Advances in big data bio analytics
File(s)1909.08254v1.pdf (359.8 KB)
Published version
Author(s)
Angelopoulos, Nicos
Wielemaker, Jan
Type
Conference Paper
Abstract
Delivering effective data analytics is of crucial importance to the interpretation of the multitude of biological datasets currently generated by an ever increasing number of high throughput techniques. Logic programming has much to offer in this area. Here, we detail advances that highlight two of the strengths of logical formalisms in developing data analytic solutions in biological settings: access to large relational databases and building analytical pipelines collecting graph information from multiple sources. We present significant advances on the bio_db package which serves biological databases as Prolog facts that can be served either by in-memory loading or via database backends. These advances include modularising the underlying architecture and the incorporation of datasets from a second organism (mouse). In addition, we introduce a number of data analytics tools that operate on these datasets and are bundled in the analysis package: bio_analytics. Emphasis in both packages is on ease of installation and use. We highlight the general architecture of our components based approach. An experimental graphical user interface via SWISH for local installation is also available. Finally, we advocate that biological data analytics is a fertile area which can drive further innovation in applied logic programming.
Date Issued
2019-09-18
Date Acceptance
2019-09-01
Citation
Electronic Proceedings in Theoretical Computer Science, 2019, 306, pp.309-322
Publisher
Open Publishing Association
Start Page
309
End Page
322
Journal / Book Title
Electronic Proceedings in Theoretical Computer Science
Volume
306
Copyright Statement
© 2019 The Author(s)
Identifier
https://arxiv.org/abs/1909.08254v1
Source
35th International Conference on Logic Programming
Subjects
cs.LO
cs.LO
cs.DB
q-bio.QM
Publication Status
Published online
Start Date
2019-09-20
Finish Date
2019-09-25
Coverage Spatial
New Mexico, USA
Date Publish Online
2019-09-19