Abstract
GMQL is a high-level query language for genomics, which operates on datasets described through GDM, a unifying data model for processed data formats. They are ingredients for the integration of processed genomic datasets, i.e. of signals produced by the genome after sequencing and long data extraction pipelines. While most of the processing load of today’s genomic platforms is due to data extraction pipelines, we anticipate soon a shift of attention towards processed datasets, as such data are being collected by large consortia and are becoming increasingly available.
In our view, biology and personalized medicine will increasingly rely on data extraction and analysis methods for inferring new knowledge from existing heterogeneous repositories of processed datasets, typically augmented with the results of experimental data targeting individuals or small populations. While today’s big data are raw reads of the sequencing machines, tomorrow’s big data will also include billions or trillions of genomic regions, each featuring specific values depending on the processing conditions.
Coherently, GMQL is a high-level, declarative language inspired by big data management, and its execution engines include classic cloud-based systems, from Pig to Flink to SciDB to Spark. In this paper, we discuss how the GMQL execution environment has been developed, by going through a major version change that marked a complete system redesign; we also discuss our experiences in comparatively evaluating the four platforms.
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Notes
- 1.
http://www.bioinformatics.deib.polimi.it/gendata/, PRIN Italian National Project, 2013–2016.
- 2.
Data-Driven Genomic Computing, http://www.bioinformatics.deib.polimi.it/geco/, ERC Advanced Grant, 2016–2021.
- 3.
GeCo V2 software is available at https://github.com/DEIB-GECO/GMQL.
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Acknowledgment
This research is funded by the ERC Advanced Grant project GeCo (Data-Driven Genomic Computing), 2016–2021.
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Ceri, S., Canakoglu, A., Kaitoua, A., Masseroli, M., Pinoli, P. (2018). Experiences in the Development of a Data Management System for Genomics. In: Filipe, J., Bernardino, J., Quix, C. (eds) Data Management Technologies and Applications. DATA 2017. Communications in Computer and Information Science, vol 814. Springer, Cham. https://doi.org/10.1007/978-3-319-94809-6_10
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