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63 results for “Biological pathways”
A Curated Gene and Biological System Annotation of Adverse Outcome Pathways Related to Human Health
<p>Adverse Outcome Pathways (AOPs) are multi-scale models of biological mechanisms connecting molecular initiating events to adverse outcomes through measurable key events. AOPs can guide the use and development of new approach methodologies (NAMs) aimed at reducing animal experimentation in chemical safety assessment. Here, we present a comprehensive molecular annotation of AOPs relevant to human health to embed the AOP framework into molecular data interpretation, which supports the development and application of novel AOP-based approaches in biomedical research.</p> <p>Please cite the following publication alongside this Zenodo entry when using the data:</p> <p>Saarimäki, L.A., Fratello, M., Pavel, A. <em>et al.</em> A curated gene and biological system annotation of adverse outcome pathways related to human health. <em>Sci Data</em> <strong>10</strong>, 409 (2023). https://doi.org/10.1038/s41597-023-02321-w</p>
Appendix 5 to "The Status of Biological Invasions and their Management in South Africa in 2019"—Pathways change tracker
<p>For more details see: http://iasreport.sanbi.org.za</p> <p>SANBI and CIB 2020. Appendix 5 to "The Status of Biological Invasions and their Management in South Africa in 2019"—Pathways change tracker. South African National Biodiversity Institute, Kirstenbosch and DSI-NRF Centre of Excellence for Invasion Biology, Stellenbosch. http://dx.doi.org/10.5281/zenodo.3947799</p>
Pathformer: a biological pathway informed Transformer for disease diagnosis and prognosis using multi-omics data
<p>Integrating multi-omics data offers a more comprehensive view of gene regulation, which would be helpful in achieving accurate diagnosis of diseases like cancer. To improve the accuracy of disease diagnosis and prognosis, we developed Pathformer, a multi-omics integration method for both tissue and liquid biopsy data. We implemented Pathformer's network architecture using the “PyTorch” package in Python v3.6.9, and our codes can be found in the GitHub repository (https://github.com/lulab/Pathformer). This repository contains preprocessed TCGA dataset data, preprocessedliquid biopsy dataset data, result of Pathformer and comparison_methods, mentioned in GitHub project and article.</p>
Appendix 1 to "The Status of Biological Invasions and their Management in South Africa in 2022"—Species level pathway data
<p>SANBI and CIB 2023. Appendix 1 to "The Status of Biological Invasions and their Management in South Africa in 2022"—Species level pathway data. South African National Biodiversity Institute, Kirstenbosch and DSI-NRF Centre of Excellence for Invasion Biology, Stellenbosch. http://dx.doi.org/10.5281/zenodo.8217192</p> <p>For more details see: http://iasreport.sanbi.org.za</p> <p>For the report itself see: http://dx.doi.org/10.5281/zenodo.8217182</p>
A machine learning framework for extracting information from biological pathway images in the literature
<p><strong>466 target chemicals_selected chemicals:</strong></p> <p>Target chemicals satisfying the criteria for biochemical reactions not covered by MetaNetX and KEGG.</p> <p> </p> <p><strong>466 target chemicals_statistics:</strong><br>Numbers of MetaCyc reactions, papers, and pathway images collected for 466 target chemicals from the bio-based chemicals map (Jang et al., Trends in Biotechnology, 2023).</p> <p> </p> <p><strong>arrow detection_bounding box labels:</strong><br>Bounding box labels for 6,471 images in the training and validation datasets and 100 images in the test dataset. The corresponding images are available in "arrow detection_training and validation datasets.zip".</p> <p> </p> <p><strong>arrow detection_test dataset:</strong></p> <p>Test dataset for arrow detection using Faster R-CNN model. A total of 100 images have been prepared from 89 papers searched through PubMed Central (PMC).</p> <p> </p> <p><strong>arrow detection_training and validation datasets:</strong></p> <p>Training and validation datasets for arrow detection using Faster R-CNN model. A total of 6,471 images have been prepared, including 2,332 images from five different sources and 4,139 augmented images.</p> <p> </p> <p><strong>EBPI outputs:</strong></p> <p>Reaction information extracted using EBPI from 49,846 biological pathway images across 466 target chemicals.</p> <p> </p> <p><strong>text classification_training, validation and test datasets:</strong></p> <p>Dataset for text classification using BioBERT. A total of 59,370 terms have been prepared, including 15,101 “gene” terms, 21,417 “protein” terms, and 22,852 “others” terms by combining the data from MetaCyc and the PaddleOCR results from the papers.</p>
Appendix 3 to "The Status of Biological Invasions and their Management in South Africa in 2019"—Data on the status of pathways
<p>For more details see: http://iasreport.sanbi.org.za</p> <p>SANBI and CIB 2020. Appendix 3 to "The Status of Biological Invasions and their Management in South Africa in 2019"—Data on the status of pathways. South African National Biodiversity Institute, Kirstenbosch and DSI-NRF Centre of Excellence for Invasion Biology, Stellenbosch. http://dx.doi.org/10.5281/zenodo.3947666</p>
Uncoupling of Behavioral and Metabolic Twenty-Four-Hour Rhythms in Reindeer (Current Biology, Meier et al. 2024): Metabolomics analysis tables: Annotation list, pathway analysis outputs, target list for targeted peak exstraction and MS/MS spectra of annotated features
<p><span>Metabolomics analysis tables: Annotation list, pathway analysis outputs, target list for targeted peak exstraction and MS/MS spectra of annotated features</span></p>
Exploration of the Activity of DNA Located Outside of Cellular Nucleus to Amplify Inflammation in Inflammatory Bowel Disease in Children Through Biological Pathway Cyclic GMP-AMP Synthase (cGAS) - Sti
ClinicalTrials.gov study NCT05916274. IPD Sharing: Not stated. Countries: 1. Publications: 8.
Data from: Transpacific coalescent pathways of coconut rhinoceros beetle biotypes: resistance to biological control catalyzes resurgence of an old pest
Open the record for dataset details and reuse information.
Supplementary material 1 from: Pergl J, Brundu G, Harrower CA, Cardoso AC, Genovesi P, Katsanevakis S, Lozano V, Perglová I, Rabitsch W, Richards G, Roques A, Rorke SL, Scalera R, Schönrogge K, Stewart A, Tricarico E, Tsiamis K, Vannini A, Vilà M, Zenetos A, Roy HE (2020) Applying the Convention on Biological Diversity Pathway Classification to alien species in Europe. In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 333-363. https://doi.org/10.3897/neobiota.62.53796
Table S1
Identifying Biomarkers & Dysregulated Biological Pathways in Blood and Urine of Congenital Central Hypoventilation Syndrome (CCHS) Patients
ClinicalTrials.gov study NCT06997146. IPD Sharing: YES. Countries: 1. Publications: 0.
MicroRNAs and their isomiRs function cooperatively to target common biological pathways
GEO Series GSE29101. Homo sapiens. 20 samples. Type: Expression profiling by array; Non-coding RNA profiling by array.
Inhalation and oropharyngeal aspiration exposure to rod-like carbon nanotubes induces highly similar airway inflammation and biological pathways in mouse lungs
GEO Series GSE85711. Mus musculus. 15 samples. Type: Expression profiling by array.
VISTA re-programs macrophage biology through the combined regulation of tolerance and anti-inflammatory pathways
GEO Series GSE157518. Homo sapiens; Mus musculus. 62 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis
GEO Series GSE74464. Homo sapiens. 14 samples. Type: Methylation profiling by high throughput sequencing.
Candidate genes and pathways involved in TTK-induced biological functions in ovarian carcinoma
GEO Series GSE176220. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide studies reveal novel biological pathways regulated by SIN3 isoforms
GEO Series GSE72173. Drosophila melanogaster. 14 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Time series integrative analysis of RNA-Seq and miRNA expression data reveals key biologic pathways during keloid formation [RNA-seq]
GEO Series GSE113619. Homo sapiens. 64 samples. Type: Expression profiling by high throughput sequencing.
Multi-omic analysis unveils biological pathways in peripheral immune system associated to minimal hepatic encephalopathy appearance in cirrhotic patients
GEO Series GSE149741. Homo sapiens. 11 samples. Type: Expression profiling by array.
beta-Arrestin Pathway-Selective G Protein-Coupled Receptor Agonists Engender Unique Biological Efficacy In Vivo
GEO Series GSE35181. Mus musculus. 18 samples. Type: Expression profiling by array.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.