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Deliverable Report D3.2 Data Management System with extended search capabilities

Nina Jeliazkova, Nikolay Kochev, Vedrin Jeliazkov, Micha Rautenberg, Egon Willighagen, Friederike Ehrhart, Penny Nymark, Barry Hardy

The eNanoMapper prototype database, described in the eNanoMapper report “Technical specification and initial implementation of the protocol and data management web services” (2015), was extended with new search functionality: chemically-aware search, several options for searching experimental data, semantic search including SPARQL endpoint free text search, supported by eNanoMapper ontology and annotated database entries. The types of the new queries are informed by the list of scientific questions identified through the requirements analysis and during the eNanoMapper ontology working meetings. Test and public instances of the prototype database are available at http://apps.ideaconsult.net/enmtest and http://data.enanomapper.net respectively. The data content of http://data.enanomapper.net has been updated. The configurable parser, enabling the import of data stored in spreadsheet templates, was enhanced with new capabilities. ISA-Tab import and export implementation is ongoing, based on a new version of the ISA-Tab specification with JSON schemas, published by the ISA team at the University of Oxford e-Research Centre. The schema and code for parsing and generation of ISA files are under active development and available on GitHub, including an ISA-Nano extension developed by eNanoMapper work supporting database develoment. The database Application Programming Interface (API) and search functionality are used by visualization (JavaScript) and modelling (R) packages, described in this report. The database API and content is also being used by the modelling prototype, currently under development within eNanoMapper.

http://www.enanomapper.net/deliverables/d3/20160420_eNanoMapper_D3.2_Data_Management_System_with_extended_search_capabilities_FINAL.pdf
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