RE: SenseDisambiguatorAnnotator in ctakes 4.0?

[Finan, Sean]

Hi Lani,

Great questions.  As far as I know nobdy is changing what is in ytex for this 
release.  So, if you run the default ctakes clinical pipeline the rare word 
lookup will be used.  If you run ytex then the old first word will still be 
used.

The gui does not support first word lookup.  Somebody may add that in the 
future (there actually is code in sandbox), but I don't plan to do it myself.

Sean




-Original Message-
From: Lani Lin [mailto:l...@informatik.uni-leipzig.de] 
Sent: Wednesday, March 29, 2017 9:59 AM
To: dev@ctakes.apache.org
Subject: Re: SenseDisambiguatorAnnotator in ctakes 4.0?

Hi Sean,

thanks. Will the new dictionary building GUI also include building dictionaries 
for first word lookup?

Another question to be clarified: if the dictionary used in ctakes FIRST word 
also the same as YTEX?

In other words, if the results from ctakes FIRST word = those from YTEX?

best,

Lani


On 29.03.2017 15:23, Finan, Sean wrote:
> Hi Lani,
>
> The rare word lookup will be the default.  The default redistributable 
> dictionary will be umls snomed and rxnorm 2016ab.
>
> Sean
>
> -Original Message-
> From: Lani Lin [mailto:l...@informatik.uni-leipzig.de]
> Sent: Wednesday, March 29, 2017 3:27 AM
> To: dev@ctakes.apache.org
> Subject: Re: SenseDisambiguatorAnnotator in ctakes 4.0?
>
> Hi Sean,
>
> thanks for your reply. I'll try to make the annotator running and see if I 
> can do more.
>
> Another question regarding ctakes 4.0,  will it use the first word or rare 
> word algorithm?
>
> best,
>
> Lani
>
>
> On 28.03.2017 17:23, Finan, Sean wrote:
>> Hi Lani,
>>
>> It will remain part of the ytex package.  There is some effort being made 
>> toward getting new wsd into ctakes, but it will not be introduced for some 
>> time.
>>
>> If anybody out there has something that they would like to contribute to 
>> ctakes, please do!
>>
>> Sean
>>
>> -Original Message-
>> From: Lani Lin [mailto:l...@informatik.uni-leipzig.de]
>> Sent: Tuesday, March 28, 2017 10:50 AM
>> To: dev@ctakes.apache.org
>> Subject: SenseDisambiguatorAnnotator in ctakes 4.0?
>>
>> Hi,
>>
>> Will the ctakes 4.0 include SenseDisambiguatorAnnotator or it will still be 
>> only part of ytex?
>>
>> best,
>> Lani
>>
>>
> --
> Ying-Chi Lin 
> (https://urldefense.proofpoint.com/v2/url?u=http-3A__dbs.uni-2Dleipzig
> .de_de_person_yingchi-5Flin=DwIDaQ=qS4goWBT7poplM69zy_3xhKwEW14JZM
> SdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=2U738MxWz
> u_mmcrY00IpwCh3R-URXYCLMzY91aNSMWQ=f_-F5l58L6ao70tJDeJOk0etiYbuplvGF
> 3f1dASrCN0= ) Database Group, Department of Computer Science, 
> Universität Leipzig
>
>

--
Ying-Chi Lin 
(https://urldefense.proofpoint.com/v2/url?u=http-3A__dbs.uni-2Dleipzig.de_de_person_yingchi-5Flin=DwIDaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=t_U9PuQaNHQ2VM8FIstsF4ug7xjcOdgug7Mg3GMZYZw=PdaX792dIQZYHdBURxYgyRLftyxqEPaP5GXCl8oFpw8=
 ) Database Group, Department of Computer Science, Universität Leipzig

Re: SenseDisambiguatorAnnotator in ctakes 4.0?

[Lani Lin]

Hi Sean,

thanks. Will the new dictionary building GUI also include building 
dictionaries for first word lookup?


Another question to be clarified: if the dictionary used in ctakes FIRST 
word also the same as YTEX?


In other words, if the results from ctakes FIRST word = those from YTEX?

best,

Lani


On 29.03.2017 15:23, Finan, Sean wrote:

Hi Lani,

The rare word lookup will be the default.  The default redistributable 
dictionary will be umls snomed and rxnorm 2016ab.

Sean

-Original Message-
From: Lani Lin [mailto:l...@informatik.uni-leipzig.de]
Sent: Wednesday, March 29, 2017 3:27 AM
To: dev@ctakes.apache.org
Subject: Re: SenseDisambiguatorAnnotator in ctakes 4.0?

Hi Sean,

thanks for your reply. I'll try to make the annotator running and see if I can 
do more.

Another question regarding ctakes 4.0,  will it use the first word or rare word 
algorithm?

best,

Lani


On 28.03.2017 17:23, Finan, Sean wrote:

Hi Lani,

It will remain part of the ytex package.  There is some effort being made 
toward getting new wsd into ctakes, but it will not be introduced for some time.

If anybody out there has something that they would like to contribute to 
ctakes, please do!

Sean

-Original Message-
From: Lani Lin [mailto:l...@informatik.uni-leipzig.de]
Sent: Tuesday, March 28, 2017 10:50 AM
To: dev@ctakes.apache.org
Subject: SenseDisambiguatorAnnotator in ctakes 4.0?

Hi,

Will the ctakes 4.0 include SenseDisambiguatorAnnotator or it will still be 
only part of ytex?

best,
Lani



--
Ying-Chi Lin 
(https://urldefense.proofpoint.com/v2/url?u=http-3A__dbs.uni-2Dleipzig.de_de_person_yingchi-5Flin=DwIDaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=2U738MxWzu_mmcrY00IpwCh3R-URXYCLMzY91aNSMWQ=f_-F5l58L6ao70tJDeJOk0etiYbuplvGF3f1dASrCN0=
 ) Database Group, Department of Computer Science, Universität Leipzig




--
Ying-Chi Lin (http://dbs.uni-leipzig.de/de/person/yingchi_lin)
Database Group, Department of Computer Science, Universität Leipzig

Re: Labs annotator?

[Pei Chen]

Kean,
This would be really useful.  If you would like make a contribution,
could you please open a Jira and attach the patch or code?  When you
submit a patch via jira/attachment, it has legal verberage about
donating the code, etc.

--Pei


On Wed, Mar 29, 2017 at 9:30 AM, Finan, Sean
 wrote:
> Fantastic!
>
> I would really like to work with you to get this into ctakes 4.1.  Let me 
> know how you would like to proceed.  Would you like to send me or another 
> committer the code or have somebody review it remotely?  The "tweaks" may be 
> something useful to ctakes, but if not I'm sure that we can create a decent 
> interfacing.
>
> Cheers,
> Sean
>
> -Original Message-
> From: Kean Kaufmann [mailto:k...@recordsone.com]
> Sent: Wednesday, March 29, 2017 7:59 AM
> To: dev@ctakes.apache.org
> Subject: Re: Labs annotator?
>
>>
>> I'm sure that people would love to see lab values in ctakes!  Could
>> you please write a small summary of what it does?  Maybe an example or
>> two could suffice.
>
>
> Hi Sean,
>
> The labs annotator identifies likely lab phrases by TUI (T059 et al.), and 
> relates them to the nearest following number-ish value -- NumToken, 
> FractionAnnotation, MeasurementAnnotation or (as a last resort) 
> RangeAnnotation -- that isn't part of a Date or TimeAnnotation.
> A whitelist of lab-value words can also be specified,  e.g. "positive", 
> "negative", "normal", "elevated", "decreased", ...
>
> For example,
>
> Weight / BMI:  Recent weight (as of 05/05/16) is
>> 45.36 kg (100 lb)
>
>
> yields
>
> "weight" -> "45.36 kg"
>
> and
>
> HEPATIC FUNCTION PANEL
>> Result Value Ref Range
>>  Albumin 2.2 (*) 3.7 - 5.1 g/dL
>>  Total Protein 5.5 (*) 5.8 - 8.0 g/dL
>>  Alkaline Phosphatase 844 (*) 42 - 121 IU/L ...
>
>
> yields
>
> "Albumin" -> "2.2"
> "Protein" -> "5.5"
> "Alkaline Phosphatase" -> "844"
>
> (without trying to fill in the units or referenceRangeNarrative values).
>
> Configuration parameters:
> * ids of segments to annotate
> * TUIs indicating labs - I use T059, T060 and T121
> * CUIs too general to be useful, e.g. C1443182, "Calculated (procedure)"
> * Whitelist of words allowed as lab values
> * Maximum number of newlines permitted between lab and value (0 = must be on 
> same line)
>
> I'd need to check in with you to make sure it plays nicely with the cTAKES 
> type system; we've tweaked ours a bit.
>
> Best,
> -kk
>
>
> On Tue, Mar 28, 2017 at 11:45 AM, Finan, Sean < 
> sean.fi...@childrens.harvard.edu> wrote:
>
>> Hi Kean,
>>
>> I'm sure that people would love to see lab values in ctakes!  Could
>> you please write a small summary of what it does?  Maybe an example or
>> two could suffice.
>>
>> We can definitely put it into ctakes in release 4.1 - maybe next quarter?
>>
>> Cheers,
>> Sean
>>
>> -Original Message-
>> From: Kean Kaufmann [mailto:k...@recordsone.com]
>> Sent: Tuesday, March 28, 2017 11:34 AM
>> To: dev@ctakes.apache.org
>> Subject: Labs annotator?
>>
>> On Tue, Mar 28, 2017 at 11:23 AM, Finan, Sean <
>> sean.fi...@childrens.harvard.edu> wrote:
>>
>> >
>> > If anybody out there has something that they would like to
>> > contribute to ctakes, please do!
>> >
>>
>> I recently wrote an annotator for lab values.  There was some
>> discussion of this on the dev list a couple of years ago; did anything come 
>> of it?
>> Happy to contribute if it's helpful.
>>
>> --
>> _
>> *Kean Kaufmann*
>> NLP Developer
>>
>> RecordsOne
>>   nSight Driven | *Priority. Clarity. Integrity. *
>>
>> *mobile* |
>> 240-401-6131
>>
>> *Twitter:  **@R1_RecordsOne*
>> *See us in Vegas @ ACDIS 2017 *
>> *See us in Los Angeles @ AHIMA 2017*
>>
>> 
>> ---
>> *Confidentiality Notice:  *This email, including any attachments is
>> the property of RecordsOne, LLC and is intended for the sole use of
>> the intended recipient(s). It may contain information that is
>> privileged and confidential. Any unauthorized review, use, disclosure,
>> or distribution is prohibited. If you are not the intended recipient,
>> please reply to the sender that you have received the message in
>> error, then delete this message.
>> 
>> ---
>> *Mailing*:  10641 Airport Pulling Road, Suite 30 | Naples, FL 34109
>> *Main*:  239.451.6112
>>
>> *Please consider the environmental impact before printing this email.
>> *
>>

RE: SenseDisambiguatorAnnotator in ctakes 4.0?

[Finan, Sean]

Hi Lani,

The rare word lookup will be the default.  The default redistributable 
dictionary will be umls snomed and rxnorm 2016ab.  

Sean

-Original Message-
From: Lani Lin [mailto:l...@informatik.uni-leipzig.de] 
Sent: Wednesday, March 29, 2017 3:27 AM
To: dev@ctakes.apache.org
Subject: Re: SenseDisambiguatorAnnotator in ctakes 4.0?

Hi Sean,

thanks for your reply. I'll try to make the annotator running and see if I can 
do more.

Another question regarding ctakes 4.0,  will it use the first word or rare word 
algorithm?

best,

Lani


On 28.03.2017 17:23, Finan, Sean wrote:
> Hi Lani,
>
> It will remain part of the ytex package.  There is some effort being made 
> toward getting new wsd into ctakes, but it will not be introduced for some 
> time.
>
> If anybody out there has something that they would like to contribute to 
> ctakes, please do!
>
> Sean
>
> -Original Message-
> From: Lani Lin [mailto:l...@informatik.uni-leipzig.de]
> Sent: Tuesday, March 28, 2017 10:50 AM
> To: dev@ctakes.apache.org
> Subject: SenseDisambiguatorAnnotator in ctakes 4.0?
>
> Hi,
>
> Will the ctakes 4.0 include SenseDisambiguatorAnnotator or it will still be 
> only part of ytex?
>
> best,
> Lani
>
>

--
Ying-Chi Lin 
(https://urldefense.proofpoint.com/v2/url?u=http-3A__dbs.uni-2Dleipzig.de_de_person_yingchi-5Flin=DwIDaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=2U738MxWzu_mmcrY00IpwCh3R-URXYCLMzY91aNSMWQ=f_-F5l58L6ao70tJDeJOk0etiYbuplvGF3f1dASrCN0=
 ) Database Group, Department of Computer Science, Universität Leipzig

Re: Labs annotator?

[Kean Kaufmann]

>
> I'm sure that people would love to see lab values in ctakes!  Could you
> please write a small summary of what it does?  Maybe an example or two
> could suffice.


Hi Sean,

The labs annotator identifies likely lab phrases by TUI (T059 et al.),
and relates them to the nearest following number-ish value --
NumToken, FractionAnnotation, MeasurementAnnotation or (as a last resort)
RangeAnnotation --
that isn't part of a Date or TimeAnnotation.
A whitelist of lab-value words can also be specified,  e.g. "positive",
"negative", "normal", "elevated", "decreased", ...

For example,

Weight / BMI:  Recent weight (as of 05/05/16) is
> 45.36 kg (100 lb)


yields

"weight" -> "45.36 kg"

and

HEPATIC FUNCTION PANEL
> Result Value Ref Range
>  Albumin 2.2 (*) 3.7 - 5.1 g/dL
>  Total Protein 5.5 (*) 5.8 - 8.0 g/dL
>  Alkaline Phosphatase 844 (*) 42 - 121 IU/L
> ...


yields

"Albumin" -> "2.2"
"Protein" -> "5.5"
"Alkaline Phosphatase" -> "844"

(without trying to fill in the units or referenceRangeNarrative values).

Configuration parameters:
* ids of segments to annotate
* TUIs indicating labs - I use T059, T060 and T121
* CUIs too general to be useful, e.g. C1443182, "Calculated (procedure)"
* Whitelist of words allowed as lab values
* Maximum number of newlines permitted between lab and value (0 = must be
on same line)

I'd need to check in with you to make sure it plays nicely with the cTAKES
type system; we've tweaked ours a bit.

Best,
-kk


On Tue, Mar 28, 2017 at 11:45 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:

> Hi Kean,
>
> I'm sure that people would love to see lab values in ctakes!  Could you
> please write a small summary of what it does?  Maybe an example or two
> could suffice.
>
> We can definitely put it into ctakes in release 4.1 - maybe next quarter?
>
> Cheers,
> Sean
>
> -Original Message-
> From: Kean Kaufmann [mailto:k...@recordsone.com]
> Sent: Tuesday, March 28, 2017 11:34 AM
> To: dev@ctakes.apache.org
> Subject: Labs annotator?
>
> On Tue, Mar 28, 2017 at 11:23 AM, Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> >
> > If anybody out there has something that they would like to contribute
> > to ctakes, please do!
> >
>
> I recently wrote an annotator for lab values.  There was some discussion
> of this on the dev list a couple of years ago; did anything come of it?
> Happy to contribute if it's helpful.
>
> --
> _
> *​Kean Kaufmann*
> ​NLP Developer
>
> RecordsOne
>   nSight Driven | *Priority. Clarity. Integrity. *
>
> *mobile* |
> ​240-401-6131
>
> *Twitter:  **@R1_RecordsOne*
> *See us in Vegas @ ACDIS 2017 *
> *See us in Los Angeles @ AHIMA 2017*
>
> 
> ---
> *Confidentiality Notice:  *This email, including any attachments is the
> property of RecordsOne, LLC and is intended for the sole use of the
> intended recipient(s). It may contain information that is privileged and
> confidential. Any unauthorized review, use, disclosure, or distribution is
> prohibited. If you are not the intended recipient, please reply to the
> sender that you have received the message in error, then delete this
> message.
> 
> ---
> *Mailing*:  10641 Airport Pulling Road, Suite 30 | Naples, FL 34109
> *Main*:  239.451.6112
>
> *Please consider the environmental impact before printing this email. *
>

Re: SenseDisambiguatorAnnotator in ctakes 4.0?

[Lani Lin]

Hi Sean,

thanks for your reply. I'll try to make the annotator running and see if 
I can do more.


Another question regarding ctakes 4.0,  will it use the first word or 
rare word algorithm?


best,

Lani


On 28.03.2017 17:23, Finan, Sean wrote:

Hi Lani,

It will remain part of the ytex package.  There is some effort being made 
toward getting new wsd into ctakes, but it will not be introduced for some time.

If anybody out there has something that they would like to contribute to 
ctakes, please do!

Sean

-Original Message-
From: Lani Lin [mailto:l...@informatik.uni-leipzig.de]
Sent: Tuesday, March 28, 2017 10:50 AM
To: dev@ctakes.apache.org
Subject: SenseDisambiguatorAnnotator in ctakes 4.0?

Hi,

Will the ctakes 4.0 include SenseDisambiguatorAnnotator or it will still be 
only part of ytex?

best,
Lani




--
Ying-Chi Lin (http://dbs.uni-leipzig.de/de/person/yingchi_lin)
Database Group, Department of Computer Science, Universität Leipzig