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meikeric / ytex

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CUIs of those labeled as medicalEvents could not found in the output database tables in drugNER test example. #4

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
1. Open CPE 
2. Set descriptor at 
yhome/config\desc\ytex\drugnerdesccollection_processing_engine/DrugNER_PlainText
_CPE.xml 
3. Set analysis_batch=“test” in Dbconsumer 
4. add analysis_engine DrugAggregatePlaintextProcessor Run.

What is the expected output? What do you see instead?
All CUIs including both medicalEventMention and  EntityMention should be seen 
in the database tables v_document_ontoanno and/or v_document_cui_sent. But only 
the latter were. 
For example, ibuprofen (C0020740), appeared in the text input file, cehcked and 
it is in my umls database, and it even also appeared  when view the analysis 
result in annotation viewer, but either of the two fore mentioned mysql tables 
contain this cui. 

What version of the product are you using? On what operating system?
Ytex0.8 and UMLS2012AB level 0. 

Please provide any additional information below.

Maybe it is hiding in some other tables that I did not go into. But I would 
rather them to be included in the above two tables too for ease of reference in 
future.

Original issue reported on code.google.com by zjz...@gmail.com on 7 Feb 2013 at 2:43

GoogleCodeExporter commented 8 years ago 
can you check the anno_ontology_concept table?  We do not map 
medicalEventMention out of the box.  You can configure ytex to map it though.  
See
http://code.google.com/p/ytex/wiki/DataModel_V07#Configuration

If you map it, please post the sql for the table you create, and we'll add it 
to the next ytex release.

Original comment by vi...@garla.net on 15 Feb 2013 at 2:46