You are viewing a plain text version of this content. The canonical link for it is here.
Posted to dev@ctakes.apache.org by Peter Abramowitsch <pa...@gmail.com> on 2021/03/18 10:18:59 UTC
Issue with dictionary creator?
Has anyone seen an issue where a dictionary is created from UMLS sources
where there is no entry in PREFTERM for a valid CUI that is present in TUI,
CUI_TERMS, and SNOMEDCT_US?.
It seems to be happening in certain medication mentions where there is a
base drug instance and then various forms. It could be that one of the
form descriptions is obsolete, but that wouldn't explain why it was only
half-present in the resulting dictionary.
for instance
clobetasol CUI 8992 has an entry in every table
clobetasol emollient CUI 4520933 has all information in every table
clobetasol topical CUI 3207574 but is missing only in PREFTERM
cui_term
'3207574','0','2','clobetasol topical','clobetasol'
'3207574','0','8','clobetasol - containing product in cutaneous dose
form','clobetasol'
Tui
'3207574','200'
Snomed
'3207574','771278006'
Prefterm
Blank.
Peter
RE: Issue with dictionary creator?
Posted by "Monogyiou, Eugenia" <Eu...@nttdata.com>.
Hi Peter,
Yes I have (before I started using the cased format) and it was only medication indeed-- however it was drugs that should not be annotated as such in the first place , e.g. today as an antibiotic which led me to think it may have had something to do with broken links, even residuals from efforts to "fix" certain entries perhaps? Our cohort was for heart attack so not a very broad range of meds were present in the letters; perhaps I did not encounter "valid" cases just out of luck because of the specific cohort...?
Kind Regards,
Eugenia Monogyiou
-----Original Message-----
From: Peter Abramowitsch <pa...@gmail.com>
Sent: 18 March 2021 10:19
To: dev@ctakes.apache.org
Subject: Issue with dictionary creator?
Has anyone seen an issue where a dictionary is created from UMLS sources where there is no entry in PREFTERM for a valid CUI that is present in TUI, CUI_TERMS, and SNOMEDCT_US?.
It seems to be happening in certain medication mentions where there is a base drug instance and then various forms. It could be that one of the form descriptions is obsolete, but that wouldn't explain why it was only half-present in the resulting dictionary.
for instance
clobetasol CUI 8992 has an entry in every table clobetasol emollient CUI 4520933 has all information in every table clobetasol topical CUI 3207574 but is missing only in PREFTERM
cui_term
'3207574','0','2','clobetasol topical','clobetasol'
'3207574','0','8','clobetasol - containing product in cutaneous dose form','clobetasol'
Tui
'3207574','200'
Snomed
'3207574','771278006'
Prefterm
Blank.
Peter
Disclaimer: This email and any attachments are sent in strictest confidence for the sole use of the addressee and may contain legally privileged, confidential, and proprietary data. If you are not the intended recipient, please advise the sender by replying promptly to this email and then delete and destroy this email and any attachments without any further use, copying or forwarding.
Re: Issue with dictionary creator? [EXTERNAL]
Posted by Peter Abramowitsch <pa...@gmail.com>.
Thanks Sean and Eugenia,
I'm glad that it's not just me. I'll do some stats on this. I also found
another possible issue where there's no current snomed mapping for a CUI
(perhaps one of them is obsolete), so what happens then that the CUI based
entry remains in TUI and in CUI_TERMS, but there's none in either SNOMEDCT
or in PREFTERM.
Peter
On Thu, Mar 18, 2021 at 1:28 PM Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Hi Peter, Eugenia,
>
> I haven't noticed the occurrence, but can believe that this could happen.
> I am not sure why or how. I suppose you could run two counts to find out
> how many are missing - I don't want to know.
>
> There are probably a few things that could be done to 'cover' this
> problem, but the best would be making the dictionary creator fill in the
> blanks.
>
> Sean
> ________________________________________
> From: Monogyiou, Eugenia <Eu...@nttdata.com>
> Sent: Thursday, March 18, 2021 6:34 AM
> To: dev@ctakes.apache.org
> Subject: RE: Issue with dictionary creator? [EXTERNAL]
>
> * External Email - Caution *
>
>
> Just to clarify the cases I encountered were not valid conceptually but
> appeared to be valid , i.e. had cui, tui and SNOMED code. I used today as
> an example to show exactly that "conceptual" issue but it has been many
> months since the last time I encountered this so I don't have any proper
> examples to list at the moment.
>
> Kind Regards,
>
> Eugenia Monogyiou | NTT Data UK
> Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG
>
> Mob: +44 (0)7971623683 Email: eugenia.monogyiou@nttdata.com
>
>
> -----Original Message-----
> From: Monogyiou, Eugenia
> Sent: 18 March 2021 10:27
> To: dev@ctakes.apache.org
> Subject: RE: Issue with dictionary creator?
>
> Hi Peter,
>
> Yes I have (before I started using the cased format) and it was only
> medication indeed-- however it was drugs that should not be annotated as
> such in the first place , e.g. today as an antibiotic which led me to think
> it may have had something to do with broken links, even residuals from
> efforts to "fix" certain entries perhaps? Our cohort was for heart attack
> so not a very broad range of meds were present in the letters; perhaps I
> did not encounter "valid" cases just out of luck because of the specific
> cohort...?
>
> Kind Regards,
>
> Eugenia Monogyiou
>
> -----Original Message-----
> From: Peter Abramowitsch <pa...@gmail.com>
> Sent: 18 March 2021 10:19
> To: dev@ctakes.apache.org
> Subject: Issue with dictionary creator?
>
> Has anyone seen an issue where a dictionary is created from UMLS sources
> where there is no entry in PREFTERM for a valid CUI that is present in TUI,
> CUI_TERMS, and SNOMEDCT_US?.
>
> It seems to be happening in certain medication mentions where there is a
> base drug instance and then various forms. It could be that one of the
> form descriptions is obsolete, but that wouldn't explain why it was only
> half-present in the resulting dictionary.
>
> for instance
>
> clobetasol CUI 8992 has an entry in every table clobetasol emollient CUI
> 4520933 has all information in every table clobetasol topical CUI 3207574
> but is missing only in PREFTERM
>
> cui_term
> '3207574','0','2','clobetasol topical','clobetasol'
> '3207574','0','8','clobetasol - containing product in cutaneous dose
> form','clobetasol'
>
> Tui
> '3207574','200'
>
> Snomed
> '3207574','771278006'
>
> Prefterm
> Blank.
>
> Peter
> Disclaimer: This email and any attachments are sent in strictest
> confidence for the sole use of the addressee and may contain legally
> privileged, confidential, and proprietary data. If you are not the intended
> recipient, please advise the sender by replying promptly to this email and
> then delete and destroy this email and any attachments without any further
> use, copying or forwarding.
>
Re: Issue with dictionary creator? [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Peter, Eugenia,
I haven't noticed the occurrence, but can believe that this could happen. I am not sure why or how. I suppose you could run two counts to find out how many are missing - I don't want to know.
There are probably a few things that could be done to 'cover' this problem, but the best would be making the dictionary creator fill in the blanks.
Sean
________________________________________
From: Monogyiou, Eugenia <Eu...@nttdata.com>
Sent: Thursday, March 18, 2021 6:34 AM
To: dev@ctakes.apache.org
Subject: RE: Issue with dictionary creator? [EXTERNAL]
* External Email - Caution *
Just to clarify the cases I encountered were not valid conceptually but appeared to be valid , i.e. had cui, tui and SNOMED code. I used today as an example to show exactly that "conceptual" issue but it has been many months since the last time I encountered this so I don't have any proper examples to list at the moment.
Kind Regards,
Eugenia Monogyiou | NTT Data UK
Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG
Mob: +44 (0)7971623683 Email: eugenia.monogyiou@nttdata.com
-----Original Message-----
From: Monogyiou, Eugenia
Sent: 18 March 2021 10:27
To: dev@ctakes.apache.org
Subject: RE: Issue with dictionary creator?
Hi Peter,
Yes I have (before I started using the cased format) and it was only medication indeed-- however it was drugs that should not be annotated as such in the first place , e.g. today as an antibiotic which led me to think it may have had something to do with broken links, even residuals from efforts to "fix" certain entries perhaps? Our cohort was for heart attack so not a very broad range of meds were present in the letters; perhaps I did not encounter "valid" cases just out of luck because of the specific cohort...?
Kind Regards,
Eugenia Monogyiou
-----Original Message-----
From: Peter Abramowitsch <pa...@gmail.com>
Sent: 18 March 2021 10:19
To: dev@ctakes.apache.org
Subject: Issue with dictionary creator?
Has anyone seen an issue where a dictionary is created from UMLS sources where there is no entry in PREFTERM for a valid CUI that is present in TUI, CUI_TERMS, and SNOMEDCT_US?.
It seems to be happening in certain medication mentions where there is a base drug instance and then various forms. It could be that one of the form descriptions is obsolete, but that wouldn't explain why it was only half-present in the resulting dictionary.
for instance
clobetasol CUI 8992 has an entry in every table clobetasol emollient CUI 4520933 has all information in every table clobetasol topical CUI 3207574 but is missing only in PREFTERM
cui_term
'3207574','0','2','clobetasol topical','clobetasol'
'3207574','0','8','clobetasol - containing product in cutaneous dose form','clobetasol'
Tui
'3207574','200'
Snomed
'3207574','771278006'
Prefterm
Blank.
Peter
Disclaimer: This email and any attachments are sent in strictest confidence for the sole use of the addressee and may contain legally privileged, confidential, and proprietary data. If you are not the intended recipient, please advise the sender by replying promptly to this email and then delete and destroy this email and any attachments without any further use, copying or forwarding.
RE: Issue with dictionary creator?
Posted by "Monogyiou, Eugenia" <Eu...@nttdata.com>.
Just to clarify the cases I encountered were not valid conceptually but appeared to be valid , i.e. had cui, tui and SNOMED code. I used today as an example to show exactly that "conceptual" issue but it has been many months since the last time I encountered this so I don't have any proper examples to list at the moment.
Kind Regards,
Eugenia Monogyiou | NTT Data UK
Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG
Mob: +44 (0)7971623683 Email: eugenia.monogyiou@nttdata.com
-----Original Message-----
From: Monogyiou, Eugenia
Sent: 18 March 2021 10:27
To: dev@ctakes.apache.org
Subject: RE: Issue with dictionary creator?
Hi Peter,
Yes I have (before I started using the cased format) and it was only medication indeed-- however it was drugs that should not be annotated as such in the first place , e.g. today as an antibiotic which led me to think it may have had something to do with broken links, even residuals from efforts to "fix" certain entries perhaps? Our cohort was for heart attack so not a very broad range of meds were present in the letters; perhaps I did not encounter "valid" cases just out of luck because of the specific cohort...?
Kind Regards,
Eugenia Monogyiou
-----Original Message-----
From: Peter Abramowitsch <pa...@gmail.com>
Sent: 18 March 2021 10:19
To: dev@ctakes.apache.org
Subject: Issue with dictionary creator?
Has anyone seen an issue where a dictionary is created from UMLS sources where there is no entry in PREFTERM for a valid CUI that is present in TUI, CUI_TERMS, and SNOMEDCT_US?.
It seems to be happening in certain medication mentions where there is a base drug instance and then various forms. It could be that one of the form descriptions is obsolete, but that wouldn't explain why it was only half-present in the resulting dictionary.
for instance
clobetasol CUI 8992 has an entry in every table clobetasol emollient CUI 4520933 has all information in every table clobetasol topical CUI 3207574 but is missing only in PREFTERM
cui_term
'3207574','0','2','clobetasol topical','clobetasol'
'3207574','0','8','clobetasol - containing product in cutaneous dose form','clobetasol'
Tui
'3207574','200'
Snomed
'3207574','771278006'
Prefterm
Blank.
Peter
Disclaimer: This email and any attachments are sent in strictest confidence for the sole use of the addressee and may contain legally privileged, confidential, and proprietary data. If you are not the intended recipient, please advise the sender by replying promptly to this email and then delete and destroy this email and any attachments without any further use, copying or forwarding.