ctakes 3.1.2 produces no medical annotations for me

["Lee, Richard A. [USA]" <le...@bah.com>]

Hi, folks.

I’ve been trying to use the new cTAKES 3.1.2 with ytex, using the AggregatePlaintextUMLSProcessor.xml AE under ctakes-ytex-uima, and so far it’s not been producing the numerous medical annotations (eg DiseaseDisorderMention) that I was getting on the same documents with cTAKES 3.1.1. Attached screenshot will hopefully make this clear.

I did use MetamorphoSys to set up the UMLS tables, and then the ytex script to populate its schema, and I now have ytex tables with hundreds of thousands of entries.

I’ve upped the logging level in the hopes the log file would provide a clue, and the only thing I’m seeing is a lot of “DEBUG [FirstTokenPermutationImpl] Window size of 8 exceeds the max permutation level of 7.”; that number varies from 8 to 12.

Would that explain the problem? If so, how do I fix it? If not, how do I find the problem? Thanks.

Re: ctakes 3.1.2 produces no medical annotations for me

[vijay garla <vn...@gmail.com>]

Hi Richard,

Did you add SNOMED-CT when creating your UMLS Subset?  The dictionary that
YTEX ships with has ~1.5 million entries.  If that doesn't work, you can
also try running the stock cTAKES AggregatePlaintextUMLSProcessor to see if
that creates different annotations.

HTH,

-vj


On Fri, May 23, 2014 at 4:58 PM, Lee, Richard A. [USA]
<le...@bah.com>wrote:

>  Hi, folks.
>
>
>
> I’ve been trying to use the new cTAKES 3.1.2 with ytex, using the
> AggregatePlaintextUMLSProcessor.xml AE under ctakes-ytex-uima, and so far
> it’s not been producing the numerous medical annotations (eg
> DiseaseDisorderMention) that I was getting on the same documents with
> cTAKES 3.1.1. Attached screenshot will hopefully make this clear.
>
>
>
> I did use MetamorphoSys to set up the UMLS tables, and then the ytex
> script to populate its schema, and I now have ytex tables with hundreds of
> thousands of entries.
>
>
>
> I’ve upped the logging level in the hopes the log file would provide a
> clue, and the only thing I’m seeing is a lot of “DEBUG
> [FirstTokenPermutationImpl] Window size of 8 exceeds the max permutation
> level of 7.”; that number varies from 8 to 12.
>
>
>
> Would that explain the problem? If so, how do I fix it? If not, how do I
> find the problem? Thanks.
>
>
>
>
>