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Posted to dev@ctakes.apache.org by "Finan, Sean" <Se...@childrens.harvard.edu> on 2018/02/23 15:34:32 UTC
RE: Fast UMLS dictionary lookup description [EXTERNAL]
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__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0-2B-2D-2BFast-2BDictionary-2BLookup&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=2lx9jiMXTJ4lNLDbef7KG0qSHxD_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_-7Emrouhiz1&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&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.
>
Re: Fast UMLS dictionary lookup description [EXTERNAL] [SUSPICIOUS]
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
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.
>