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From "Abramowitsch, Peter" <pabramowit...@hearst.com>
Subject Re: How to use external CSV or BSV in addition to FastUMLS attention Sean [EXTERNAL]
Date Thu, 04 Jan 2018 12:51:46 GMT
Thanks Tim,  

I did see that folder and its contents and it seemed the right place to
begin.  What I couldn't find was how/where to refer to one of those
CustomCuiTui.Xml files in an engine description.

Peter

On 1/4/18, 1:41 PM, "Miller, Timothy"
<Timothy.Miller@childrens.harvard.edu> wrote:

>Peter, I know Sean is busy this week and he may not see this for a while.
>But I tried this method over the summer and got it to work so I'm fairly
>confident that's the right approach still. Some of the details may have
>changed from two years ago, so I would also check out this directory as a
>starting point:
>https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_viewvc_
>ctakes_trunk_ctakes-2Ddictionary-2Dlookup-2Dfast-2Dres_src_main_resources_
>org_apache_ctakes_dictionary_lookup_fast_example_bsv_&d=DwIFAw&c=B73tqXN8E
>c0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK5Orm10&m=j2h_timB4skc
>lRz6ICf0XlmaUgJekZOOgGo_WF-iuDw&s=qbZInrnxDgeP2prW-pOoOFkVLFweja-ct48H8NWy
>dIM&e=
>
>Tim
>
>________________________________________
>From: Abramowitsch, Peter <pabramowitsch@hearst.com>
>Sent: Thursday, January 4, 2018 7:28 AM
>To: dev@ctakes.apache.org
>Subject: Re: How to use external CSV or BSV in addition to FastUMLS
>attention Sean [EXTERNAL]
>
>Further to my previous message, Sean, I was wondering if you could tell
>me whether this answer you gave in 2015, is still the right way to do
>things in ctakes4.x
>
>permalink:  
>https://urldefense.proofpoint.com/v2/url?u=http-3A__markmail.org_message_s
>3ztinppusvsciss&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=H
>eup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Xq7U7BTl
>hofW8xpZfuBKuudNTqry4yt5RzaoBoPLRIg&s=BSEa_ZZMusVnqd2JbfeyoBxsDD1ZdfsHVXO5
>6wR8erA&e=
>
>Subject:        RE: How to update cTAKES so that new top level categories
>come out based on local
>dictionary?<https://urldefense.proofpoint.com/v2/url?u=http-3A__markmail.o
>rg_message_s3ztinppusvsciss&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdio
>CoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674
>h&m=Xq7U7BTlhofW8xpZfuBKuudNTqry4yt5RzaoBoPLRIg&s=BSEa_ZZMusVnqd2JbfeyoBxs
>DD1ZdfsHVXO56wR8erA&e=>     [permalink]
><https://urldefense.proofpoint.com/v2/url?u=http-3A__markmail.org_message_
>s3ztinppusvsciss&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
>Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Xq7U7BT
>lhofW8xpZfuBKuudNTqry4yt5RzaoBoPLRIg&s=BSEa_ZZMusVnqd2JbfeyoBxsDD1ZdfsHVXO
>56wR8erA&e=>
>From:   Finan, Sean (Sean...@childrens.harvard.edu)
>Date:   Oct 6, 2015 2:04:56 pm
>List:   org.apache.incubator.ctakes-dev
>
>
>Regards
>Peter
>
>From: <Abramowitsch>, Peter Abramowitsch
><pabramowitsch@hearst.com<mailto:pabramowitsch@hearst.com>>
>Date: Thursday, January 4, 2018 at 12:50 PM
>To: "dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>"
><dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>>
>Subject: How to use external CSV or BSV in addition to FastUMLS
>
>Can someone point me to any up-to-date how-tos on how to include external
>CSV/BSV type resources to add synonyms, and other terms for dictionary
>lookup to augment the FAST UMLS resources that comes out of the box.
>Perhaps I have missed something, but looking at the
>CTakesDictionaryCreator UI, it looks like it is designed only to choose
>subsets of the UMLS data set rather than allowing one to bring in
>completely new information sources.  I scoured the Marklogic ctakes user
>archive, but so many of the entries are old and I'm not sure they
>describe the current way of doing things.
>
>The only approach I could see would be to take use the AggregateEngine
>description and have it point to the CSV annotator, creating a completely
>new AE but this would build other types of annotation, whereas what I'm
>thinking about is a case for creating identified mentions such as a
>DiseaseDisorderMention based on finding an acronym that the UMLS resource
>doesn't know about, even though the concept in its full textual form is
>there.
>
>I'm sure this is not a unique request and apologize in advance if it has
>already been answered somewhere
>
>- Peter


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