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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
PurificationDB: database of purification conditions for proteins
Olivia Garland and others
Database, Volume 2023, 2023, baad016, https://doi.org/10.1093/database/baad016
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Correction
Correction to: Standardized naming of microbiome samples in Genomes OnLine Database
Database, Volume 2023, 2023, baad032, https://doi.org/10.1093/database/baad032
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
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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