Volume 2023

2023

(In Progress)

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EISSN 1758-0463

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IN PROGRESS

Volume 2023, 2023

CiliaMiner: an integrated database for ciliopathy genes and ciliopathies

Merve Gül Turan and others

Database, Volume 2023, 2023, baad047, https://doi.org/10.1093/database/baad047

TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria

Andrzej Zielezinski and others

Database, Volume 2023, 2023, baad058, https://doi.org/10.1093/database/baad058

Tissue-specific transcriptomes reveal potential mechanisms of microbiome heterogeneity in an ancient fish

Matt J Thorstensen and others

Database, Volume 2023, 2023, baad055, https://doi.org/10.1093/database/baad055

PolyQ Database—an integrated database on polyglutamine diseases

Bernardo Estevam and others

Database, Volume 2023, 2023, baad060, https://doi.org/10.1093/database/baad060

Original Articles

Developing a disease-specific annotation protocol for VHL gene curation using Hypothes.is

Dena Salehipour and others

Database, Volume 2023, 2023, baac109, https://doi.org/10.1093/database/baac109

ENCD: a manually curated database of experimentally supported endocrine system disease and lncRNA associations

Ming Hao and others

Database, Volume 2023, 2023, baac113, https://doi.org/10.1093/database/baac113

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Automatic Extraction of Medication Mentions from Tweets—Overview of the BioCreative VII Shared Task 3 Competition

Davy Weissenbacher and others

Database, Volume 2023, 2023, baac108, https://doi.org/10.1093/database/baac108

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SalivaDB—a comprehensive database for salivary biomarkers in humans

Akanksha Arora and others

Database, Volume 2023, 2023, baad002, https://doi.org/10.1093/database/baad002

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Coronavirus Immunotherapeutic Consortium Database

Jarjapu Mahita and others

Database, Volume 2023, 2023, baac112, https://doi.org/10.1093/database/baac112

Standardized naming of microbiome samples in Genomes OnLine Database

Supratim Mukherjee and others

Database, Volume 2023, 2023, baad001, https://doi.org/10.1093/database/baad001

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FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes

Muhammad Rashid and others

Database, Volume 2023, 2023, baad004, https://doi.org/10.1093/database/baad004

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Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII

Robert Leaman and others

Database, Volume 2023, 2023, baad005, https://doi.org/10.1093/database/baad005

Assessing resource use: a case study with the Human Disease Ontology

J. Allen Baron and Lynn M Schriml

Database, Volume 2023, 2023, baad007, https://doi.org/10.1093/database/baad007

AIMedGraph: a comprehensive multi-relational knowledge graph for precision medicine

Xueping Quan and others

Database, Volume 2023, 2023, baad006, https://doi.org/10.1093/database/baad006

lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs

Giacomo B Marino and others

Database, Volume 2023, 2023, baad009, https://doi.org/10.1093/database/baad009

dbAQP-SNP: a database of missense single-nucleotide polymorphisms in human aquaporins

Rachana Dande and Ramasubbu Sankararamakrishnan

Database, Volume 2023, 2023, baad012, https://doi.org/10.1093/database/baad012

AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold

Jimin Pei and Qian Cong

Database, Volume 2023, 2023, baad008, https://doi.org/10.1093/database/baad008

A review of the International Seabed Authority database DeepData from a biological perspective: challenges and opportunities in the UN Ocean Decade

M Rabone and others

Database, Volume 2023, 2023, baad013, https://doi.org/10.1093/database/baad013

NbThermo: a new thermostability database for nanobodies

Mario S Valdés-Tresanco and others

Database, Volume 2023, 2023, baad021, https://doi.org/10.1093/database/baad021

CARD*Shark: automated prioritization of literature curation for the Comprehensive Antibiotic Resistance Database

Arman Edalatmand and Andrew G McArthur

Database, Volume 2023, 2023, baad023, https://doi.org/10.1093/database/baad023

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A combinatorial approach implementing new database structures to facilitate practical data curation management of QTL, association, correlation and heritability data on trait variants

Zhi-Liang Hu and others

Database, Volume 2023, 2023, baad024, https://doi.org/10.1093/database/baad024

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MBS: a genome browser annotation track for high-confident microRNA binding sites in whole human transcriptome

Walter Arancio and others

Database, Volume 2023, 2023, baad015, https://doi.org/10.1093/database/baad015

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OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology

Angela L Riffo-Campos and others

Database, Volume 2023, 2023, baad029, https://doi.org/10.1093/database/baad029

TRSRD: a database for research on risky substances in tea using natural language processing and knowledge graph-based techniques

Yongmei Wang and others

Database, Volume 2023, 2023, baad031, https://doi.org/10.1093/database/baad031

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CaviDB: a database of cavities and their features in the structural and conformational space of proteins

Ana Julia Velez Rueda and others

Database, Volume 2023, 2023, baad010, https://doi.org/10.1093/database/baad010

PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes

Liskin Swint-Kruse and others

Database, Volume 2023, 2023, baad030, https://doi.org/10.1093/database/baad030

SmartWoodID—an image collection of large end-grain surfaces to support wood identification systems

Ruben De Blaere and others

Database, Volume 2023, 2023, baad034, https://doi.org/10.1093/database/baad034

IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2)

Abhishek Khatri and others

Database, Volume 2023, 2023, baad039, https://doi.org/10.1093/database/baad039

PLBD: protein–ligand binding database of thermodynamic and kinetic intrinsic parameters

Darius Lingė and others

Database, Volume 2023, 2023, baad040, https://doi.org/10.1093/database/baad040

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Neodb: a comprehensive neoantigen database and discovery platform for cancer immunotherapy

Tao Wu and others

Database, Volume 2023, 2023, baad041, https://doi.org/10.1093/database/baad041

GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture

Noam Hadar and others

Database, Volume 2023, 2023, baad043, https://doi.org/10.1093/database/baad043

RNA-Chrom: a manually curated analytical database of RNA–chromatin interactome

G K Ryabykh and others

Database, Volume 2023, 2023, baad025, https://doi.org/10.1093/database/baad025

PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines

Qinyun Cai and others

Database, Volume 2023, 2023, baad042, https://doi.org/10.1093/database/baad042

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VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants

Pietro Pinoli and others

Database, Volume 2023, 2023, baad044, https://doi.org/10.1093/database/baad044

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PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study

Jian Hu and others

Database, Volume 2023, 2023, baad050, https://doi.org/10.1093/database/baad050

CropGF: a comprehensive visual platform for crop gene family mining and analysis

Jingtian Xu and others

Database, Volume 2023, 2023, baad051, https://doi.org/10.1093/database/baad051

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APDB: a database on air pollutant characterization and similarity prediction

Eva Viesi and others

Database, Volume 2023, 2023, baad046, https://doi.org/10.1093/database/baad046

scBrainMap: a landscape for cell types and associated genetic markers in the brain

Yuhao Chi and others

Database, Volume 2023, 2023, baad035, https://doi.org/10.1093/database/baad035

BLAB2CancerKD: a knowledge graph database focusing on the association between lactic acid bacteria and cancer, but beyond

Yi Jing and others

Database, Volume 2023, 2023, baad036, https://doi.org/10.1093/database/baad036

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PurificationDB: database of purification conditions for proteins

Olivia Garland and others

Database, Volume 2023, 2023, baad016, https://doi.org/10.1093/database/baad016

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Assessing the use of supplementary materials to improve genomic variant discovery

Emilie Pasche and others

Database, Volume 2023, 2023, baad017, https://doi.org/10.1093/database/baad017

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PDC: a highly compact file format to store protein 3D coordinates

Chengxin Zhang and Anna Marie Pyle

Database, Volume 2023, 2023, baad018, https://doi.org/10.1093/database/baad018

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Semi-automatic translation of medicine usage data (in Dutch, free-text) from Lifelines COVID-19 questionnaires to ATC codes

Alexander J Kellmann and others

Database, Volume 2023, 2023, baad019, https://doi.org/10.1093/database/baad019

Developing TeroENZ and TeroMAP modules for the terpenome research platform TeroKit

Nianhang Chen and others

Database, Volume 2023, 2023, baad020, https://doi.org/10.1093/database/baad020

CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines

Zhi-Hui Luo and others

Database, Volume 2023, 2023, baad022, https://doi.org/10.1093/database/baad022

The landscape of health disparities in the UK Biobank

Shashwat Deepali Nagar and others

Database, Volume 2023, 2023, baad026, https://doi.org/10.1093/database/baad026

AI4FoodDB: a database for personalized e-Health nutrition and lifestyle through wearable devices and artificial intelligence

Sergio Romero-Tapiador and others

Database, Volume 2023, 2023, baad049, https://doi.org/10.1093/database/baad049

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Biomedical relation extraction with knowledge base–refined weak supervision

Wonjin Yoon and others

Database, Volume 2023, 2023, baad054, https://doi.org/10.1093/database/baad054

The MetaGens algorithm for metagenomic database lossy compression and subject alignment

Gustavo Henrique Cervi and others

Database, Volume 2023, 2023, baad053, https://doi.org/10.1093/database/baad053

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CBPDdb: a curated database of compounds derived from Coumarin–Benzothiazole–Pyrazole

Shailima Rampogu and others

Database, Volume 2023, 2023, baad062, https://doi.org/10.1093/database/baad062

Building a large gene expression-cancer knowledge base with limited human annotations

Stefano Marchesin and others

Database, Volume 2023, 2023, baad061, https://doi.org/10.1093/database/baad061

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Review

New approaches in developing medicinal herbs databases

Zahra Fathifar and others

Database, Volume 2023, 2023, baac110, https://doi.org/10.1093/database/baac110

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Review of databases for experimentally validated human microRNA–mRNA interactions

Dorian Kariuki and others

Database, Volume 2023, 2023, baad014, https://doi.org/10.1093/database/baad014

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The importance of graph databases and graph learning for clinical applications

Daniel Walke and others

Database, Volume 2023, 2023, baad045, https://doi.org/10.1093/database/baad045

Technical report

WASP: the World Archives of Species Perception

Tuan Nguyen and others

Database, Volume 2023, 2023, baad003, https://doi.org/10.1093/database/baad003

Database tool

Improved insights into the SABIO-RK database via visualization

Dorotea Dudaš and others

Database, Volume 2023, 2023, baad011, https://doi.org/10.1093/database/baad011

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SyntenyViewer: a comparative genomics-driven translational research tool

Raphael Flores and others

Database, Volume 2023, 2023, baad027, https://doi.org/10.1093/database/baad027

MantaID: a machine learning–based tool to automate the identification of biological database IDs

Zhengpeng Zeng and others

Database, Volume 2023, 2023, baad028, https://doi.org/10.1093/database/baad028

Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine

Raghunandan Wable and others

Database, Volume 2023, 2023, baad033, https://doi.org/10.1093/database/baad033

ChagasDB: 80 years of publicly available data on the molecular host response to Trypanosoma cruzi infection in a single database

Pauline Brochet and others

Database, Volume 2023, 2023, baad037, https://doi.org/10.1093/database/baad037

CIGAF—a database and interactive platform for insect-associated trichomycete fungi

Shalini Chaudhary and others

Database, Volume 2023, 2023, baad038, https://doi.org/10.1093/database/baad038

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MineProt: a stand-alone server for structural proteome curation

Yunchi Zhu and others

Database, Volume 2023, 2023, Page 0, https://doi.org/10.1093/database/baad059

CCIDB: a manually curated cell–cell interaction database with cell context information

Jin Young Noh and others

Database, Volume 2023, 2023, baad057, https://doi.org/10.1093/database/baad057

AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV

Shahid Ullah and others

Database, Volume 2023, 2023, baad056, https://doi.org/10.1093/database/baad056

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Perspective/Opinion

Unified and pluralistic ideals for data sharing and reuse in biodiversity

Beckett Sterner and others

Database, Volume 2023, 2023, baad048, https://doi.org/10.1093/database/baad048

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Correction

Correction to: Standardized naming of microbiome samples in Genomes OnLine Database

Database, Volume 2023, 2023, baad032, https://doi.org/10.1093/database/baad032

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Correction to: RNA-Chrom: a manually curated analytical database of RNA–chromatin interactome

Database, Volume 2023, 2023, baad052, https://doi.org/10.1093/database/baad052

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