The supplementary material is available in the electronic version of this article: http://dx.doi.org/ 10.3233/JAD-151178.
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SUMMARY
Biological knowledge is fundamentally complicated, and over time, a high volume of correspondingly complex and highly heterogeneous data has been generated using high-throughput technologies. The use of ontologies and terminologies is prevalent to a greater extent in the life sciences domain as these can be used for collecting, organizing and storing the vast volume of biological data in a standardized manner. The advantages of using biomedical ontologies are: (i) it enables easy interoperability of resources between linked databases, (ii) an efficient search and query of different resources are possible, (iii) it allows for
context-specific information retrieval, and (iv) automatic reasoning of data can be performed.
However, with the growing number of molecular databases, one major challenge for the ontology community is in the lack of semantic mapping from a database to an ontology. For instance, there are more than 170 pathway databases which vary widely in form and content; with the multiplicity of information stored in these databases concordant with a lack of quality check over them, raising simple questions often becomes a daunting task for researchers. Furthermore, there also exists a lack of order in the existing pathway ontologies, which motivated us to develop the pathway terminology system (PTS), which combines signaling pathways and biological events to ensure broad coverage of the entire pathway knowledge domain. We have also demonstrated the usability of this system to answer complex questions in any context, especially in the field of NDD.
Molecular pathways consist of the interactions of bimolecular entities triggering a flow of chemical chain-like reactions for regulating or disregarding a biological process. Hence, pathways become an essential target for monitoring disease
progression and for optimized drug treatment. Moreover, they form an integral part of complex, multi-scale modeling approaches, mainly due to the full range of functionality of specific chemical reactions where the effect of genetic and proteomic alterations canforcibly alter metabolic and biochemical reactions, and trespassing of the blood-brain barrier is rendered possible. Additionally, incorporation of context-specific pathway models is highly relevant for gaining more profound insight into bridging the molecular underpinnings of biological processes with significant impact on clinical modalities of the brain.