Semantic Web repositories for genomics data using the eXframe platform

Abstract

BackgroundWith the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well as the number of databases in which it is stored. In these databases, sample annotation using ontologies and controlled vocabularies is becoming more common. However, the annotation is rarely available as Linked Data, in a machine-readable format, or for standardized queries using SPARQL. This makes large-scale reuse, or integration with other knowledge bases very difficult.MethodsTo address this challenge, we have developed the second generation of our eXframe platform, a reusable framework for creating online repositories of genomics experiments. This second generation model now publishes Semantic Web data. To accomplish this, we created an experiment model that covers provenance, citations, external links, assays, biomaterials used in the experiment, and the data collected during the process. The elements of our model are mapped to classes and properties from various established biomedical ontologies. Resource Description Framework (RDF) data is automatically produced using these mappings and indexed in an RDF store with a built-in Sparql Protocol and RDF Query Language (SPARQL) endpoint.ConclusionsUsing the open-source eXframe software, institutions and laboratories can create Semantic Web repositories of their experiments, integrate it with heterogeneous resources and make it interoperable with the vast Semantic Web of biomedical knowledge.

Harnessing Big Data for Systems Pharmacology

“…For example, BioGateway uses the semantic web to integrate the OBO foundry ontology, Gene Ontology, NCBI taxonomy, and UniProt (78). eXFrame provides a reusable framework for creating semantic web repositories of genomics experiments (79). Bio2RDF release 2 links 19 datasets (80).…”

Knowledge Representation and Management: a Linked Data Perspective

“…Both RDF and ontologies are used in two particular cases, viii and xi. In the first one, data from Bio2RDF platform is used as well as NIF Standard ontology (NIF-STD), NCI Thesaurus (NCI), Gene Regulation Ontology (GRO), SemanticScience Integrated Ontology (SIO) Cases, 2014 [33] Hettne, 2014 [34] Navas¬Delgado, 2015 [35] Davies, 2015 [36] Personeni, 2014 [37] Bertel¬Paternina, 2014 [38] Mina, 2015 [39] Merrill, 2014 [40] Ranzinger, 2015 [41] Hoehndhorf, 2015 [42] Wolstencroft, 2015 [43] Kawano, 2014 [44] Rebholz¬Schuhmann, 2014 [45] and Sequence Ontology (SO). The former, a bio-ontology repository, used several ontologies and RDF data to create the platform.…”

Selected papers from the 16th Annual Bio-Ontologies Special Interest Group Meeting

“…The six papers selected for this supplement are extended versions of the original papers and flash updates presented at the 2013 SIG. The papers include research on such classic but nevertheless crucially important problems as ontology-based data integration [ 1 - 3 ], ontology-based annotation of scientific literature [ 1 - 4 ], ontology and data model development [ 2 , 3 , 5 ], representation of scientific results [ 5 ] and gene candidate prediction [ 6 ].…”

“…Merrill et al in their paper "Semantic Web repositories for genomics data using the eXframe platform" addresses the critical task of the integration of genomic databases and data re-use [ 3 ]. They developed the second generation of the eXframe platform that supports the creation of online repositories to deposit genomics data as Linked Data.…”