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From Bruce Tietjen <bruce.tiet...@perfectsearchcorp.com>
Subject Re: Differences in MedicationMention annotations on subsequent processing runs
Date Wed, 08 Oct 2014 15:51:30 GMT
If I understand correctly, I would need new dictionary resources to run the
rare word lookup method.

Where can I find the necessary dictionary(ies) or how do I build them?


 [image: IMAT Solutions] <http://imatsolutions.com>
 Bruce Tietjen
Senior Software Engineer
[image: Mobile:] 801.634.1547
bruce.tietjen@imatsolutions.com

On Wed, Oct 8, 2014 at 9:46 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

>  Hi Bruce,
>
> I would venture to say that this is neither expected nor desired.
>
>
>
> Before you fix it (or in addition to a fix), try to run with the new
> dictionary lookup.   It will have a different behavior, and it will be the
> default dictionary lookup in future releases of cTakes – making fixes to
> the current module slightly less urgent.
>
>
>
> Sean
>
>
>
> *From:* Bruce Tietjen [mailto:bruce.tietjen@perfectsearchcorp.com]
> *Sent:* Wednesday, October 08, 2014 11:38 AM
> *To:* dev@ctakes.apache.org
> *Subject:* Differences in MedicationMention annotations on subsequent
> processing runs
>
>
>
>
>
> I have encountered a situation in which the cTakes clinical pipeline
> output differs between multiple runs on the same text with the same
> configuration.
>
> The following snippets from a single document are sufficient to
> demonstrate the issue:
>
>  a gentle curve going into. irrigated with Bacitracin.
>
>
>
> The source of the difference is that the DictionaryLookupAnnotator uses a
> map to filter out duplicate annotations for a single document location:
>
>     // used to prevent duplicate hits
>     // key = hit begin,end key (java.lang.String)
>     // val = Set of MetaDataHit objects
>     private Map<String,Set<MetaDataHit>> iv_dupMap = new HashMap<>();
>
>  This map is shared between both the umls_ms_2011ab lookup and the
> umls_ms_2011an_rxnorm lookup,
>
>
>
> If both dictionaries contain the same term, the order of dictionary lookup
> execution determines the output.If the rxnorm lookup runs first, then a
> MedicationMention annotation for Bacitracin appears in the final output. If
> the standard umls lookup runs first, then there is no MedicationMention
> annotation for Bacitracin.
>
> I will attach the output from the subsequent runs. (Hopefully the
> attachment will make it through the system)
>
>
>
> Is this expected behavior? If not, what would be the expected behavior?
>
>
>
> [image: Image removed by sender. IMAT Solutions]
> <http://imatsolutions.com>
>
> *Bruce Tietjen*
> Senior Software Engineer
> [image: Image removed by sender. Mobile:]801.634.1547
> bruce.tietjen@imatsolutions.com
>

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