@Christian_Reich: re: “Well, the first is really a dumb code: “Apparent life threatening event in infant”. How do you do analytics on that?” Term of art - think of it as “chest pain” for infants.
For additional analytic fun, what I’ll call “sociology” is keeping the diagnostic landscape interesting: ALTEs are now officially BRUEs (http://emedicine.medscape.com/article/1418765-overview). But I trust in the ability of concept_relationship to iron out the bumps between “near-SIDS”, “ALTE”, and “BRUE” and make standard analytics possible.
does not properly append to CONCEPT.csv, but rather produces a lower-case concept.csv. I thought this problem had been fixed, per this post. If I append concept.csv to CONCEPT.csv, the problems with CONCEPT_RELATIONSHIP.csv, CONCEPT_ANCESTOR.csv, and CONCEPT_SYNONYM.csv having terms that do not appear in CONCEPT.csv go away.
Ah. Regression problem. Sorry about that. Glad it works. Keep it coming.
We are still on the NDC problem, but it looks like that RxNorm made a change to prefabricated injectables (like syringes with the substance in there as powder): Instead of the concentration they provide the total amount. They provide new codes for these and proper upgrades for the old ones, but only for those that are currently prescribable. I am still finding out and will as RxNorm what’s going on. It may take a little.
We have examples of the condition codes from various site’s source data in our network that currently have a deprecated mapping in concept_relationship. Would you like us to send you our full list for your team to investigate?
I believe cpt4.jar is either broken again, or there is a problem with the server side. I downloaded the vocabulary with the default vocabularies on 6/12/2016, and got this error:
$java -jar cpt4.jar 5
Exception in thread "main" com.sun.xml.internal.ws.fault.ServerSOAPFaultException: Client received SOAP Fault from server: Java heap space Please see the server log to find more detail regarding exact cause of the failure.
at com.sun.xml.internal.ws.fault.SOAP11Fault.getProtocolException(SOAP11Fault.java:178)
at com.sun.xml.internal.ws.fault.SOAPFaultBuilder.createException(SOAPFaultBuilder.java:116)
at com.sun.xml.internal.ws.client.sei.StubHandler.readResponse(StubHandler.java:238)
at com.sun.xml.internal.ws.db.DatabindingImpl.deserializeResponse(DatabindingImpl.java:189)
at com.sun.xml.internal.ws.db.DatabindingImpl.deserializeResponse(DatabindingImpl.java:276)
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:104)
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:77)
at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(SEIStub.java:147)
at com.sun.proxy.$Proxy34.getCode(Unknown Source)
at org.odhsi.utils.cpt.Application.process(Application.java:113)
at org.odhsi.utils.cpt.Application.main(Application.java:84)
Has anyone else had this problem? It occurs on both Windows and Linux.
@Vladimir_Nikolaenko
Also, I was surprised to see that when running the cpt4.jar two times on the same data I got the 14580 CPT4 codes tacked onto the CONCEPT.csv file in a different order each time. I would recommend that it be stable from one run to the next – perhaps printing them out in the same order as they appear in CONCEPT_CPT4.csv. That way, we can readily run a diff between changing versions of vocabularies. Note: I am not 100% sure that it is not a matter of CONCEPT_CPT4.csv coming back in two different orders (sorry).