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Posted to user@ctakes.apache.org by David Kincaid <ki...@gmail.com> on 2014/12/27 04:47:46 UTC

DrugNER working?

Is the ctakes-drug-ner AE supposed to be working in the newest versions of
cTakes (3.2.x)? I'm getting the following error and confirm that that
TypeSystem.xml doesn't exist anywhere.

Has ctakes-drug-ner been supersceded by something else?


InvalidXMLException An import could not be resolved.  No .xml file with
name "org.apache.ctakes.drugner.types.TypeSystem" was found in the class
path or data path. (Descriptor:
file:/home/davek/apps/apache-ctakes-3.2.1/desc/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml)


Thanks,

Dave

Re: DrugNER working?

Posted by David Kincaid <ki...@gmail.com>.

Thanks, Pei. I was able to get it working by including the
org.apache.ctakes/ctakes-drug-ner library in my project. But the accuracy
isn't anywhere near where I would need it to be, so I'm looking at other
options. Has anyone tried integrating MedXN with cTAKES? MedXN performs
extremely well on the handful of test medical notes that I ran it on.

Thanks,

Dave

On Wed, Dec 31, 2014 at 10:13 AM, Pei Chen <ch...@apache.org> wrote:

> Dave,
> There was a related email one [1].
> Essentially, you shouldn't need a secondary/redundant lookup window and
> dictionary.  It should just iterate through all of the Medications
> previously identified by the Dictionary Lookup Component.
> See sample config [2] in how to add that to your existing pipeline.  Let
> us know if that works for you.
>
> [1]
> http://mail-archives.apache.org/mod_mbox/ctakes-dev/201412.mbox/%3c924DE05C19409B438EB81DE683A942D916DB2493@CHEXMBX1A.CHBOSTON.ORG%3e
> [2]
> https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml
>
> On Fri, Dec 26, 2014 at 10:47 PM, David Kincaid <ki...@gmail.com>
> wrote:
>
>> Is the ctakes-drug-ner AE supposed to be working in the newest versions
>> of cTakes (3.2.x)? I'm getting the following error and confirm that that
>> TypeSystem.xml doesn't exist anywhere.
>>
>> Has ctakes-drug-ner been supersceded by something else?
>>
>>
>> InvalidXMLException An import could not be resolved.  No .xml file with
>> name "org.apache.ctakes.drugner.types.TypeSystem" was found in the class
>> path or data path. (Descriptor:
>> file:/home/davek/apps/apache-ctakes-3.2.1/desc/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml)
>>
>>
>> Thanks,
>>
>> Dave
>>
>
>

Re: DrugNER working?

Posted by Pei Chen <ch...@apache.org>.

Dave,
There was a related email one [1].
Essentially, you shouldn't need a secondary/redundant lookup window and
dictionary.  It should just iterate through all of the Medications
previously identified by the Dictionary Lookup Component.
See sample config [2] in how to add that to your existing pipeline.  Let us
know if that works for you.

[1]
http://mail-archives.apache.org/mod_mbox/ctakes-dev/201412.mbox/%3c924DE05C19409B438EB81DE683A942D916DB2493@CHEXMBX1A.CHBOSTON.ORG%3e
[2]
https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml

On Fri, Dec 26, 2014 at 10:47 PM, David Kincaid <ki...@gmail.com>
wrote:

> Is the ctakes-drug-ner AE supposed to be working in the newest versions of
> cTakes (3.2.x)? I'm getting the following error and confirm that that
> TypeSystem.xml doesn't exist anywhere.
>
> Has ctakes-drug-ner been supersceded by something else?
>
>
> InvalidXMLException An import could not be resolved.  No .xml file with
> name "org.apache.ctakes.drugner.types.TypeSystem" was found in the class
> path or data path. (Descriptor:
> file:/home/davek/apps/apache-ctakes-3.2.1/desc/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml)
>
>
> Thanks,
>
> Dave
>