Volume 2023

2023

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EISSN 1758-0463

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Volume 2023, 2023

Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific

Takashi Hosono and others

Database, Volume 2023, 2023, baad081, https://doi.org/10.1093/database/baad081

A dataset of tumour-infiltrating lymphocytes in colorectal cancer patients using limited resources

Anis Hasnaoui and others

Database, Volume 2023, 2023, Page 0, https://doi.org/10.1093/database/baad089

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Original Articles

Benchmarks for measurement of duplicate detection methods in nucleotide databases

Qingyu Chen and others

Database, Volume 2023, 2023, baw164, https://doi.org/10.1093/database/baw164

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PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins

Hiroko X Kondo and others

Database, Volume 2023, 2023, baaa066, https://doi.org/10.1093/database/baaa066

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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

PolyQ Database—an integrated database on polyglutamine diseases

Bernardo Estevam and others

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

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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BCEDB: a linear B-cell epitopes database for SARS-CoV-2

Chengzheng Tai and others

Database, Volume 2023, 2023, baad065, https://doi.org/10.1093/database/baad065

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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

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

The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study

Panni Simona and others

Database, Volume 2023, 2023, baad066, https://doi.org/10.1093/database/baad066

Fisheries data management systems in the NW Mediterranean: from data collection to web visualization

Jordi Ribera-Altimir and others

Database, Volume 2023, 2023, baad067, https://doi.org/10.1093/database/baad067

InCliniGene enables high-throughput and comprehensive in vivo clonal tracking toward clinical genomics data integration

Ivan Merelli and others

Database, Volume 2023, 2023, baad069, https://doi.org/10.1093/database/baad069

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Notes on the data quality of bibliographic records from the MEDLINE database

Robin Bramley and others

Database, Volume 2023, 2023, baad070, https://doi.org/10.1093/database/baad070

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LeishMANIAdb: a comparative resource for Leishmania proteins

Gábor E Tusnády and others

Database, Volume 2023, 2023, baad074, https://doi.org/10.1093/database/baad074

OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis

Quan Xu and others

Database, Volume 2023, 2023, baad077, https://doi.org/10.1093/database/baad077

Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications

Shatabdi Sen and others

Database, Volume 2023, 2023, baad078, https://doi.org/10.1093/database/baad078

FooDrugs: a comprehensive food–drug interactions database with text documents and transcriptional data

Blanca Lacruz-Pleguezuelos and others

Database, Volume 2023, 2023, baad075, https://doi.org/10.1093/database/baad075

PlantIntronDB: a database for plant introns that host functional elements

Weiping Wang and others

Database, Volume 2023, 2023, baad082, https://doi.org/10.1093/database/baad082

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An online database for einkorn wheat to aid in gene discovery and functional genomics studies

Parva Kumar Sharma and others

Database, Volume 2023, 2023, baad079, https://doi.org/10.1093/database/baad079

Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical–protein relations

Antonio Miranda-Escalada and others

Database, Volume 2023, 2023, baad080, https://doi.org/10.1093/database/baad080

LncPCD: a manually curated database of experimentally supported associations between lncRNA-mediated programmed cell death and diseases

Ni He and others

Database, Volume 2023, 2023, baad087, https://doi.org/10.1093/database/baad087

aSynPEP-DB: a database of biogenic peptides for inhibiting α-synuclein aggregation

Carlos Pintado-Grima and others

Database, Volume 2023, 2023, baad084, https://doi.org/10.1093/database/baad084

Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium

Jennifer L Clarke and others

Database, Volume 2023, 2023, baad076, https://doi.org/10.1093/database/baad076

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Managing and monitoring a pandemic: showcasing a practical approach for the genomic surveillance of SARS-CoV-2

Mateusz Jundzill and others

Database, Volume 2023, 2023, baad071, https://doi.org/10.1093/database/baad071

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DISPEL: database for ascertaining the best medicinal plants to cure human diseases

Kavya Singh and others

Database, Volume 2023, 2023, baad073, https://doi.org/10.1093/database/baad073

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Design of the formalized and integrated Alzheimer’s Disease Ontology and its application in retrieving textual data via text mining

Bide Zhang and others

Database, Volume 2023, 2023, baad085, https://doi.org/10.1093/database/baad085

Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases

Ling-Ping Cen and others

Database, Volume 2023, 2023, baad083, https://doi.org/10.1093/database/baad083

SplicingLore: a web resource for studying the regulation of cassette exons by human splicing factors

Hélène Polvèche and others

Database, Volume 2023, 2023, baad091, https://doi.org/10.1093/database/baad091

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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Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences

Cecilia H Deng and others

Database, Volume 2023, 2023, baad088, https://doi.org/10.1093/database/baad088

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

Preproject ‘Swiss Virtual Natural History Collection’

Ana Petrus and others

Database, Volume 2023, 2023, baad072, https://doi.org/10.1093/database/baad072

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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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AgingReG: a curated database of aging regulatory relationships in humans

Minghui Piao and others

Database, Volume 2023, 2023, baad064, https://doi.org/10.1093/database/baad064

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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

ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer

Asma Sindhoo and others

Database, Volume 2023, 2023, baad063, https://doi.org/10.1093/database/baad063

iCAZyGFADB: an insect CAZyme and gene function annotation database

Chun Fu and YaoJun Yang

Database, Volume 2023, 2023, baad086, https://doi.org/10.1093/database/baad086

EnzyMine: a comprehensive database for enzyme function annotation with enzymatic reaction chemical feature

Dandan Sun and others

Database, Volume 2023, 2023, baaa065, https://doi.org/10.1093/database/baaa065

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DrugGen: a database of de novo-generated molecular binders for specified target proteins

Hao Qian and others

Database, Volume 2023, 2023, baad090, https://doi.org/10.1093/database/baad090

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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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Correction to: H3ABioNet genomic medicine and microbiome data portals hackathon proceedings

Database, Volume 2023, 2023, baad068, https://doi.org/10.1093/database/baad068

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