Motivation: To provide high quality computationally tractable enzyme annotation in UniProtKB using Rhea, a comprehensive expert-curated knowledgebase of biochemical reactions which describes reaction participants using the ChEBI (Chemical Entities of Biological Interest) ontology.
Results: We replaced existing textual descriptions of biochemical reactions in UniProtKB with their equivalents from Rhea, which is now the standard for annotation of enzymatic reactions in UniProtKB. We developed improved search and query facilities for the UniProt website, REST API and SPARQL endpoint that leverage the chemical structure data, nomenclature and classification that Rhea and ChEBI provide.
Availability And Implementation: UniProtKB at https://www.uniprot.org; UniProt REST API at https://www.uniprot.org/help/api; UniProt SPARQL endpoint at https://sparql.uniprot.org/; Rhea at https://www.rhea-db.org.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162351 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btz817 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Decoding the mA epitranscriptomic landscape for biotechnological applications using a direct RNA sequencing approach.
Nat Commun
January 2025
National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.
Epitranscriptomic modifications, particularly N6-methyladenosine (mA), are crucial regulators of gene expression, influencing processes such as RNA stability, splicing, and translation. Traditional computational methods for detecting mA from Nanopore direct RNA sequencing (DRS) data are constrained by their reliance on experimentally validated labels, often resulting in the underestimation of modification sites. Here, we introduce pum6a, an innovative attention-based framework that integrates positive and unlabeled multi-instance learning (MIL) to address the challenges of incomplete labeling and missing read-level annotations.
View Article and Find Full Text PDFQuantitative analysis of the polar cod (Boreogadus saida) hepatic proteome highlights interconnected responses in cellular adaptation and defence mechanisms after dietary benzo[a]pyrene exposure.
Sci Total Environ
January 2025
Department of Arctic and Marine Biology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway.
Increased industrial offshore activities in northern waters raise the question of impact of polycyclic aromatic hydrocarbons (PAHs) on key Arctic marine species. One of these is the ecologically important polar cod (Boreogadus saida), which is the primary food source for Arctic marine mammals and seabirds. In the present work, we have conducted the first comprehensive proteomics study with this species by exploring the effects of dietary PAH exposure on the hepatic proteome, using benzo[a]pyrene (BaP) as a PAH model-compound.
View Article and Find Full Text PDFActionable Gene Alterations Identified in Patients With Malignant Melanoma by Targeted Sequencing in Japan.
JCO Precis Oncol
January 2025
Department of Medical Oncology, Hokkaido University Hospital, Sapporo, Hokkaido, Japan.
Purpose: Precision medicine plays an important role in the treatment of patients with advanced melanoma. Despite its high incidence in White patients, advanced melanoma is rare in Asian countries, hampering prospective clinical trials targeting the Asian population. This retrospective study aimed to elucidate the real-world molecular diagnoses and outcomes of Japanese patients with melanoma using comprehensive genome profiling (CGP).
View Article and Find Full Text PDFPhysio-biochemical and molecular mechanisms of low nitrogen stress tolerance in peanut (Arachis hypogaea L.).
Plant Mol Biol
January 2025
Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat and Xinxiang Key Laboratory of Crop Root Biology and Green Efficient Production, School of Life Sciences, Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China.
Nitrogen (N) is a major plant nutrient and its deficiency can arrest plant growth. However, how low-N stress impair plant growth and its related tolerance mechanisms in peanut seedlings has not yet been explored. To counteract this issue, a hydroponic study was conducted to explore low N stress (0.
View Article and Find Full Text PDFImpact of rare non-coding variants on human diseases through alternative polyadenylation outliers.
Nat Commun
January 2025
Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
Although rare non-coding variants (RVs) play crucial roles in complex traits and diseases, understanding their mechanisms and identifying disease-associated RVs continue to be major challenges. Here we constructed a comprehensive atlas of alternative polyadenylation (APA) outliers (aOutliers), including 1334 3' UTR and 200 intronic aOutliers, from 15,201 samples across 49 human tissues. These aOutliers exhibit unique characteristics from transcription or splicing outliers, with a pronounced RV enrichment.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!