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From a Conceptual Model to a Knowledge Graph for Genomic Datasets

  • Anna BernasconiEmail author
  • Arif Canakoglu
  • Stefano Ceri
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11788)

Abstract

Data access at genomic repositories is problematic, as data is described by heterogeneous and hardly comparable metadata. We previously introduced a unified conceptual schema, collected metadata in a single repository and provided classical search methods upon them. We here propose a new paradigm to support semantic search of integrated genomic metadata, based on the Genomic Knowledge Graph, a semantic graph of genomic terms and concepts, which combines the original information provided by each source with curated terminological content from specialized ontologies.

Commercial knowledge-assisted search is designed for transparently supporting keyword-based search without explaining inferences; in biology, inference understanding is instead critical. For this reason, we propose a graph-based visual search for data exploration; some expert users can navigate the semantic graph along the conceptual schema, enriched with simple forms of homonyms and term hierarchies, thus understanding the semantic reasoning behind query results.

Keywords

Knowledge graph Semantic search Conceptual model Data integration Genomics Next Generation Sequencing Open data 

Notes

Acknowledgement

This research is funded by the ERC Advanced Grant 693174 GeCo (Data-Driven Genomic Computing), 2016-2021.

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Dipartimento di Elettronica, Informazione e BioingegneriaPolitecnico di MilanoMilanItaly

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