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FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-03-27 Tan Meng, Hanqing Jiao, Yi Zhang, Yi Zhou, Shaoying Chen, Xinrui Wang, Bowen Yang, Jie Sun, Xin Geng, Dilay Hazal Ayhan, Li Guo
Pangenomes, capturing the genetic diversity of a species or genus, are essential to understanding the ecology, pathobiology and evolutionary mechanisms of fungi that cause infection in crops and humans. However, fungal pangenome databases remain unavailable. Here, we report the first fungal pangenome database, specifically for Fusarium oxysporum species complex (FOSC), a group of cross-kingdom pathogens
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BioKC: a collaborative platform for curation and annotation of molecular interactions Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-03-27 Carlos Vega, Marek Ostaszewski, Valentin Grouès, Reinhard Schneider, Venkata Satagopam
Curation of biomedical knowledge into systems biology diagrammatic or computational models is essential for studying complex biological processes. However, systems-level curation is a laborious manual process, especially when facing ever-increasing growth of domain literature. New findings demonstrating elaborate relationships between multiple molecules, pathways and cells have to be represented in
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ESKtides: a comprehensive database and mining method for ESKAPE phage-derived antimicrobial peptides Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-03-26 Hongfang Wu, Rongxian Chen, Xuejian Li, Yue Zhang, Jianwei Zhang, Yanbo Yang, Jun Wan, Yang Zhou, Huanchun Chen, Jinquan Li, Runze Li, Geng Zou
‘Superbugs’ have received increasing attention from researchers, such as ESKAPE bacteria (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.), which directly led to about 1 270 000 death cases in 2019. Recently, phage peptidoglycan hydrolases (PGHs)–derived antimicrobial peptides were proposed as new antibacterial
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Development of marine biodiversity database (BISMaL) to enable estimations past habitat conditions for marine life in the northwestern Pacific Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-03-20 Takashi Hosono, Tomoaki Kitayama, Hideaki Saito, Katsunori Fujikura
Global activities involving the collection of marine biodiversity information have provided a large amount of biological observation records that cover various spatiotemporal areas. To predict biological responses or distribution changes in response to environmental changes by using these observation records, it is essential to analyze not only the current marine physicochemical environmental conditions
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Best practices for the manual curation of intrinsically disordered proteins in DisProt Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-03-20 Federica Quaglia, Anastasia Chasapi, Maria Victoria Nugnes, Maria Cristina Aspromonte, Emanuela Leonardi, Damiano Piovesan, Silvio C E Tosatto
The DisProt database is a resource containing manually curated data on experimentally validated intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) from the literature. Developed in 2005, its primary goal was to collect structural and functional information into proteins that lack a fixed three-dimensional structure. Today, DisProt has evolved into a major repository
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FGCD: a database of fungal gene clusters related to secondary metabolism Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-03-19 Fuyuan Zhang, Hongzhe Cao, Helong Si, Jinping Zang, Jingao Dong, Jihong Xing, Kang Zhang
Fungal secondary metabolites are not necessary for growth, but they are important for fungal metabolism and ecology because they provide selective advantages for competition, survival and interactions with the environment. These various metabolites are widely used as medicinal precursors and insecticides. Secondary metabolism genes are commonly arranged in clusters along chromosomes, which allow for
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ThermoPCD: a database of molecular dynamics trajectories of antibody–antigen complexes at physiologic and fever-range temperatures Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-03-19 Puneet K Singh, Razvan C Stan
Progression of various cancers and autoimmune diseases is associated with changes in systemic or local tissue temperatures, which may impact current therapies. The role of fever and acute inflammation-range temperatures on the stability and activity of antibodies relevant for cancers and autoimmunity is unknown. To produce molecular dynamics (MD) trajectories of immune complexes at relevant temperatures
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AagingBase: a comprehensive database of anti-aging peptides Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-03-12 Kunjulakshmi R, Ambuj Kumar, Keerthana Vinod Kumar, Avik Sengupta, Kavita Kundal, Simran Sharma, Ankita Pawar, Pithani Sai Krishna, Mohammad Alfatah, Sandipan Ray, Bhavana Tiwari, Rahul Kumar
The process of aging is an intrinsic and inevitable aspect of life that impacts every living organism. As biotechnological advancements continue to shape our understanding of medicine, peptide therapeutics have emerged as a promising strategy for anti-aging interventions. This is primarily due to their favorable attributes, such as low immunogenicity and cost-effective production. Peptide-based treatments
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SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-03-09 Zhiwei Zhou, Jingyi Du, Jianhua Wang, Liangyi Liu, M Gracie Gordon, Chun Jimmie Ye, Joseph E Powell, Mulin Jun Li, Shuquan Rao
Mapping of expression quantitative trait loci (eQTLs) and other molecular QTLs can help characterize the modes of action of disease-associated genetic variants. However, current eQTL databases present data from bulk RNA-seq approaches, which cannot shed light on the cell type- and environment-specific regulation of disease-associated genetic variants. Here, we introduce our Single-cell eQTL Interactive
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SEPDB: a database of secreted proteins Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-02-12 Ruiqing Wang, Chao Ren, Tian Gao, Hao Li, Xiaochen Bo, Dahai Zhu, Dan Zhang, Hebing Chen, Yong Zhang
Detecting changes in the dynamics of secreted proteins in serum has been a challenge for proteomics. Enter secreted protein database (SEPDB), an integrated secretory proteomics database offering human, mouse and rat secretory proteomics datasets collected from serum, exosomes and cell culture media. SEPDB compiles secreted protein information from secreted protein database, UniProt and Human Protein
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ARAapp: filling gaps in the ecological knowledge of spiders using an automated and dynamic approach to analyze systematically collected community data Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-02-02 Alexander Bach, Florian Raub, Hubert Höfer, Richard Ottermanns, Martina Roß-Nickoll
The ARAMOB data repository compiles meticulously curated spider community datasets from systematical collections, ensuring a high standard of data quality. These datasets are enriched with crucial methodological data that enable the datasets to be aligned in time and space, facilitating data synthesis across studies, respectively, collections. To streamline the analysis of these datasets in a species-specific
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NanoLAS: a comprehensive nanobody database with data integration, consolidation and application Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-02-01 Shuchang Xiong, Zhengwen Liu, Xin Yi, Kai Liu, Bingding Huang, Xin Wang
Nanobodies, a unique subclass of antibodies first discovered in camelid animals, are composed solely of a single heavy chain’s variable region. Their significantly reduced molecular weight, in comparison to conventional antibodies, confers numerous advantages in the treatment of various diseases. As research and applications involving nanobodies expand, the quantity of identified nanobodies is also
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Filling knowledge gaps in insect conservation by leveraging genetic data from public archives Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-01-29 Serena Baini, Alessio De Biase
Insect decline has become a growing concern in recent years, with studies showing alarming declines in populations of several taxa. Our knowledge about genetic spatial patterns and evolutionary history of insects still exhibits significant gaps hindering our ability to effectively conserve and manage insect populations and species. Genetic data may provide valuable insights into the diversity and the
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AHP DB: a reference database of proteins in the human aqueous humor Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-01-29 Tae Jin Lee, Arnav Goyal, Garrett Jones, Joshua Glass, Vishal Doshi, Kathryn Bollinger, Lane Ulrich, Saleh Ahmed, Sai Karthik Kodeboyina, Amy Estes, Marc Töteberg-Harms, Wenbo Zhi, Shruti Sharma, Ashok Sharma
The aqueous humor (AH) is a low-viscosity biofluid that continuously circulates from the posterior chamber to the anterior chamber of the eye. Recent advances in high-resolution mass-spectrometry workflows have facilitated the study of proteomic content in small-volume biofluids like AH, highlighting the potential clinical implications of the AH proteome. Nevertheless, in-depth investigations into
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Analysis and review of techniques and tools based on machine learning and deep learning for prediction of lysine malonylation sites in protein sequences Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-01-21 Shahin Ramazi, Seyed Amir Hossein Tabatabaei, Elham Khalili, Amirhossein Golshan Nia, Kiomars Motarjem
The post-translational modifications occur as crucial molecular regulatory mechanisms utilized to regulate diverse cellular processes. Malonylation of proteins, a reversible post-translational modification of lysine/k residues, is linked to a variety of biological functions, such as cellular regulation and pathogenesis. This modification plays a crucial role in metabolic pathways, mitochondrial functions
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DAPredict: a database for drug action phenotype prediction Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-01-20 Qingkang Meng, Yiyang Cai, Kun Zhou, Fei Xu, Diwei Huo, Hongbo Xie, Meini Yu, Denan Zhang, Xiujie Chen
The phenotypes of drug action, including therapeutic actions and adverse drug reactions (ADRs), are important indicators for evaluating the druggability of new drugs and repositioning the approved drugs. Here, we provide a user-friendly database, DAPredict (http://bio-bigdata.hrbmu.edu.cn/DAPredict), in which our novel original drug action phenotypes prediction algorithm (Yang,J., Zhang,D., Liu,L.
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An optimized relational database for querying structural patterns in proteins Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-01-18 Renzo Angles, Mauricio Arenas-Salinas, Roberto García, Ben Ingram
A database is an essential component in almost any software system, and its creation involves more than just data modeling and schema design. It also includes query optimization and tuning. This paper focuses on a web system called GSP4PDB, which is used for searching structural patterns in proteins. The system utilizes a normalized relational database, which has proven to be inefficient even for simple
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An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP) Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-01-16 Nie Kai, Cai Qingsong, Ma Kejia, Luo Weiwei, Wu Xing, Chen Xuejie, Cai Lixia, Deng Minzi, Yang Yuanyuan, Wang Xiaoyan
IBD, including ulcerative colitis and Crohn’s disease, is a chronic and debilitating gastrointestinal disorder that affects millions of people worldwide. Research on IBD has generated massive amounts of data, including literature, metagenomics, metabolomics, bioresources and databases. We aim to create an IBD Integrated Resources Portal (IBDIRP) that provides the most comprehensive resources for IBD
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The African Human Microbiome Portal: a public web portal of curated metagenomic metadata Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-01-10 Anmol Kiran, Mariem Hanachi, Nihad Alsayed, Meriem Fassatoui, Ovokeraye H Oduaran, Imane Allali, Suresh Maslamoney, Ayton Meintjes, Lyndon Zass, Jorge Da Rocha, Rym Kefi, Alia Benkahla, Kais Ghedira, Sumir Panji, Nicola Mulder, Faisal M Fadlelmola, Oussema Souiai
There is growing evidence that comprehensive and harmonized metadata are fundamental for effective public data reusability. However, it is often challenging to extract accurate metadata from public repositories. Of particular concern is the metagenomic data related to African individuals, which often omit important information about the particular features of these populations. As part of a collaborative
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piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2024-01-10 Kai Wang, Bambarendage P U Perera, Rachel K Morgan, Kimberley Sala-Hamrick, Viviana Geron, Laurie K Svoboda, Christopher Faulk, Dana C Dolinoy, Maureen A Sartor
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that are highly expressed and extensively studied from the germline. piRNAs associate with PIWI proteins to maintain DNA methylation for transposon silencing and transcriptional gene regulation for genomic stability. Mature germline piRNAs have distinct characteristics including a 24- to 32-nucleotide length and a 2ʹ-O-methylation
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DrugGen: a database of de novo-generated molecular binders for specified target proteins Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-12-27 Hao Qian, Jingyuan Zhou, Shikui Tu, Lei Xu
De novo molecular generation is a promising approach to drug discovery, building novel molecules from the scratch that can bind the target proteins specifically. With the increasing availability of machine learning algorithms and computational power, artificial intelligence (AI) has emerged as a valuable tool for this purpose. Here, we have developed a database of 3D ligands that collects six AI models
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A dataset of tumour-infiltrating lymphocytes in colorectal cancer patients using limited resources Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-12-16 Anis Hasnaoui, Imen Helal, Zouhour Ben Azouz, Amira Hmidi, Raja Jouini, Aschraf Chadli-Debbiche
In the realm of cancer research, specifically focusing on colorectal carcinomas (CRCs), a novel diagnostic test referred to as ‘Immunoscore’ (IS) has emerged. This test relies on assessing the density of tumour-infiltrating lymphocytes, specifically CD3 and CD8, in both the centre of the tumour (CT) and its invasive margin (IM). IS holds promise as a potential prognostic factor. A retrospective descriptive
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Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-12-15 Ling-Ping Cen, Tsz Kin Ng, Jie Ji, Jian-Wei Lin, Yao Yao, Rucui Yang, Geng Dong, Yingjie Cao, Chongbo Chen, Shi-Qi Yao, Wen-Ying Wang, Zijing Huang, Kunliang Qiu, Chi Pui Pang, Qingping Liu, Mingzhi Zhang
The aim of the study is to establish an online database for predicting protein structures altered in ocular diseases by Alphafold2 and RoseTTAFold algorithms. Totally, 726 genes of multiple ocular diseases were collected for protein structure prediction. Both Alphafold2 and RoseTTAFold algorithms were built locally using the open-source codebases. A dataset with 48 protein structures from Protein Data
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Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-12-12 Cecilia H Deng, Sushma Naithani, Sunita Kumari, Irene Cobo-Simón, Elsa H Quezada-Rodríguez, Maria Skrabisova, Nick Gladman, Melanie J Correll, Akeem Babatunde Sikiru, Olusola O Afuwape, Annarita Marrano, Ines Rebollo, Wentao Zhang, Sook Jung
Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources
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Design of the formalized and integrated Alzheimer’s Disease Ontology and its application in retrieving textual data via text mining Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-12-02 Bide Zhang, Vanessa Lage-Rupprecht, Philipp Wegner, Astghik Sargsyan, Stephan Gebel, Marc Jacobs, Jürgen Klein, Martin Hofmann-Apitius, Alpha Tom Kodamullil
As one of the leading causes for dementia in the population, it is imperative that we discern exactly why Alzheimer’s disease (AD) has a strong molecular association with beta-amyloid and tau. Although a clear understanding about etiology and pathogenesis of AD remains unsolved, scientists worldwide have dedicated significant efforts to discovering the molecular interactions linked to the pathological
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iCAZyGFADB: an insect CAZyme and gene function annotation database Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-11-28 Chun Fu, YaoJun Yang
With the continuous upgrading of high-throughput sequencing technology, a large amount of biological genome data has been deciphered and published. The research on functional genes of biological genomes urgently needs a collection of service websites with user-friendly and full annotation functions for a variety of gene function annotation tools. In this study, iCAZyGFADB, which is a database website
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Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical–protein relations Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-11-28 Antonio Miranda-Escalada, Farrokh Mehryary, Jouni Luoma, Darryl Estrada-Zavala, Luis Gasco, Sampo Pyysalo, Alfonso Valencia, Martin Krallinger
It is getting increasingly challenging to efficiently exploit drug-related information described in the growing amount of scientific literature. Indeed, for drug–gene/protein interactions, the challenge is even bigger, considering the scattered information sources and types of interactions. However, their systematic, large-scale exploitation is key for developing tools, impacting knowledge fields as
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LncPCD: a manually curated database of experimentally supported associations between lncRNA-mediated programmed cell death and diseases Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-11-27 Ni He, Danyang Li, Fanfan Xu, Jingnan Jin, Lifang Li, Liting Tian, Biying Chen, Xiaoju Li, Shangwei Ning, Lihua Wang, Jianjian Wang
Programmed cell death (PCD) refers to controlled cell death that is conducted to keep the internal environment stable. Long noncoding RNAs (lncRNAs) participate in the progression of PCD in a variety of diseases. However, no specialized online repository is available to collect and store the associations between lncRNA-mediated PCD and diseases. Here, we developed LncPCD, a comprehensive database that
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aSynPEP-DB: a database of biogenic peptides for inhibiting α-synuclein aggregation Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-11-27 Carlos Pintado-Grima, Oriol Bárcenas, Valentín Iglesias, Jaime Santos, Zoe Manglano-Artuñedo, Irantzu Pallarès, Michał Burdukiewicz, Salvador Ventura
Parkinson’s disease (PD) is the second most prevalent neurodegenerative disorder, yet effective treatments able to stop or delay disease progression remain elusive. The aggregation of a presynaptic protein, α-synuclein (aSyn), is the primary neurological hallmark of PD and, thus, a promising target for therapeutic intervention. However, the lack of consensus on the molecular properties required to
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An online database for einkorn wheat to aid in gene discovery and functional genomics studies Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-11-16 Parva Kumar Sharma, Hanin Ibrahim Ahmed, Matthias Heuberger, Dal-Hoe Koo, Jesus Quiroz-Chavez, Laxman Adhikari, John Raupp, Stéphane Cauet, Nathalie Rodde, Charlotte Cravero, Caroline Callot, Inderjit Singh Yadav, Nagarajan Kathiresan, Naveenkumar Athiyannan, Ricardo H Ramirez-Gonzalez, Cristobal Uauy, Thomas Wicker, Michael Abrouk, Yong Q Gu, Jesse Poland, Simon G Krattinger, Gerard R Lazo, Vijay
Diploid A-genome wheat (einkorn wheat) presents a nutrition-rich option as an ancient grain crop and a resource for the improvement of bread wheat against abiotic and biotic stresses. Realizing the importance of this wheat species, reference-level assemblies of two einkorn wheat accessions were generated (wild and domesticated). This work reports an einkorn genome database that provides an interface
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Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-11-16 Jennifer L Clarke, Laurel D Cooper, Monica F Poelchau, Tanya Z Berardini, Justin Elser, Andrew D Farmer, Stephen Ficklin, Sunita Kumari, Marie-Angélique Laporte, Rex T Nelson, Rie Sadohara, Peter Selby, Anne E Thessen, Brandon Whitehead, Taner Z Sen
Over the last couple of decades, there has been a rapid growth in the number and scope of agricultural genetics, genomics and breeding databases and resources. The AgBioData Consortium (https://www.agbiodata.org/) currently represents 44 databases and resources (https://www.agbiodata.org/databases) covering model or crop plant and animal GGB data, ontologies, pathways, genetic variation and breeding
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FooDrugs: a comprehensive food–drug interactions database with text documents and transcriptional data Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-11-12 Blanca Lacruz-Pleguezuelos, Oscar Piette, Marco Garranzo, David Pérez-Serrano, Jelena Milešević, Isabel Espinosa-Salinas, Ana Ramírez de Molina, Teresa Laguna, Enrique Carrillo de Santa Pau
Food–drug interactions (FDIs) occur when a food item alters the pharmacokinetics or pharmacodynamics of a drug. FDIs can be clinically relevant, as they can hamper or enhance the therapeutic effects of a drug and impact both their efficacy and their safety. However, knowledge of FDIs in clinical practice is limited. This is partially due to the lack of resources focused on FDIs. Here, we describe FooDrugs
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PlantIntronDB: a database for plant introns that host functional elements Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-11-12 Weiping Wang, Jiming Hu, Han Li, Jun Yan, Xiaoyong Sun
Although more and more attention has been focused on introns and the important role of plant introns in plant growth and development has been discovered, there is still a lack of an open and comprehensive database on plant introns with functional elements in current research. In order to make full use of large-scale sequencing data and help researchers in related fields to achieve high-throughput functional
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Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications. Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-11-06 Shatabdi Sen,Margaret R Woodhouse,John L Portwood,Carson M Andorf
The big-data analysis of complex data associated with maize genomes accelerates genetic research and improves agronomic traits. As a result, efforts have increased to integrate diverse datasets and extract meaning from these measurements. Machine learning models are a powerful tool for gaining knowledge from large and complex datasets. However, these models must be trained on high-quality features
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LeishMANIAdb: a comparative resource for Leishmania proteins Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-11-06 Gábor E Tusnády, András Zeke, Zsófia E Kálmán, Marie Fatoux, Sylvie Ricard-Blum, Toby J Gibson, Laszlo Dobson
Leishmaniasis is a detrimental disease causing serious changes in quality of life and some forms can lead to death. The disease is spread by the parasite Leishmania transmitted by sandfly vectors and their primary hosts are vertebrates including humans. The pathogen penetrates host cells and secretes proteins (the secretome) to repurpose cells for pathogen growth and to alter cell signaling via host–pathogen
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Preproject ‘Swiss Virtual Natural History Collection’ Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-11-06 Ana Petrus, Tobias Wildi, Stefanie Müller
The initiative ‘Swiss Natural History Collection Network’ (SwissCollNet) aims to improve the accessibility of the Swiss natural history collections for research, education and the wider public. In the 2021–24 funding period, SwissCollNet is identifying, prioritizing and digitizing as many collections as possible and building an online portal called the ‘Swiss Virtual Natural History Collection’ (hereafter
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InCliniGene enables high-throughput and comprehensive in vivo clonal tracking toward clinical genomics data integration. Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-11-02 Ivan Merelli,Stefano Beretta,Daniela Cesana,Alessandro Gennari,Fabrizio Benedicenti,Giulio Spinozzi,Daniele Cesini,Eugenio Montini,Daniele D'Agostino,Andrea Calabria
High-throughput clonal tracking in patients under hematopoietic stem cell gene therapy with integrating vector is instrumental in assessing bio-safety and efficacy. Monitoring the fate of millions of transplanted clones and their progeny across differentiation and proliferation over time leverages the identification of the vector integration sites, used as surrogates of clonal identity. Although γ-tracking
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Fisheries data management systems in the NW Mediterranean: from data collection to web visualization. Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-10-20 Jordi Ribera-Altimir,Gerard Llorach-Tó,Joan Sala-Coromina,Joan B Company,Eve Galimany
The European Union Data Collection Framework (DCF) states that scientific data-driven assessments are essential to achieve sustainable fisheries. To respond to the DCF call, this study introduces the information systems developed and used by Institut Català de Recerca per a la Governança del Mar (ICATMAR), the Catalan Institute of Research for the Governance of the Seas. The information systems include
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Managing and monitoring a pandemic: showcasing a practical approach for the genomic surveillance of SARS-CoV-2 Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-10-17 Mateusz Jundzill, Riccardo Spott, Mara Lohde, Martin Hölzer, Adrian Viehweger, Christian Brandt
With the rapidly growing amount of biological data, powerful but also flexible data management and visualization systems are of increasingly crucial importance. The COVID-19 pandemic has more than highlighted this need and the challenges scientists are facing. Here, we provide an example and a step-by-step template for non-IT personnel to easily implement an intuitive, interactive data management solution
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DISPEL: database for ascertaining the best medicinal plants to cure human diseases Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-10-17 Kavya Singh, Harshit Maurya, Parthasarathi Singh, Pujarani Panda, Amit Kumar Behera, Arshad Jamal, Ganesh Eslavath, Somesh Mohapatra, Harsh Chauhan, Deepak Sharma
Medicinal plants are anticipated to be one of the most valuable resources for the remedial usage in the treatment of various ailments. The data on key medicinal plants and their therapeutic efficacy against various ailments are quite scattered and not available on a single platform. Moreover, currently there is no means/mechanism of finding the best medicinal plant(s) from numerous plants known to
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Correction to: H3ABioNet genomic medicine and microbiome data portals hackathon proceedings. Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-10-13
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The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-10-11 Panni Simona, Kalpana Panneerselvam, Pablo Porras, Margaret Duesbury, Livia Perfetto, Luana Licata, Henning Hermjakob, Sandra Orchard
In recent years, a huge amount of data on ncRNA interactions has been described in scientific papers and databases. Although considerable effort has been made to annotate the available knowledge in public repositories, there are still significant discrepancies in how different resources capture and interpret data on ncRNA functional and physical associations. In the present paper, we present a collection
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ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-10-10 Asma Sindhoo, Saima Sipy, Abbas Khan, Gurudeeban Selvaraj, Abdulrahman Alshammari, Mark Earl Casida, Dong-Qing Wei
‘Esophageal cancer’ (EC) is a highly aggressive and deadly complex disease. It comprises two types, esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC), with Barrett’s esophagus (BE) being the only known precursor. Recent research has revealed that microRNAs (miRNAs) play a crucial role in the development, prognosis and treatment of EC and are involved in various human diseases
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AgingReG: a curated database of aging regulatory relationships in humans Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-10-06 Minghui Piao, Ke Feng, Xinyu Liu, Xuefeng Bai, Yuqi Zheng, Meiling Sun, Peng Zhao, Yani Wang, Xiaofang Ban, Jie Xiong, Chengyu Shi, Li Meng, Yuxin Liu, Li Yu, Jing Li, Shan Zhong, Xinjian Jiang, Yu Chen, Xin Sun, Yan Zheng, Jinwei Tian
Aging and cellular senescence are characterized by a progressive loss of physiological integrity, which could be triggered by aging factors such as physiological, pathological and external factors. Numerous studies have shown that gene regulatory events play crucial roles in aging, increasing the need for a comprehensive repository of regulatory relationships during aging. Here, we established a manually
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BCEDB: a linear B-cell epitopes database for SARS-CoV-2 Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-09-30 Chengzheng Tai, Hongjun Li, Jing Zhang
The 2019 Novel Coronavirus (SARS-CoV-2) has infected millions of people worldwide and caused millions of deaths. The virus has gone numerous mutations to replicate faster, which can overwhelm the immune system of the host. Linear B-cell epitopes are becoming promising in prevention of various deadly infectious diseases, breaking the general idea of their low immunogenicity and partial protection. However
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Building a large gene expression-cancer knowledge base with limited human annotations. Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-09-27 Stefano Marchesin,Laura Menotti,Fabio Giachelle,Gianmaria Silvello,Omar Alonso
Cancer prevention is one of the most pressing challenges that public health needs to face. In this regard, data-driven research is central to assist medical solutions targeting cancer. To fully harness the power of data-driven research, it is imperative to have well-organized machine-readable facts into a knowledge base (KB). Motivated by this urgent need, we introduce the Collaborative Oriented Relation
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CBPDdb: a curated database of compounds derived from Coumarin-Benzothiazole-Pyrazole. Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-09-13 Shailima Rampogu,Mohammed Rafi Shaik,Merajuddin Khan,Mujeeb Khan,Tae Hwan Oh,Baji Shaik
The present article describes the building of a small-molecule web server, CBPDdb, employing R-shiny. For the generation of the web server, three compounds were chosen, namely coumarin, benzothiazole and pyrazole, and their derivatives were curated from the literature. The two-dimensional (2D) structures were drawn using ChemDraw, and the .sdf file was created employing Discovery Studio Visualizer
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PolyQ Database—an integrated database on polyglutamine diseases Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-08-21 Bernardo Estevam, Carlos A Matos, Clévio Nóbrega
Polyglutamine (polyQ) diseases are neurodegenerative disorders caused by abnormally expanded Cytosine, Adenine, Guanine (CAG) triplet repeat sequences in the coding region of otherwise unrelated genes. Until now, nine different polyQ diseases have been described: Huntington’s disease, dentatorubral-pallidoluysian atrophy, spinal and bulbar muscular atrophy and six types of spinocerebellar ataxias—1
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AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-08-18 Shahid Ullah, Wajeeha Rahman, Farhan Ullah, Anees Ullah, Gulzar Ahmad, Muhammad Ijaz, Hameed Ullah, Zilong Zheng, Tianshun Gao
Serious illnesses caused by viruses are becoming the world’s most critical public health issues and lead millions of deaths each year in the world. Thousands of studies confirmed that the plant-derived medicines could play positive therapeutic effects on the patients with viral diseases. Since thousands of antiviral phytochemicals have been identified as lifesaving drugs in medical research, a comprehensive
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Tissue-specific transcriptomes reveal potential mechanisms of microbiome heterogeneity in an ancient fish. Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-08-17 Matt J Thorstensen,Alyssa M Weinrauch,William S Bugg,Ken M Jeffries,W Gary Anderson
The lake sturgeon (Acipenser fulvescens) is an ancient, octoploid fish faced with conservation challenges across its range in North America, but a lack of genomic resources has hindered molecular research in the species. To support such research, we created a transcriptomic database from 13 tissues: brain, esophagus, gill, head kidney, heart, white muscle, liver, glandular stomach, muscular stomach
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The MetaGens algorithm for metagenomic database lossy compression and subject alignment Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-08-11 Gustavo Henrique Cervi, Cecilia Dias Flores, Claudia Elizabeth Thompson
The advancement of genetic sequencing techniques led to the production of a large volume of data. The extraction of genetic material from a sample is one of the early steps of the metagenomic study. With the evolution of the processes, the analysis of the sequenced data allowed the discovery of etiological agents and, by corollary, the diagnosis of infections. One of the biggest challenges of the technique
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CCIDB: a manually curated cell–cell interaction database with cell context information Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-08-11 Jin Young Noh, Hae In Lee, Ji-Hye Choi, Seong-Ho Cho, Yoon Hui Yi, Ji Hyun Lim, Eun Been Myung, Ye Ju Shin, Hyo Jin Shin, Hyun Goo Woo
Cell–cell interaction (CCI) is a crucial event in the development and function of multicellular organisms. The development of CCI databases is beneficial for researchers who want to analyze single-cell sequencing data or study CCI through molecular experiments. CCIs are known to act differently according to cellular and biological contexts such as cell types, gene mutations or disease status; however
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MineProt: a stand-alone server for structural proteome curation Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-08-10 Yunchi Zhu, Chengda Tong, Zuohan Zhao, Zuhong Lu
AlphaFold-like systems are rapidly expanding the scale of proteome structuring, and MineProt provides an effective solution for custom curation of these novel high-throughput data. It enables researchers to build their own server in simple steps, run almost out-of-the-box scripts to annotate and curate their proteins, analyze their data via a user-friendly online interface, and utilize plugins to extend
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Biomedical relation extraction with knowledge base-refined weak supervision. Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-07-26 Wonjin Yoon,Sean Yi,Richard Jackson,Hyunjae Kim,Sunkyu Kim,Jaewoo Kang
Biomedical relation extraction (BioRE) is the task of automatically extracting and classifying relations between two biomedical entities in biomedical literature. Recent advances in BioRE research have largely been powered by supervised learning and large language models (LLMs). However, training of LLMs for BioRE with supervised learning requires human-annotated data, and the annotation process often
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AI4FoodDB: a database for personalized e-Health nutrition and lifestyle through wearable devices and artificial intelligence. Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-07-18 Sergio Romero-Tapiador,Blanca Lacruz-Pleguezuelos,Ruben Tolosana,Gala Freixer,Roberto Daza,Cristina M Fernández-Díaz,Elena Aguilar-Aguilar,Jorge Fernández-Cabezas,Silvia Cruz-Gil,Susana Molina,Maria Carmen Crespo,Teresa Laguna,Laura Judith Marcos-Zambrano,Ruben Vera-Rodriguez,Julian Fierrez,Ana Ramírez de Molina,Javier Ortega-Garcia,Isabel Espinosa-Salinas,Aythami Morales,Enrique Carrillo de Santa
The increasing prevalence of diet-related diseases calls for an improvement in nutritional advice. Personalized nutrition aims to solve this problem by adapting dietary and lifestyle guidelines to the unique circumstances of each individual. With the latest advances in technology and data science, researchers can now automatically collect and analyze large amounts of data from a variety of sources
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Unified and pluralistic ideals for data sharing and reuse in biodiversity. Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-07-18 Beckett Sterner,Steve Elliott,Edward E Gilbert,Nico M Franz
How should billions of species observations worldwide be shared and made reusable? Many biodiversity scientists assume the ideal solution is to standardize all datasets according to a single, universal classification and aggregate them into a centralized, global repository. This ideal has known practical and theoretical limitations, however, which justifies investigating alternatives. To support better
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APDB: a database on air pollutant characterization and similarity prediction Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-07-14 Eva Viesi, Davide Stefano Sardina, Ugo Perricone, Rosalba Giugno
The World Health Organization estimates that 9 out of 10 people worldwide breathe air containing high levels of pollutants. Long-term and chronic exposure to high concentrations of air pollutants is associated with deleterious effects on vital organs, including increased inflammation in the lungs, oxidative stress in the heart and disruption of the blood–brain barrier. For this reason, in an effort
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The importance of graph databases and graph learning for clinical applications Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-07-11 Daniel Walke, Daniel Micheel, Kay Schallert, Thilo Muth, David Broneske, Gunter Saake, Robert Heyer
The increasing amount and complexity of clinical data require an appropriate way of storing and analyzing those data. Traditional approaches use a tabular structure (relational databases) for storing data and thereby complicate storing and retrieving interlinked data from the clinical domain. Graph databases provide a great solution for this by storing data in a graph as nodes (vertices) that are connected
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PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-07-06 Jian Hu, Baisha Huang, Hao Yin, Kaijie Qi, Yuanyuan Jia, Zhihua Xie, Yuan Gao, Hongxiang Li, Qionghou Li, Zewen Wang, Ying Zou, Shaoling Zhang, Xin Qiao
Pear (Pyrus ssp.) belongs to Rosaceae and is an important fruit tree widely cultivated around the world. Currently, challenges to cope with the burgeoning sets of multiomics data are rapidly increasing. Here, we constructed the Pear Multiomics Database (PearMODB) by integrating genome, transcriptome, epigenome and population variation data, and aimed to provide a portal for accessing and analyzing
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VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants Database J. Biol. Databases Curation (IF 5.8) Pub Date : 2023-07-06 Pietro Pinoli, Arif Canakoglu, Stefano Ceri, Matteo Chiara, Erika Ferrandi, Luca Minotti, Anna Bernasconi
With the progression of the COVID-19 pandemic, large datasets of SARS-CoV-2 genome sequences were collected to closely monitor the evolution of the virus and identify the novel variants/strains. By analyzing genome sequencing data, health authorities can ‘hunt’ novel emerging variants of SARS-CoV-2 as early as possible, and then monitor their evolution and spread. We designed VariantHunter, a highly