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Using GMQL-Web for Querying, Downloading and Integrating Public with Private Genomic Datasets

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Mario CannataroAuthors Info & Claims

BCB '19: Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics

Pages 688 - 693

https://doi.org/10.1145/3307339.3343466

Published: 04 September 2019 Publication History

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Abstract

Recent integrative analyses using data from TCGA permit GWAS investigation of the genetic variants function, providing more insight than single-platform approaches. Although there has been much progress, the integration across data sets and data types remains limited. In this work we illustrate a workflow, based on the use of GMQL-Web, for combining private cancer datasets with datasets of genomic features and biological/clinical metadata sourcing from ENCODE, Roadmap Epigenomics, TCGA, as well as annotations from GENCODE and RefSeq. GMQL-Web is a web-based interface with the goal of providing a user-friendly intuitive environment for bioinformaticians and biologists who need to query genomic processed data (including public dataset not already available in the GMQL Repository) and combine them with their private datasets. Finally, we present a case study that illustrates the workflow steps to find samples extracted from a pharmacogenomic drug metabolism multi-gene platform, i.e. the Affymetrix DMET Plus platform that contain single-nucleotide polymorphisms (SNPs) that overlap with exon regions. The DMET platform is able to identify the relationship among the patients' genomic variations and drug metabolism by detecting SNPs on genes related to drug metabolism. From the obtained result, we identify only the SNPs overlapping with genes whose expression level is above a given threshold.

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Bernasconi ACanakoglu AComolli F(2023)Processing genome-wide association studies within a repository of heterogeneous genomic datasetsBMC Genomic Data10.1186/s12863-023-01111-y24:1Online publication date: 3-Mar-2023
https://doi.org/10.1186/s12863-023-01111-y
Settino MCannataro M(2023)MMRFVariant: Prioritizing variants in Multiple MyelomaInformatics in Medicine Unlocked10.1016/j.imu.2023.10127139(101271)Online publication date: 2023
https://doi.org/10.1016/j.imu.2023.101271
Bernasconi AGarcía S. ACeri SPastor O(2023)PoliViews: A comprehensive and modular approach to the conceptual modeling of genomic dataData & Knowledge Engineering10.1016/j.datak.2023.102201147(102201)Online publication date: Sep-2023
https://doi.org/10.1016/j.datak.2023.102201

Index Terms

Using GMQL-Web for Querying, Downloading and Integrating Public with Private Genomic Datasets
1. Information systems
  1. Data management systems
    1. Information integration
      1. Extraction, transformation and loading

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BCB '19: Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics

September 2019

716 pages

ISBN:9781450366663

DOI:10.1145/3307339

General Chairs:
Xinghua (Mindy) Shi
Temple University, USA
,
Michael Buck
University of Buffalo, USA
,
Program Chairs:
Jian Ma
Carnegie Mellon University, USA
,
Pierangelo Veltri
University Magna Graecia of Catanzaro, Italy

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 04 September 2019

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BCB '19: 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics

September 7 - 10, 2019

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Bernasconi ACanakoglu AComolli F(2023)Processing genome-wide association studies within a repository of heterogeneous genomic datasetsBMC Genomic Data10.1186/s12863-023-01111-y24:1Online publication date: 3-Mar-2023
https://doi.org/10.1186/s12863-023-01111-y
Settino MCannataro M(2023)MMRFVariant: Prioritizing variants in Multiple MyelomaInformatics in Medicine Unlocked10.1016/j.imu.2023.10127139(101271)Online publication date: 2023
https://doi.org/10.1016/j.imu.2023.101271
Bernasconi AGarcía S. ACeri SPastor O(2023)PoliViews: A comprehensive and modular approach to the conceptual modeling of genomic dataData & Knowledge Engineering10.1016/j.datak.2023.102201147(102201)Online publication date: Sep-2023
https://doi.org/10.1016/j.datak.2023.102201

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Intra-relation Reconstruction from Inter-relation: miRNA to Gene Expression

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An integrative analysis of ATAC-seq and RNA-seq data in activated, CD4+CD45RO+CD196+ human T cells treated with IL-1B and IL-23 with or without PGE2

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