ABSTRACT
MOTIVATION: Knowledge graphs (KGs) are being adopted in industry, commerce and academia. Biomedical KG presents a challenge due to the complexity, size and heterogeneity of the underlying information. RESULTS: In this work, we present the Scalable Precision Medicine Open Knowledge Engine (SPOKE), a biomedical KG connecting millions of concepts via semantically meaningful relationships. SPOKE contains 27 million nodes of 21 different types and 53 million edges of 55 types downloaded from 41 databases. The graph is built on the framework of 11 ontologies that maintain its structure, enable mappings and facilitate navigation. SPOKE is built weekly by python scripts which download each resource, check for integrity and completeness, and then create a 'parent table' of nodes and edges. Graph queries are translated by a REST API and users can submit searches directly via an API or a graphical user interface. Conclusions/Significance: SPOKE enables the integration of seemingly disparate information to support precision medicine efforts. AVAILABILITY AND IMPLEMENTATION: The SPOKE neighborhood explorer is available at https://spoke.rbvi.ucsf.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Subject(s)
Pattern Recognition, Automated , Precision Medicine , Databases, FactualABSTRACT
Osteoarthritis is a prevalent degenerative disease affecting a large portion of the world's aging population. Currently, nonsteroidal anti-inflammatory drugs and acetaminophen are first-line medications for treating osteoarthritis patients' pain. However, several studies have noted that while these medications control pain they do not halt progressive degeneration and tend to have an unfavorable side-effect profile with prolonged use. Recently, due to their more favorable side-effect profiles, herbal alternatives for controlling osteoarthritis symptoms and for alleviating the progression of the disease are being increasingly studied. Synogesic is a newly developed herbal supplement blend by renowned orthopedic surgeons and physiatrists consisting of turmeric, rutin, ginger root, vitamin C, vitamin D, and boswellia extracts. A study by Sharkey et al. has commented on the efficacy of the blend on the patients with knee osteoarthritis. So far, a review on the ingredients of the blend has not yet carried outbeen. By exploring prominent literature databases including PubMed and ScienceDirect, our aim is to write a narrative review to explore the individual ingredients of this blend and delve into their characteristics, as well as the most recent literature on their mechanism and efficacy in patients with osteoarthritis. Through this, we hope to inform clinicians and patients alike on relevant up-to-date research on the supplement and provide insight on the potential for this supplement for alleviating the disease course of patients with osteoarthritis.
ABSTRACT
Oral squamous cell carcinoma (OSCC) is the most common type of head and neck cancer and, as indicated by The Oral Cancer Foundation, kills at an alarming rate of roughly one person per hour. With this study, we aimed at better understanding disease mechanisms and identifying minimally invasive disease biomarkers by profiling novel small non-coding RNAs (specifically, tRNA halves and YRNA fragments) in both serum and tumor tissue from humans. Small RNA-Sequencing identified multiple 5' tRNA halves and 5' YRNA fragments that displayed significant differential expression levels in circulation and/or tumor tissue, as compared to control counterparts. In addition, by implementing a modification of weighted gene coexpression network analysis, we identified an upregulated genetic module comprised of 5' tRNA halves and miRNAs (miRNAs were described in previous study using the same samples) with significant association with the cancer trait. By consequently implementing miRNA-overtargeting network analysis, the biological function of the module (and by "guilt by association," the function of the 5' tRNA-Val-CAC-2-1 half) was found to involve the transcriptional targeting of specific genes involved in the negative regulation of the G1/S transition of the mitotic cell cycle. These findings suggest that 5' tRNA-Val-CAC-2-1 half (reduced in serum of OSCC patients and elevated in the tumor tissue) could potentially serve as an OSCC circulating biomarker and/or target for novel anticancer therapies. To our knowledge, this is the first time that the specific molecular function of a 5'-tRNA half is specifically pinpointed in OSCC.
