About

Features

• Support for operations:
  • empty graph,
  • import RDF files to the graph,
  • extract meta data into the graph,
  • export RDF data from the graph,
  • and query RDF data using SPARQL.
• Sequential operations processing. You can activate one or more operations by selecting command line options.
• Extract meta data from selected files or the whole input data directories or files recursively.
• Use a file with the list of input data files which enable you to select files for meta data extraction. Each file's (absolute or relative) path on a one row.
• Graph can be stored:
  • in-memory only,
  • in-memory, but always automatically backed from/to specified file system root directory (Note: If graph in file system exists it is loaded into the memory automatically and before application exit it is stored back to the file system. The store/load delay is significant with a large graph.),
  • in OpenLink Virtuoso OpenSource database.
• Export an application built-in prefix map into a text file.
• Set the graph name.
• Empty the the graph.
• Can print the graph size automatically before and after operations.
• Import RDF files(s) to the graph.
• Import GZipped RDF files is possible with all data stores. MetaMed will gunzip file when reading.
• Set the directory with SPARQL files. One query per file with prefixes or without them when known to MetaMed. All queries will be automatically extended with build-in prefixes and processed.
• Select output format for all queries.
• Export an application built-in prefix map into a text file.
• Export the whole RDF graph to a file with specified RDF serialization.
• Merge RDF files – using import and export options (e.g. with in-memory graph).
• Use this tool for RDF serialization conversion (e.g. with in-memory graph, you can use export RDF graph property).
• Plugable file format support for extractors. You can implement own plugins with support for other file formats.
• Parallel data processing - you can set number of threads for:
  • meta data extraction
  • querying data by SPARQL
  • graph export (when extracted by more threads)
• Configuration file order:
  • user specific ~/.mre/connection.properties.
  • or system configuration in the /etc/mre/connection.properties files.
  • specify your own file by -virt argument.
• The file connection.properties content looks like:

          url=jdbc:virtuoso://localhost:1111
          user=username
          password=password
          graph=https://mre.zcu.cz/dataset/example

  Property graph is the default graph name. It is used when connecting/opening graph. You can change used graph by --graph argument.

Input and output format support

Implemented support of file formats:

• DASTA – DAta STAndard (the Czech language only) is national standard for medical data by Ministry of Health of the Czech Republic,
• HL7 – Health Level Seven (HL7) – partial/development support only, because (still) it is not a national standard in the Czech Republic.
• DICOM – Digital Imaging and Communications in Medicine,
• Stroke data – our internal XML format for diagnostic data and treatment results during three months after the stroke incident,
• PNG – Portable Network Graphics
• JFIF/JPEG – JPEG File Interchange Format/Joint Photographic Experts Group
• TIFF – Tag Image File Format

RDF serialization formats support:

• RDF/XML,
• RDF/XML-ABBREV,
• TURTLE,
• N3,
• N-TRIPLE.

Supported (query) output formats:

• text,
• csv, tsv,
• rdf,
• sse,
• json,
• xml and xmlstring.

SPARQL is supported for RDF data queries.