Database : The Journal of Biological Databases and Curation 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.

UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase –substrate interactions
AbstractUbiquitination is an important post-translational modification, which controls protein turnover by labeling malfunctional and redundant proteins for proteasomal degradation, and also serves intriguing non-proteolytic regulatory functions. E3 ubiquitin ligases, whose substrate specificity determines the recognition of target proteins of ubiquitination, play crucial roles in ubiquitin –proteasome system. UbiNet 2.0 is an updated version of the database UbiNet. It contains 3332 experimentally verified E3–substrate interactions (ESIs) in 54 organisms and rich annotations useful for investigating the regulation of u...
Source: Database : The Journal of Biological Databases and Curation - March 8, 2021 Category: Databases & Libraries Source Type: research

HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis
AbstractTo facilitate biomedical studies of disease mechanisms, a high-quality interactome that connects functionally related genes is needed to help investigators formulate pathway hypotheses and to interpret the biological logic of a phenotype at the biological process level. Interactions in the updated version of the human interactome resource (HIR V2) were inferred from 36 mathematical characterizations of six types of data that suggest functional associations between genes. This update of the HIR consists of 88  069 pairs of genes (23.2% functional interactions of HIR V2 are in common with the previous version of HI...
Source: Database : The Journal of Biological Databases and Curation - March 2, 2021 Category: Databases & Libraries Source Type: research

An update of KAIKObase, the silkworm genome database
AbstractKAIKObase was established in 2009 as the genome database of the domesticated silkwormBombyx mori. It provides several gene sets and genetic maps as well as genome annotation obtained from the sequencing project of the International Silkworm Genome Consortium in 2008. KAIKObase has been used widely for silkworm and insect studies even though there are some erroneous predicted genes due to misassembly and gaps in the genome. In 2019, we released a new silkworm genome assembly, showing improvements in gap closure and covering more and longer gene models. Therefore, there is a need to include new genome and new gene mo...
Source: Database : The Journal of Biological Databases and Curation - February 27, 2021 Category: Databases & Libraries Source Type: research

Extraction of causal relations based on SBEL and BERT model
AbstractExtraction of causal relations between biomedical entities in the form of Biological Expression Language (BEL) poses a new challenge to the community of biomedical text mining due to the complexity of BEL statements. We propose a simplified form of BEL statements [Simplified Biological Expression Language (SBEL)] to facilitate BEL extraction and employ BERT (Bidirectional Encoder Representation from Transformers) to improve the performance of causal relation extraction (RE). On the one hand, BEL statement extraction is transformed into the extraction of an intermediate form —SBEL statement, which is then further ...
Source: Database : The Journal of Biological Databases and Curation - February 18, 2021 Category: Databases & Libraries Source Type: research

bc-GenExMiner 4.5: new mining module computes breast cancer differential gene expression analyses
Abstract‘Breast cancer gene-expression miner’ (bc-GenExMiner) is a breast cancer–associated web portal (http://bcgenex.ico.unicancer.fr). Here, we describe the development of a new statistical mining module, which permits several differential gene expression analyses, i.e. ‘Expression’ module. Sixty-two breast cancer cohorts and one healthy breast cohort with their corresponding clinicopathological information are included in bc-GenExMiner v4.5 version. Analyses are based on microarray or RNAseq transcriptomic data. Thirty-nine differential gene expression analyse s, grouped into 13 categories, according to clini...
Source: Database : The Journal of Biological Databases and Curation - February 18, 2021 Category: Databases & Libraries Source Type: research

Curation of over 10  000 transcriptomic studies to enable data reuse
AbstractVast amounts of transcriptomic data reside in public repositories, but effective reuse remains challenging. Issues include unstructured dataset metadata, inconsistent data processing and quality control, and inconsistent probe –gene mappings across microarray technologies. Thus, extensive curation and data reprocessing are necessary prior to any reuse. The Gemma bioinformatics system was created to help address these issues. Gemma consists of a database of curated transcriptomic datasets, analytical software, a web inte rface and web services. Here we present an update on Gemma’s holdings, data processing and a...
Source: Database : The Journal of Biological Databases and Curation - February 18, 2021 Category: Databases & Libraries Source Type: research

Converting disease maps into heavyweight ontologies: general methodology and application to Alzheimer ’s disease
AbstractOmics technologies offer great promises for improving our understanding of diseases. The integration and interpretation of such data pose major challenges, calling for adequate knowledge models. Disease maps provide curated knowledge about disorders ’ pathophysiology at the molecular level adapted to omics measurements. However, the expressiveness of disease maps could be increased to help in avoiding ambiguities and misinterpretations and to reinforce their interoperability with other knowledge resources. Ontology is an adequate framework to overcome this limitation, through their axiomatic definitions and logic...
Source: Database : The Journal of Biological Databases and Curation - February 16, 2021 Category: Databases & Libraries Source Type: research

CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator
AbstractMolecular causal interactions are defined as regulatory connections between biological components. They are commonly retrieved from biological experiments and can be used for connecting biological molecules together to enable the building of regulatory computational models that represent biological systems. However, including a molecular causal interaction in a model requires assessing its relevance to that model, based on the detailed knowledge about the biomolecules, interaction type and biological context. In order to standardize the representation of this knowledge in ‘causal statements’, we recently develo...
Source: Database : The Journal of Biological Databases and Curation - February 6, 2021 Category: Databases & Libraries Source Type: research

InSexBase: an annotated genomic resource of sex chromosomes and sex-biased genes in insects
AbstractSex determination and the regulation of sexual dimorphism are among the most fascinating topics in modern biology. As the most species-rich group of sexually reproducing organisms on Earth, insects have multiple sex determination systems. Though sex chromosomes and sex-biased genes are well-studied in dozens of insects, their gene sequences are scattered in various databases. Moreover, a shortage of annotation hinders the deep mining of these data. Here, we collected the chromosome-level sex chromosome data of 49 insect species, including 34 X chromosomes, 15 Z chromosomes, 5 W chromosomes and 2 Y chromosomes. We a...
Source: Database : The Journal of Biological Databases and Curation - January 28, 2021 Category: Databases & Libraries Source Type: research

SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences
AbstractSingle-exon coding sequences (CDSs), also known as ‘single-exon genes’ (SEGs), are defined as nuclear, protein-coding genes that lack introns in their CDSs. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancers and neurological/developmental dis orders, and many exhibit tissue-specific transcription. We developed SinEx DB that houses DNA and protein sequence information of SEGs from 10 mammalian genomes including human. SinEx DB includes their functional predictions (KOG (euKaryotic Orthologous Groups)) and the...
Source: Database : The Journal of Biological Databases and Curation - January 28, 2021 Category: Databases & Libraries Source Type: research

The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research
AbstractInformatics has become an essential component of research in the past few decades, capitalizing on the efficiency and power of computation to improve the knowledge gained from increasing quantities and types of data. While other fields of research such as genomics are well represented in informatics resources, nutrition remains underrepresented. Nutrition is one of the most integral components of human life, and it impacts individuals far beyond just nutrient provisions. For example, nutrition plays a role in cultural practices, interpersonal relationships and body image. Despite this, integrated computational inve...
Source: Database : The Journal of Biological Databases and Curation - January 25, 2021 Category: Databases & Libraries Source Type: research

Large-scale regulatory and signaling network assembly through linked open data
AbstractHuge efforts are currently underway to address the organization of biological knowledge through linked open databases. These databases can be automatically queried to reconstruct regulatory and signaling networks. However, assembling networks implies manual operations due to source-specific identification of biological entities and relationships, multiple life-science databases with redundant information and the difficulty of recovering logical flows in biological pathways. We propose a framework based on Semantic Web technologies to automate the reconstruction of large-scale regulatory and signaling networks in th...
Source: Database : The Journal of Biological Databases and Curation - January 18, 2021 Category: Databases & Libraries Source Type: research

HGFDB: a collective database of helmeted guinea fowl genomics
AbstractAs a vigorous and hardy and an almost disease-free game bird, the domestic helmeted guinea fowl (Numida meleagris, hereafter HGF) has attracted considerable attention in a large number of genetic study projects. However, none of the current/recent avian databases are related to this agriculturally and commercially important poultry species. To address this data gap, we developed Helmeted Guinea Fowl Database (HGFDB), which manages and shares HGF genomic and genetic data. By processing the data of genome assembly, sequencing reads and genetic variations, we organized them into eight modules, which correspond to ‘H...
Source: Database : The Journal of Biological Databases and Curation - January 8, 2021 Category: Databases & Libraries Source Type: research

HeartBioPortal2.0: new developments and updates for genetic ancestry and cardiometabolic quantitative traits in diverse human populations
AbstractCardiovascular disease (CVD) is the leading cause of death worldwide for all genders and across most racial and ethnic groups. However, different races and ethnicities exhibit different rates of CVD and its related cardiorenal and metabolic comorbidities, suggesting differences in genetic predisposition and risk of onset, as well as socioeconomic and lifestyle factors (diet, exercise, etc.) that act upon an individual ’s unique underlying genetic background. Here, we present HeartBioPortal2.0, a major update to HeartBioPortal, the world’s largest CVD genetics data precision medicine platform for harmonized CVD-...
Source: Database : The Journal of Biological Databases and Curation - December 31, 2020 Category: Databases & Libraries Source Type: research

CorkOakDB —The Cork Oak Genome Database Portal
AbstractQuercus suber (cork oak) is an evergreen tree native to the Mediterranean basin, which plays a key role in the ecology and economy of this area. Over the last decades, this species has gone through an observable decline, mostly due to environmental factors. Deciphering the mechanisms of cork oak ’s response to the environment and getting a deep insight into its biology are crucial to counteract biotic and abiotic stresses compromising the stability of a unique ecosystem. In the light of these setbacks, the publication of the genome in 2018 was a major step towards understanding the geneti c make-up of this specie...
Source: Database : The Journal of Biological Databases and Curation - December 31, 2020 Category: Databases & Libraries Source Type: research