A Cloud-Based Metabolite and Chemical Prioritization System for the Biology/Disease-Driven Human Proteome Project
| Autor: | Christopher Ré, Tsung-Lu Michael Lee, Samuel C. Kou, Kun-Hsing Yu, Michael Snyder, Yu-Ju Chen, Isaac S. Kohane, Jung-Hsien Chiang |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Proteome Metabolite Cloud computing Computational biology Biology Proteomics Biochemistry Article Unique identifier 03 medical and health sciences chemistry.chemical_compound Metabolomics Human proteome project Data Mining Humans business.industry General Chemistry Cloud Computing Automatic summarization Search Engine 030104 developmental biology chemistry business Precision and recall Algorithms |
| Zdroj: | Journal of Proteome Research. 17:4345-4357 |
| ISSN: | 1535-3907 1535-3893 |
| Popis: | Targeted metabolomics and biochemical studies complement the ongoing investigations led by the Human Proteome Organization (HUPO) Biology/Disease-driven-Human Proteome Project (B/D-HPP). However, it is challenging to identify and prioritize metabolite and chemical targets. Literature mining-based approaches have been proposed for target proteomics studies, but text mining methods for metabolite and chemical prioritization is hindered by a large number of synonyms and non-standardized names of each entity. In this study, we developed a cloud-based literature mining and summarization platform that maps metabolites and chemicals in the literature to unique identifiers and summarizes the co-publication trends of metabolite/chemicals and B/D-HPP topics using the Protein Universal Reference Publication-Originated Search Engine (PURPOSE) scores. We successfully prioritized metabolites and chemicals associated with the B/D-HPP targeted fields, with the results validated by checking against expert-curated associations and enrichment analyses. Comparing with existing algorithms, our system achieved better precision and recall in retrieving chemicals related to B/D-HPP focused area. Our cloud-based platform enables queries on all biological terms in multiple species, which will contribute to B/D-HPP and targeted metabolomics/chemical studies. |
| Databáze: | OpenAIRE |
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