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From Justin Zhang <justinzhang...@gmail.com>
Subject Re: how to run i2b2 data
Date Fri, 07 Aug 2015 14:44:29 GMT
Thanks Sean for your understanding, and I am in hope now.

Where is the best place to start looking at regarding "create a collection
reader that works similarly to org.apache.ctakes.core.cr.


On Wed, Aug 5, 2015 at 7:24 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Hi Justin,
> A shot in the dark:
> You could create a collection reader that works similarly to
> org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader , but instead of
> grabbing all of the files in a directory it grabs all the records parsed
> from a single .xml and runs a pipeline per record.  Basically, swap a
> directory for an .xml, a text file for an xml element containing a record.
> Somebody out there might have something that already does as much.
> Sean
> -----Original Message-----
> From: Justin Zhang [mailto:justinzhang.xl@gmail.com]
> Sent: Wednesday, August 05, 2015 6:40 PM
> To: user@ctakes.apache.org; dev@ctakes.apache.org
> Subject: how to run i2b2 data
> Hello everyone,
> I am running ctakes with i2b2 data
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.i2b2.org_NLP_DataSets_Main.php&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=IygWj6YGkcjofGRbrDiFJacJHMaBveHR9qzY0VD1AAE&s=swpt3QP4-B392iLlJ9wypBwD17tRDOCxPdSZOW1rS8s&e=
> In each xml file, there are multiple patient records. I am able to
> separate each patient into single files and process them with "runCPE.sh"
> Is there a way to convert this single xml file into the format "ctakes"
> accepted, and process as a single input file, and generate a single output
> file (results labelled by patient id). For example, each patient id has a
> "smoking status".
> Thanks,
> --
> Justin


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