ArticleDatabase : the journal of biological databases and curation2015
Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.
Article in Database : the journal of biological databases and curation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Tobacco Alkaloid Assessment in a DSS-Induced Colitis Mouse Model with a Fully Humanized Immune System.International journal of molecular sciences · 2023Article
- Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery.PLoS computational biology · 2022Article
- Causal Biological Network Model for Inflammasome Signaling Applied for Interpreting Transcriptomic Changes in Various Inflammatory States.International journal of inflammation · 2022Article
- From Causal Networks to Adverse Outcome Pathways: A Developmental Neurotoxicity Case Study.Frontiers in toxicology · 2022Article
- Impact of whole-body versus nose-only inhalation exposure systems on systemic, respiratory, and cardiovascular endpoints in a 2-month cigarette smoke exposure study in the ApoEJournal of applied toxicology : JAT · 2021Article
- LINPS: a database for cancer-cell-specific perturbations of biological networks.Database : the journal of biological databases and curation · 2021Article
- Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review.Biomolecules · 2021Review
- Signaling pathway perturbation analysis for assessment of biological impact of cigarette smoke on lung cells.Scientific reports · 2021Article
- Identification of Mucus-Associated Molecular Subtypes of Chronic Obstructive Pulmonary Disease: A Latent Profile Analysis Based on MUC5B-Associated Genes.Medical science monitor : international medical journal of experimental and clinical research · 2021Article
- The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling.Briefings in bioinformatics · 2021Article
- Systems biology approach highlights mechanistic differences between Crohn's disease and ulcerative colitis.Scientific reports · 2021Article
- CaNDis: a web server for investigation of causal relationships between diseases, drugs and drug targets.Bioinformatics (Oxford, England) · 2021Article
- A 6-month inhalation toxicology study in ApoeArchives of toxicology · 2021Article
- The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).Bioinformatics (Oxford, England) · 2021Article
- Assembling Disease Networks From Causal Interaction Resources.Frontiers in genetics · 2021Review
- Systems Toxicology Approach for Assessing Developmental Neurotoxicity in Larval Zebrafish.Frontiers in genetics · 2021Article
- Respiratory Effects of Exposure to Aerosol From the Candidate Modified-Risk Tobacco Product THS 2.2 in an 18-Month Systems Toxicology Study With A/J Mice.Toxicological sciences : an official journal of the Society of Toxicology · 2020Article
- Multi-omics systems toxicology study of mouse lung assessing the effects of aerosols from two heat-not-burn tobacco products and cigarette smoke.Computational and structural biotechnology journal · 2020Article
- Machine learning applications in drug development.Computational and structural biotechnology journal · 2020Review
- Systems toxicology assessment of a representative e-liquid formulation using human primary bronchial epithelial cells.Toxicology reports · 2020Article
Corrections and comments
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.