Volume 2020, 2020

Original Articles

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

Antonia Lock and others

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 and others

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

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

Xiangying Jiang and others

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 and Geng Meng

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

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

Lei Zhao and others

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 and others

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 and 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 and others

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

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

Ruixia Niu and others

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

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

Kwang Su Jung and others

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

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WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans

Basten L Snoek and others

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

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

Giulia Antonazzo and others

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 and others

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 and others

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

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

Rongrong Wu and others

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

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

Erik Czipa and others

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

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

Ibrahim Burak Ozyurt and others

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 and others

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 and others

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 and Julie A Hawkins

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

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GREG—studying transcriptional regulation using integrative graph databases

Songqing Mei and others

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

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HSPMdb: a computational repository of heat shock protein modulators

Prashant Singh and others

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 and others

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

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dbPepNeo: a manually curated database for human tumor neoantigen peptides

Xiaoxiu Tan and others

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

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

Xiao-Bao Ding and others

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

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

Valerio Arnaboldi and others

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

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Database Updates

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

Robert S Nash and others

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 and others

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 and others

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 and others

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 and others

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 and others

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

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

Mercy Rophina and others

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 and others

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

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MMHub, a database for the mulberry metabolome

Dong Li and others

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

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Human Breathomics Database

Tien-Chueh Kuo and others

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

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Tripal EUtils: a Tripal module to increase exchange and reuse of genome assembly metadata

B Condon and others

Database, Volume 2020, 2020, baz143, https://doi.org/10.1093/database/baz143

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miR-TV: an interactive microRNA Target Viewer for microRNA and target gene expression interrogation for human cancer studies

Chao-Yu Pan and Wen-Chang Lin

Database, Volume 2020, 2020, baz148, https://doi.org/10.1093/database/baz148

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RBPTD: a database of cancer-related RNA-binding proteins in humans

Kun Li and others

Database, Volume 2020, 2020, baz156, https://doi.org/10.1093/database/baz156

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GXD’s RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest

Constance M Smith and others

Database, Volume 2020, 2020, baaa002, https://doi.org/10.1093/database/baaa002

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PncStress: a manually curated database of experimentally validated stress-responsive non-coding RNAs in plants

Wenyi Wu and others

Database, Volume 2020, 2020, baaa001, https://doi.org/10.1093/database/baaa001

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Reviews

Artificial intelligence with multi-functional machine learning platform development for better healthcare and precision medicine

Zeeshan Ahmed and others

Database, Volume 2020, 2020, baaa010, https://doi.org/10.1093/database/baaa010

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Articles

Geographic assessment of cancer genome profiling studies

Paula Carrio-Cordo and others

Database, Volume 2020, 2020, baaa009, https://doi.org/10.1093/database/baaa009

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Technical report

A negative storage model for precise but compact storage of genetic variation data

Guillermo Gonzalez-Calderon and others

Database, Volume 2020, 2020, baz158, https://doi.org/10.1093/database/baz158

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Corrigendum

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

Kwang Su Jung and others

Database, Volume 2020, 2020, baaa030, https://doi.org/10.1093/database/baaa030

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