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Posted to dev@ctakes.apache.org by Tomasz Oliwa <ol...@uchicago.edu> on 2015/11/13 00:27:42 UTC
cTAKES dictionary lookup behavior question
Hi,
cTAKES has a dictionary lookup behavior that I cannot explain, you can verify the queries via the cTAKES demo that has been posted here at: http://52.27.22.206:8080/index.jsp but it also happens with the current 3.2.2 version and the fast dictionary UMLS lookup
SENTENCE: Took the baby to the hospital.
VB DT NN IN DT NN
|===| |======|
Event Anatomy
C1305907
It finds the "baby tooth" annotation. The only CUI texts in the default fast dictionary for C1305907 are
C1305907|primary tooth
C1305907|milk tooth
C1305907|baby tooth
How can "baby to" trigger the "baby tooth" annotation?
Regards,
Tomasz
RE: cTAKES dictionary lookup behavior question
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
You are welcome - thank you for finding and reporting the bug!
-----Original Message-----
From: Tomasz Oliwa [mailto:oliwa@uchicago.edu]
Sent: Monday, November 16, 2015 4:08 PM
To: dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
Sean,
I checked out 'ctakes/trunk' with this fix and run it on the examples from the Description. It no longer finds the incorrect annotations mentioned in the Description. I closed the JIRA entry. Thanks for the quick fix.
Regards,
Tomasz
________________________________________
From: Finan, Sean [Sean.Finan@childrens.harvard.edu]
Sent: Monday, November 16, 2015 11:25 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
Hi Tomasz,
I just checked in a fix. Could you please re-run your tests and close the issue if it passes?
Thanks,
Sean
-----Original Message-----
From: Tomasz Oliwa [mailto:oliwa@uchicago.edu]
Sent: Monday, November 16, 2015 11:36 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
Sean,
I created a JIRA entry for this bug at: https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D389&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=1RTSCop2kmDAXve36EPdNJo6avl2B2SPpQcxCZZdeFw&s=2TRn9S89nvbp0TDN_LC1xTglF3VWlqnkgV5KdURu4KM&e=
It would be great you could check in a fix for it.
Regards,
Tomasz
________________________________________
From: Finan, Sean [Sean.Finan@childrens.harvard.edu]
Sent: Monday, November 16, 2015 10:20 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
Hi all,
This is not intended behavior, it is a bug. I will check in a fix soon ...
-----Original Message-----
From: Tomasz Oliwa [mailto:oliwa@uchicago.edu]
Sent: Thursday, November 12, 2015 6:53 PM
To: britt fitch; dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
Britt,
I observed it also depends on what the "missed" word is.
"baby to" , "baby too" match C1305907 of "baby tooth", however "baby token" does not match it.
"electrolyte le", "electrolyte lev" match C0428284 "electrolyte level", but "electrolyte dev" does not match.
It seems if the "missed" word contains the same characters that the word found in the fast dictionary starts with, a match is made?
Is there any way to tweak or customize this behavior?
Thanks,
Tomasz
________________________________
From: britt fitch [britt.fitch@wiredinformatics.com]
Sent: Thursday, November 12, 2015 5:36 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES dictionary lookup behavior question
The rare words, given the example terms below are "primary", "milk", and "baby".
The lookup allows for a certain number of "misses".
The "baby to" hits on "baby" as the rare word.
"baby to" compared to "baby tooth" is 1 "miss" and qualifies as a match. (in practice, if I recall correctly, "to" is actually discarded entirely, so the comparison is actually "baby" : "baby tooth").
Others can correct my napkin logic though.
This is a pretty common scenario when a single term ends up matching to a larger term because of the allowance of misses.
For example:
"oxygen" > "oxygen therapy"
"pathology" > "pathology department" , "pathology procedure"
"exercise" > "exercise pain management"
Those are just some quick examples. It depends heavily on what the ontology contains though.
Cheers,
Britt
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
https://urldefense.proofpoint.com/v2/url?u=http-3A__wiredinformatics.com&d=BQIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=nrheHTAYzgKYX9njwAR5G_NJXfSe_sbYbOMaifjWZwQ&s=6LcknYupSIqPd8Uml-tNRhwLudfDpVLBcC5JjZFhFQo&e=
Britt.Fitch@wiredinformatics.com
On Nov 12, 2015, at 6:27 PM, Tomasz Oliwa <ol...@uchicago.edu>> wrote:
Hi,
cTAKES has a dictionary lookup behavior that I cannot explain, you can verify the queries via the cTAKES demo that has been posted here at: https://urldefense.proofpoint.com/v2/url?u=http-3A__52.27.22.206-3A8080_index.jsp&d=BQIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=nrheHTAYzgKYX9njwAR5G_NJXfSe_sbYbOMaifjWZwQ&s=UmyBQ5X4UBJggOqmIQkANeD0eUz0nrLqGN8Z6__iB8o&e= but it also happens with the current 3.2.2 version and the fast dictionary UMLS lookup
SENTENCE: Took the baby to the hospital.
VB DT NN IN DT NN
|===| |======|
Event Anatomy
C1305907
It finds the "baby tooth" annotation. The only CUI texts in the default fast dictionary for C1305907 are
C1305907|primary tooth
C1305907|milk tooth
C1305907|baby tooth
How can "baby to" trigger the "baby tooth" annotation?
Regards,
Tomasz
RE: cTAKES dictionary lookup behavior question
Posted by Tomasz Oliwa <ol...@uchicago.edu>.
Sean,
I checked out 'ctakes/trunk' with this fix and run it on the examples from the Description. It no longer finds the incorrect annotations mentioned in the Description. I closed the JIRA entry. Thanks for the quick fix.
Regards,
Tomasz
________________________________________
From: Finan, Sean [Sean.Finan@childrens.harvard.edu]
Sent: Monday, November 16, 2015 11:25 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
Hi Tomasz,
I just checked in a fix. Could you please re-run your tests and close the issue if it passes?
Thanks,
Sean
-----Original Message-----
From: Tomasz Oliwa [mailto:oliwa@uchicago.edu]
Sent: Monday, November 16, 2015 11:36 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
Sean,
I created a JIRA entry for this bug at: https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D389&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=1RTSCop2kmDAXve36EPdNJo6avl2B2SPpQcxCZZdeFw&s=2TRn9S89nvbp0TDN_LC1xTglF3VWlqnkgV5KdURu4KM&e=
It would be great you could check in a fix for it.
Regards,
Tomasz
________________________________________
From: Finan, Sean [Sean.Finan@childrens.harvard.edu]
Sent: Monday, November 16, 2015 10:20 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
Hi all,
This is not intended behavior, it is a bug. I will check in a fix soon ...
-----Original Message-----
From: Tomasz Oliwa [mailto:oliwa@uchicago.edu]
Sent: Thursday, November 12, 2015 6:53 PM
To: britt fitch; dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
Britt,
I observed it also depends on what the "missed" word is.
"baby to" , "baby too" match C1305907 of "baby tooth", however "baby token" does not match it.
"electrolyte le", "electrolyte lev" match C0428284 "electrolyte level", but "electrolyte dev" does not match.
It seems if the "missed" word contains the same characters that the word found in the fast dictionary starts with, a match is made?
Is there any way to tweak or customize this behavior?
Thanks,
Tomasz
________________________________
From: britt fitch [britt.fitch@wiredinformatics.com]
Sent: Thursday, November 12, 2015 5:36 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES dictionary lookup behavior question
The rare words, given the example terms below are "primary", "milk", and "baby".
The lookup allows for a certain number of "misses".
The "baby to" hits on "baby" as the rare word.
"baby to" compared to "baby tooth" is 1 "miss" and qualifies as a match. (in practice, if I recall correctly, "to" is actually discarded entirely, so the comparison is actually "baby" : "baby tooth").
Others can correct my napkin logic though.
This is a pretty common scenario when a single term ends up matching to a larger term because of the allowance of misses.
For example:
"oxygen" > "oxygen therapy"
"pathology" > "pathology department" , "pathology procedure"
"exercise" > "exercise pain management"
Those are just some quick examples. It depends heavily on what the ontology contains though.
Cheers,
Britt
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
https://urldefense.proofpoint.com/v2/url?u=http-3A__wiredinformatics.com&d=BQIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=nrheHTAYzgKYX9njwAR5G_NJXfSe_sbYbOMaifjWZwQ&s=6LcknYupSIqPd8Uml-tNRhwLudfDpVLBcC5JjZFhFQo&e=
Britt.Fitch@wiredinformatics.com
On Nov 12, 2015, at 6:27 PM, Tomasz Oliwa <ol...@uchicago.edu>> wrote:
Hi,
cTAKES has a dictionary lookup behavior that I cannot explain, you can verify the queries via the cTAKES demo that has been posted here at: https://urldefense.proofpoint.com/v2/url?u=http-3A__52.27.22.206-3A8080_index.jsp&d=BQIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=nrheHTAYzgKYX9njwAR5G_NJXfSe_sbYbOMaifjWZwQ&s=UmyBQ5X4UBJggOqmIQkANeD0eUz0nrLqGN8Z6__iB8o&e= but it also happens with the current 3.2.2 version and the fast dictionary UMLS lookup
SENTENCE: Took the baby to the hospital.
VB DT NN IN DT NN
|===| |======|
Event Anatomy
C1305907
It finds the "baby tooth" annotation. The only CUI texts in the default fast dictionary for C1305907 are
C1305907|primary tooth
C1305907|milk tooth
C1305907|baby tooth
How can "baby to" trigger the "baby tooth" annotation?
Regards,
Tomasz
RE: cTAKES dictionary lookup behavior question
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Tomasz,
I just checked in a fix. Could you please re-run your tests and close the issue if it passes?
Thanks,
Sean
-----Original Message-----
From: Tomasz Oliwa [mailto:oliwa@uchicago.edu]
Sent: Monday, November 16, 2015 11:36 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
Sean,
I created a JIRA entry for this bug at: https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D389&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=1RTSCop2kmDAXve36EPdNJo6avl2B2SPpQcxCZZdeFw&s=2TRn9S89nvbp0TDN_LC1xTglF3VWlqnkgV5KdURu4KM&e=
It would be great you could check in a fix for it.
Regards,
Tomasz
________________________________________
From: Finan, Sean [Sean.Finan@childrens.harvard.edu]
Sent: Monday, November 16, 2015 10:20 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
Hi all,
This is not intended behavior, it is a bug. I will check in a fix soon ...
-----Original Message-----
From: Tomasz Oliwa [mailto:oliwa@uchicago.edu]
Sent: Thursday, November 12, 2015 6:53 PM
To: britt fitch; dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
Britt,
I observed it also depends on what the "missed" word is.
"baby to" , "baby too" match C1305907 of "baby tooth", however "baby token" does not match it.
"electrolyte le", "electrolyte lev" match C0428284 "electrolyte level", but "electrolyte dev" does not match.
It seems if the "missed" word contains the same characters that the word found in the fast dictionary starts with, a match is made?
Is there any way to tweak or customize this behavior?
Thanks,
Tomasz
________________________________
From: britt fitch [britt.fitch@wiredinformatics.com]
Sent: Thursday, November 12, 2015 5:36 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES dictionary lookup behavior question
The rare words, given the example terms below are "primary", "milk", and "baby".
The lookup allows for a certain number of "misses".
The "baby to" hits on "baby" as the rare word.
"baby to" compared to "baby tooth" is 1 "miss" and qualifies as a match. (in practice, if I recall correctly, "to" is actually discarded entirely, so the comparison is actually "baby" : "baby tooth").
Others can correct my napkin logic though.
This is a pretty common scenario when a single term ends up matching to a larger term because of the allowance of misses.
For example:
"oxygen" > "oxygen therapy"
"pathology" > "pathology department" , "pathology procedure"
"exercise" > "exercise pain management"
Those are just some quick examples. It depends heavily on what the ontology contains though.
Cheers,
Britt
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
https://urldefense.proofpoint.com/v2/url?u=http-3A__wiredinformatics.com&d=BQIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=nrheHTAYzgKYX9njwAR5G_NJXfSe_sbYbOMaifjWZwQ&s=6LcknYupSIqPd8Uml-tNRhwLudfDpVLBcC5JjZFhFQo&e=
Britt.Fitch@wiredinformatics.com
On Nov 12, 2015, at 6:27 PM, Tomasz Oliwa <ol...@uchicago.edu>> wrote:
Hi,
cTAKES has a dictionary lookup behavior that I cannot explain, you can verify the queries via the cTAKES demo that has been posted here at: https://urldefense.proofpoint.com/v2/url?u=http-3A__52.27.22.206-3A8080_index.jsp&d=BQIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=nrheHTAYzgKYX9njwAR5G_NJXfSe_sbYbOMaifjWZwQ&s=UmyBQ5X4UBJggOqmIQkANeD0eUz0nrLqGN8Z6__iB8o&e= but it also happens with the current 3.2.2 version and the fast dictionary UMLS lookup
SENTENCE: Took the baby to the hospital.
VB DT NN IN DT NN
|===| |======|
Event Anatomy
C1305907
It finds the "baby tooth" annotation. The only CUI texts in the default fast dictionary for C1305907 are
C1305907|primary tooth
C1305907|milk tooth
C1305907|baby tooth
How can "baby to" trigger the "baby tooth" annotation?
Regards,
Tomasz
RE: cTAKES dictionary lookup behavior question
Posted by Tomasz Oliwa <ol...@uchicago.edu>.
Sean,
I created a JIRA entry for this bug at: https://issues.apache.org/jira/browse/CTAKES-389
It would be great you could check in a fix for it.
Regards,
Tomasz
________________________________________
From: Finan, Sean [Sean.Finan@childrens.harvard.edu]
Sent: Monday, November 16, 2015 10:20 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
Hi all,
This is not intended behavior, it is a bug. I will check in a fix soon ...
-----Original Message-----
From: Tomasz Oliwa [mailto:oliwa@uchicago.edu]
Sent: Thursday, November 12, 2015 6:53 PM
To: britt fitch; dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
Britt,
I observed it also depends on what the "missed" word is.
"baby to" , "baby too" match C1305907 of "baby tooth", however "baby token" does not match it.
"electrolyte le", "electrolyte lev" match C0428284 "electrolyte level", but "electrolyte dev" does not match.
It seems if the "missed" word contains the same characters that the word found in the fast dictionary starts with, a match is made?
Is there any way to tweak or customize this behavior?
Thanks,
Tomasz
________________________________
From: britt fitch [britt.fitch@wiredinformatics.com]
Sent: Thursday, November 12, 2015 5:36 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES dictionary lookup behavior question
The rare words, given the example terms below are "primary", "milk", and "baby".
The lookup allows for a certain number of "misses".
The "baby to" hits on "baby" as the rare word.
"baby to" compared to "baby tooth" is 1 "miss" and qualifies as a match. (in practice, if I recall correctly, "to" is actually discarded entirely, so the comparison is actually "baby" : "baby tooth").
Others can correct my napkin logic though.
This is a pretty common scenario when a single term ends up matching to a larger term because of the allowance of misses.
For example:
"oxygen" > "oxygen therapy"
"pathology" > "pathology department" , "pathology procedure"
"exercise" > "exercise pain management"
Those are just some quick examples. It depends heavily on what the ontology contains though.
Cheers,
Britt
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
https://urldefense.proofpoint.com/v2/url?u=http-3A__wiredinformatics.com&d=BQIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=nrheHTAYzgKYX9njwAR5G_NJXfSe_sbYbOMaifjWZwQ&s=6LcknYupSIqPd8Uml-tNRhwLudfDpVLBcC5JjZFhFQo&e=
Britt.Fitch@wiredinformatics.com
On Nov 12, 2015, at 6:27 PM, Tomasz Oliwa <ol...@uchicago.edu>> wrote:
Hi,
cTAKES has a dictionary lookup behavior that I cannot explain, you can verify the queries via the cTAKES demo that has been posted here at: https://urldefense.proofpoint.com/v2/url?u=http-3A__52.27.22.206-3A8080_index.jsp&d=BQIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=nrheHTAYzgKYX9njwAR5G_NJXfSe_sbYbOMaifjWZwQ&s=UmyBQ5X4UBJggOqmIQkANeD0eUz0nrLqGN8Z6__iB8o&e= but it also happens with the current 3.2.2 version and the fast dictionary UMLS lookup
SENTENCE: Took the baby to the hospital.
VB DT NN IN DT NN
|===| |======|
Event Anatomy
C1305907
It finds the "baby tooth" annotation. The only CUI texts in the default fast dictionary for C1305907 are
C1305907|primary tooth
C1305907|milk tooth
C1305907|baby tooth
How can "baby to" trigger the "baby tooth" annotation?
Regards,
Tomasz
RE: cTAKES dictionary lookup behavior question
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi all,
This is not intended behavior, it is a bug. I will check in a fix soon ...
-----Original Message-----
From: Tomasz Oliwa [mailto:oliwa@uchicago.edu]
Sent: Thursday, November 12, 2015 6:53 PM
To: britt fitch; dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
Britt,
I observed it also depends on what the "missed" word is.
"baby to" , "baby too" match C1305907 of "baby tooth", however "baby token" does not match it.
"electrolyte le", "electrolyte lev" match C0428284 "electrolyte level", but "electrolyte dev" does not match.
It seems if the "missed" word contains the same characters that the word found in the fast dictionary starts with, a match is made?
Is there any way to tweak or customize this behavior?
Thanks,
Tomasz
________________________________
From: britt fitch [britt.fitch@wiredinformatics.com]
Sent: Thursday, November 12, 2015 5:36 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES dictionary lookup behavior question
The rare words, given the example terms below are "primary", "milk", and "baby".
The lookup allows for a certain number of "misses".
The "baby to" hits on "baby" as the rare word.
"baby to" compared to "baby tooth" is 1 "miss" and qualifies as a match. (in practice, if I recall correctly, "to" is actually discarded entirely, so the comparison is actually "baby" : "baby tooth").
Others can correct my napkin logic though.
This is a pretty common scenario when a single term ends up matching to a larger term because of the allowance of misses.
For example:
"oxygen" > "oxygen therapy"
"pathology" > "pathology department" , "pathology procedure"
"exercise" > "exercise pain management"
Those are just some quick examples. It depends heavily on what the ontology contains though.
Cheers,
Britt
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
https://urldefense.proofpoint.com/v2/url?u=http-3A__wiredinformatics.com&d=BQIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=nrheHTAYzgKYX9njwAR5G_NJXfSe_sbYbOMaifjWZwQ&s=6LcknYupSIqPd8Uml-tNRhwLudfDpVLBcC5JjZFhFQo&e=
Britt.Fitch@wiredinformatics.com
On Nov 12, 2015, at 6:27 PM, Tomasz Oliwa <ol...@uchicago.edu>> wrote:
Hi,
cTAKES has a dictionary lookup behavior that I cannot explain, you can verify the queries via the cTAKES demo that has been posted here at: https://urldefense.proofpoint.com/v2/url?u=http-3A__52.27.22.206-3A8080_index.jsp&d=BQIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=nrheHTAYzgKYX9njwAR5G_NJXfSe_sbYbOMaifjWZwQ&s=UmyBQ5X4UBJggOqmIQkANeD0eUz0nrLqGN8Z6__iB8o&e= but it also happens with the current 3.2.2 version and the fast dictionary UMLS lookup
SENTENCE: Took the baby to the hospital.
VB DT NN IN DT NN
|===| |======|
Event Anatomy
C1305907
It finds the "baby tooth" annotation. The only CUI texts in the default fast dictionary for C1305907 are
C1305907|primary tooth
C1305907|milk tooth
C1305907|baby tooth
How can "baby to" trigger the "baby tooth" annotation?
Regards,
Tomasz
RE: cTAKES dictionary lookup behavior question
Posted by Tomasz Oliwa <ol...@uchicago.edu>.
Britt,
I observed it also depends on what the "missed" word is.
"baby to" , "baby too" match C1305907 of "baby tooth", however "baby token" does not match it.
"electrolyte le", "electrolyte lev" match C0428284 "electrolyte level", but "electrolyte dev" does not match.
It seems if the "missed" word contains the same characters that the word found in the fast dictionary starts with, a match is made?
Is there any way to tweak or customize this behavior?
Thanks,
Tomasz
________________________________
From: britt fitch [britt.fitch@wiredinformatics.com]
Sent: Thursday, November 12, 2015 5:36 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES dictionary lookup behavior question
The rare words, given the example terms below are “primary”, “milk”, and “baby”.
The lookup allows for a certain number of “misses”.
The “baby to” hits on “baby” as the rare word.
“baby to” compared to “baby tooth” is 1 “miss” and qualifies as a match. (in practice, if I recall correctly, “to” is actually discarded entirely, so the comparison is actually “baby” : “baby tooth”).
Others can correct my napkin logic though.
This is a pretty common scenario when a single term ends up matching to a larger term because of the allowance of misses.
For example:
“oxygen” > “oxygen therapy”
“pathology” > “pathology department” , “pathology procedure”
“exercise” > “exercise pain management”
Those are just some quick examples. It depends heavily on what the ontology contains though.
Cheers,
Britt
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
Britt.Fitch@wiredinformatics.com
On Nov 12, 2015, at 6:27 PM, Tomasz Oliwa <ol...@uchicago.edu>> wrote:
Hi,
cTAKES has a dictionary lookup behavior that I cannot explain, you can verify the queries via the cTAKES demo that has been posted here at: http://52.27.22.206:8080/index.jsp but it also happens with the current 3.2.2 version and the fast dictionary UMLS lookup
SENTENCE: Took the baby to the hospital.
VB DT NN IN DT NN
|===| |======|
Event Anatomy
C1305907
It finds the "baby tooth" annotation. The only CUI texts in the default fast dictionary for C1305907 are
C1305907|primary tooth
C1305907|milk tooth
C1305907|baby tooth
How can "baby to" trigger the "baby tooth" annotation?
Regards,
Tomasz
Re: cTAKES dictionary lookup behavior question
Posted by britt fitch <br...@wiredinformatics.com>.
The rare words, given the example terms below are “primary”, “milk”, and “baby”.
The lookup allows for a certain number of “misses”.
The “baby to” hits on “baby” as the rare word.
“baby to” compared to “baby tooth” is 1 “miss” and qualifies as a match. (in practice, if I recall correctly, “to” is actually discarded entirely, so the comparison is actually “baby” : “baby tooth”).
Others can correct my napkin logic though.
This is a pretty common scenario when a single term ends up matching to a larger term because of the allowance of misses.
For example:
“oxygen” > “oxygen therapy”
“pathology” > “pathology department” , “pathology procedure”
“exercise” > “exercise pain management”
Those are just some quick examples. It depends heavily on what the ontology contains though.
Cheers,
Britt
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
Britt.Fitch@wiredinformatics.com
> On Nov 12, 2015, at 6:27 PM, Tomasz Oliwa <ol...@uchicago.edu> wrote:
>
> Hi,
>
> cTAKES has a dictionary lookup behavior that I cannot explain, you can verify the queries via the cTAKES demo that has been posted here at: http://52.27.22.206:8080/index.jsp but it also happens with the current 3.2.2 version and the fast dictionary UMLS lookup
>
> SENTENCE: Took the baby to the hospital.
> VB DT NN IN DT NN
> |===| |======|
> Event Anatomy
> C1305907
>
> It finds the "baby tooth" annotation. The only CUI texts in the default fast dictionary for C1305907 are
>
> C1305907|primary tooth
> C1305907|milk tooth
> C1305907|baby tooth
>
> How can "baby to" trigger the "baby tooth" annotation?
>
> Regards,
> Tomasz