Database : The Journal of Biological Databases and Curation 
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This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.met v1: expanding on old estimations of biodiversity from eDNA with a new database framework
This article introduces a new software framework, met, which utilizes large numbers of metabarcode datasets to draw conclusions about patterns of diversity at large spatial scales. Given more accurate estimations on the distribution of variance in metabarcode datasets, this software framework could facilitate novel analyses that are outside the scope of currently available similar platforms.Database URLhttps://osf.io/spb8v/ (Source: Database : The Journal of Biological Databases and Curation)
Source: Database : The Journal of Biological Databases and Curation - May 11, 2022 Category: Databases & Libraries Source Type: research
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants
AbstractCancer is a somatic disease. The lack of Indian-specific reference germline variation resources limits the ability to identify true cancer-associated somatic variants among Indian cancer patients. We integrate two recent studies, the GenomeAsia 100K and the Genomics for Public Health in India (IndiGen) program, describing genome sequence variations across 598 and 1029 healthy individuals of Indian origin, respectively, along with the unique variants generated from our in-house 173 normal germline samples derived from cancer patients to generate the Tata Memorial Centre-SNP database (TMC-SNPdb) 2.0. To show its util...
Source: Database : The Journal of Biological Databases and Curation - May 11, 2022 Category: Databases & Libraries Source Type: research
XePhIR: the zebrafish xenograft phenotype interactive repository
AbstractZebrafish xenografts are an established model in cancer biology, with a steadily rising number of models and users. However, as of yet, there is no platform dedicated to standardizing protocols and sharing data regarding zebrafish xenograft phenotypes. Here, we present the Xenograft Phenotype Interactive Repository (XePhIR,https://www.xephir.org) as an independent data-sharing platform to deposit, share and repurpose zebrafish xenograft data. Deposition of data and publication with XePhIR will be done after the acceptation of the original publication. This will enhance the reach of the original research article, en...
Source: Database : The Journal of Biological Databases and Curation - April 28, 2022 Category: Databases & Libraries Source Type: research
PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes
AbstractMore accurate and more complete predictions of cis-regulatory modules (CRMs) and constituent transcription factor (TF) binding sites (TFBSs) in genomes can facilitate characterizing functions of regulatory sequences. Here, we developed a database predictedcis-regulatory modules (PCRMS) (https://cci-bioinfo.uncc.edu) that stores highly accurate and unprecedentedly complete maps of predicted CRMs and TFBSs in the human and mouse genomes. The web interface allows the user to browse CRMs and TFBSs in an organism, find the closest CRMs to a gene, search CRMs around a gene and find all TFBSs of a TF. PCRMS can be a usefu...
Source: Database : The Journal of Biological Databases and Curation - April 22, 2022 Category: Databases & Libraries Source Type: research
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe
AbstractSequence alignments are models that capture the structural, functional and evolutionary relationships between proteins. Structure-guided sequence alignments are helpful in the case of distantly related proteins with poor sequence identity, thus rendering routine sequence alignment methods ineffective. Protein Alignment organized as Structural Superfamilies or PASS2 database provides such sequence alignments of protein domains within a superfamily as per the Structural Classification of Proteins extended (SCOPe) database. The current update of PASS2 (i.e. PASS2.7) is following the latest release of SCOPe (2.07) and ...
Source: Database : The Journal of Biological Databases and Curation - April 12, 2022 Category: Databases & Libraries Source Type: research
SwissBioPics —an interactive library of cell images for the visualization of subcellular location data
AbstractSwissBioPics (www.swissbiopics.org) is a freely available resource of interactive, high-resolution cell images designed for the visualization of subcellular location data. SwissBioPics provides images describing cell types from all kingdoms of life —from the specialized muscle, neuronal and epithelial cells of animals, to the rods, cocci, clubs and spirals of prokaryotes. All cell images in SwissBioPics are drawn in Scalable Vector Graphics (SVG), with each subcellular location tagged with a unique identifier from the controlled vocabulary o f subcellular locations and organelles of UniProt (https://www.uniprot.o...
Source: Database : The Journal of Biological Databases and Curation - April 12, 2022 Category: Databases & Libraries Source Type: research
Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database
AbstractImproving the understanding of the oligogenic nature of diseases requires access to high-quality, well-curated Findable, Accessible, Interoperable, Reusable (FAIR) data. Although first steps were taken with the development of the Digenic Diseases Database, leading to novel computational advancements to assist the field, these were also linked with a number of limitations, for instance, thead hoc curation protocol and the inclusion of only digenic cases. The OLIgogenic diseases DAtabase (OLIDA) presents a novel, transparent and rigorous curation protocol, introducing a confidence scoring mechanism for the published ...
Source: Database : The Journal of Biological Databases and Curation - April 12, 2022 Category: Databases & Libraries Source Type: research
Conference report: Biocuration 2021 Virtual Conference
AbstractThe International Society for Biocuration (ISB) aims to promote the field of biocuration and provide a community forum for information exchange and networking. Over the past 14 years, the ISB has hosted annual international conferences, entirely dedicated to the field of biocuration, that rotate between regions across the world. These meetings bring together biocurators from various roles, including database curators, bioinformaticians, ontology developers and students. Due to the ongoing global pandemic, the 14th Annual ISB Biocuration Conference (ISB2021) was held virtually in the form of four sessions and one...
Source: Database : The Journal of Biological Databases and Curation - April 9, 2022 Category: Databases & Libraries Source Type: research
BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins
AbstractPesticidal proteins derived from the bacteriumBacillus thuringiensis, have provided the bases for a diverse array of pest management tools ranging from natural products used in organic agriculture, to modern biotechnological approaches. With advances in genome sequencing technologies and protein structure determination, an increasing number of pesticidal proteins from myriad bacterial species have been identified. The Bacterial Pesticidal Protein Resource Center (BPPRC) has been established to provide informational and analytical resources on the wide range of pesticidal proteins derived from bacteria that have pot...
Source: Database : The Journal of Biological Databases and Curation - April 4, 2022 Category: Databases & Libraries Source Type: research
ImmuMethy, a database of DNA methylation plasticity at a single cytosine resolution in human blood and immune cells
In this study, we carried out a systematic analysis of methylome data derived from human blood and immune cells and constructed the ImmuMethy database. ImmuMethy allows interrogation of DNA methylation plasticity (MPL) at the single cytosine level. MPL, which refers to the variability of DNA methylation, is quantitatively measured in multiple ways, such as quartiles and standard deviations. ImmuMethy comprises over 36 000 samples from the Human Methylation450 and MethylationEPIC BeadChips platforms and provides multiple applications, such as an overview of methylation status and plasticity, differential methylation anal...
Source: Database : The Journal of Biological Databases and Curation - April 1, 2022 Category: Databases & Libraries Source Type: research
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation
AbstractThe Sickle Cell Disease (SCD) Ontology (SCDO,https://scdontology.h3abionet.org/) provides a comprehensive knowledge base of SCD management, systems and standardized human and machine-readable resources that unambiguously describe terminology and concepts about SCD for researchers, patients and clinicians. The SCDO was launched in 2016 and is continuously updated in quantity, as well as in quality, to effectively support the curation of SCD research, patient databasing and clinical informatics applications. SCD knowledge from the scientific literature is used to update existing SCDO terms and create new terms where ...
Source: Database : The Journal of Biological Databases and Curation - April 1, 2022 Category: Databases & Libraries Source Type: research
https://invertebratefungi.org/: an expert-curated web-based platform for the identification and classification of invertebrate-associated fungi and fungus-like organisms
AbstractFungi are the major decomposers in terrestrial and aquatic ecosystems, playing essential roles in biogeochemical cycles and food webs. The Fungi kingdom encompasses a diverse array of taxa that often form intimate relationships with other organisms, including plants, insects, algae, cyanobacteria and even other fungi. Fungal parasites of insects are known as entomopathogenic fungi and are the causative agents of serious disease and/or mortality of their hosts. Entomopathogens produce distinct metabolic compounds with roles in pathogenicity, virulence and host –parasite interactions. Thus, the potential of discove...
Source: Database : The Journal of Biological Databases and Curation - April 1, 2022 Category: Databases & Libraries Source Type: research
hCoronavirusesDB: an integrated bioinformatics resource for human coronaviruses
AbstractIn the twenty-first century, three new human coronaviruses have been identified with known zoonotic origins: severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, and Middle East respiratory syndrome coronavirus (MERS-CoV). SARS-CoV-2 was identified in November 2019 and is associated with an ongoing pandemic. Molecular surveillance and monitoring studies are essential for containing viral outbreaks, epidemics, and pandemics. In addition, the development and deployment of bioinformatics resources for highly pathogenic human coronaviruses are crucial for understanding the genetic and immunogenic lands...
Source: Database : The Journal of Biological Databases and Curation - March 26, 2022 Category: Databases & Libraries Source Type: research
Diseases 2.0: a weekly updated database of disease –gene associations from text mining and data integration
AbstractThe scientific knowledge about which genes are involved in which diseases grows rapidly, which makes it difficult to keep up with new publications and genetics datasets. The DISEASES database aims to provide a comprehensive overview by systematically integrating and assigning confidence scores to evidence for disease –gene associations from curated databases, genome-wide association studies (GWAS) and automatic text mining of the biomedical literature. Here, we present a major update to this resource, which greatly increases the number of associations from all these sources. This is especially true for the tex t-...
Source: Database : The Journal of Biological Databases and Curation - March 24, 2022 Category: Databases & Libraries Source Type: research
Correction to: DDPD 1.0: a manually curated and standardized database of digital properties of approved drugs for drug-likeness evaluation and drug development
(Source: Database : The Journal of Biological Databases and Curation)
Source: Database : The Journal of Biological Databases and Curation - March 23, 2022 Category: Databases & Libraries Source Type: research
