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Posted to dev@ctakes.apache.org by "Chen, Pei" <Pe...@childrens.harvard.edu> on 2014/11/06 21:55:23 UTC
ctakes-dictionary-lookup-fast
Hi,
The original plan was to update AggregatePlaintextUMLSProcessor.xml to use the new ultrafast dictionary lookup in the upcoming 3.2.1 release.
However, the output is slightly different the old cTAKES dictionary where it no longer has a SNOMED/RXNORM consumer (Returns CUI's only and doesn't post process map back to the SNOMED/RXNORM codes.) This can certainly be done again, but I am not sure how many people are dependent on the AggregatePlaintextUMLSProcessor.xml to consider this a patch release.
Some Options/Ideas:
1) Create a AggreatePlaintextUMLSFastProcessor.xml which defaults to dictionary-lookup-fast. But doesn't return the codes for now. We replace the default pipeline when SNOMED/RXNORM codes are returned again.
2) Push forward with defaulting to the new dictionary-lookup-fast in AggregatePlaintextUMLSProcessor.xml
Example output of dictionary-lookup-fast:
[cid:image001.png@01CFF9D9.E5D2CA50]
RE: ctakes-dictionary-lookup-fast
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
By Pei:
> As much as I hate maintaining more desc xml's, but I think it's prudent to create a separate one for a patch release temporarily for ctakes-dictionary-lookup-fast so users do not get blindsided by the change in output.
By Sean:
Excellent idea
-----Original Message-----
From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
Sent: Friday, November 07, 2014 11:13 AM
To: dev@ctakes.apache.org
Subject: RE: ctakes-dictionary-lookup-fast
sounds good to me.
thanks for attaching the images to the JIRA.
-- James
________________________________________
From: Chen, Pei [Pei.Chen@childrens.harvard.edu]
Sent: Friday, November 07, 2014 10:00 AM
To: dev@ctakes.apache.org
Subject: RE: ctakes-dictionary-lookup-fast
Attached screenshots of CVD output to the Jira[1].
As much as I hate maintaining more desc xml's, but I think it's prudent to create a separate one for a patch release temporarily for ctakes-dictionary-lookup-fast so users do not get blindsided by the change in output.
So users can still choose the existing behavior: AggregatePlaintextUMLSProcessor.xml
Or the new dictionary lookup: AggregatePlaintextFastUMLSProcessor.xml
[1] https://issues.apache.org/jira/browse/CTAKES-325
We can replace the xml's in the next major/minor release...
--Pei
> -----Original Message-----
> From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
> Sent: Thursday, November 06, 2014 10:17 PM
> To: 'dev@ctakes.apache.org'
> Subject: RE: ctakes-dictionary-lookup-fast
>
> The image didn't come through for me. Can you post the image
> somewhere and send the url? Thanks.
>
>
> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> Sent: Thursday, November 06, 2014 2:55 PM
> To: dev@ctakes.apache.org
> Subject: ctakes-dictionary-lookup-fast
>
> Hi,
> The original plan was to update AggregatePlaintextUMLSProcessor.xml to
> use the new ultrafast dictionary lookup in the upcoming 3.2.1 release.
> However, the output is slightly different the old cTAKES dictionary
> where it no longer has a SNOMED/RXNORM consumer (Returns CUI's only
> and doesn't post process map back to the SNOMED/RXNORM codes.) This
> can certainly be done again, but I am not sure how many people are
> dependent on the AggregatePlaintextUMLSProcessor.xml to consider this
> a patch release.
> Some Options/Ideas:
>
> 1) Create a AggreatePlaintextUMLSFastProcessor.xml which defaults to
> dictionary-lookup-fast. But doesn't return the codes for now. We
> replace the default pipeline when SNOMED/RXNORM codes are returned again.
>
> 2) Push forward with defaulting to the new dictionary-lookup-fast in
> AggregatePlaintextUMLSProcessor.xml
>
> Example output of dictionary-lookup-fast:
>
> [cid:image001.png@01CFF9D9.E5D2CA50]
RE: ctakes-dictionary-lookup-fast
Posted by "Masanz, James J." <Ma...@mayo.edu>.
sounds good to me.
thanks for attaching the images to the JIRA.
-- James
________________________________________
From: Chen, Pei [Pei.Chen@childrens.harvard.edu]
Sent: Friday, November 07, 2014 10:00 AM
To: dev@ctakes.apache.org
Subject: RE: ctakes-dictionary-lookup-fast
Attached screenshots of CVD output to the Jira[1].
As much as I hate maintaining more desc xml's, but I think it's prudent to create a separate one for a patch release temporarily for ctakes-dictionary-lookup-fast so users do not get blindsided by the change in output.
So users can still choose the existing behavior: AggregatePlaintextUMLSProcessor.xml
Or the new dictionary lookup: AggregatePlaintextFastUMLSProcessor.xml
[1] https://issues.apache.org/jira/browse/CTAKES-325
We can replace the xml's in the next major/minor release...
--Pei
> -----Original Message-----
> From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
> Sent: Thursday, November 06, 2014 10:17 PM
> To: 'dev@ctakes.apache.org'
> Subject: RE: ctakes-dictionary-lookup-fast
>
> The image didn't come through for me. Can you post the image somewhere
> and send the url? Thanks.
>
>
> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> Sent: Thursday, November 06, 2014 2:55 PM
> To: dev@ctakes.apache.org
> Subject: ctakes-dictionary-lookup-fast
>
> Hi,
> The original plan was to update AggregatePlaintextUMLSProcessor.xml to
> use the new ultrafast dictionary lookup in the upcoming 3.2.1 release.
> However, the output is slightly different the old cTAKES dictionary where it
> no longer has a SNOMED/RXNORM consumer (Returns CUI's only and
> doesn't post process map back to the SNOMED/RXNORM codes.) This can
> certainly be done again, but I am not sure how many people are dependent
> on the AggregatePlaintextUMLSProcessor.xml to consider this a patch
> release.
> Some Options/Ideas:
>
> 1) Create a AggreatePlaintextUMLSFastProcessor.xml which defaults to
> dictionary-lookup-fast. But doesn't return the codes for now. We replace
> the default pipeline when SNOMED/RXNORM codes are returned again.
>
> 2) Push forward with defaulting to the new dictionary-lookup-fast in
> AggregatePlaintextUMLSProcessor.xml
>
> Example output of dictionary-lookup-fast:
>
> [cid:image001.png@01CFF9D9.E5D2CA50]
RE: ctakes-dictionary-lookup-fast
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Attached screenshots of CVD output to the Jira[1].
As much as I hate maintaining more desc xml's, but I think it's prudent to create a separate one for a patch release temporarily for ctakes-dictionary-lookup-fast so users do not get blindsided by the change in output.
So users can still choose the existing behavior: AggregatePlaintextUMLSProcessor.xml
Or the new dictionary lookup: AggregatePlaintextFastUMLSProcessor.xml
[1] https://issues.apache.org/jira/browse/CTAKES-325
We can replace the xml's in the next major/minor release...
--Pei
> -----Original Message-----
> From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
> Sent: Thursday, November 06, 2014 10:17 PM
> To: 'dev@ctakes.apache.org'
> Subject: RE: ctakes-dictionary-lookup-fast
>
> The image didn't come through for me. Can you post the image somewhere
> and send the url? Thanks.
>
>
> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> Sent: Thursday, November 06, 2014 2:55 PM
> To: dev@ctakes.apache.org
> Subject: ctakes-dictionary-lookup-fast
>
> Hi,
> The original plan was to update AggregatePlaintextUMLSProcessor.xml to
> use the new ultrafast dictionary lookup in the upcoming 3.2.1 release.
> However, the output is slightly different the old cTAKES dictionary where it
> no longer has a SNOMED/RXNORM consumer (Returns CUI's only and
> doesn't post process map back to the SNOMED/RXNORM codes.) This can
> certainly be done again, but I am not sure how many people are dependent
> on the AggregatePlaintextUMLSProcessor.xml to consider this a patch
> release.
> Some Options/Ideas:
>
> 1) Create a AggreatePlaintextUMLSFastProcessor.xml which defaults to
> dictionary-lookup-fast. But doesn't return the codes for now. We replace
> the default pipeline when SNOMED/RXNORM codes are returned again.
>
> 2) Push forward with defaulting to the new dictionary-lookup-fast in
> AggregatePlaintextUMLSProcessor.xml
>
> Example output of dictionary-lookup-fast:
>
> [cid:image001.png@01CFF9D9.E5D2CA50]
RE: ctakes-dictionary-lookup-fast
Posted by "Masanz, James J." <Ma...@mayo.edu>.
The image didn't come through for me. Can you post the image somewhere and send the url? Thanks.
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: Thursday, November 06, 2014 2:55 PM
To: dev@ctakes.apache.org
Subject: ctakes-dictionary-lookup-fast
Hi,
The original plan was to update AggregatePlaintextUMLSProcessor.xml to use the new ultrafast dictionary lookup in the upcoming 3.2.1 release.
However, the output is slightly different the old cTAKES dictionary where it no longer has a SNOMED/RXNORM consumer (Returns CUI's only and doesn't post process map back to the SNOMED/RXNORM codes.) This can certainly be done again, but I am not sure how many people are dependent on the AggregatePlaintextUMLSProcessor.xml to consider this a patch release.
Some Options/Ideas:
1) Create a AggreatePlaintextUMLSFastProcessor.xml which defaults to dictionary-lookup-fast. But doesn't return the codes for now. We replace the default pipeline when SNOMED/RXNORM codes are returned again.
2) Push forward with defaulting to the new dictionary-lookup-fast in AggregatePlaintextUMLSProcessor.xml
Example output of dictionary-lookup-fast:
[cid:image001.png@01CFF9D9.E5D2CA50]