Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems
| Autor: | William Hayes, Jurjen W. Westra, Stéphanie Boué, Alain Sewer, Emilija Veljkovic, Julia Hoeng, Brett Fields, Manuel C. Peitsch, Sam Ansari, Jennifer Park, Renee Deehan Kenney, Marja Talikka, Florian Martin, Anselmo Di Fabio, Walter K. Schlage |
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| Rok vydání: | 2015 |
| Předmět: |
Databases
Factual Computer science Neovascularization Physiologic Context (language use) computer.software_genre Cardiovascular System General Biochemistry Genetics and Molecular Biology Set (abstract data type) World Wide Web Stress Physiological Animals Humans Lung Cell Proliferation computer.programming_language Information retrieval Database Models Cardiovascular Cell Differentiation Tissue repair JSON Expression (mathematics) Visualization Cell stress Original Article General Agricultural and Biological Sciences computer Biological network Information Systems |
| Zdroj: | Database: The Journal of Biological Databases and Curation |
| ISSN: | 1758-0463 |
| Popis: | 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 |
| Databáze: | OpenAIRE |
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