Hi Abad,
Since you are changing code ...
Line #320 of AbstractJcasTermAnnotator:
final boolean isNonLookup = baseToken instanceof PunctuationToken
|| baseToken instanceof NumToken
|| baseToken instanceof ContractionToken
|| baseToken instanceof SymbolToken;
Comment out:
|| baseToken instanceof NumToken
Sean
________________________________________
From: [email protected] <[email protected]>
Sent: Wednesday, September 16, 2020 1:01 PM
To: [email protected]
Subject: RE: Building a new custom dictionary or Updating/Adding values to the
existing dictionary in cTAKES [EXTERNAL]
* External Email - Caution *
Hi Sean,
We tried setting the exclusion tags="". PFB the changes we did
1. Set the value of String DEFAULT_EXCLUSION_TAGS = "" ; in
JCasTermAnnotator.java file
2. Removed the values of <value> tag of <nameValuePair > with <name> tag as
'exclusionTags' in UmlsLookupAnnotator.xml & UmlsOverlapLookupAnnotator.xml
But still we could see that "97112" was not getting picked up from dictionary.
Is there anywhere else we need to try the changes. Kindly advise
Thanks & Regards
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028
-----Original Message-----
From: Finan, Sean <[email protected]>
Sent: Tuesday, September 15, 2020 9:06 PM
To: [email protected]
Subject: Re: Building a new custom dictionary or Updating/Adding values to the
existing dictionary in cTAKES [EXTERNAL]
[External]
Hi Abad,
The first thing that I would try for the "97112" problem is changing the parts
of speech that are ignored for lookup. Right now a pure number is ignored - it
is not a word. So, similar to what I said in my previous email, change the
dictionary lookup parameter exclusionTags. But to make sure that you get
everything, you can first try no exclusions:
set exclusionTags=""
My guess with the F84.1 problem is that your sentence splitter is splitting
"F84.1" but not splitting "F84 . 1".
I think that the best way to start debugging is adding the PrettyTextWriter to
the end of the piper and looking at its output (see my previous email). It
will print each sentence on a line and indicate the part of speech for each
token. If you can quickly and easily see what the system is doing then you
might start to understand what needs to be changed to fit your data.
Sean
________________________________________
From: [email protected] <[email protected]>
Sent: Tuesday, September 15, 2020 11:15 AM
To: [email protected]
Subject: RE: Building a new custom dictionary or Updating/Adding values to the
existing dictionary in cTAKES [EXTERNAL]
* External Email - Caution *
Thank you Sean for the detailed response. I think there was miscommunication
from our end with the requirement. Your solution of adding spaces between the
entries worked but it required the input text also to have the spaces. If the
text comes in as 'F84.1' cTAKES didn't reckon the token but if the text came as
'F84 . 1' then cTAKES was recognizing the tokens for the below INSERT scripts.
INSERT INTO CUI_TERMS VALUES(4352,0,3, ‘F84 . 1’,’F84’)
But we encountered a similar issue when we configured an INSERT entry as below
for CPT codes,
INSERT INTO CUI_TERMS VALUES(41154,0,1, ‘97112’,’97112’)
Where 97112 is a CPT code(which usually doesn’t have decimals or '.'). We
expected cTAKES to recognize the CPT code '97112' as a separate token but it
didn't. Could you pls. advise us on why this issue came up.
Is there something wrong in the configuration. Do we need to have something
additional for cTAKES to recognize the code alone as a separate token Is there
any other way in which we can try to get the respective ICD/CPT code of the
identified annotation from cTAKES, like querying the CPT/ICD table using the
fetched CUI? Kindly advise.
Thanks & Regards
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028
-----Original Message-----
From: Finan, Sean <[email protected]>
Sent: Monday, September 14, 2020 9:35 PM
To: [email protected]
Subject: Re: Building a new custom dictionary or Updating/Adding values to the
existing dictionary in cTAKES [EXTERNAL]
[External]
Hi Abad,
I think that you need to make only one minor change.
ctakes uses "tokens" for identification and not the actual text. Tokenization
turns text such as "F84.1" into "F84 . 1" The first token being F84, followed
by a token encompassing '.' and another with '1'. The manner in which this is
indicated in the .script file is by adding a space between each token. This
makes the full entry:
INSERT INTO CUI_TERMS VALUES(4352,0,3, ‘F84 . 1’,’F84’)
Notice that the token length is now 3 and the full text contains the
between-token spaces. This would carry forward for the other entries, such as:
INSERT INTO CUI_TERMS VALUES(4352,3,4, ‘F84 . 1 pdd’, ‘pdd’)
Sean
________________________________
From: [email protected] <[email protected]>
Sent: Monday, September 14, 2020 11:32 AM
To: [email protected]
Subject: RE: Building a new custom dictionary or Updating/Adding values to the
existing dictionary in cTAKES [EXTERNAL]
* External Email - Caution *
Hi Team,
I hope you all are doing good. With your support ,We were able to successfully
add our required synonyms into existing dictionary and could see that it was
getting successfully picked up by cTAKES. Now we have a requirement to
configure the ICD and CPT also, where we followed the steps as mentioned in
cTAKES wiki and generated the respective .script file.
The newly created dictionary which comprises of SNOMEDCT_US,RxNORM,ICD10,CPT
are identifying the descriptions as expected but we have a requirement to
extract the ICD code for the respective description . so the scenario would be
like for a text like below
‘F84.1 pervasive developmental disorders’
We would need cTAKES to reckon F84.1 as a token or at least as an attribute in
any of the ‘IdentifiedAnnotation’. So for achieving the same based on our prior
experience we tried to tweak the dictionary where we added a synonym for the
existing CUI as below
INSERT INTO CUI_TERMS VALUES(4352,1,4, ‘F84.1 pervasive developmental
disorders’, ‘pervasive’) INSERT INTO CUI_TERMS VALUES(4352,1,2, ‘F84.1 pdd’,
‘pdd’) INSERT INTO CUI_TERMS VALUES(4352,0,1, ‘F84.1’,’F84.1’)
Though we have seen cTAKES can identify ‘F84’ alone as a token but it won’t
consider whenever a ‘.’ Has been encountered. As an end result cTAKES won’t be
able to give the ICD codes like F84.1,M25.6 as separate tokens. Since almost
all of the ICD codes have a ‘.’ Associated with it, this way of tweaking the
dictionary is not working. Infact cTAKES is recognizing the digit after decimal
within the ‘FractionAnnotation’
Does cTAKES have the capability to return the code like ICD code while
retrieving the token as an individual token or as an attribute in any of the
tokens
Is there any other way in which the dictionary can be tweaked , so that a
synonym addition as below will recognize the ICD code as a token and will be
returned from cTAKES
INSERT INTO CUI_TERMS VALUES(4352,0,1, ‘F84.1’,’F84.1’)
Kindly check and advise us on how to proceed on this situation
Thanks & Regards
[cid:D3145E69-CD94-48C1-877F-5134EEAFB598]
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028
From: Remy Sanouillet <[email protected]>
Sent: Tuesday, June 2, 2020 7:23 AM
To: [email protected]
Subject: Re: Building a new custom dictionary or Updating/Adding values to the
existing dictionary in cTAKES
[External]
Hi Abad,
• How can we point cTAKES application to multiple dictionaries. Currently
only sno_rx_16ab is pointed to the application, how can I tweak it to point
that to multiple dictionary simultaneously. Or you meant to say create a fresh
dictionary with all the vocabularies and point just that in cTAKES.
If you go back in the archive a bit, you should find a thread where I went into
detail on how to add multiple dictionaries. Combining all dictionaries into a
fresh dictionary is not recommended for obvious reasons. If you can't find the
thread, I will dig it up.
• So for these edits I will have to add INSERT queries to respective
tables in the sno_rx_16ab.script file right? Do I need to make any more changes
for these tokens to get reflected in cTAKES.
Nope! That is all that is needed and next time you launch cTakes, it should
recognize your new entries.
• If it is a non-existing CUI , I can get the respective CUI,TUI from
here
https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__apc01.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Futs.nlm.nih.gov-252F-252Fmetathesaurus.html-26amp-3Bdata-3D02-257C01-257CAbad.Ayyub-2540cognizant.com-257C28b35c064d474a289fbd08d858c7ea90-257Cde08c40719b9427d9fe8edf254300ca7-257C0-257C0-257C637356962959976394-26amp-3Bsdata-3D2tgzGJUzWdtDSTyT7MI93e2i17aeFW8Nqp3s4D1cj8g-253D-26amp-3Breserved-3D0%26d%3DDwIGaQ%26c%3DqS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU%26r%3Dfs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao%26m%3DhNvrRzAHvcCXfHnoaSacGNAAqM4UXu0zPaOlGH4K5ME%26s%3DWuQh-Ty9Xl9rlhk8J3aOBylaw9UQLLQxEGwKQGUOBZw%26e%3D&data=02%7C01%7CAbad.Ayyub%40cognizant.com%7Ccf606465888d49e922fa08d8598d0fec%7Cde08c40719b9427d9fe8edf254300ca7%7C0%7C0%7C637357809711644893&sdata=hXu2kXG4Xt%2Bw2kh61fAPVD0FRW25XcZWhcRAJtIGkf0%3D&reserved=0
<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__apc01.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Futs.nlm.nih.gov-252Fmetathesaurus.html-26data-3D02-257C01-257CAbad.Ayyub-2540cognizant.com-257Cc8b0b69302014cff91ac08d80697c6a7-257Cde08c40719b9427d9fe8edf254300ca7-257C0-257C0-257C637266596246493365-26sdata-3DhNixbxffJ9-252Fx-252Bho9J41gjonaT9IGLsxIqABKq1dpzG8-253D-26reserved-3D0%26d%3DDwMGaQ%26c%3DqS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU%26r%3Dfs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao%26m%3DYKrpBhJM7sqCBY3Ow1jSUhu5QBdlnoqFGZbsVZIHH8U%26s%3DAks7ZCfU7hTRPTyJJdrrdupKbd1n1TpuFdf-10yQtrA%26e%3D&data=02%7C01%7CAbad.Ayyub%40cognizant.com%7Ccf606465888d49e922fa08d8598d0fec%7Cde08c40719b9427d9fe8edf254300ca7%7C0%7C0%7C637357809711649892&sdata=vBFcrxWI0hFUqB%2B1s0F%2FWqPN%2F%2BNFTXm4pCaJB16qCfI%3D&reserved=0>
right?
Correct! Remember that the ontology has multiple-inheritance so you need to
grab all the TUIs for a given CUI.
• Based on the source I will have to add entry to respective table right?
Like SNOMED,RxNORM,ICD 10 and a CUI will belong to either one of it and not in
all. Correct me if am wrong on this understanding
That is also correct. And most of the time, the dictionaries only contain one
CODE table so it is not even a question. However, sno_rx_16ab is an exception
with both a CODE table for SNOMEDCT_US and RXNORM. They mostly do not overlap.
I do remember that there were a couple of exceptions but, in the case where
that happens, the metathesaurus will show it.
For example: 'Acebutolol' (CUI: C0000946) has two SNOMEDCT_US codes (372815001
and 68088000) *and* an RXNORM of 149.
• PREFTERM table will be having only one entry for each CUI right?
Basically it’s a one-to-one mapping between CUI and PREFTERM . Correct me if am
wrong on this understanding.
You are correct here also. It is a one-to-one mapping although the system
appears to tolerate when the PREFTERM is missing.
Rémy Sanouillet
NLP Engineer
[email protected]<mailto:[email protected]>
[image.png]
ForeSee Medical, Inc.
12555 High Bluff Drive, Suite 100
San Diego, CA 92130
NOTICE: This e-mail message and all attachments transmitted with it are
intended solely for the use of the addressee and may contain legally privileged
and confidential information. If the reader of this message is not the intended
recipient, or an employee or agent responsible for delivering this message to
the intended recipient, you are hereby notified that any dissemination,
distribution, copying, or other use of this message or its attachments is
strictly prohibited. If you have received this message in error, please notify
the sender immediately by replying to this message and please delete it from
your computer.
On Mon, Jun 1, 2020 at 7:56 AM
<[email protected]<mailto:[email protected]>> wrote:
Thank you Remy and Peter for your responses. I hope you guys are doing good and
safe in this lock down period. Could you pls. help me on my below queries in
creating an additional dictionary.
• How to create additional dictionary. You meant to say using the UMLS
tool , so that using that tool we create .script files from .RRF files?
• How can we point cTAKES application to multiple dictionaries. Currently
only sno_rx_16ab is pointed to the application, how can I tweak it to point
that to multiple dictionary simultaneously. Or you meant to say create a fresh
dictionary with all the vocabularies and point just that in cTAKES.
I hope Remy was explaining editing the existing dictionary where I would deal
with two scenarios where one was with existing CUI and other was with
Non-existing CUI. Could you pls. resolve the below queries regarding the same.
• So for these edits I will have to add INSERT queries to respective
tables in the sno_rx_16ab.script file right? Do I need to make any more changes
for these tokens to get reflected in cTAKES.
• If it is a non-existing CUI , I can get the respective CUI,TUI from
here
https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__apc01.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Futs.nlm.nih.gov-252F-252Fmetathesaurus.html-26amp-3Bdata-3D02-257C01-257CAbad.Ayyub-2540cognizant.com-257C28b35c064d474a289fbd08d858c7ea90-257Cde08c40719b9427d9fe8edf254300ca7-257C0-257C0-257C637356962959976394-26amp-3Bsdata-3D2tgzGJUzWdtDSTyT7MI93e2i17aeFW8Nqp3s4D1cj8g-253D-26amp-3Breserved-3D0%26d%3DDwIGaQ%26c%3DqS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU%26r%3Dfs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao%26m%3DhNvrRzAHvcCXfHnoaSacGNAAqM4UXu0zPaOlGH4K5ME%26s%3DWuQh-Ty9Xl9rlhk8J3aOBylaw9UQLLQxEGwKQGUOBZw%26e%3D&data=02%7C01%7CAbad.Ayyub%40cognizant.com%7Ccf606465888d49e922fa08d8598d0fec%7Cde08c40719b9427d9fe8edf254300ca7%7C0%7C0%7C637357809711649892&sdata=5ffFqKOHKUDW8hrOw2%2Ftbg%2FumJa%2FbE%2B7oB84PMgUAbo%3D&reserved=0
<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__apc01.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Futs.nlm.nih.gov-252Fmetathesaurus.html-26data-3D02-257C01-257CAbad.Ayyub-2540cognizant.com-257Cc8b0b69302014cff91ac08d80697c6a7-257Cde08c40719b9427d9fe8edf254300ca7-257C0-257C0-257C637266596246503352-26sdata-3DbbpLuRz7gcbSopU7kFxTJrlsAiqZY4TiK15eq1l4qVs-253D-26reserved-3D0%26d%3DDwMGaQ%26c%3DqS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU%26r%3Dfs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao%26m%3DYKrpBhJM7sqCBY3Ow1jSUhu5QBdlnoqFGZbsVZIHH8U%26s%3D3BlK-CxQfaf_mvf6rMZ7MK1GJIEnflO1MlbEZ1oTsEM%26e%3D&data=02%7C01%7CAbad.Ayyub%40cognizant.com%7Ccf606465888d49e922fa08d8598d0fec%7Cde08c40719b9427d9fe8edf254300ca7%7C0%7C0%7C637357809711649892&sdata=UR%2F623xDp4qXTS7p%2BRxux0I0CN4w0rtyd4a13RxIMuU%3D&reserved=0>
right?
• Based on the source I will have to add entry to respective table right?
Like SNOMED,RxNORM,ICD 10 and a CUI will belong to either one of it and not in
all. Correct me if am wrong on this understanding
• PREFTERM table will be having only one entry for each CUI right?
Basically it’s a one-to-one mapping between CUI and PREFTERM . Correct me if am
wrong on this understanding.
Thanks & Regards
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028
From: Remy Sanouillet <[email protected]<mailto:[email protected]>>
Sent: Friday, May 29, 2020 9:25 PM
To: [email protected]<mailto:[email protected]>
Cc: [email protected]<mailto:[email protected]>
Subject: Re: Building a new custom dictionary or Updating/Adding values to the
existing dictionary in cTAKES
[External]
Hello Abad,
The short answer is, yes, the sno_rx_16ab can be "hacked". A couple of caveats
are that any mistake can stop all recognition and you will lose all your mods
on updates. So an additional dictionary is a recommended approach.
There are two cases. EIther the CUI you are adding already exists and you are
just adding a synonym. In that case, you only need to add one line:
INSERT INTO CUI_TERMS VALUES(CUI,RINDEX,TCOUNT,TEXT,RWORD)
where:
* CUI is the cui, nuf'said
* TEXT is the tokenized lowercase string for the entry. In your case 'pap
smear'. Most punctuation is a separate token. Single quotes are escaped by
doubling them
* RWORD is the one token in TEXT that is the most indicative (least common)
which will be used as the index in the lookup. In your case probably 'pap'
since it is not as common as 'smear'
* RINDEX is the index of RWORD in TEXT. First token is 0 which is the case
for 'pap'
* TCOUNT is the token count for TEXT. In your case, 2
So you would want to add:
INSERT INTO CUI_TERMS VALUES(200845,0,2,'pap smear','pap')
If the entry is a non-existing one, you will need to add a few more lines.
Their positions are unimportant as long as they are below the header lines
(below the final "SET SCHEMA PUBLIC" line).
1. INSERT INTO TUI VALUES(CUI,TUI)
One line for each TUI in the taxonomy
2. INSERT INTO SNOMEDCT_US VALUES(CUI,SNOMED) assuming you are adding a
SNOMED
3. INSERT INTO PREFTERM VALUES(CUI,PREFTERM) where PREFTERM is the pretty
string to describe the entry. It need not correspond to any indexed entry. It
is used for display once the lookup has been successful.
That's it. Use at your own discretion. No guarantees.
Rémy Sanouillet
NLP Engineer
[email protected]<mailto:[email protected]>
ForeSee Medical, Inc.
12555 High Bluff Drive, Suite 100
San Diego, CA 92130
NOTICE: This e-mail message and all attachments transmitted with it are
intended solely for the use of the addressee and may contain legally privileged
and confidential information. If the reader of this message is not the intended
recipient, or an employee or agent responsible for delivering this message to
the intended recipient, you are hereby notified that any dissemination,
distribution, copying, or other use of this message or its attachments is
strictly prohibited. If you have received this message in error, please notify
the sender immediately by replying to this message and please delete it from
your computer.
On Fri, May 29, 2020 at 7:34 AM
<[email protected]<mailto:[email protected]>> wrote:
Hi Team,
We set up cTAKES4.0.0 as our NLP engine for our profile recently . We have
faced situations where some of the expected tokens are not picked up by cTAKES
during clinical text extraction. So our first thought process was to identify
where the dictionary is configured and how that can be updated. After some code
analysis it was found that the dictionary is configured in the below path
under ctakes/resources for sources RxNorm and SNOMEDCT_US
We were able to open the hsqldb using the hsql db gui and found out that some
of our required entries are already there . So if I come specifically to our
current problem. The Pap Smear and Mamogram are two clinical terms which are
not currently recognized by cTAKES in our profile.
• If I look into the .script file , Pap Smear and Mammogram/Mammography
is already present in the .script file and in the respective tables. PFB a
snapshot as below
But still this was not recogonised by cTAKES. I see there are some filters
working on top of the available entries in dictionary(ctakes-gui and
ctake-gui-res). Will that be because of these filters the tokens are not
recognized as expected. Could you pls. share us what exactly these filters do.
This will help us in future also when we are trying to add new terms into the
dictionary
• What are the steps to do if we need to add/edit entries into the
existing dictionaries. I see we can add/edit the existing values in .scripts
files but our primary doubt is if suppose I have a term ‘xyz’ to be added to
dictionary how can I get the CUI and other values like TUI,RINDEX,TCOUNT and
PREFTERM. Is it fine if I can give any random value for the
TUI/CUI/RINDEX/TCOUNT. I could also see options to create custom bsv
dictionaries but couldn’t see much documentation for it. Kindly advise which is
the better option from the below 3.
o Generate a custom dictionary using METAMORPHOSYS UML installation
tool(where we provide sources as ICD10,RxNORM,SNOMEDCT_US) and leverage the
full set of .rrf files in the meta folder . Is this approach better if the
entries to be populated are maximal?
o Add/edit the available dictionary sno_rx_16ab and in that case how to
provide valid values for each columns like CUI, TUI,RINDEX,TCOUNT and PREFTERM.
If the entries to be populated are minimal is this approach would be better?.
o Use a custom bsv , in that case how should we add values to custom bsv.
Could you also provide a sample in that case.
I found a Metathesaurus browser in the below url , where I can search for the
terms and get the CUI and the respective source like ICD/CPT/MDR. But still I
was unable to get the other required attributes to be populated like
TUI,RINDEX,TCOUNT and PREFTERM. Could you pls. brief what these attributes
signifies
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Kindly advise us on how to proceed on this and correct us if we went wrong
somewhere. This would be of great help for us
P.S : We comply with UMLS license
Thanks & Regards
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028
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