CTS2-LE Supported Terminologies - Versionsgeschichte

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@@ Zeile 170: / Zeile 170: @@
 </ul>
 <h3 id="note">Note</h3>
-<p>Depending on the kubernetes settings, a timeout ca occur. Nevertheless, the loading process is started and can be observed in the container logs. Future versions could introduce a task-concept for such purposes.</p>
+<p>Depending on the kubernetes settings, a timeout can occur. Nevertheless, the loading process is started and can be observed in the container logs. Future versions could introduce a task-concept for such purposes.</p>
 <p>Afterwards an update of the suggester (used by the navigator) has to be performed:</p>
 <ul>

@@ Zeile 93: / Zeile 93: @@
 <p>downloads all to the directory <code>packages</code> (call <code>./download.sh --help</code> for details).</p>
 <h4 id="structure">Structure</h4>
-<p>The packages downloaded from bfarm must be located in a dedicated directory (e.g. <code>bfarm</code> as <strong>LD</strong>). The following structure is an example for two packages (ICDGM, OPS).</p>
+<p>The directory <code>packages</code> downloaded from bfarm must be located in a dedicated directory (e.g. <code>bfarm</code> as <strong>LD</strong>). The following structure is an example for two packages (ICDGM, OPS).</p>
 <pre>
 bfarm
@@ Zeile 175: / Zeile 175: @@
 <li>HTTP GET <code>&lt;host-cts2le&gt;/WebCts2LE/service/manage/index/suggester/update</code></li>
 </ul>
-<h2 id="notes">Notes</h2>
+<h2 id="metrics">Metrics</h2>
 <h3 id="removal">Removal</h3>
 <p>Removal time is nearly equal load time due to the RDF store. It is recommended that the terminology is not present in the store beforehand. The following numbers assume an empty store.</p>

@@ Zeile 3: / Zeile 3: @@
 <p>To load a standard terminology the customer has to copy the input files to a dedicated directory (called <strong>LD</strong> in the following) together with a specification json file (<strong>SF</strong>). In context of docker, kubernetes etc. a dedicated volume should be used. To avoid inconsistencies, services should not be accessed during load.</p>
 <h2 id="terminology-directory-ld">Terminology Directory (<strong>LD</strong>)</h2>
-<p>Directory <strong>LD</strong> contains all files required for a specific standard terminology. There should be a separate directory for each terminology (currently Snomed, Loinc, Mesh, and BfArM).</p>
+<p>A dedicated directory, called <strong>LD</strong> in the following, contains all files required for a specific standard terminology or terminology packet. There should be a separate directory for each, currently Snomed, Loinc, Mesh, and BfArM.</p>
 <p>The deployment for Kubernetes provides an extra volume with the path</p>
 <ul>
 <li><code>/etc/webcts2le/inst/terminologies</code></li>
 </ul>
-<p>Subdirectories within this path should be used for <strong>LD</strong>, which is specified when starting the load (see [[#rest-interface|REST interface for loading]]).</p>
+<p>Subdirectories prefixed with this path should be used for <strong>LD</strong>, which is specified when starting the load (see [[#rest-interface|REST interface for loading]]).</p>
 <h2 id="standard-terminologies">Standard Terminologies</h2>
 <h3 id="specification-file-sf">Specification File (<strong>SF</strong>)</h3>
@@ Zeile 52: / Zeile 52: @@
      "groupName": "loinc-tree",
      "resourceId": "Loinc-2.80",
-     // defines the corr. display name
+     // defines the corr. display language
      "defaultLanguage" : "de",
      // the following linguistic variants must be exist at directory 'AccessoryFiles/LinguisticVariants',
@@ Zeile 139: / Zeile 139: @@
 <li>this filter loads only packages whose <em>canonical package name</em> conforms to <code>&lt;regex&gt;</code>. The <em>canonical package name</em> ist defined as the form <code>&lt;name&gt;|&lt;version&gt;</code> where <code>name</code> and <code>version</code> are the properties in the package definition file
 <ul>
-<li><code>bfarm/packages/bfarm.terminologien.icd10gm-2025.0.0.tar.gz/package/package.json</code> (see section Packages above).</li>
+<li><code>bfarm/packages/bfarm.terminologien.icd10gm-2025.0.0.tar.gz/package/package.json</code> (see section [[#packages|Packages]] above).</li>
 <li>E.g., regex <code>.*(icd10gm\\|2025|ops\\|2025).*</code> will only load the ICD and OPS package.</li>
 </ul>
@@ Zeile 177: / Zeile 177: @@
 <h2 id="notes">Notes</h2>
 <h3 id="removal">Removal</h3>
-<p>Removal time is nearly equal load time due to the RDF store. It is recommended that the terminology is not present in the store beforehand.</p>
+<p>Removal time is nearly equal load time due to the RDF store. It is recommended that the terminology is not present in the store beforehand. The following numbers assume an empty store.</p>
 <h3 id="loading-time">Loading Time</h3>
 <p>Due to used RDF quad store technology, the loading time (i.e. 'weaving' the RDF-triple knowledge graph based on the flat files) on e.g. openshift is</p>

@@ Zeile 80: / Zeile 80: @@
 </syntaxhighlight>
 <h2 id="bfarm-terminologies">BfArM Terminologies</h2>
-<p>BfArM (Bundesinstitut für Arzneimittel und Medizinprodukte) provides the standard terminologies for Germany. To load these standard terminologies the customer has to create a dedicated directory (called <strong>LD</strong> in the following) together with a specification json file (<strong>SF</strong>). In context of docker, kubernetes etc. a dedicated volume should be used.</p>
+<p>BfArM (Bundesinstitut für Arzneimittel und Medizinprodukte) provides the standard terminologies for Germany.</p>
 <h3 id="packages">Packages</h3>
-<p>The packages downloaded from bfarm must be located in a dedicated directory (e.g. <code>bfarm</code>). The following structure is an example for two packages (ICDGM, OPS).</p>
+<p>To download these terminologies, the</p>
 <pre>
 bfarm
@@ Zeile 95: / Zeile 106: @@
 |_ fhir-packs.jsonc
 </pre>
 <h3 id="specification-file-sf-1">Specification File (<strong>SF</strong>)</h3>
-<p>for BfArM terminologies, the following specification file is used.</p>
+<p>For BfArM terminologies, the following specification file is used.</p>
 <syntaxhighlight lang="json" line>
+{
@@ Zeile 178: / Zeile 190: @@
 <p>It is a known restriction for quad stores that loading time is high compared to other nosql data stores. On the other hand it offers elaborated functionality based on semantic web technologies. Future versions of CTS2-LE could utilize nosql data stores.</p>
 <h3 id="disk-space">Disk Space</h3>
-<p>Initially, the following disk space (per container) is occupied for the complete terminology set</p>
+<p>The following disk space (per container) is occupied for the complete terminology set after loading</p>
 <ul>
 <li><em>cts2le</em>: ~3 GB</li>

@@ Zeile 144: / Zeile 144: @@
 <p>In this example only the terminologies for age rejection and the exotic one of the ICD as well as the one-time codes of the OPS package will be loaded.</p>
 <h2 id="rest-interface">REST interface</h2>
-<pre>
+<ul>
-GET HOST/WebCts2LE/service/crud/bulk/load-std-terminology
+<li>HTTP GET <code>&lt;host-cts2le&gt;/WebCts2LE/service/crud/bulk/load-std-terminology</code></li>
-</pre>
+</ul>
 <h3 id="query-parameters">Query Parameters</h3>
 <ul>
@@ Zeile 153: / Zeile 154: @@
 </ul>
 <h3 id="example-1">Example</h3>
-<pre>
+<ul>
-GET HOST/WebCts2LE/service/crud/bulk/load-std-terminology?directory=/etc/webcts2le/inst/terminologies/loinc&loadSpec=load-spec-2.80.json
+<li>HTTP GET <code>&lt;host-cts2le&gt;/WebCts2LE/service/crud/bulk/load-std-terminology?directory=/etc/webcts2le/inst/terminologies/loinc&amp;loadSpec=load-spec-2.80.json</code></li>
-</pre>
+</ul>
 <h3 id="note">Note</h3>
 <p>Afterwards an update of the suggester (used by the navigator) has to be performed:</p>
-<pre>
+<ul>
-GET HOST/WebCts2LE/service/manage/index/suggester/update
+<li>HTTP GET <code>&lt;host-cts2le&gt;/WebCts2LE/service/manage/index/suggester/update</code></li>
-</pre>
+</ul>
 <h2 id="notes">Notes</h2>
 <h3 id="removal">Removal</h3>
 <p>Removal time is nearly equal load time due to the RDF store. It is recommended that the terminology is not present in the store beforehand.</p>
 <h3 id="loading-time">Loading Time</h3>
-<p>Due to used RDF quad store technology the loading time (i.e. 'weaving' the RDF-triple knowledge graph based on the flat files) on a notebook (~2 GHz throttled, 16 GB RAM) is:</p>
+<p>Due to used RDF quad store technology, the loading time (i.e. 'weaving' the RDF-triple knowledge graph based on the flat files) on e.g. openshift is</p>
 <ul>
-<li>Smomed: ~90 min</li>
+<li>Smomed: ~15 min</li>
-<li>Loinc: ~45 min</li>
+<li>Loinc: ~9 min</li>
-<li>MeSH: ~15 min</li>
+<li>MeSH: ~7 min</li>
 </ul>
-<p>It is recommended in the context of docker, kubernetes, etc. to define high CPU/RAM resources for the <em>fuseki</em> container to decrease loading time.</p>
+<p>(CPU ~2.7 GHz (cat /proc/cpuinfo); OS UI POD metrics: ~7.6 GB used memory)</p>
 <p>It is a known restriction for quad stores that loading time is high compared to other nosql data stores. On the other hand it offers elaborated functionality based on semantic web technologies. Future versions of CTS2-LE could utilize nosql data stores.</p>
-<h3 id="database-space">Database Space</h3>
+<h3 id="disk-space">Disk Space</h3>
-<p>Quad stores usually occupies huge space on disk because every quad is indexed. E.g. Snomed has ~18.000.000 quads and the quad store <em>fuseki</em> can occupies ~50 GB after loading. But <em>fuseki</em> offers a compaction of the database to ~8 GB with the call</p>
+<p>Initially, the following disk space (per container) is occupied for the complete terminology set</p>
 <pre>
-curl --request POST --url 'http://localhost:3030/$/compact/cts2le?deleteOld=true'
+curl --request POST --url 'http://fuseki:3030/$/compact/cts2le?deleteOld=true'
 </pre>
+<p>For details, please visit <code>https://jena.apache.org/documentation/fuseki2/fuseki-server-protocol.html#compact</code> or contact the Fhg Fokus team.</p>

@@ Zeile 48: / Zeile 48: @@
 GET <HOST>/WebCts2LE/service/crud/bulk/load-std-terminology?directory=terminologies/loinc&loadSpec=load-spec-2.71.json
 </pre>
-<h2 id="supported-terminologies">Supported Terminologies</h2>
+<h1 id="supported-terminologies">Supported Terminologies</h1>
 <pre>
+{
@@ Zeile 126: / Zeile 126: @@
+}
 </pre>
-<h2 id="notes">Notes</h2>
+<h1 id="notes">Notes</h1>
 <h2 id="removal">Removal</h2>
 <p>Removal time is nearly equal load time. It is recommended that the terminology is not contained in the store.</p>

@@ Zeile 12: / Zeile 12: @@
 </li>
 </ul>
-<h2 id="1-specification-file-sf">1. Specification File (<strong>SF</strong>)</h2>
+<h2 id="specification-file-sf">Specification File (<strong>SF</strong>)</h2>
 <pre>
+{
@@ Zeile 30: / Zeile 30: @@
 </pre>
 <p>!!! In case of designator <code>hl7Fhir</code> the version, groupName and resourceId property is defined by the standard itself and defining these properties has no effect.</p>
-<h2 id="2-rest-interface">2. REST interface</h2>
+<h2 id="rest-interface">REST interface</h2>
 <pre>
 GET <HOST>/WebCts2LE/service/crud/bulk/load-std-terminology
@@ Zeile 48: / Zeile 48: @@
 GET <HOST>/WebCts2LE/service/crud/bulk/load-std-terminology?directory=terminologies/loinc&loadSpec=load-spec-2.71.json
 </pre>
-<h2 id="3-supported-terminologies">3. Supported Terminologies</h2>
+<h2 id="supported-terminologies">Supported Terminologies</h2>
 <pre>
+{

← Nächstältere Version		Version vom 18. Januar 2022, 17:02 Uhr
Zeile 1:		Zeile 1:
−	Many widely used terminologies are only available in a proprietary format and therefore need specific loaders that map this proprietary format onto the CTS2 data model. This section lists the '''main''' terminologies which are recently supported.	+	Many widely used terminologies are only available in a proprietary format and therefore need specific loaders that map this proprietary format onto the FHIR/CTS2 data model. This section lists the '''main''' terminologies which are recently supported.

	CTS2-LE currently provides specific loaders for the following terminologies:		CTS2-LE currently provides specific loaders for the following terminologies: