Re: Fast UMLS dictionary lookup description [EXTERNAL] [SUSPICIOUS]
Didn't you have some slides at some point as well? I don't know if they are suitable for public consumption but I remember it was helpful for me at least. Tim On Fri, 2018-02-23 at 15:34 +, Finan, Sean wrote: > Unfortunately, writing is not my jam. I wrote about 50% of a paper > and then shoved it aside for other tasks. Now I have no idea where I > saved it ... > > However, there is an outline of sorts in the code repository within > the ctakes-dictionary-lookup-fast module. The doc/ directory > contains a few files and the DictionaryLookupHelp document may > address your question. I apparently wrote it in March of 2014 (time > flies) so I am guessing that some minor details have changed, but the > main flow is the same. > > Sean > > -Original Message- > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > > Sent: Friday, February 23, 2018 2:57 AM > To: dev@ctakes.apache.org > Subject: RE: Fast UMLS dictionary lookup description [EXTERNAL] > > Hi Masoud, > > > > In this link - https://urldefense.proofpoint.com/v2/url?u=https-3A__c > wiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0-2B-2D-2BFast- > 2BDictionary- > 2BLookup&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs6 > 7GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=2lx9jiMXTJ4lNLDbef7KG0qSHx > D_AZH_DYqrQyAZWSY&s=UpxVWvyK8fZ_8vnYhIrFZlUza0qBHuqVme5n-8zEeqw&e=, I > could see an information stating " A paper on rare word indexing is > currently in progress." > > > > May be Sean or Tim will be able to provide info on this I feel. > > > > Regards, > > Gandhi > > > > -Original Message- > > From: Masoud Rouhizadeh [mailto:m...@jhu.edu] > > Sent: Thursday, February 22, 2018 9:57 PM > > To: dev@ctakes.apache.org > > Subject: Fast UMLS dictionary lookup description > > > > Hello, cTAKES developing team, > > > > We are using and comparing various NLP tools (including cTAKES) for > processing over 5 million clinical notes within Johns Hopkins Medical > Institutes. As a part of our comparisons, we are exploring the > architecture of the NER and (UMLS) concept linking components of the > tools. > > > > I was able to find the description on the cTAKES default/original > dictionary look up in the Savova et. al. 2010 paper but I was not > able to find a paper or tech report describing the fast UMLS > dictionary lookup (Fast UMLS Processor) yet. > > > > Any description of the fast dictionary lookup algorithm is highly > appreciated. > > > > Thank you, > > Masoud Rouhizadeh > > > > > > Masoud Rouhizadeh, PhD > > > > NLP Specialist / Software Engineer > > Institute for Clinical and Translational Research Center for Clinical > Data Analysis School of Medicine, Johns Hopkins University > > https://urldefense.proofpoint.com/v2/url?u=http-3A__pages.jh.edu_-7Em > rouhiz1&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67 > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=2lx9jiMXTJ4lNLDbef7KG0qSHxD > _AZH_DYqrQyAZWSY&s=sqC6maCH-rhpZGJ_y6zc1q1K1z5FDYjcN6HhX8e_ZbY&e= > > > > This email and any files transmitted with it are confidential and > intended solely for the use of the individual or entity to whom they > are addressed. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > or system manager by email immediately if you have received this e- > mail by mistake and delete this e-mail from your system. If you are > not the intended recipient you are notified that disclosing, copying, > distributing or taking any action in reliance on the contents of this > information is strictly prohibited and against the law. >
RE: Fast UMLS dictionary lookup description [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
I did have slides. I suppose that I can do some digging through my old laptop's crowded disk ... Sean -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Friday, February 23, 2018 11:16 AM To: dev@ctakes.apache.org Subject: Re: Fast UMLS dictionary lookup description [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] Didn't you have some slides at some point as well? I don't know if they are suitable for public consumption but I remember it was helpful for me at least. Tim On Fri, 2018-02-23 at 15:34 +, Finan, Sean wrote: > Unfortunately, writing is not my jam. I wrote about 50% of a paper > and then shoved it aside for other tasks. Now I have no idea where I > saved it ... > > However, there is an outline of sorts in the code repository within > the ctakes-dictionary-lookup-fast module. The doc/ directory contains > a few files and the DictionaryLookupHelp document may address your > question. I apparently wrote it in March of 2014 (time > flies) so I am guessing that some minor details have changed, but the > main flow is the same. > > Sean > > -Original Message- > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > > Sent: Friday, February 23, 2018 2:57 AM > To: dev@ctakes.apache.org > Subject: RE: Fast UMLS dictionary lookup description [EXTERNAL] > > Hi Masoud, > > > > In this link - https://urldefense.proofpoint.com/v2/url?u=https-3A__c > wiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0-2B-2D-2BFast- > 2BDictionary- > 2BLookup&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs6 > 7GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=2lx9jiMXTJ4lNLDbef7KG0qSHx > D_AZH_DYqrQyAZWSY&s=UpxVWvyK8fZ_8vnYhIrFZlUza0qBHuqVme5n-8zEeqw&e=, I > could see an information stating " A paper on rare word indexing is > currently in progress." > > > > May be Sean or Tim will be able to provide info on this I feel. > > > > Regards, > > Gandhi > > > > -Original Message- > > From: Masoud Rouhizadeh [mailto:m...@jhu.edu] > > Sent: Thursday, February 22, 2018 9:57 PM > > To: dev@ctakes.apache.org > > Subject: Fast UMLS dictionary lookup description > > > > Hello, cTAKES developing team, > > > > We are using and comparing various NLP tools (including cTAKES) for > processing over 5 million clinical notes within Johns Hopkins Medical > Institutes. As a part of our comparisons, we are exploring the > architecture of the NER and (UMLS) concept linking components of the > tools. > > > > I was able to find the description on the cTAKES default/original > dictionary look up in the Savova et. al. 2010 paper but I was not able > to find a paper or tech report describing the fast UMLS dictionary > lookup (Fast UMLS Processor) yet. > > > > Any description of the fast dictionary lookup algorithm is highly > appreciated. > > > > Thank you, > > Masoud Rouhizadeh > > > > > > Masoud Rouhizadeh, PhD > > > > NLP Specialist / Software Engineer > > Institute for Clinical and Translational Research Center for Clinical > Data Analysis School of Medicine, Johns Hopkins University > > https://urldefense.proofpoint.com/v2/url?u=http-3A__pages.jh.edu_-7Em > rouhiz1&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67 > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=2lx9jiMXTJ4lNLDbef7KG0qSHxD > _AZH_DYqrQyAZWSY&s=sqC6maCH-rhpZGJ_y6zc1q1K1z5FDYjcN6HhX8e_ZbY&e= > > > > This email and any files transmitted with it are confidential and > intended solely for the use of the individual or entity to whom they > are addressed. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > or system manager by email immediately if you have received this e- > mail by mistake and delete this e-mail from your system. If you are > not the intended recipient you are notified that disclosing, copying, > distributing or taking any action in reliance on the contents of this > information is strictly prohibited and against the law. >
Re: Fast UMLS dictionary lookup description [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Thanks so much, everyone for your helpful messages and pointers. It’s wonderful
to see how responsive you are!
Sean: I’m looking forward to seeing your slides in case you could find them on
your old machine
Thanks!
Masoud
On 2/23/18, 11:20 AM, "Finan, Sean" wrote:
I did have slides. I suppose that I can do some digging through my old
laptop's crowded disk ...
Sean
-Original Message-
From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
Sent: Friday, February 23, 2018 11:16 AM
To: dev@ctakes.apache.org
Subject: Re: Fast UMLS dictionary lookup description [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Didn't you have some slides at some point as well? I don't know if they are
suitable for public consumption but I remember it was helpful for me at least.
Tim
On Fri, 2018-02-23 at 15:34 +, Finan, Sean wrote:
> Unfortunately, writing is not my jam. I wrote about 50% of a paper
> and then shoved it aside for other tasks. Now I have no idea where I
> saved it ...
>
> However, there is an outline of sorts in the code repository within
> the ctakes-dictionary-lookup-fast module. The doc/ directory contains
> a few files and the DictionaryLookupHelp document may address your
> question. I apparently wrote it in March of 2014 (time
> flies) so I am guessing that some minor details have changed, but the
> main flow is the same.
>
> Sean
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
>
> Sent: Friday, February 23, 2018 2:57 AM
> To: dev@ctakes.apache.org
> Subject: RE: Fast UMLS dictionary lookup description [EXTERNAL]
>
> Hi Masoud,
>
>
>
> In this link - https://urldefense.proofpoint.com/v2/url?u=https-3A__c
> wiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0-2B-2D-2BFast-
> 2BDictionary-
> 2BLookup&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs6
> 7GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=2lx9jiMXTJ4lNLDbef7KG0qSHx
> D_AZH_DYqrQyAZWSY&s=UpxVWvyK8fZ_8vnYhIrFZlUza0qBHuqVme5n-8zEeqw&e=, I
> could see an information stating " A paper on rare word indexing is
> currently in progress."
>
>
>
> May be Sean or Tim will be able to provide info on this I feel.
>
>
>
> Regards,
>
> Gandhi
>
>
>
> -Original Message-
>
> From: Masoud Rouhizadeh [mailto:m...@jhu.edu]
>
> Sent: Thursday, February 22, 2018 9:57 PM
>
> To: dev@ctakes.apache.org
>
> Subject: Fast UMLS dictionary lookup description
>
>
>
> Hello, cTAKES developing team,
>
>
>
> We are using and comparing various NLP tools (including cTAKES) for
> processing over 5 million clinical notes within Johns Hopkins Medical
> Institutes. As a part of our comparisons, we are exploring the
> architecture of the NER and (UMLS) concept linking components of the
> tools.
>
>
>
> I was able to find the description on the cTAKES default/original
> dictionary look up in the Savova et. al. 2010 paper but I was not able
> to find a paper or tech report describing the fast UMLS dictionary
> lookup (Fast UMLS Processor) yet.
>
>
>
> Any description of the fast dictionary lookup algorithm is highly
> appreciated.
>
>
>
> Thank you,
>
> Masoud Rouhizadeh
>
>
>
>
>
> Masoud Rouhizadeh, PhD
>
>
>
> NLP Specialist / Software Engineer
>
> Institute for Clinical and Translational Research Center for Clinical
> Data Analysis School of Medicine, Johns Hopkins University
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__pages.jh.edu_-7Em
> rouhiz1&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67
> GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=2lx9jiMXTJ4lNLDbef7KG0qSHxD
> _AZH_DYqrQyAZWSY&s=sqC6maCH-rhpZGJ_y6zc1q1K1z5FDYjcN6HhX8e_ZbY&e=
>
>
>
> This email and any files transmitted with it are confidential and
> intended solely for the use of the individual or entity to whom they
> are addressed. If you are not the named addressee you should not
> disseminate, distribute or copy this e-mail. Please notify the sender
> or system manager by email immediately if you have received this e-
> mail by mistake and delete this e-mail from your system. If you are
> not the intended recipient you are notified that disclosing, copying,
> distributing or taking any action in reliance on the contents of this
> information is strictly prohibited and against the law.
>
