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Posted to user@ctakes.apache.org by "Hari, Sekhar" <se...@cgi.com> on 2017/03/28 13:12:31 UTC
Popular terminology support in cTAKES
Hi there -
I have large number of PDF documents containing clinical and discharge narratives (all PHIs are de-identified). The healthcare organization from where I received these files use non-SNOMEDCT codes and descriptions such as CPT for procedures, ICD10 for diagnoses, LOINC for laboratory results and NDC for medications. Does cTAKES support / recognize these terms and return the corresponding non-SNOMEDCT code while processing the clinical narratives?
Thanks
Sekhar Hari | Program Lead
Health Sciences Business Innovation
ASDC CGI Health Solutions
Electronic City, Bangalore
Karnataka, India 560100
814 7027 779 (C)
080 6642 2536 (D)
RE: Popular terminology support in cTAKES
Posted by "Hari, Sekhar" <se...@cgi.com>.
Hi Sean - That's good news! Thanks.
Any chance you can share some details regarding ontology mapping to SNOMEDCT?
Many thanks,
Sekhar H.
________________________________________
From: Finan, Sean [Sean.Finan@childrens.harvard.edu]
Sent: 28 March 2017 22:33
To: dev@ctakes.apache.org
Subject: RE: Popular terminology support in cTAKES
Hi Sekhar,
Ctakes 4.0 will include a gui that can create a custom dictionary from a local copy of the umls .rrf files. We will have quick-start type documentation available after the release.
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Tuesday, March 28, 2017 12:55 PM
To: dev@ctakes.apache.org
Subject: RE: Popular terminology support in cTAKES
Ok, thanks! Any chance you can supply any guidance for creating such a dictionary?
And also, do you know if any comprehensive mapping (for meaningful use) exists for CPT to SNOMEDCT and LOINC to SNOMEDCT? I have downloaded the mapping from NLM for ICD9CM to SNOMEDCT, ICD10CM to SNOMEDCT as well as ICD10PCS to SNOMEDCT.
Thanks,
Sekhar H.
________________________________________
From: Finan, Sean [Sean.Finan@childrens.harvard.edu]
Sent: 28 March 2017 18:53
To: dev@ctakes.apache.org
Subject: RE: Popular terminology support in cTAKES
Hi Sekhar,
Short answer: yes. Longer answer: You need to create a custom dictionary and then set ctakes to use it. You also need to make sure that your output is providing the icd, loinc, etc. codes in addition to the standard umls cuis.
Our ctakes 4.0 is scheduled to be release in April, and we will try to document procedures such as what you would need necessary as best we can.
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Tuesday, March 28, 2017 9:13 AM
To: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: Popular terminology support in cTAKES
Hi there -
I have large number of PDF documents containing clinical and discharge narratives (all PHIs are de-identified). The healthcare organization from where I received these files use non-SNOMEDCT codes and descriptions such as CPT for procedures, ICD10 for diagnoses, LOINC for laboratory results and NDC for medications. Does cTAKES support / recognize these terms and return the corresponding non-SNOMEDCT code while processing the clinical narratives?
Thanks
Sekhar Hari | Program Lead
Health Sciences Business Innovation
ASDC CGI Health Solutions
Electronic City, Bangalore
Karnataka, India 560100
814 7027 779 (C)
080 6642 2536 (D)
RE: Popular terminology support in cTAKES
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Sekhar,
Ctakes 4.0 will include a gui that can create a custom dictionary from a local copy of the umls .rrf files. We will have quick-start type documentation available after the release.
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Tuesday, March 28, 2017 12:55 PM
To: dev@ctakes.apache.org
Subject: RE: Popular terminology support in cTAKES
Ok, thanks! Any chance you can supply any guidance for creating such a dictionary?
And also, do you know if any comprehensive mapping (for meaningful use) exists for CPT to SNOMEDCT and LOINC to SNOMEDCT? I have downloaded the mapping from NLM for ICD9CM to SNOMEDCT, ICD10CM to SNOMEDCT as well as ICD10PCS to SNOMEDCT.
Thanks,
Sekhar H.
________________________________________
From: Finan, Sean [Sean.Finan@childrens.harvard.edu]
Sent: 28 March 2017 18:53
To: dev@ctakes.apache.org
Subject: RE: Popular terminology support in cTAKES
Hi Sekhar,
Short answer: yes. Longer answer: You need to create a custom dictionary and then set ctakes to use it. You also need to make sure that your output is providing the icd, loinc, etc. codes in addition to the standard umls cuis.
Our ctakes 4.0 is scheduled to be release in April, and we will try to document procedures such as what you would need necessary as best we can.
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Tuesday, March 28, 2017 9:13 AM
To: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: Popular terminology support in cTAKES
Hi there -
I have large number of PDF documents containing clinical and discharge narratives (all PHIs are de-identified). The healthcare organization from where I received these files use non-SNOMEDCT codes and descriptions such as CPT for procedures, ICD10 for diagnoses, LOINC for laboratory results and NDC for medications. Does cTAKES support / recognize these terms and return the corresponding non-SNOMEDCT code while processing the clinical narratives?
Thanks
Sekhar Hari | Program Lead
Health Sciences Business Innovation
ASDC CGI Health Solutions
Electronic City, Bangalore
Karnataka, India 560100
814 7027 779 (C)
080 6642 2536 (D)
RE: Popular terminology support in cTAKES
Posted by "Hari, Sekhar" <se...@cgi.com>.
Ok, thanks! Any chance you can supply any guidance for creating such a dictionary?
And also, do you know if any comprehensive mapping (for meaningful use) exists for CPT to SNOMEDCT and LOINC to SNOMEDCT? I have downloaded the mapping from NLM for ICD9CM to SNOMEDCT, ICD10CM to SNOMEDCT as well as ICD10PCS to SNOMEDCT.
Thanks,
Sekhar H.
________________________________________
From: Finan, Sean [Sean.Finan@childrens.harvard.edu]
Sent: 28 March 2017 18:53
To: dev@ctakes.apache.org
Subject: RE: Popular terminology support in cTAKES
Hi Sekhar,
Short answer: yes. Longer answer: You need to create a custom dictionary and then set ctakes to use it. You also need to make sure that your output is providing the icd, loinc, etc. codes in addition to the standard umls cuis.
Our ctakes 4.0 is scheduled to be release in April, and we will try to document procedures such as what you would need necessary as best we can.
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Tuesday, March 28, 2017 9:13 AM
To: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: Popular terminology support in cTAKES
Hi there -
I have large number of PDF documents containing clinical and discharge narratives (all PHIs are de-identified). The healthcare organization from where I received these files use non-SNOMEDCT codes and descriptions such as CPT for procedures, ICD10 for diagnoses, LOINC for laboratory results and NDC for medications. Does cTAKES support / recognize these terms and return the corresponding non-SNOMEDCT code while processing the clinical narratives?
Thanks
Sekhar Hari | Program Lead
Health Sciences Business Innovation
ASDC CGI Health Solutions
Electronic City, Bangalore
Karnataka, India 560100
814 7027 779 (C)
080 6642 2536 (D)
RE: Popular terminology support in cTAKES
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Sekhar,
Short answer: yes. Longer answer: You need to create a custom dictionary and then set ctakes to use it. You also need to make sure that your output is providing the icd, loinc, etc. codes in addition to the standard umls cuis.
Our ctakes 4.0 is scheduled to be release in April, and we will try to document procedures such as what you would need necessary as best we can.
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Tuesday, March 28, 2017 9:13 AM
To: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: Popular terminology support in cTAKES
Hi there -
I have large number of PDF documents containing clinical and discharge narratives (all PHIs are de-identified). The healthcare organization from where I received these files use non-SNOMEDCT codes and descriptions such as CPT for procedures, ICD10 for diagnoses, LOINC for laboratory results and NDC for medications. Does cTAKES support / recognize these terms and return the corresponding non-SNOMEDCT code while processing the clinical narratives?
Thanks
Sekhar Hari | Program Lead
Health Sciences Business Innovation
ASDC CGI Health Solutions
Electronic City, Bangalore
Karnataka, India 560100
814 7027 779 (C)
080 6642 2536 (D)