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Development of biomedical infrastructure for drug/compound annotations
Adesara, Julee Pratik
Su, AndrewKelley, Scott
The effects of compounds and drugs on biological system make them an exceptionally important bio-entity among a set of bio-entities, such as gene, genetic variant, drug, disease, pathway, in a wide range of application. Understanding these effects (therapeutic, investigational or adverse effect) of compounds and drugs on biological system is crucial to research in chemical biology, pharmacology, toxicology and related fields. Vast amount of data describing bioactivity of large chemical libraries and biological roles or effects of metabolites, drugs and small molecules has accumulated in public repositories, due to development of high-throughput screening technologies. Attempts to comprehensively annotate drugs or compounds are distributed across numerous efforts. There is no one-fits-all database which can capture the entire knowledge space (chemically and clinically oriented annotations) of drugs or compounds. To allow systematic interpretation and alleviate fragmentation of drugs or compounds data, c.biothings.io is developed. c.biothings.io is an aggregation of drug or compounds data sources into a unified, queryable web service. Development of this web service required loading, aggregating, and indexing data and developing a programmatic interface for exploring and interactively querying annotations. Pathway analysis of drug targets retrieved from this web service demonstrate the use case of this web service. Analysis of obtained enriched biological pathways may direct to the mechanism of action or therapeutic effects of drugs. This approach can be beneficial to investigate additional clinical uses of the drugs or in drug repositioning studies.
Bioinformatics And Medical Informatics
Biological and Medical Informatics Research Center
Master Of Science (M.S.) San Diego State University, 2017
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