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CTS2-LE currently provides specific loaders for the below listed terminological resources. Due to the fact that file structures or entire file representations of a code system/value set may change when new versions are published, the usage of a loader is always bound to a specific terminology version. Thus, if a user wishes to import vocabulary that is not represented through a FHIR value set definition, he or she has to send a request to the contact partner at Fraunhofer FOKUS.  
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= Overview =
 +
CTS2-LE currently provides specific loaders for the below listed terminological resources. Due to the fact that file structures or entire file representations of a code system/value set may change when new versions are published, the usage of a loader is always bound to a specific terminology version. Thus, if a user wishes to import a vocabulary that is not represented through a FHIR value set definition, he or she has to send a request to the contact partner at Fraunhofer FOKUS.  
  
 
{| class="wikitable"
 
{| class="wikitable"
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! Terminology !! Version, Language !! System Intern Identifier !! Obtained from, file format  
 
! Terminology !! Version, Language !! System Intern Identifier !! Obtained from, file format  
 
|-
 
|-
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| International Classification of Diseases (ICD) || 2010, Englisch || ICD10en-v10 || [http://apps.who.int/classifications/apps/icd/ClassificationDownloadNR/login.aspx?ReturnUrl=%2fclassifications%2fapps%2ficd%2fClassificationDownload%2fdefault.aspx World Health Organization], ClaML  
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| International Classification of Diseases (ICD) || 2010, English || ICD10en-v10 || [http://apps.who.int/classifications/apps/icd/ClassificationDownloadNR/login.aspx?ReturnUrl=%2fclassifications%2fapps%2ficd%2fClassificationDownload%2fdefault.aspx World Health Organization], ClaML  
 
|-
 
|-
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| Internationale statistische Klassifikation der Krankheiten und verwandter Gesundheitsprobleme || 2013, Deutsch || ICD10de-v13 || [http://www.dimdi.de/dynamic/de/klassi/downloadcenter/icd-10-gm/vorgaenger/version2013/ Dimdi downloads], ClaML  
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| Internationale statistische Klassifikation der Krankheiten und verwandter Gesundheitsprobleme || 2013, German|| ICD10de-v13 || [http://www.dimdi.de/dynamic/de/klassi/downloadcenter/icd-10-gm/vorgaenger/version2013/ DIMDI downloads], ClaML  
 
|-
 
|-
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| Alphabetisches Verzeichnis zur ICD-10-GM || 2013, Deutsch || alphaID || [http://www.dimdi.de/dynamic/de/klassi/downloadcenter/alpha-id/vorgaenger/alphaid2013.zip Dimdi downloads], TXT (CSV)  
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| Internationale statistische Klassifikation der Krankheiten und verwandter Gesundheitsprobleme || 2015, German|| ICD10de-v15 || [http://www.dimdi.de/dynamic/de/klassi/downloadcenter/icd-10-gm/vorgaenger/version2015/ DIMDI downloads], ClaML
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|-
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| Internationale statistische Klassifikation der Krankheiten und verwandter Gesundheitsprobleme || 2016, German|| ICD10de-v16 || [http://www.dimdi.de/dynamic/de/klassi/downloadcenter/icd-10-gm/vorgaenger/version2016/ DIMDI downloads], ClaML
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|-
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| Alphabetisches Verzeichnis zur ICD-10-GM || 2013, German|| alphaID-v13 || [http://www.dimdi.de/dynamic/de/klassi/downloadcenter/alpha-id/vorgaenger/alphaid2013.zip DIMDI downloads], TXT (CSV)
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|-
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| Alphabetisches Verzeichnis zur ICD-10-GM || 2015, German|| alphaID-v15 || [http://www.dimdi.de/dynamic/de/klassi/downloadcenter/alpha-id/vorgaenger/alphaid2015.zip DIMDI downloads], TXT (CSV)
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|-
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| Alphabetisches Verzeichnis zur ICD-10-GM || 2016, German|| alphaID-v16 || [https://www.dimdi.de/dynamic/de/klassi/downloadcenter/alpha-id/vorgaenger/alphaid2016.zip DIMDI downloads], TXT (CSV)  
 
|-  
 
|-  
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| Operationen- und Prozedurenschlüssel || 2013, Deutsch || ops13 || [http://www.dimdi.de/dynamic/de/klassi/downloadcenter/ops/vorgaenger/version2013/ Dimdi downloads], ClaML  
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| Operationen- und Prozedurenschlüssel || 2013, German|| ops13 || [http://www.dimdi.de/dynamic/de/klassi/downloadcenter/ops/vorgaenger/version2013/ DIMDI downloads], ClaML  
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|-
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| Operationen- und Prozedurenschlüssel || 2015, German|| ops15 || [https://www.dimdi.de/dynamic/de/klassi/downloadcenter/ops/version2015/systematik/ DIMDI downloads], ClaML
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|-
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| Medical Subject Headings || 2012, English || mesh12 || [http://www.nlm.nih.gov/mesh/filelist.html NIH downloads] (U.S. National Library of Medicine), XML
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|-
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| Medical Subject Headings || 2014, English + additional German designations || mesh14 || [http://www.nlm.nih.gov/mesh/filelist.html NIH downloads] (U.S. National Library of Medicine), XML
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|-
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| Medical Subject Headings || 2014, German|| mesh14-de || [http://www.dimdi.de/static/de/klassi/mesh_umls/mesh/bestell.htm DIMDI downloads], XML
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|-
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| Medical Subject Headings || 2017, English|| mesh17 || [https://www.nlm.nih.gov/mesh/filelist.html NIH downloads], XML
 
|-
 
|-
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| Medical Subject Headings || 2014, Englisch || mesh14 || [http://www.nlm.nih.gov/mesh/filelist.html NIH downloads] (U.S. National Library of Medicine), XML  
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<!--| Medical Subject Headings Supplementary || 2014, English || meshSupp14|| [http://www.nlm.nih.gov/mesh/filelist.html NIH downloads] (U.S. National Library of Medicine), XML  
 
|-
 
|-
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| Medical Subject Headings || 2014, Deutsch || mesh14-de || [http://www.dimdi.de/static/de/klassi/mesh_umls/mesh/bestell.htm Dimdi downloads], XML
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| HL7-v3- and FHIR- value sets || 2013, English || hl7-fhir  || [http://www.hl7.org/implement/standards/fhir/downloads.html FHIR downloads] (Health Level Seven - FHIR V0.12), XML
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|- -->
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| Anatomisch Therapeutisch Chemische Klassifikation mit definierten Tagesdosen (ATC DDD) || 2013, German|| ATC_DDD_v13 || [http://wido.de/amtl_atc-code.html WiDO downloads] (Wissenschaftliches Institut der AOK), XML
 
|-
 
|-
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| HL7-v3- and FHIR- value sets || 2013, Englisch || hl7-fhir  || [http://www.hl7.org/implement/standards/fhir/downloads.html FHIR downloads] (Health Level Seven - FHIR V0.12), XML
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| Anatomisch Therapeutisch Chemische Klassifikation mit definierten Tagesdosen (ATC DDD) || 2015, German|| ATC_DDD_v15 || [http://wido.de/amtl_atc-code.html WiDO downloads] (Wissenschaftliches Institut der AOK), XML
 
|-
 
|-
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| Anatomisch Therapeutisch Chemische Klassifikation || 2015, Deutsch || ATC_DDD_v15 || [http://wido.de/amtl_atc-code.html WiDO downloads] (Wissenschaftliches Institut der AOK), XML
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| Unified Code for Units of Measure || 2013, English || ucum || [http://unitsofmeasure.org/trac/ UCUM downloads], TSV
 
|-
 
|-
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| Unified Code for Units of Measure || 2013, Englisch || ucum || [http://unitsofmeasure.org/trac/ UCUM downloads], TSV
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| Logical Observation Identifiers Names and Codes || 2.44, English || loinc || [https://loinc.org/downloads/accessory-files LOINC downloads] (Regenstrief Institute, Inc.), XML
 
|-
 
|-
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| Logical Observation Identifiers Names and Codes || 2.44, Englisch || loinc || [https://loinc.org/downloads/accessory-files LOINC downloads] (Regenstrief Institute, Inc.), XML
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| SNOMED CT || 2015, English || snomed || [http://www.ihtsdo.org/ IHTSDO (International Health Terminology Standards Development Organisation)]
 
|-
 
|-
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| SNOMED CT || 2015, Englisch || snomed || [http://www.ihtsdo.org/ IHTSDO (International Health Terminology Standards Development Organisation)]
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| PathLex || 2015, English || pathlex || [http://bioportal.bioontology.org/ontologies/PATHLEX Anatomic Pathology Lexicon], OWL/RDF
 
|-
 
|-
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| PathLex || 2015, Englisch || pathlex || [http://bioportal.bioontology.org/ontologies/PATHLEX Anatomic Pathology Lexicon], OWL/RDF
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| Bundeslebensmittelschlüssel || 3.02 , German + English || bls|| [https://www.mri.bund.de/de/service/datenbanken/bundeslebensmittelschluessel/ Max Rubner Institut], TXT
 
|}
 
|}
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= Activating a Loader =
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This section refers to some notations (e.g. <code>'''''<H>'''''</code>) that were introduced in the [[Installation and Setup V2|Installation and Setup Guide]].
 +
<ol>
 +
<li> Ensure that the server is not running </li>
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<li> Open <code>'''''<H>'''''\CTS2LE_resources\resources-custom\cts2_conf.xml</code> </li>
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Example cts2_conf.xml file
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<syntaxhighlight lang="xml">
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<conf>
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<vocabularies loadAll="false" fresh="false" index="false" sigCheck="false">
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<vocabulary load="true" friendly-name="Example code system" resourceID="exa"/>
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</vocabularies>
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</conf>
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</syntaxhighlight>
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<li>Adapt the following attributes according to your needs; i.e. fill in '''true''' to enable the described behaviour:</li>
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* attributes of the <code><vocabularies></code>-element
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** '''loadAll''': load all vocabularies stated by means of the child <code><vocabulary></code> elements
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** '''fresh''': discards the entire store content before loading
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** '''index''': build an index based on concept designations
 +
** '''sigCheck''': check the integrated vocabularies for schema conformance
 +
 +
* attribute of individual <code><vocabulary></code> elements
 +
** '''load''': load the respective vocabulary
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** '''friendly-name''': is the human readable name for a terminology - changing the value of this attribute will not have any effect at all
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** '''resourceID''': is a system intern identifier for the terminology;  <span style="color:red">must not be changed</span>
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<li> Save the file</li>
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<li> Change to directory '''''<H>'''''</li>
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<li> - On Windows: Run <code>bin\SuperLoader.bat</code> <br> - On Linux: Run <code>./bin/SuperLoader.sh</code></li>
 +
</ol>

Aktuelle Version vom 2. Oktober 2017, 09:22 Uhr

Overview

CTS2-LE currently provides specific loaders for the below listed terminological resources. Due to the fact that file structures or entire file representations of a code system/value set may change when new versions are published, the usage of a loader is always bound to a specific terminology version. Thus, if a user wishes to import a vocabulary that is not represented through a FHIR value set definition, he or she has to send a request to the contact partner at Fraunhofer FOKUS.

Terminology Version, Language System Intern Identifier Obtained from, file format
International Classification of Diseases (ICD) 2010, English ICD10en-v10 World Health Organization, ClaML
Internationale statistische Klassifikation der Krankheiten und verwandter Gesundheitsprobleme 2013, German ICD10de-v13 DIMDI downloads, ClaML
Internationale statistische Klassifikation der Krankheiten und verwandter Gesundheitsprobleme 2015, German ICD10de-v15 DIMDI downloads, ClaML
Internationale statistische Klassifikation der Krankheiten und verwandter Gesundheitsprobleme 2016, German ICD10de-v16 DIMDI downloads, ClaML
Alphabetisches Verzeichnis zur ICD-10-GM 2013, German alphaID-v13 DIMDI downloads, TXT (CSV)
Alphabetisches Verzeichnis zur ICD-10-GM 2015, German alphaID-v15 DIMDI downloads, TXT (CSV)
Alphabetisches Verzeichnis zur ICD-10-GM 2016, German alphaID-v16 DIMDI downloads, TXT (CSV)
Operationen- und Prozedurenschlüssel 2013, German ops13 DIMDI downloads, ClaML
Operationen- und Prozedurenschlüssel 2015, German ops15 DIMDI downloads, ClaML
Medical Subject Headings 2012, English mesh12 NIH downloads (U.S. National Library of Medicine), XML
Medical Subject Headings 2014, English + additional German designations mesh14 NIH downloads (U.S. National Library of Medicine), XML
Medical Subject Headings 2014, German mesh14-de DIMDI downloads, XML
Medical Subject Headings 2017, English mesh17 NIH downloads, XML
Anatomisch Therapeutisch Chemische Klassifikation mit definierten Tagesdosen (ATC DDD) 2013, German ATC_DDD_v13 WiDO downloads (Wissenschaftliches Institut der AOK), XML
Anatomisch Therapeutisch Chemische Klassifikation mit definierten Tagesdosen (ATC DDD) 2015, German ATC_DDD_v15 WiDO downloads (Wissenschaftliches Institut der AOK), XML
Unified Code for Units of Measure 2013, English ucum UCUM downloads, TSV
Logical Observation Identifiers Names and Codes 2.44, English loinc LOINC downloads (Regenstrief Institute, Inc.), XML
SNOMED CT 2015, English snomed IHTSDO (International Health Terminology Standards Development Organisation)
PathLex 2015, English pathlex Anatomic Pathology Lexicon, OWL/RDF
Bundeslebensmittelschlüssel 3.02 , German + English bls Max Rubner Institut, TXT

Activating a Loader

This section refers to some notations (e.g. <H>) that were introduced in the Installation and Setup Guide.

  1. Ensure that the server is not running
  2. Open <H>\CTS2LE_resources\resources-custom\cts2_conf.xml
    3. Example cts2_conf.xml file 
    <conf>	
 <vocabularies loadAll="false" fresh="false" index="false" sigCheck="false">
	 <vocabulary load="true" friendly-name="Example code system" resourceID="exa"/>
 </vocabularies>
</conf>
  3. Adapt the following attributes according to your needs; i.e. fill in true to enable the described behaviour:
    • attributes of the <vocabularies>-element
      • loadAll: load all vocabularies stated by means of the child <vocabulary> elements
      • fresh: discards the entire store content before loading
      • index: build an index based on concept designations
      • sigCheck: check the integrated vocabularies for schema conformance
    • attribute of individual <vocabulary> elements
      • load: load the respective vocabulary
      • friendly-name: is the human readable name for a terminology - changing the value of this attribute will not have any effect at all
      • resourceID: is a system intern identifier for the terminology; must not be changed
  4. Save the file
  5. Change to directory <H>
  6. - On Windows: Run bin\SuperLoader.bat
    - On Linux: Run ./bin/SuperLoader.sh
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