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dc.contributor.authorMerrill, Emilyen_US
dc.contributor.authorCorlosquet, Stéphaneen_US
dc.contributor.authorCiccarese, Paoloen_US
dc.contributor.authorClark, Timen_US
dc.contributor.authorDas, Sudeshnaen_US
dc.date.accessioned2014-09-08T15:37:25Z
dc.date.issued2014en_US
dc.identifier.citationMerrill, Emily, Stéphane Corlosquet, Paolo Ciccarese, Tim Clark, and Sudeshna Das. 2014. “Semantic Web repositories for genomics data using the eXframe platform.” Journal of Biomedical Semantics 5 (Suppl 1): S3. doi:10.1186/2041-1480-5-S1-S3. http://dx.doi.org/10.1186/2041-1480-5-S1-S3.en
dc.identifier.issn2041-1480en
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:12785937
dc.description.abstractBackground: With 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. Methods: To 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. Conclusions: Using 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.en
dc.language.isoen_USen
dc.publisherBioMed Centralen
dc.relation.isversionofdoi:10.1186/2041-1480-5-S1-S3en
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108874/pdf/en
dash.licenseLAAen_US
dc.titleSemantic Web repositories for genomics data using the eXframe platformen
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden
dc.relation.journalJournal of Biomedical Semanticsen
dash.depositing.authorCiccarese, Paoloen_US
dc.date.available2014-09-08T15:37:25Z
dc.identifier.doi10.1186/2041-1480-5-S1-S3*
dash.contributor.affiliatedDas, Sudeshna
dash.contributor.affiliatedCiccarese, Paolo Nunzio
dash.contributor.affiliatedClark, Tim


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