CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining
Year: 2007
Type: article
Abstract: CMGSDB (Database for Computational Modeling of Gene Silencing) is an integration of heterogeneous data sources about Caenorhabditis elegans with capabilities for compositional data mining (CDM) across diverse domains. Besides gene, protein and functional annotations, CMGSDB currently unifies information about 531 RNAi phenotypes obtained from heterogeneous databases using a hierarchical scheme. A phenotype browser at the CMGSDB website serves this hierarchy and relates phenotypes to other biological entities. The application of CDM to CMGSDB produces 'chains' of relationships in the data by finding two-way connections between sets of biological entities. Chains can, for example, relate the knock down of a set of genes during an RNAi experiment to the disruption of a pathway or specific gene expression through another set of genes not directly related to the former set. The web interface for CMGSDB is available at https://bioinformatics.cs.vt.edu/cmgs/CMGSDB/, and serves individual biological entity information as well as details of all chains computed by CDM.
Source: Nucleic Acids Research
DOI: 10.1093/nar/gkm804
Institution: Virginia Tech
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,992
Funder: National Science Foundation
OpenAlex ID: W2040539769