Integrated querying and version control of context-specific biological networks

• DOI: 10.1093/database/baaa018
• Publication Date: 2020-03-02T20:16:55Z
• Authors: Tyler Cowman; Mustafa Coşkun; Ananth Grama; Mehmet Koyutürk
• Keywords: 0301 basic medicine; Internet; Databases, Factual; Computational Biology; DISEASE; 3. Good health; User-Computer Interface; 03 medical and health sciences; Data Mining; Humans; Original Article; Gene Regulatory Networks; ALGORITHM; Protein Interaction Maps; Algorithms; Data Curation

Biomolecular data stored in public databases is increasingly specialized to organisms, context/pathology and tissue type, potentially resulting significant overhead for analyses. These networks are often specializations of generic interaction sets, presenting opportunities reducing storage computational cost. Therefore, it desirable develop effective compression techniques, along with efficient algorithms a flexible query interface capable operating on compressed structures. Current graph offer varying levels support network integration. However, these solutions do not provide methods the querying versioned networks. We present VerTIoN, framework consisting novel structures associated mechanisms integrated context-specific biological As use case our framework, we study proximity queries which user can select compose combination tissue-specific Using version tree structure, conjunction state-of-the-art numerical demonstrate real-time large databases. Our results show that possible defined heterogeneous composed at time while drastically response multiple simultaneous queries. The flexibility offered by VerTIoN composing versions opens new avenues utilization ever increasing volume broad range biomedical applications. implemented as C++ library available http://compbio.case.edu/omics/software/vertion https://github.com/tjcowman/vertion. [e-mail].