Motivation: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. Pathways are arranged in a hierarchical structure that largely corresponds to the GO biological process hierarchy, allowing the user to navigate from high level concepts like immune system to detailed pathway diagrams showing biomolecular events like membrane transport or phosphorylation. Here, we present new developments in the Reactome visualization system that facilitate navigation through the pathway hierarchy and enable efficient reuse of Reactome visualizations for users' own research presentations and publications.
Results: For the higher levels of the hierarchy, Reactome now provides scalable, interactive textbook-style diagrams in SVG format, which are also freely downloadable and editable. Repeated diagram elements like 'mitochondrion' or 'receptor' are available as a library of graphic elements. Detailed lower-level diagrams are now downloadable in editable PPTX format as sets of interconnected objects.
Availability And Implementation: http://reactome.org.
Contact: fabregat@ebi.ac.uk or hhe@ebi.ac.uk.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860170 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btx441 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Aligning Large Language Models with Humans: A Comprehensive Survey of ChatGPT's Aptitude in Pharmacology.
Drugs
December 2024
Department of Pharmacy and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China.
Background: Due to the lack of a comprehensive pharmacology test set, evaluating the potential and value of large language models (LLMs) in pharmacology is complex and challenging.
Aims: This study aims to provide a test set reference for assessing the application potential of both general-purpose and specialized LLMs in pharmacology.
Methods: We constructed a pharmacology test set consisting of three tasks: drug information retrieval, lead compound structure optimization, and research trend summarization and analysis.
AAindexNC: Estimating the Physicochemical Properties of Non-Canonical Amino Acids, Including Those Derived from the PDB and PDBeChem Databank.
Int J Mol Sci
November 2024
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia.
The physicochemical properties of amino acid residues from the AAindex database are widely used as predictors in building models for predicting both protein structures and properties. It should be noted, however, that the AAindex database contains data only for the 20 canonical amino acids. Non-canonical amino acids, while less common, are not rare; the Protein Data Bank includes proteins with more than 1000 distinct non-canonical amino acids.
View Article and Find Full Text PDFUsing artificial intelligence (AI) to assess the prevalence of false or misleading health-related claims.
R Soc Open Sci
October 2024
Independent Information Scientist, Oadby, Leicestershire, UK.
Article Synopsis
- Complementary healthcare in the UK is voluntarily regulated, but many practices are based on pseudoscience and may include misleading health claims.
- An AI tool analyzed websites of 872 clinics registered under the Complementary and Natural Healthcare Council, finding that 704 (97%) contained false or misleading claims.
- The AI's accuracy was comparable to human assessors, identifying nearly the same number of misleading claims while misidentifying fewer, suggesting that AI could enhance regulatory effectiveness.
Understanding Voriconazole Metabolism: A Middle-Out Physiologically-Based Pharmacokinetic Modelling Framework Integrating In Vitro and Clinical Insights.
Clin Pharmacokinet
November 2024
Department of Clinical Pharmacy and Biochemistry, Institute of Pharmacy, Freie Universitaet Berlin, Berlin, Germany.
Background And Objective: Voriconazole (VRC), a broad-spectrum antifungal drug, exhibits nonlinear pharmacokinetics (PK) due to saturable metabolic processes, autoinhibition and metabolite-mediated inhibition on their own formation. VRC PK is also characterised by high inter- and intraindividual variability, primarily associated with cytochrome P450 (CYP) 2C19 genetic polymorphism. Additionally, recent in vitro findings indicate that VRC main metabolites, voriconazole N-oxide (NO) and hydroxyvoriconazole (OHVRC), inhibit CYP enzymes responsible for VRC metabolism, adding to its PK variability.
View Article and Find Full Text PDFC→U transition biases in SARS-CoV-2: still rampant 4 years from the start of the COVID-19 pandemic.
mBio
December 2024
Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom.
Unlabelled: The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the pandemic and post-pandemic periods has been characterized by rapid adaptive changes that confer immune escape and enhanced human-to-human transmissibility. Sequence change is additionally marked by an excess number of C→U transitions suggested as being due to host-mediated genome editing. To investigate how these influence the evolutionary trajectory of SARS-CoV-2, 2,000 high-quality, coding complete genome sequences of SARS-CoV-2 variants collected pre-September 2020 and from each subsequently appearing alpha, delta, BA.
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!