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Posted to dev@ctakes.apache.org by "Miller, Timothy" <Ti...@childrens.harvard.edu> on 2018/02/23 16:15:48 UTC

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 +0000, 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.Natarajan@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:mrou@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]

Posted by Masoud Rouhizadeh <mr...@jhu.edu>.

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" <Se...@childrens.harvard.edu> 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.Miller@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 +0000, 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.Natarajan@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:mrou@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]

Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.

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.Miller@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 +0000, 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.Natarajan@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:mrou@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.
>