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dicom2rdf ========= Author: Michael Brunnbauer, Bonubase GmbH (www.bonubase.com) The author's email address is email@example.com This is free software, see the file LICENCE for details dicom2rdf.py generates RDF/XML files from metadata found in DICOM files (.dcm) DICOM = Digital Imaging and Communications in Medicine http://dicom.nema.org/ dicom2rdf.py needs Python 2.x and the following Python modules: pydicom: http://code.google.com/p/pydicom/ rdflib: https://github.com/RDFLib Usage ----- $ ./dicom2rdf.py file1.dcm file2.dcm file3.dcm ... Will generate file1.rdf file2.rdf file3.rdf ... We strongly recommend to: 1) De-identify DICOM files before conversion. 2) Not making the resulting triples public (for example by publishing the RDF/XML files on the web or operating an open SPARQL endpoint). Ontology / Namespace -------------------- The ontology used can be found at http://purl.org/healthcarevocab/v1 It has been generated by the program found in the directory gen_ontology. See http://purl.org/healthcarevocab/v1help for an explanation of the basic concepts of the ontology. The source files containing dictionaries have been generated from the DICOM standard by the parsers found in gen_source. Warnings -------- A warning of the form SOP Class 1.2.840.10008... not found means that dicom2rdf does not know what IOD is assigned to the given SOP Class UID. The list defined in sopclasses.py is still incomplete. All Attributes in this information object will be related to the information object instead of the correct information entities. Please search for the UID in PS 3.4 of the DICOM standard: http://medical.nema.org/Dicom/2011/11_04pu.pdf Then search for the IOD name in iods.py, add the assignment to sopclasses.py and give us a note. A Warning of the form IE ... not in IOD for ... means that an attribute was used in an information object that is not defined in the corresponding information object definition. This warning is caused by non standard conformant DICOM files or an irregularity in our parsing of PS 3.3. URI creation ------------ -Every dataset having a SOP Instance UID will get a urn:oid: URI with that UID -Every Study, Series or Frame of Reference with a UID will also get a urn:oid: URI -Every other entity will get a generated hash URI relative to the created RDF/XML document Triples generated ----------------- -A URI will be created for the DICOM file with the filename as rdfs:label and dcterms:format http://purl.org/NET/mediatypes/application/dicom Triples will be added for the Attributes that pydicom has identified as relating to the DICOM file. -A URI will be determined or created for the main information object which is asserted to be in the class corresponding to its SOP Class UID (a urn:oid URI for the class is generated from the SOP Class UID). -For every attribute in the current information object, the information entity it relates to according to the information object definition is determined. A URI is determined or created for this IE and membership in the corresponding IE class is asserted. If the information entity cannot be determined unambiguously, the subject of the triple will be the information object itself. The information object will be connected to the information entities with dcterms:subject. -For every item in a sequence, a URI will be determined or created and the attributes for that item relate to the item by default. If the item is an information object, attributes can relate to an information entity instead like with the main information object. -Extra triples may be generated using other ontologies, e.G. with foaf:familyName and foaf:givenName for components of the PN VR.