Executing Complexity-Increasing Queries in Relational (MySQL) and NoSQL (MongoDB and EXist) Size-Growing ISO/EN 13606 Standardized EHR Databases

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Castro, Antonio; Moreno, Oscar; Pascual, Mario

doi:10.3791/57439

Cited by 15 publications

(7 citation statements)

References 5 publications

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“…Database development. All the database files were stored as JavaScript Object Notation (JSON) 51 files in MongoDB database 52 . These JSON files was uploaded on the server localhost using pymongo and query commands were made in the command line client in MongoDB compass.…”

Section: Discussionmentioning

confidence: 99%

MyomirDB: A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons

Gupta

Srivastava

Suryakumar

et al. 2020

Sci Rep

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Muscular atrophy or muscle loss is a multifactorial clinical condition during many critical illnesses like cancer, cardiovascular diseases, diabetes, pulmonary diseases etc. leading to fatigue and weakness and contributes towards a decreased quality of life. The proportion of older adults (>65 y) in the overall population is also growing and aging is another important factor causing muscle loss. Some muscle miRNAs (myomiRs) and their target genes have even been proposed as potential diagnostic, therapeutic and predictive markers for muscular atrophy. MyomirDB (http://www.myomirdb.in/) is a unique resource that provides a comprehensive, curated, user-friendly and detailed compilation of various miRNA bio-molecular interactions; miRNA-Transcription Factor-Target Gene co-regulatory networks and ~8000 tripartite regulons associated with 247 myomiRs which have been experimentally validated to be associated with various muscular atrophy conditions. For each database entry, MyomirDB compiles source organism, muscle atrophic condition, experiment duration, its level of expression, fold change, tissue of expression, experimental validation, disease and drug association, tissue-specific expression level, Gene Ontology and KEGG pathway associations. The web resource is a unique server platform which uses in-house scripts to construct miRNA-Transcription Factor-Target Gene co-regulatory networks and extract tri-partite regulons also called Feed Forward Loops. These unique features helps to offer mechanistic insights in disease pathology. Hence, MyomirDB is a unique platform for researchers working in this area to explore, fetch, compare and analyse atrophy associated miRNAs, their co-regulatory networks and FFL regulons.

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Section: Discussionmentioning

confidence: 99%

MyomirDB: A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons

Gupta

Srivastava

Suryakumar

et al. 2020

Sci Rep

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“…EHR-derived PheWAS codes in MGI library 17 to map object oriented models onto MySQL database. 18 A gene-centered Manhattan plot represents noticed SNP to gene associations a round gene of curiosity, and an SNP-centered line chart illustrates observed eQTLs surrounding SNPs of interest. Tested on a Bluegene super computing with ∼32 GB of RAM in response to set a parameters based on load samples and component for dynamic balancing of virtual machines within the cloud infrastructure resource, as soon as it is uploaded, our server can fetch per SNP-probe pairs from these >75 people in <0.0257s from the database, and calculates Spearman’s rhos and nominal P -values for 486 SNP-probe pairs in 3 s.…”

Section: Methodsmentioning

confidence: 99%

Prevalence of the Factor V Leiden Mutation Arg534Gln in Western Region of Saudi Arabia: Functional Alteration and Association Study With Different Populations

Athar

Abduljaleel

Ghita

et al. 2021

Clin Appl Thromb Hemost

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The rare Gln534 (Factor V Leiden; FVL) allele (1:169,519,049 T>C) is associated with an increased risk of venous thrombosis. The purpose of this study was to measure the prevalence of Factor V Leiden mutation in thrombophilia patients with deep vein thrombosis. Also, we investigated the functional and structural characteristics of this mutation p.(Arg534Gln) to be examined the cumulative impact on venous thrombosis risk as well correlated with different populations by Genome Wide Association Studies (GWAS). A total of 108 patients with idiopathic deep vein thrombosis were examined for Factor V Leiden gene mutation. Our preliminary data show that about 10% of patients were detected with the heterozygous and homozygous form of the Factor V Leiden mutation. An association analysis confirmed that the Factor V SNP variant (rs6025) was highly associated ( P-value 4.91 x10-^ -39) with an increased risk of venous thrombosis. Also, we found that the recognized SNP was important among HapMap populations. Our results indicated that among the 3 populations (Asian, African, and American) studied, this association was highest in the African population based on the r(2) significant threshold ( P-value 5e-190). In addition, this mutation was located at the domain F5/8 type A 2, which can disturb this domain and abolish its function. Because of aspartic acid nearby wild type position as form in the salt bridge due to this discharge will disturb the ionic interaction made by the wild type residue Arg534. This residue was not found to be in contact with other domains of which the function was known. However, contact with other molecules or domains (THPH2: MIM: 188055) were still possible and might be affected by this mutation that may cause thrombophilia due to activated protein C resistance.

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“…Finally, after collection, processing and enrichment of the data, all the database files were stored as JavaScript Object Notation (JSON) files in MongoDB database relational database ( 50 ). These JSON files were uploaded on the server localhost using PyMongo, and query commands were made in the command line client in MongoDB compass.…”

Section: Methodsmentioning

confidence: 99%

HAHmiR.DB: a server platform for high-altitude human miRNA–gene coregulatory networks and associated regulatory circuits

et al. 2020

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Around 140 million people live in high-altitude (HA) conditions! and even a larger number visit such places for tourism, adventure-seeking or sports training. Rapid ascent to HA can cause severe damage to the body organs and may lead to many fatal disorders. During induction to HA, human body undergoes various physiological, biochemical, hematological and molecular changes to adapt to the extreme environmental conditions. Several literature references hint that gene-expression-regulation and regulatory molecules like miRNAs and transcription factors (TFs) control adaptive responses during HA stress. These biomolecules are known to interact in a complex combinatorial manner to fine-tune the gene expression and help in controlling the molecular responses during this stress and ultimately help in acclimatization. High-Altitude Human miRNA Database (HAHmiR.DB) is a unique, comprehensive and curated collection of miRNAs that have been experimentally validated to be associated with HA stress, their level of expression in different altitudes, fold change, experiment duration, biomarker association, disease and drug association, tissue-specific expression level, Gene Ontology (GO) and Kyoto Encyclopaedia of Gene and Genomes (KEGG) pathway associations. As a server platform, it also uniquely constructs and analyses interactive miRNA–TF–gene coregulatory networks and extracts regulatory circuits/feed-forward loops (FFLs). These regulatory circuits help to offer mechanistic insights into complex regulatory mechanisms during HA stress. The server can also build these regulatory networks between two and more miRNAs of the database and also identify the regulatory circuits from this network. Hence, HAHmiR.DB is the first-of-its-kind database in HA research, which is a reliable platform to explore, compare, analyse and retrieve miRNAs associated with HA stress, their coregulatory networks and FFL regulatory-circuits. HAHmiR.DB is freely accessible at http://www.hahmirdb.in

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Executing Complexity-Increasing Queries in Relational (MySQL) and NoSQL (MongoDB and EXist) Size-Growing ISO/EN 13606 Standardized EHR Databases

Cited by 15 publications

References 5 publications

MyomirDB: A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons

MyomirDB: A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons

Prevalence of the Factor V Leiden Mutation Arg534Gln in Western Region of Saudi Arabia: Functional Alteration and Association Study With Different Populations

HAHmiR.DB: a server platform for high-altitude human miRNA–gene coregulatory networks and associated regulatory circuits

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