: a COVID-19 resource compendium

Rohit Satyam, Malik Yousef, Sahar Qazi, Adil Manzoor Bhat, Khalid Raza

Database, Volume 2021, 2021, baab057, https://doi.org/10.1093/database/baab057

EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species

Anna Bernasconi, Luca Cilibrasi, Ruba Al Khalaf, Tommaso Alfonsi, Stefano Ceri, Pietro Pinoli, Arif Canakoglu

Database, Volume 2021, 2021, baab059, https://doi.org/10.1093/database/baab059

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Classifying domain-specific text documents containing ambiguous keywords

Kamran Karimi, Sergei Agalakov, Cheryl A Telmer, Thomas R Beatman, Troy J Pells, Bradley Im Arshinoff, Carolyn J Ku, Saoirse Foley, Veronica F Hinman, Charles A Ettensohn, Peter D Vize

Database, Volume 2021, 2021, baab062, https://doi.org/10.1093/database/baab062

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Review

The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research

Lauren Chan, Nicole Vasilevsky, Anne Thessen, Julie McMurry, Melissa Haendel

Database, Volume 2021, 2021, baab003, https://doi.org/10.1093/database/baab003

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Post-translational modifications in proteins: resources, tools and prediction methods

Shahin Ramazi, Javad Zahiri

Database, Volume 2021, 2021, baab012, https://doi.org/10.1093/database/baab012

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An overview of graph databases and their applications in the biomedical domain

Santiago Timón-Reina, Mariano Rincón, Rafael Martínez-Tomás

Database, Volume 2021, 2021, baab026, https://doi.org/10.1093/database/baab026

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Database tool

InSexBase: an annotated genomic resource of sex chromosomes and sex-biased genes in insects

X i Chen, Yang Mei, Mengyao Chen, Dong Jing, Yumin He, Feiling Liu, Kang He, Fei Li

Database, Volume 2021, 2021, baab001, https://doi.org/10.1093/database/baab001

bc-GenExMiner 4.5: new mining module computes breast cancer differential gene expression analyses

Pascal Jézéquel, Wilfried Gouraud, Fadoua Ben Azzouz, Catherine Guérin-Charbonnel, Philippe P Juin, Hamza Lasla, Mario Campone

Database, Volume 2021, 2021, baab007, https://doi.org/10.1093/database/baab007

CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator

Vasundra Touré, John Zobolas, Martin Kuiper, Steven Vercruysse

Database, Volume 2021, 2021, baaa107, https://doi.org/10.1093/database/baaa107

MENSAdb: a thorough structural analysis of membrane protein dimers

Pedro Matos-Filipe, António J Preto, Panagiotis I Koukos, Joana Mourão, Alexandre M J J Bonvin, Irina S Moreira

Database, Volume 2021, 2021, baab013, https://doi.org/10.1093/database/baab013

H3ABioNet genomic medicine and microbiome data portals hackathon proceedings

Faisal M Fadlelmola, Kais Ghedira, Yosr Hamdi, Mariem Hanachi, Fouzia Radouani, Imane Allali, Anmol Kiran, Lyndon Zass, Nihad Alsayed, Meriem Fassatoui, Chaimae Samtal, Samah Ahmed, Jorge Da Rocha, Souad Chaqsare, Reem M Sallam, Melek Chaouch, Mohammed A Farahat, Alfred Ssekagiri, Ziyaad Parker … Nicola Mulder

Database, Volume 2021, 2021, baab016, https://doi.org/10.1093/database/baab016

BC-TFdb: a database of transcription factor drivers in breast cancer

Abbas Khan, Taimoor Khan, Syed Nouman Nasir, Syed Shujait Ali, Muhammad Suleman, Muhammad Rizwan, Muhammad Waseem, Shahid Ali, Xia Zhao, Dong-Qing Wei

Database, Volume 2021, 2021, baab018, https://doi.org/10.1093/database/baab018

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IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease

Farhat Khan, Aleksandar Radovanovic, Takashi Gojobori, Mandeep Kaur

Database, Volume 2021, 2021, baab022, https://doi.org/10.1093/database/baab022

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mPPI: a database extension to visualize structural interactome in a one-to-many manner

Yekai Zhou, Hongjun Chen, Sida Li, Ming Chen

Database, Volume 2021, 2021, baab036, https://doi.org/10.1093/database/baab036

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LINPS: a database for cancer-cell-specific perturbations of biological networks

Mahmoud Ahmed, Deok Ryong Kim

Database, Volume 2021, 2021, baab048, https://doi.org/10.1093/database/baab048

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Database update

SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences

R Jorquera, C González, P T L C Clausen, B Petersen, D S Holmes

Database, Volume 2021, 2021, baab002, https://doi.org/10.1093/database/baab002

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An update of KAIKObase, the silkworm genome database

Ching-chia Yang, Kakeru Yokoi, Kimiko Yamamoto, Akiya Jouraku

Database, Volume 2021, 2021, baaa099, https://doi.org/10.1093/database/baaa099

Integration of 1:1 orthology maps and updated datasets into Echinobase

Saoirse Foley, Carolyn Ku, Brad Arshinoff, Vaneet Lotay, Kamran Karimi, Peter D Vize, Veronica Hinman

Database, Volume 2021, 2021, baab030, https://doi.org/10.1093/database/baab030

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The Progenetix oncogenomic resource in 2021

Qingyao Huang, Paula Carrio-Cordo, Bo Gao, Rahel Paloots, Michael Baudis

Database, Volume 2021, 2021, baab043, https://doi.org/10.1093/database/baab043

Technical report

Bioinformatics tools developed to support BioCompute Objects

Janisha A Patel, Dennis A Dean, Charles Hadley King, Nan Xiao, Soner Koc, Ekaterina Minina, Anton Golikov, Phillip Brooks, Robel Kahsay, Rahi Navelkar, Manisha Ray, Dave Roberson, Chris Armstrong, Raja Mazumder, Jonathon Keeney

Database, Volume 2021, 2021, baab008, https://doi.org/10.1093/database/baab008

Standardization of assay representation in the Ontology for Biomedical Investigations

Randi Vita, Jie Zheng, Rebecca Jackson, Damion Dooley, James A Overton, Mark A Miller, Daniel C Berrios, Richard H Scheuermann, Yongqun He, Hande Küçük McGinty, Mathias Brochhausen, Aisyah Yu Lin, Sagar B Jain, Marcus C Chibucos, John Judkins, Michelle G Giglio, Irene Y Feng, Gully Burns, Matthew H Brush … Christian J Stoeckert Jr

Database, Volume 2021, 2021, baab040, https://doi.org/10.1093/database/baab040

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