Glad you got it running. Part of the SHARP initiative was to standardize/normalize the type systems used in medical annotations.
http://www.healthit.gov/policy-researchers-implementers/strategic-health-it-advanced-research-projects-sharp Regarding your second question I am not sure I understand your workaround scenario. I suggest you repost your question to the cTAKES community again to see if they can provide an answer. Thanks. Sent from my iPhone On Mar 12, 2014, at 8:40 AM, "ravi garg" <[email protected]<mailto:[email protected]>> wrote: Hey, I have got it working now. But I wanted to know, just out of curiosity, why to remove all the drugner typesystem annotations. Also can you please let me know if there is any workaround to get all the annotations from the plain text in one output.xml file. Regards, Ravi On Tue, Mar 11, 2014 at 10:21 PM, ravi garg <[email protected]<mailto:[email protected]>> wrote: Hey, Thanks I will look in to it and let you know if I run into any trouble. Thank you once again for the help. On Tue, Mar 11, 2014 at 9:54 PM, Murphy, Sean P. <[email protected]<mailto:[email protected]>> wrote: The source code containing the lines to be modified are in ctakes-drug-ner\src\main\java\org\apache\ctakes\drugner\ae\DrugMentionAnnotator.java . I had it backwards in that the lines need to be commented out to enable the annotations to be generated again. Specifically, lines ~ 275 to 290 have the actual types that can be commented out to be included (e.g. org.apache.ctakes.drugner.type.SubSectionAnnotation.type is already commented out thus should already be included in existing annotations). Or by commenting out line 264 < removeDrugNerTypes(jcas, intermediateTypesToRemove)> all legacy types should be included. Thanks, ~Sean From: ravi garg [mailto:[email protected]<mailto:[email protected]>] Sent: Tuesday, March 11, 2014 11:17 AM To: [email protected]<mailto:[email protected]> Subject: Re: How to use Drug NER Hey, Yes, It is populated with the medication. I was actually getting that before too but not the drug ner type system part.. Also when I browse the inner annotations of MedicationMention, I can finally see other annotations too like medicationFrequency, medicationRoute etc in the refsem typesystem. Thank you very much for the help. I would try to uncomment the code you are referring and try to rebuild that part.Just one final help can you please kindly point me to the code you are talking about. Thanks, Ravi On Tue, Mar 11, 2014 at 9:18 PM, Murphy, Sean P. <[email protected]<mailto:[email protected]>> wrote: Ravi, Can you look at the list of IdentifiedAnnotation to see if the entities include the drugs in question. Specifically, the ‘ctakes.typesystem.type.textsem.MedicationMention’ should be populated. Additionally, there should be the missing drug related annotations, such as strength in that list. The problem is that the drug ner was migrated to use the new type system a release or two back. However, the old type system format was allowed to remain in the event that someone required that legacy handling. These can actually be populated by uncommenting some code that exists in the DrugMention source code and rerunning. I had forgotten about these changes. Hopefully, that explains what you’re seeing. Thanks, ~Sean From: ravi garg [mailto:[email protected]<mailto:[email protected]>] Sent: Tuesday, March 11, 2014 10:15 AM To: [email protected]<mailto:[email protected]> Subject: Re: How to use Drug NER Hey, I am using ctakes-drug-ner/desc/analysis_engine/AggregatePlainTextUMLSProcessor.xml as the Analysis Engine in the CVD where in I am getting the other annotations such as Medication Annotations Fraction Annotation which are of ctakes.typesystem.type.textsem.IdentifiedAnnotation but do not get any of the ctakes.drugner.type annotations for eg Frequency Annotation Drug Strength Annotations etc. I dont get any errors though but I feel DrugMentionAnnotator descriptor which extracts the strength, frequency, route etc is not working for me. Thanks, Ravi On Tue, Mar 11, 2014 at 8:18 PM, Murphy, Sean P. <[email protected]<mailto:[email protected]>> wrote: Ravi, I assume you’re just using plain text as the input for the pipeline. Did you use the provided sample DrugNER_PlainText_CPE.xml available in the ctakes-drug-ner/desc/collection_processing_engine/ folder to see if it can run the provided sample? If my assumption is correct than make sure you’re using the Analysis Engines provided for the plain text path (i.e. no aggregates with ‘CDA’ in the name should be utilized). This also pertains to the consumer which output ( make sure to use this one ‘AggregatePlaintextProcessor.xml’). If you are using the CVD (cas visual debugger) then everything but the consumer would still apply. Just be sure that you are loading the DrugAggregatePlaintextUMLSProcessor AE specifier. BTW. Are you seeing other annotations other than the drugner type? Thanks, ~Sean From: ravi garg [mailto:[email protected]<mailto:[email protected]>] Sent: Tuesday, March 11, 2014 2:38 AM To: [email protected]<mailto:[email protected]> Subject: Re: How to use Drug NER Ohh Okay, I am sorry Sean, I didn't actually knew Rxnorm is an umls dictionary and you need to have a license to use it. I have got that working but still I dont get any annotations in drugner.type for example RouteAnnotation, DurationAnnotation etc. Any ideas on how to get that working Thanks, Ravi On Mon, Mar 10, 2014 at 11:56 PM, ravi garg <[email protected]<mailto:[email protected]>> wrote: Hey Xiayuan, I ensured that the directory of the resource that is the rxnorm_index is correct and cTAKES is also actually using it. I can see the logs wherein cTAKES actually parses 16k docs. I get no errors though on using the pipeline but nothing is extracted or annotated. Even the dosage, frequency and route which I believe are not dependent on drug dictionary are also not getting identified. I have worked on the main clinical pipeline before but am working on the Drug pipeline for the first time so no idea whats wrong. Regards, Ravi On Mon, Mar 10, 2014 at 11:38 PM, Xiayuan Huang <[email protected]<mailto:[email protected]>> wrote: Hi Ravi, Currently I am doing one project using cTAKES. I am trying to use a pipeline for identifying smoking status, SimulatedProdSmokingTAE.xml. And I also encountered some problem on executing those pipelines. Some possible errors will be the directory of UIMA resource, you have to set that correctly. And I got some exceptions when I try to run pipelines. We can discuss how to implement cTAKES later on, I guess I really need someone to discuss and help out on this cTAKES system. Best, Xiayuan Huang On 2014-03-10 11:05, ravi garg wrote: Hey, I am using DrugAggregatePlainTextProcessor.xml as my analysis engine annotator. I have downloaded all the required resources by cTAKES 3.1 . I guess it uses the rxnorm_index as the drug database. But I am not getting any annotations as the output. Please let me know the correct way using Drug NER Thanks, Ravi -- Ravi Garg 4th Year MSc (hons) Biological Sciences B.E (hons) Computer Science and Engineering BITS Pilani KK Birla Goa Campus -- Ravi Garg 4th Year MSc (hons) Biological Sciences B.E (hons) Computer Science and Engineering BITS Pilani KK Birla Goa Campus -- Ravi Garg 4th Year MSc (hons) Biological Sciences B.E (hons) Computer Science and Engineering BITS Pilani KK Birla Goa Campus -- Ravi Garg 4th Year MSc (hons) Biological Sciences B.E (hons) Computer Science and Engineering BITS Pilani KK Birla Goa Campus -- Ravi Garg 4th Year MSc (hons) Biological Sciences B.E (hons) Computer Science and Engineering BITS Pilani KK Birla Goa Campus -- Ravi Garg 4th Year MSc (hons) Biological Sciences B.E (hons) Computer Science and Engineering BITS Pilani KK Birla Goa Campus -- Ravi Garg 4th Year MSc (hons) Biological Sciences B.E (hons) Computer Science and Engineering BITS Pilani KK Birla Goa Campus
