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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject Re: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Date Fri, 11 Jan 2019 16:36:29 GMT
Thanks Tim.
There is a patch in the jira item, but I don't know if it was ever applied (checked in).
Does anybody know?

________________________________________
From: Miller, Timothy <Timothy.Miller@childrens.harvard.edu>
Sent: Friday, January 11, 2019 11:32 AM
To: dev@ctakes.apache.org
Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]

Looks like someone fixed that as part of a different issue:
https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D500&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=1stOSUyvduxWyRf5ExkM407a94mlzdOtd52cdYQb3WQ&s=eSMr6VoSvH5sGvOa4s3OzFHOWPSUigB1hED4x2wu27A&e=
Tim


-----Original Message-----
From: "Finan, Sean" <Sean.Finan@childrens.harvard.edu<mailto:%22Finan,%20Sean%22%20%3cSean.Finan@childrens.harvard.edu%3e>>
Reply-to: <dev@ctakes.apache.org>
To: dev@ctakes.apache.org <dev@ctakes.apache.org<mailto:%22dev@ctakes.apache.org%22%20%3cdev@ctakes.apache.org%3e>>
Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL]
[SUSPICIOUS]
Date: Fri, 11 Jan 2019 16:05:21 +0000


Hi Sana,

This might be related to

https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D450-3Ffilter-3D-2D5-26jql-3Dproject-2520-253D-2520CTAKES-2520AND-2520resolution-2520-253D-2520Unresolved-2520AND-2520-2522Attachment-2520count-2522-2520-253C-253D-2520-25222-2522-2520AND-2520-2522Attachment-2520count-2522-2520-253E-253D-2520-25221-2522-2520order-2520by-2520priority-2520DESC-252Cupdated-2520DESC&d=DwIFAw&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Ojz-Ww86QvcLG1VBfECfCcNudtXNQIe7c-jJ_UMXtiE&s=sd2GH6n5nOzk4vtOA4qKh0kULci4rCiBDMWyM0IKU0Y&e=

If anybody has time to test and approve the patch attached to that tar please let me know
so that it can be checked in.

Thanks,
Sean
________________________________________
From: Sana Riaz <sana.riaz@xflowresearch.com<mailto:sana.riaz@xflowresearch.com>>
Sent: Friday, January 11, 2019 5:33 AM
To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>
Subject: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL]

Hi,
I am trying to process CDA documents with AggregateCdaUMLSProcessor.xml
descriptor (clinical-pipeline). The cda document includes sections like
problems, medications, allergies, tests etc. In the plain_view, all these
section are visible in CVD but all the annotations extracted by
AggregateCdaUMLSProcessor are only on last section. i.e. there's no
annotation on the medications or problems.

I've looked into CdaCasInitializer output , and it only passes one segment
(the last one) so all the other annotators only process on that. In
addition to that, every section's id (including last) is assigned null as
[start section id="null"]
....
[end section id="null"]

Do i have to assign section id's myself? Any suggestion would be very
helpful.

Warm Regards,

Sana Riaz


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