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Posted to user@ctakes.apache.org by "Rooney, Niall" <nf...@ulster.ac.uk> on 2013/04/12 13:05:47 UTC
concept identification query
Hi,
I have question concerning concept identification. I have modifying the example text given in the installation instructions to demonstrate the use of CAS Visual Debugger.
My text is:
Dr. Nutritious
Medical Nutrition Therapy for Hyperlipidemia and Aphasia
Referral from: Julie Tester, RD, LD, CNSD
Phone contact: (555) 555-1212
Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
Diet: General
Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity and blood pressure.
Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
Pt has been on a 3-day calorie count and has had an average intake of 1100 calories. She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.
She agrees with the plan and has my number for further assessment. May want a Metabolic Rate as well. She takes Codeine a day for knee and stomach pain.
Original entities and concepts are identified such as "Hyperlidemia" , "knee","pain". However concepts associated with addition to the text are not identified such as "Aphasia", "blood pressure", "stomach". Also "metabolic rate" is not identified. Does anyone know why this is?
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
RE: concept identification query
Posted by "Rooney, Niall" <nf...@ulster.ac.uk>.
Yes. I followed the instructions for cTAKES resources<http://sourceforge.net/projects/ctakesresources/files/>. I am not aware if I need to download and install anything else?
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: 12 April 2013 12:49
To: <us...@ctakes.apache.org>
Cc: user@ctakes.apache.org
Subject: Re: concept identification query
Thanks. We'll take a closer look.
I also presume you're using the *UMLS* dictionaries/pipeline?
Sent from my iPad
On Apr 12, 2013, at 7:27 AM, "Rooney, Niall" <nf...@ulster.ac.uk>> wrote:
Dear Pei,
I have attached the xmi export. I am using the most recent version of CTakes 3.0 on Windows 7.
Best Regards
Niall
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: 12 April 2013 12:20
To: <us...@ctakes.apache.org>>
Cc: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: concept identification query
Hi Niall,
Could you please also send the xml/xmi export from the CVD?
Also, which version of cTAKES are you using?
Sent from my iPad
On Apr 12, 2013, at 7:06 AM, "Rooney, Niall" <nf...@ulster.ac.uk>> wrote:
Hi,
I have question concerning concept identification. I have modifying the example text given in the installation instructions to demonstrate the use of CAS Visual Debugger.
My text is:
Dr. Nutritious
Medical Nutrition Therapy for Hyperlipidemia and Aphasia
Referral from: Julie Tester, RD, LD, CNSD
Phone contact: (555) 555-1212
Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
Diet: General
Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity and blood pressure.
Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
Pt has been on a 3-day calorie count and has had an average intake of 1100 calories. She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.
She agrees with the plan and has my number for further assessment. May want a Metabolic Rate as well. She takes Codeine a day for knee and stomach pain.
Original entities and concepts are identified such as "Hyperlidemia" , "knee","pain". However concepts associated with addition to the text are not identified such as "Aphasia", "blood pressure", "stomach". Also "metabolic rate" is not identified. Does anyone know why this is?
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
<result.xmi>
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
Re: concept identification query
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Thanks. We'll take a closer look.
I also presume you're using the *UMLS* dictionaries/pipeline?
Sent from my iPad
On Apr 12, 2013, at 7:27 AM, "Rooney, Niall" <nf...@ulster.ac.uk>> wrote:
Dear Pei,
I have attached the xmi export. I am using the most recent version of CTakes 3.0 on Windows 7.
Best Regards
Niall
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: 12 April 2013 12:20
To: <us...@ctakes.apache.org>>
Cc: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: concept identification query
Hi Niall,
Could you please also send the xml/xmi export from the CVD?
Also, which version of cTAKES are you using?
Sent from my iPad
On Apr 12, 2013, at 7:06 AM, "Rooney, Niall" <nf...@ulster.ac.uk>> wrote:
Hi,
I have question concerning concept identification. I have modifying the example text given in the installation instructions to demonstrate the use of CAS Visual Debugger.
My text is:
Dr. Nutritious
Medical Nutrition Therapy for Hyperlipidemia and Aphasia
Referral from: Julie Tester, RD, LD, CNSD
Phone contact: (555) 555-1212
Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
Diet: General
Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity and blood pressure.
Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
Pt has been on a 3-day calorie count and has had an average intake of 1100 calories. She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.
She agrees with the plan and has my number for further assessment. May want a Metabolic Rate as well. She takes Codeine a day for knee and stomach pain.
Original entities and concepts are identified such as “Hyperlidemia” , “knee”,“pain”. However concepts associated with addition to the text are not identified such as “Aphasia”, “blood pressure”, “stomach”. Also “metabolic rate” is not identified. Does anyone know why this is?
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
<result.xmi>
RE: concept identification query
Posted by "Rooney, Niall" <nf...@ulster.ac.uk>.
Dear Pei,
I have attached the xmi export. I am using the most recent version of CTakes 3.0 on Windows 7.
Best Regards
Niall
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: 12 April 2013 12:20
To: <us...@ctakes.apache.org>
Cc: user@ctakes.apache.org
Subject: Re: concept identification query
Hi Niall,
Could you please also send the xml/xmi export from the CVD?
Also, which version of cTAKES are you using?
Sent from my iPad
On Apr 12, 2013, at 7:06 AM, "Rooney, Niall" <nf...@ulster.ac.uk>> wrote:
Hi,
I have question concerning concept identification. I have modifying the example text given in the installation instructions to demonstrate the use of CAS Visual Debugger.
My text is:
Dr. Nutritious
Medical Nutrition Therapy for Hyperlipidemia and Aphasia
Referral from: Julie Tester, RD, LD, CNSD
Phone contact: (555) 555-1212
Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
Diet: General
Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity and blood pressure.
Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
Pt has been on a 3-day calorie count and has had an average intake of 1100 calories. She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.
She agrees with the plan and has my number for further assessment. May want a Metabolic Rate as well. She takes Codeine a day for knee and stomach pain.
Original entities and concepts are identified such as "Hyperlidemia" , "knee","pain". However concepts associated with addition to the text are not identified such as "Aphasia", "blood pressure", "stomach". Also "metabolic rate" is not identified. Does anyone know why this is?
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
Re: concept identification query
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Hi Niall,
Could you please also send the xml/xmi export from the CVD?
Also, which version of cTAKES are you using?
Sent from my iPad
On Apr 12, 2013, at 7:06 AM, "Rooney, Niall" <nf...@ulster.ac.uk>> wrote:
Hi,
I have question concerning concept identification. I have modifying the example text given in the installation instructions to demonstrate the use of CAS Visual Debugger.
My text is:
Dr. Nutritious
Medical Nutrition Therapy for Hyperlipidemia and Aphasia
Referral from: Julie Tester, RD, LD, CNSD
Phone contact: (555) 555-1212
Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
Diet: General
Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity and blood pressure.
Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
Pt has been on a 3-day calorie count and has had an average intake of 1100 calories. She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.
She agrees with the plan and has my number for further assessment. May want a Metabolic Rate as well. She takes Codeine a day for knee and stomach pain.
Original entities and concepts are identified such as “Hyperlidemia” , “knee”,“pain”. However concepts associated with addition to the text are not identified such as “Aphasia”, “blood pressure”, “stomach”. Also “metabolic rate” is not identified. Does anyone know why this is?
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
Re: concept identification query
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
+1
Sent from my iPhone
On Apr 12, 2013, at 12:19 PM, "Tim Miller" <ti...@childrens.harvard.edu>> wrote:
Troy,
My vote would be to mention in the user guide that "real" entity recognition requires the umls component, and maybe a link to the developers guide where that is explained? Probably there are some people who wouldn't know what to expect out of the box and will be disappointed that it doesn't find much. (Luckily some of them email our lists and we can help them figure it out, but there may be people who just figure it doesn't work very well and give up.)
Btw, the guides are really nice, great job on that.
Tim
On 04/12/2013 12:12 PM, Bleeker, Troy C. wrote:
The Developer install guide talks about UMLS integration: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Developer+Install+Guide
Search for UMLS. It is described for Eclipse and for command line. Users that are just trying out cTAKES don’t have those instructions. Do you think they should be part of the User Guide?
Troy
From: user-return-110-Bleeker.Troy=mayo.edu@ctakes.apache.org<ma...@ctakes.apache.org> [mailto:user-return-110-Bleeker.Troy=mayo.edu@ctakes.apache.org] On Behalf Of giri vara prasad nambari
Sent: Friday, April 12, 2013 11:06 AM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: RE: concept identification query
Hi All,
Where do we need to update this UMLS key in ctakes?
Thanks for your time and help.
Thank you,
Giri
On Apr 12, 2013 10:59 AM, "Savova, Guergana" <Gu...@childrens.harvard.edu>> wrote:
You would need to get a UMLS license to get the full functionality. It takes 2-3 days to be approved for it.
Hope this helps.
--Guergana
From: Rooney, Niall [mailto:nf.rooney@ulster.ac.uk<ma...@ulster.ac.uk>]
Sent: Friday, April 12, 2013 10:26 AM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: RE: concept identification query
Pei,
I don’t have a UMLS license yet but thanks for looking into this.
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu<ma...@childrens.harvard.edu>]
Sent: 12 April 2013 15:10
To: <us...@ctakes.apache.org>>
Subject: Re: concept identification query
Thanks Tim for confirming...
AggregatePlaintextUMLSProcessor.xmlshould pick up stomach and aphasia etc.
Sent from my iPhone
On Apr 12, 2013, at 9:25 AM, "Tim Miller" <ti...@childrens.harvard.edu>> wrote:
Niall,
I'm sure Pei will get back to you soon, but just wanted to let you know, many of those entities will be found by the standard ctakes installation. I get aphasia and stomach. It does not get blood pressure, I think because this is filtered out by UMLS semantic class - I think it is categorized as a "measurement," and cTAKES will find things like disease/disorder, signs/symptoms, and a few others, which this does not fit into exactly. It may be worth thinking about how to include it if it will be useful. In this example it looks like it's linked to some assessment "HB +20%", I assume that is some measurement that would be useful to extract?
Tim
On 04/12/2013 07:05 AM, Rooney, Niall wrote:
Hi,
I have question concerning concept identification. I have modifying the example text given in the installation instructions to demonstrate the use of CAS Visual Debugger.
My text is:
Dr. Nutritious
Medical Nutrition Therapy for Hyperlipidemia and Aphasia
Referral from: Julie Tester, RD, LD, CNSD
Phone contact: (555) 555-1212
Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
Diet: General
Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity and blood pressure.
Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
Pt has been on a 3-day calorie count and has had an average intake of 1100 calories. She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.
She agrees with the plan and has my number for further assessment. May want a Metabolic Rate as well. She takes Codeine a day for knee and stomach pain.
Original entities and concepts are identified such as “Hyperlidemia” , “knee”,“pain”. However concepts associated with addition to the text are not identified such as “Aphasia”, “blood pressure”, “stomach”. Also “metabolic rate” is not identified. Does anyone know why this is?
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
RE: concept identification query
Posted by "Savova, Guergana" <Gu...@childrens.harvard.edu>.
+1.
Excellent job on the documentation, Troy!
--Guergana
From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
Sent: Friday, April 12, 2013 1:02 PM
To: 'user@ctakes.apache.org'
Subject: RE: concept identification query
+1, and I suggest it not just be mentioned, but that it be strongly mentioned. Maybe even change some headings on that User Guide page to indicate the "Install" is of the code, not of the real dictionaries.
Perhaps the heading "Install cTAKES" could be changed to "Install cTAKES without UMLS dictionaries"
Or add a new section between these two
Install cTAKES
Process documents using cTAKES
Something like this
Install cTAKES
Install UMLS dictionaries (optional, but required to test Concept Identification on your own data)
Process documents using cTAKES
And under Process documents using cTAKES" we could have a big NOTE that says something like "Be aware that if you have not installed the UMLS dictionaries, you only have a tiny sample dictionary...."
Troy, you have done such a good job at the docs, I'll leave these are suggestions for you, but I'd be happy to take a pass at drafting something on the Wiki if you'd prefer.
Regards,
James Masanz
From: user-return-113-Masanz.James=mayo.edu@ctakes.apache.org [mailto:user-return-113-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of giri vara prasad nambari
Sent: Friday, April 12, 2013 11:34 AM
To: user
Subject: Re: concept identification query
I second Tim's comment. Information in the link provided by Troy is really helpful, if "user guide" has this link may be in ctakes-resources downloaded section, that helps users.
Right now I am limited myself as user of ctakes and trying to understand what I may get our of the box, how much I need to customize to develop my idea into a to prototype.
You guys have been really helpful with quick replies with solution pointers. Few days back, I was about to give-up, but with the help and pointers I am getting from you guys, motivated me to stay with ctakes and explore more. Now I am almost ready to finalize infrastructure and take-off for prototype development(few more things to hash-out and hoping they will be quick).
Thanks again for your time and help.
Thank you,
Giri
On Fri, Apr 12, 2013 at 12:19 PM, Tim Miller <ti...@childrens.harvard.edu>> wrote:
Troy,
My vote would be to mention in the user guide that "real" entity recognition requires the umls component, and maybe a link to the developers guide where that is explained? Probably there are some people who wouldn't know what to expect out of the box and will be disappointed that it doesn't find much. (Luckily some of them email our lists and we can help them figure it out, but there may be people who just figure it doesn't work very well and give up.)
Btw, the guides are really nice, great job on that.
Tim
On 04/12/2013 12:12 PM, Bleeker, Troy C. wrote:
The Developer install guide talks about UMLS integration: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Developer+Install+Guide
Search for UMLS. It is described for Eclipse and for command line. Users that are just trying out cTAKES don't have those instructions. Do you think they should be part of the User Guide?
Troy
From: user-return-110-Bleeker.Troy=mayo.edu@ctakes.apache.org [mailto:user-return-110-Bleeker.Troy=mayo.edu@ctakes.apache.org] On Behalf Of giri vara prasad nambari
Sent: Friday, April 12, 2013 11:06 AM
To: user@ctakes.apache.org
Subject: RE: concept identification query
Hi All,
Where do we need to update this UMLS key in ctakes?
Thanks for your time and help.
Thank you,
Giri
On Apr 12, 2013 10:59 AM, "Savova, Guergana" <Gu...@childrens.harvard.edu>> wrote:
You would need to get a UMLS license to get the full functionality. It takes 2-3 days to be approved for it.
Hope this helps.
--Guergana
From: Rooney, Niall [mailto:nf.rooney@ulster.ac.uk]
Sent: Friday, April 12, 2013 10:26 AM
To: user@ctakes.apache.org
Subject: RE: concept identification query
Pei,
I don't have a UMLS license yet but thanks for looking into this.
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: 12 April 2013 15:10
To: <us...@ctakes.apache.org>
Subject: Re: concept identification query
Thanks Tim for confirming...
AggregatePlaintextUMLSProcessor.xmlshould pick up stomach and aphasia etc.
Sent from my iPhone
On Apr 12, 2013, at 9:25 AM, "Tim Miller" <ti...@childrens.harvard.edu>> wrote:
Niall,
I'm sure Pei will get back to you soon, but just wanted to let you know, many of those entities will be found by the standard ctakes installation. I get aphasia and stomach. It does not get blood pressure, I think because this is filtered out by UMLS semantic class - I think it is categorized as a "measurement," and cTAKES will find things like disease/disorder, signs/symptoms, and a few others, which this does not fit into exactly. It may be worth thinking about how to include it if it will be useful. In this example it looks like it's linked to some assessment "HB +20%", I assume that is some measurement that would be useful to extract?
Tim
On 04/12/2013 07:05 AM, Rooney, Niall wrote:
Hi,
I have question concerning concept identification. I have modifying the example text given in the installation instructions to demonstrate the use of CAS Visual Debugger.
My text is:
Dr. Nutritious
Medical Nutrition Therapy for Hyperlipidemia and Aphasia
Referral from: Julie Tester, RD, LD, CNSD
Phone contact: (555) 555-1212
Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
Diet: General
Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity and blood pressure.
Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
Pt has been on a 3-day calorie count and has had an average intake of 1100 calories. She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.
She agrees with the plan and has my number for further assessment. May want a Metabolic Rate as well. She takes Codeine a day for knee and stomach pain.
Original entities and concepts are identified such as "Hyperlidemia" , "knee","pain". However concepts associated with addition to the text are not identified such as "Aphasia", "blood pressure", "stomach". Also "metabolic rate" is not identified. Does anyone know why this is?
________________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
________________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
RE: concept identification query
Posted by "Bleeker, Troy C." <Bl...@mayo.edu>.
James,
As we discussed you can make changes to the User's Guide. I will review at a later date.
Thanks
Troy
From: user-return-115-Bleeker.Troy=mayo.edu@ctakes.apache.org [mailto:user-return-115-Bleeker.Troy=mayo.edu@ctakes.apache.org] On Behalf Of Masanz, James J.
Sent: Friday, April 12, 2013 12:01 PM
To: 'user@ctakes.apache.org'
Subject: RE: concept identification query
+1, and I suggest it not just be mentioned, but that it be strongly mentioned. Maybe even change some headings on that User Guide page to indicate the "Install" is of the code, not of the real dictionaries.
Perhaps the heading "Install cTAKES" could be changed to "Install cTAKES without UMLS dictionaries"
Or add a new section between these two
Install cTAKES
Process documents using cTAKES
Something like this
Install cTAKES
Install UMLS dictionaries (optional, but required to test Concept Identification on your own data)
Process documents using cTAKES
And under Process documents using cTAKES" we could have a big NOTE that says something like "Be aware that if you have not installed the UMLS dictionaries, you only have a tiny sample dictionary...."
Troy, you have done such a good job at the docs, I'll leave these are suggestions for you, but I'd be happy to take a pass at drafting something on the Wiki if you'd prefer.
Regards,
James Masanz
From: user-return-113-Masanz.James=mayo.edu@ctakes.apache.org<ma...@ctakes.apache.org> [mailto:user-return-113-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of giri vara prasad nambari
Sent: Friday, April 12, 2013 11:34 AM
To: user
Subject: Re: concept identification query
I second Tim's comment. Information in the link provided by Troy is really helpful, if "user guide" has this link may be in ctakes-resources downloaded section, that helps users.
Right now I am limited myself as user of ctakes and trying to understand what I may get our of the box, how much I need to customize to develop my idea into a to prototype.
You guys have been really helpful with quick replies with solution pointers. Few days back, I was about to give-up, but with the help and pointers I am getting from you guys, motivated me to stay with ctakes and explore more. Now I am almost ready to finalize infrastructure and take-off for prototype development(few more things to hash-out and hoping they will be quick).
Thanks again for your time and help.
Thank you,
Giri
On Fri, Apr 12, 2013 at 12:19 PM, Tim Miller <ti...@childrens.harvard.edu>> wrote:
Troy,
My vote would be to mention in the user guide that "real" entity recognition requires the umls component, and maybe a link to the developers guide where that is explained? Probably there are some people who wouldn't know what to expect out of the box and will be disappointed that it doesn't find much. (Luckily some of them email our lists and we can help them figure it out, but there may be people who just figure it doesn't work very well and give up.)
Btw, the guides are really nice, great job on that.
Tim
On 04/12/2013 12:12 PM, Bleeker, Troy C. wrote:
The Developer install guide talks about UMLS integration: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Developer+Install+Guide
Search for UMLS. It is described for Eclipse and for command line. Users that are just trying out cTAKES don't have those instructions. Do you think they should be part of the User Guide?
Troy
From: user-return-110-Bleeker.Troy=mayo.edu@ctakes.apache.org<ma...@ctakes.apache.org> [mailto:user-return-110-Bleeker.Troy=mayo.edu@ctakes.apache.org] On Behalf Of giri vara prasad nambari
Sent: Friday, April 12, 2013 11:06 AM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: RE: concept identification query
Hi All,
Where do we need to update this UMLS key in ctakes?
Thanks for your time and help.
Thank you,
Giri
On Apr 12, 2013 10:59 AM, "Savova, Guergana" <Gu...@childrens.harvard.edu>> wrote:
You would need to get a UMLS license to get the full functionality. It takes 2-3 days to be approved for it.
Hope this helps.
--Guergana
From: Rooney, Niall [mailto:nf.rooney@ulster.ac.uk]
Sent: Friday, April 12, 2013 10:26 AM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: RE: concept identification query
Pei,
I don't have a UMLS license yet but thanks for looking into this.
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: 12 April 2013 15:10
To: <us...@ctakes.apache.org>>
Subject: Re: concept identification query
Thanks Tim for confirming...
AggregatePlaintextUMLSProcessor.xmlshould pick up stomach and aphasia etc.
Sent from my iPhone
On Apr 12, 2013, at 9:25 AM, "Tim Miller" <ti...@childrens.harvard.edu>> wrote:
Niall,
I'm sure Pei will get back to you soon, but just wanted to let you know, many of those entities will be found by the standard ctakes installation. I get aphasia and stomach. It does not get blood pressure, I think because this is filtered out by UMLS semantic class - I think it is categorized as a "measurement," and cTAKES will find things like disease/disorder, signs/symptoms, and a few others, which this does not fit into exactly. It may be worth thinking about how to include it if it will be useful. In this example it looks like it's linked to some assessment "HB +20%", I assume that is some measurement that would be useful to extract?
Tim
On 04/12/2013 07:05 AM, Rooney, Niall wrote:
Hi,
I have question concerning concept identification. I have modifying the example text given in the installation instructions to demonstrate the use of CAS Visual Debugger.
My text is:
Dr. Nutritious
Medical Nutrition Therapy for Hyperlipidemia and Aphasia
Referral from: Julie Tester, RD, LD, CNSD
Phone contact: (555) 555-1212
Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
Diet: General
Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity and blood pressure.
Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
Pt has been on a 3-day calorie count and has had an average intake of 1100 calories. She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.
She agrees with the plan and has my number for further assessment. May want a Metabolic Rate as well. She takes Codeine a day for knee and stomach pain.
Original entities and concepts are identified such as "Hyperlidemia" , "knee","pain". However concepts associated with addition to the text are not identified such as "Aphasia", "blood pressure", "stomach". Also "metabolic rate" is not identified. Does anyone know why this is?
________________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
________________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
RE: concept identification query
Posted by "Masanz, James J." <Ma...@mayo.edu>.
+1, and I suggest it not just be mentioned, but that it be strongly mentioned. Maybe even change some headings on that User Guide page to indicate the "Install" is of the code, not of the real dictionaries.
Perhaps the heading "Install cTAKES" could be changed to "Install cTAKES without UMLS dictionaries"
Or add a new section between these two
Install cTAKES
Process documents using cTAKES
Something like this
Install cTAKES
Install UMLS dictionaries (optional, but required to test Concept Identification on your own data)
Process documents using cTAKES
And under Process documents using cTAKES" we could have a big NOTE that says something like "Be aware that if you have not installed the UMLS dictionaries, you only have a tiny sample dictionary...."
Troy, you have done such a good job at the docs, I'll leave these are suggestions for you, but I'd be happy to take a pass at drafting something on the Wiki if you'd prefer.
Regards,
James Masanz
From: user-return-113-Masanz.James=mayo.edu@ctakes.apache.org [mailto:user-return-113-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of giri vara prasad nambari
Sent: Friday, April 12, 2013 11:34 AM
To: user
Subject: Re: concept identification query
I second Tim's comment. Information in the link provided by Troy is really helpful, if "user guide" has this link may be in ctakes-resources downloaded section, that helps users.
Right now I am limited myself as user of ctakes and trying to understand what I may get our of the box, how much I need to customize to develop my idea into a to prototype.
You guys have been really helpful with quick replies with solution pointers. Few days back, I was about to give-up, but with the help and pointers I am getting from you guys, motivated me to stay with ctakes and explore more. Now I am almost ready to finalize infrastructure and take-off for prototype development(few more things to hash-out and hoping they will be quick).
Thanks again for your time and help.
Thank you,
Giri
On Fri, Apr 12, 2013 at 12:19 PM, Tim Miller <ti...@childrens.harvard.edu> wrote:
Troy,
My vote would be to mention in the user guide that "real" entity recognition requires the umls component, and maybe a link to the developers guide where that is explained? Probably there are some people who wouldn't know what to expect out of the box and will be disappointed that it doesn't find much. (Luckily some of them email our lists and we can help them figure it out, but there may be people who just figure it doesn't work very well and give up.)
Btw, the guides are really nice, great job on that.
Tim
On 04/12/2013 12:12 PM, Bleeker, Troy C. wrote:
The Developer install guide talks about UMLS integration: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Developer+Install+Guide
Search for UMLS. It is described for Eclipse and for command line. Users that are just trying out cTAKES don't have those instructions. Do you think they should be part of the User Guide?
Troy
From: user-return-110-Bleeker.Troy=mayo.edu@ctakes.apache.org [mailto:user-return-110-Bleeker.Troy=mayo.edu@ctakes.apache.org] On Behalf Of giri vara prasad nambari
Sent: Friday, April 12, 2013 11:06 AM
To: user@ctakes.apache.org
Subject: RE: concept identification query
Hi All,
Where do we need to update this UMLS key in ctakes?
Thanks for your time and help.
Thank you,
Giri
On Apr 12, 2013 10:59 AM, "Savova, Guergana" <Gu...@childrens.harvard.edu> wrote:
You would need to get a UMLS license to get the full functionality. It takes 2-3 days to be approved for it.
Hope this helps.
--Guergana
From: Rooney, Niall [mailto:nf.rooney@ulster.ac.uk]
Sent: Friday, April 12, 2013 10:26 AM
To: user@ctakes.apache.org
Subject: RE: concept identification query
Pei,
I don't have a UMLS license yet but thanks for looking into this.
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: 12 April 2013 15:10
To: <us...@ctakes.apache.org>
Subject: Re: concept identification query
Thanks Tim for confirming...
AggregatePlaintextUMLSProcessor.xmlshould pick up stomach and aphasia etc.
Sent from my iPhone
On Apr 12, 2013, at 9:25 AM, "Tim Miller" <ti...@childrens.harvard.edu> wrote:
Niall,
I'm sure Pei will get back to you soon, but just wanted to let you know, many of those entities will be found by the standard ctakes installation. I get aphasia and stomach. It does not get blood pressure, I think because this is filtered out by UMLS semantic class - I think it is categorized as a "measurement," and cTAKES will find things like disease/disorder, signs/symptoms, and a few others, which this does not fit into exactly. It may be worth thinking about how to include it if it will be useful. In this example it looks like it's linked to some assessment "HB +20%", I assume that is some measurement that would be useful to extract?
Tim
On 04/12/2013 07:05 AM, Rooney, Niall wrote:
Hi,
I have question concerning concept identification. I have modifying the example text given in the installation instructions to demonstrate the use of CAS Visual Debugger.
My text is:
Dr. Nutritious
Medical Nutrition Therapy for Hyperlipidemia and Aphasia
Referral from: Julie Tester, RD, LD, CNSD
Phone contact: (555) 555-1212
Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
Diet: General
Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity and blood pressure.
Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
Pt has been on a 3-day calorie count and has had an average intake of 1100 calories. She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.
She agrees with the plan and has my number for further assessment. May want a Metabolic Rate as well. She takes Codeine a day for knee and stomach pain.
Original entities and concepts are identified such as "Hyperlidemia" , "knee","pain". However concepts associated with addition to the text are not identified such as "Aphasia", "blood pressure", "stomach". Also "metabolic rate" is not identified. Does anyone know why this is?
________________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
________________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
Re: concept identification query
Posted by giri vara prasad nambari <gi...@gmail.com>.
I second Tim's comment. Information in the link provided by Troy is really
helpful, if "user guide" has this link may be in ctakes-resources
downloaded section, that helps users.
Right now I am limited myself as user of ctakes and trying to understand
what I may get our of the box, how much I need to customize to develop my
idea into a to prototype.
You guys have been really helpful with quick replies with solution
pointers. Few days back, I was about to give-up, but with the help and
pointers I am getting from you guys, motivated me to stay with ctakes and
explore more. Now I am almost ready to finalize infrastructure and take-off
for prototype development(few more things to hash-out and hoping they will
be quick).
Thanks again for your time and help.
Thank you,
Giri
On Fri, Apr 12, 2013 at 12:19 PM, Tim Miller <
timothy.miller@childrens.harvard.edu> wrote:
> Troy,
> My vote would be to mention in the user guide that "real" entity
> recognition requires the umls component, and maybe a link to the developers
> guide where that is explained? Probably there are some people who wouldn't
> know what to expect out of the box and will be disappointed that it doesn't
> find much. (Luckily some of them email our lists and we can help them
> figure it out, but there may be people who just figure it doesn't work very
> well and give up.)
>
> Btw, the guides are really nice, great job on that.
> Tim
>
>
> On 04/12/2013 12:12 PM, Bleeker, Troy C. wrote:
>
> The Developer install guide talks about UMLS integration:
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Developer+Install+Guide
> ****
>
> Search for UMLS. It is described for Eclipse and for command line. Users
> that are just trying out cTAKES don’t have those instructions. Do you think
> they should be part of the User Guide?****
>
>
> Troy ****
>
> *From:* user-return-110-Bleeker.Troy=mayo.edu@ctakes.apache.org [
> mailto:user-return-110-Bleeker.Troy=mayo.edu@ctakes.apache.org<us...@ctakes.apache.org>]
> *On Behalf Of *giri vara prasad nambari
> *Sent:* Friday, April 12, 2013 11:06 AM
> *To:* user@ctakes.apache.org
> *Subject:* RE: concept identification query****
>
> ** **
>
> Hi All,****
>
> Where do we need to update this UMLS key in ctakes? ****
>
> Thanks for your time and help.****
>
> Thank you,
> Giri****
>
> On Apr 12, 2013 10:59 AM, "Savova, Guergana" <
> Guergana.Savova@childrens.harvard.edu> wrote:****
>
> You would need to get a UMLS license to get the full functionality. It
> takes 2-3 days to be approved for it.****
>
> Hope this helps.****
>
> --Guergana****
>
> ****
>
> *From:* Rooney, Niall [mailto:nf.rooney@ulster.ac.uk]
> *Sent:* Friday, April 12, 2013 10:26 AM
> *To:* user@ctakes.apache.org
> *Subject:* RE: concept identification query****
>
> ****
>
> Pei,****
>
> ****
>
> I don’t have a UMLS license yet but thanks for looking into this.****
>
> ****
>
> *From:* Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> *Sent:* 12 April 2013 15:10
> *To:* <us...@ctakes.apache.org>
> *Subject:* Re: concept identification query****
>
> ****
>
> Thanks Tim for confirming...****
>
> AggregatePlaintextUMLSProcessor.xmlshould pick up stomach and aphasia etc.
>
> Sent from my iPhone****
>
>
> On Apr 12, 2013, at 9:25 AM, "Tim Miller" <
> timothy.miller@childrens.harvard.edu> wrote:****
>
> Niall,
> I'm sure Pei will get back to you soon, but just wanted to let you know,
> many of those entities will be found by the standard ctakes installation. I
> get aphasia and stomach. It does not get blood pressure, I think because
> this is filtered out by UMLS semantic class - I think it is categorized as
> a "measurement," and cTAKES will find things like disease/disorder,
> signs/symptoms, and a few others, which this does not fit into exactly. It
> may be worth thinking about how to include it if it will be useful. In this
> example it looks like it's linked to some assessment "HB +20%", I assume
> that is some measurement that would be useful to extract?
> Tim****
>
> On 04/12/2013 07:05 AM, Rooney, Niall wrote:****
>
> Hi,****
>
> ****
>
> I have question concerning concept identification. I have modifying the
> example text given in the installation instructions to demonstrate the use
> of CAS Visual Debugger.****
>
> ****
>
> My text is:****
>
> ****
>
> Dr. Nutritious****
>
> ****
>
> Medical Nutrition Therapy for Hyperlipidemia and Aphasia****
>
> ****
>
> Referral from: Julie Tester, RD, LD, CNSD****
>
> Phone contact: (555) 555-1212****
>
> Height: 144 cm Current Weight: 45 kg Date of current weight:
> 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2****
>
> Diet: General****
>
> Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for
> activity and blood pressure.****
>
> Daily Protein needs: 40 grams, assessed as 1.0 g/kg.****
>
> Pt has been on a 3-day calorie count and has had an average intake of 1100
> calories. She was instructed to drink 2-3 cans of liquid supplement to
> help promote weight gain. ****
>
> She agrees with the plan and has my number for further assessment. May
> want a Metabolic Rate as well. She takes Codeine a day for knee and stomach
> pain. ****
>
> ****
>
> ****
>
> Original entities and concepts are identified such as “Hyperlidemia” ,
> “knee”,“pain”. However concepts associated with addition to the text are
> not identified such as “Aphasia”, “blood pressure”, “stomach”. Also
> “metabolic rate” is not identified. Does anyone know why this is? ****
>
> ****
>
> ****
>
> ****
> ------------------------------
>
>
> This email and any attachments are confidential and intended solely for
> the use of the addressee and may contain information which is covered by
> legal, professional or other privilege. If you have received this email in
> error please notify the system manager at postmaster@ulster.ac.uk and
> delete this email immediately. Any views or opinions expressed are solely
> those of the author and do not necessarily represent those of the
> University of Ulster. The University's computer systems may be monitored
> and communications carried out on them may be recorded to secure the
> effective operation of the system and for other lawful purposes. The
> University of Ulster does not guarantee that this email or any attachments
> are free from viruses or 100% secure. Unless expressly stated in the body
> of a separate attachment, the text of email is not intended to form a
> binding contract. Correspondence to and from the University may be subject
> to requests for disclosure by 3rd parties under relevant legislation. The
> University of Ulster was founded by Royal Charter in 1984 and is registered
> with company number RC000726 and VAT registered number GB672390524.The
> primary contact address for the University of Ulster in Northern Ireland
> is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA ****
>
> ****
>
> ****
> ------------------------------
>
>
> This email and any attachments are confidential and intended solely for
> the use of the addressee and may contain information which is covered by
> legal, professional or other privilege. If you have received this email in
> error please notify the system manager at postmaster@ulster.ac.uk and
> delete this email immediately. Any views or opinions expressed are solely
> those of the author and do not necessarily represent those of the
> University of Ulster. The University's computer systems may be monitored
> and communications carried out on them may be recorded to secure the
> effective operation of the system and for other lawful purposes. The
> University of Ulster does not guarantee that this email or any attachments
> are free from viruses or 100% secure. Unless expressly stated in the body
> of a separate attachment, the text of email is not intended to form a
> binding contract. Correspondence to and from the University may be subject
> to requests for disclosure by 3rd parties under relevant legislation. The
> University of Ulster was founded by Royal Charter in 1984 and is registered
> with company number RC000726 and VAT registered number GB672390524.The
> primary contact address for the University of Ulster in Northern Ireland
> is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA ****
>
>
>
Re: concept identification query
Posted by Tim Miller <ti...@childrens.harvard.edu>.
Troy,
My vote would be to mention in the user guide that "real" entity
recognition requires the umls component, and maybe a link to the
developers guide where that is explained? Probably there are some people
who wouldn't know what to expect out of the box and will be disappointed
that it doesn't find much. (Luckily some of them email our lists and we
can help them figure it out, but there may be people who just figure it
doesn't work very well and give up.)
Btw, the guides are really nice, great job on that.
Tim
On 04/12/2013 12:12 PM, Bleeker, Troy C. wrote:
>
> The Developer install guide talks about UMLS integration:
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Developer+Install+Guide
>
> Search for UMLS. It is described for Eclipse and for command line.
> Users that are just trying out cTAKES don't have those instructions.
> Do you think they should be part of the User Guide?
>
>
> Troy
>
> *From:*user-return-110-Bleeker.Troy=mayo.edu@ctakes.apache.org
> [mailto:user-return-110-Bleeker.Troy=mayo.edu@ctakes.apache.org] *On
> Behalf Of *giri vara prasad nambari
> *Sent:* Friday, April 12, 2013 11:06 AM
> *To:* user@ctakes.apache.org
> *Subject:* RE: concept identification query
>
> Hi All,
>
> Where do we need to update this UMLS key in ctakes?
>
> Thanks for your time and help.
>
> Thank you,
> Giri
>
> On Apr 12, 2013 10:59 AM, "Savova, Guergana"
> <Guergana.Savova@childrens.harvard.edu
> <ma...@childrens.harvard.edu>> wrote:
>
> You would need to get a UMLS license to get the full functionality. It
> takes 2-3 days to be approved for it.
>
> Hope this helps.
>
> --Guergana
>
> *From:*Rooney, Niall [mailto:nf.rooney@ulster.ac.uk
> <ma...@ulster.ac.uk>]
> *Sent:* Friday, April 12, 2013 10:26 AM
> *To:* user@ctakes.apache.org <ma...@ctakes.apache.org>
> *Subject:* RE: concept identification query
>
> Pei,
>
> I don't have a UMLS license yet but thanks for looking into this.
>
> *From:*Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu
> <ma...@childrens.harvard.edu>]
> *Sent:* 12 April 2013 15:10
> *To:* <user@ctakes.apache.org <ma...@ctakes.apache.org>>
> *Subject:* Re: concept identification query
>
> Thanks Tim for confirming...
>
> AggregatePlaintextUMLSProcessor.xmlshould pick up stomach and aphasia etc.
>
> Sent from my iPhone
>
>
> On Apr 12, 2013, at 9:25 AM, "Tim Miller"
> <timothy.miller@childrens.harvard.edu
> <ma...@childrens.harvard.edu>> wrote:
>
> Niall,
> I'm sure Pei will get back to you soon, but just wanted to let you
> know, many of those entities will be found by the standard ctakes
> installation. I get aphasia and stomach. It does not get blood
> pressure, I think because this is filtered out by UMLS semantic
> class - I think it is categorized as a "measurement," and cTAKES
> will find things like disease/disorder, signs/symptoms, and a few
> others, which this does not fit into exactly. It may be worth
> thinking about how to include it if it will be useful. In this
> example it looks like it's linked to some assessment "HB +20%", I
> assume that is some measurement that would be useful to extract?
> Tim
>
> On 04/12/2013 07:05 AM, Rooney, Niall wrote:
>
> Hi,
>
> I have question concerning concept identification. I have
> modifying the example text given in the installation
> instructions to demonstrate the use of CAS Visual Debugger.
>
> My text is:
>
> Dr. Nutritious
>
> Medical Nutrition Therapy for Hyperlipidemia and Aphasia
>
> Referral from: Julie Tester, RD, LD, CNSD
>
> Phone contact: (555) 555-1212
>
> Height: 144 cm Current Weight: 45 kg Date of current
> weight: 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
>
> Diet: General
>
> Daily Calorie needs (kcals): 1500 calories, assessed as HB +
> 20% for activity and blood pressure.
>
> Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
>
> Pt has been on a 3-day calorie count and has had an average
> intake of 1100 calories. She was instructed to drink 2-3 cans
> of liquid supplement to help promote weight gain.
>
> She agrees with the plan and has my number for further
> assessment. May want a Metabolic Rate as well. She takes
> Codeine a day for knee and stomach pain.
>
> Original entities and concepts are identified such as
> "Hyperlidemia" , "knee","pain". However concepts associated
> with addition to the text are not identified such as
> "Aphasia", "blood pressure", "stomach". Also "metabolic rate"
> is not identified. Does anyone know why this is?
>
> ------------------------------------------------------------------------
>
>
> This email and any attachments are confidential and intended
> solely for the use of the addressee and may contain
> information which is covered by legal, professional or other
> privilege. If you have received this email in error please
> notify the system manager at postmaster@ulster.ac.uk
> <ma...@ulster.ac.uk> and delete this email
> immediately. Any views or opinions expressed are solely those
> of the author and do not necessarily represent those of the
> University of Ulster. The University's computer systems may be
> monitored and communications carried out on them may be
> recorded to secure the effective operation of the system and
> for other lawful purposes. The University of Ulster does not
> guarantee that this email or any attachments are free from
> viruses or 100% secure. Unless expressly stated in the body of
> a separate attachment, the text of email is not intended to
> form a binding contract. Correspondence to and from the
> University may be subject to requests for disclosure by 3rd
> parties under relevant legislation. The University of Ulster
> was founded by Royal Charter in 1984 and is registered with
> company number RC000726 and VAT registered number
> GB672390524.The primary contact address for the University of
> Ulster in Northern Ireland is,Cromore Road, Coleraine, Co.
> Londonderry BT52 1SA
>
> ------------------------------------------------------------------------
>
>
> This email and any attachments are confidential and intended solely
> for the use of the addressee and may contain information which is
> covered by legal, professional or other privilege. If you have
> received this email in error please notify the system manager at
> postmaster@ulster.ac.uk <ma...@ulster.ac.uk> and delete
> this email immediately. Any views or opinions expressed are solely
> those of the author and do not necessarily represent those of the
> University of Ulster. The University's computer systems may be
> monitored and communications carried out on them may be recorded to
> secure the effective operation of the system and for other lawful
> purposes. The University of Ulster does not guarantee that this email
> or any attachments are free from viruses or 100% secure. Unless
> expressly stated in the body of a separate attachment, the text of
> email is not intended to form a binding contract. Correspondence to
> and from the University may be subject to requests for disclosure by
> 3rd parties under relevant legislation. The University of Ulster was
> founded by Royal Charter in 1984 and is registered with company number
> RC000726 and VAT registered number GB672390524.The primary contact
> address for the University of Ulster in Northern Ireland is,Cromore
> Road, Coleraine, Co. Londonderry BT52 1SA
>
RE: concept identification query
Posted by "Bleeker, Troy C." <Bl...@mayo.edu>.
The Developer install guide talks about UMLS integration: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Developer+Install+Guide
Search for UMLS. It is described for Eclipse and for command line. Users that are just trying out cTAKES don't have those instructions. Do you think they should be part of the User Guide?
Troy
From: user-return-110-Bleeker.Troy=mayo.edu@ctakes.apache.org [mailto:user-return-110-Bleeker.Troy=mayo.edu@ctakes.apache.org] On Behalf Of giri vara prasad nambari
Sent: Friday, April 12, 2013 11:06 AM
To: user@ctakes.apache.org
Subject: RE: concept identification query
Hi All,
Where do we need to update this UMLS key in ctakes?
Thanks for your time and help.
Thank you,
Giri
On Apr 12, 2013 10:59 AM, "Savova, Guergana" <Gu...@childrens.harvard.edu>> wrote:
You would need to get a UMLS license to get the full functionality. It takes 2-3 days to be approved for it.
Hope this helps.
--Guergana
From: Rooney, Niall [mailto:nf.rooney@ulster.ac.uk<ma...@ulster.ac.uk>]
Sent: Friday, April 12, 2013 10:26 AM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: RE: concept identification query
Pei,
I don't have a UMLS license yet but thanks for looking into this.
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu<ma...@childrens.harvard.edu>]
Sent: 12 April 2013 15:10
To: <us...@ctakes.apache.org>>
Subject: Re: concept identification query
Thanks Tim for confirming...
AggregatePlaintextUMLSProcessor.xmlshould pick up stomach and aphasia etc.
Sent from my iPhone
On Apr 12, 2013, at 9:25 AM, "Tim Miller" <ti...@childrens.harvard.edu>> wrote:
Niall,
I'm sure Pei will get back to you soon, but just wanted to let you know, many of those entities will be found by the standard ctakes installation. I get aphasia and stomach. It does not get blood pressure, I think because this is filtered out by UMLS semantic class - I think it is categorized as a "measurement," and cTAKES will find things like disease/disorder, signs/symptoms, and a few others, which this does not fit into exactly. It may be worth thinking about how to include it if it will be useful. In this example it looks like it's linked to some assessment "HB +20%", I assume that is some measurement that would be useful to extract?
Tim
On 04/12/2013 07:05 AM, Rooney, Niall wrote:
Hi,
I have question concerning concept identification. I have modifying the example text given in the installation instructions to demonstrate the use of CAS Visual Debugger.
My text is:
Dr. Nutritious
Medical Nutrition Therapy for Hyperlipidemia and Aphasia
Referral from: Julie Tester, RD, LD, CNSD
Phone contact: (555) 555-1212
Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
Diet: General
Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity and blood pressure.
Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
Pt has been on a 3-day calorie count and has had an average intake of 1100 calories. She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.
She agrees with the plan and has my number for further assessment. May want a Metabolic Rate as well. She takes Codeine a day for knee and stomach pain.
Original entities and concepts are identified such as "Hyperlidemia" , "knee","pain". However concepts associated with addition to the text are not identified such as "Aphasia", "blood pressure", "stomach". Also "metabolic rate" is not identified. Does anyone know why this is?
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
RE: concept identification query
Posted by giri vara prasad nambari <gi...@gmail.com>.
Hi All,
Where do we need to update this UMLS key in ctakes?
Thanks for your time and help.
Thank you,
Giri
On Apr 12, 2013 10:59 AM, "Savova, Guergana" <
Guergana.Savova@childrens.harvard.edu> wrote:
> You would need to get a UMLS license to get the full functionality. It
> takes 2-3 days to be approved for it.****
>
> Hope this helps.****
>
> --Guergana****
>
> ** **
>
> *From:* Rooney, Niall [mailto:nf.rooney@ulster.ac.uk]
> *Sent:* Friday, April 12, 2013 10:26 AM
> *To:* user@ctakes.apache.org
> *Subject:* RE: concept identification query****
>
> ** **
>
> Pei,****
>
> ****
>
> I don’t have a UMLS license yet but thanks for looking into this.****
>
> ****
>
> *From:* Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> *Sent:* 12 April 2013 15:10
> *To:* <us...@ctakes.apache.org>
> *Subject:* Re: concept identification query****
>
> ****
>
> Thanks Tim for confirming...****
>
> AggregatePlaintextUMLSProcessor.xmlshould pick up stomach and aphasia etc.
>
> Sent from my iPhone****
>
>
> On Apr 12, 2013, at 9:25 AM, "Tim Miller" <
> timothy.miller@childrens.harvard.edu> wrote:****
>
> Niall,
> I'm sure Pei will get back to you soon, but just wanted to let you know,
> many of those entities will be found by the standard ctakes installation. I
> get aphasia and stomach. It does not get blood pressure, I think because
> this is filtered out by UMLS semantic class - I think it is categorized as
> a "measurement," and cTAKES will find things like disease/disorder,
> signs/symptoms, and a few others, which this does not fit into exactly. It
> may be worth thinking about how to include it if it will be useful. In this
> example it looks like it's linked to some assessment "HB +20%", I assume
> that is some measurement that would be useful to extract?
> Tim****
>
> On 04/12/2013 07:05 AM, Rooney, Niall wrote:****
>
> Hi,****
>
> ****
>
> I have question concerning concept identification. I have modifying the
> example text given in the installation instructions to demonstrate the use
> of CAS Visual Debugger.****
>
> ****
>
> My text is:****
>
> ****
>
> Dr. Nutritious****
>
> ****
>
> Medical Nutrition Therapy for Hyperlipidemia and Aphasia****
>
> ****
>
> Referral from: Julie Tester, RD, LD, CNSD****
>
> Phone contact: (555) 555-1212****
>
> Height: 144 cm Current Weight: 45 kg Date of current weight:
> 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2****
>
> Diet: General****
>
> Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for
> activity and blood pressure.****
>
> Daily Protein needs: 40 grams, assessed as 1.0 g/kg.****
>
> Pt has been on a 3-day calorie count and has had an average intake of 1100
> calories. She was instructed to drink 2-3 cans of liquid supplement to
> help promote weight gain. ****
>
> She agrees with the plan and has my number for further assessment. May
> want a Metabolic Rate as well. She takes Codeine a day for knee and stomach
> pain. ****
>
> ****
>
> ****
>
> Original entities and concepts are identified such as “Hyperlidemia” ,
> “knee”,“pain”. However concepts associated with addition to the text are
> not identified such as “Aphasia”, “blood pressure”, “stomach”. Also
> “metabolic rate” is not identified. Does anyone know why this is? ****
>
> ****
>
> ****
>
> ****
> ------------------------------
>
>
> This email and any attachments are confidential and intended solely for
> the use of the addressee and may contain information which is covered by
> legal, professional or other privilege. If you have received this email in
> error please notify the system manager at postmaster@ulster.ac.uk and
> delete this email immediately. Any views or opinions expressed are solely
> those of the author and do not necessarily represent those of the
> University of Ulster. The University's computer systems may be monitored
> and communications carried out on them may be recorded to secure the
> effective operation of the system and for other lawful purposes. The
> University of Ulster does not guarantee that this email or any attachments
> are free from viruses or 100% secure. Unless expressly stated in the body
> of a separate attachment, the text of email is not intended to form a
> binding contract. Correspondence to and from the University may be subject
> to requests for disclosure by 3rd parties under relevant legislation. The
> University of Ulster was founded by Royal Charter in 1984 and is registered
> with company number RC000726 and VAT registered number GB672390524.The
> primary contact address for the University of Ulster in Northern Ireland
> is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA ****
>
> ****
>
> ** **
> ------------------------------
>
>
> This email and any attachments are confidential and intended solely for
> the use of the addressee and may contain information which is covered by
> legal, professional or other privilege. If you have received this email in
> error please notify the system manager at postmaster@ulster.ac.uk and
> delete this email immediately. Any views or opinions expressed are solely
> those of the author and do not necessarily represent those of the
> University of Ulster. The University's computer systems may be monitored
> and communications carried out on them may be recorded to secure the
> effective operation of the system and for other lawful purposes. The
> University of Ulster does not guarantee that this email or any attachments
> are free from viruses or 100% secure. Unless expressly stated in the body
> of a separate attachment, the text of email is not intended to form a
> binding contract. Correspondence to and from the University may be subject
> to requests for disclosure by 3rd parties under relevant legislation. The
> University of Ulster was founded by Royal Charter in 1984 and is registered
> with company number RC000726 and VAT registered number GB672390524.The
> primary contact address for the University of Ulster in Northern Ireland
> is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA ****
>
RE: concept identification query
Posted by "Savova, Guergana" <Gu...@childrens.harvard.edu>.
You would need to get a UMLS license to get the full functionality. It takes 2-3 days to be approved for it.
Hope this helps.
--Guergana
From: Rooney, Niall [mailto:nf.rooney@ulster.ac.uk]
Sent: Friday, April 12, 2013 10:26 AM
To: user@ctakes.apache.org
Subject: RE: concept identification query
Pei,
I don't have a UMLS license yet but thanks for looking into this.
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: 12 April 2013 15:10
To: <us...@ctakes.apache.org>
Subject: Re: concept identification query
Thanks Tim for confirming...
AggregatePlaintextUMLSProcessor.xmlshould pick up stomach and aphasia etc.
Sent from my iPhone
On Apr 12, 2013, at 9:25 AM, "Tim Miller" <ti...@childrens.harvard.edu>> wrote:
Niall,
I'm sure Pei will get back to you soon, but just wanted to let you know, many of those entities will be found by the standard ctakes installation. I get aphasia and stomach. It does not get blood pressure, I think because this is filtered out by UMLS semantic class - I think it is categorized as a "measurement," and cTAKES will find things like disease/disorder, signs/symptoms, and a few others, which this does not fit into exactly. It may be worth thinking about how to include it if it will be useful. In this example it looks like it's linked to some assessment "HB +20%", I assume that is some measurement that would be useful to extract?
Tim
On 04/12/2013 07:05 AM, Rooney, Niall wrote:
Hi,
I have question concerning concept identification. I have modifying the example text given in the installation instructions to demonstrate the use of CAS Visual Debugger.
My text is:
Dr. Nutritious
Medical Nutrition Therapy for Hyperlipidemia and Aphasia
Referral from: Julie Tester, RD, LD, CNSD
Phone contact: (555) 555-1212
Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
Diet: General
Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity and blood pressure.
Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
Pt has been on a 3-day calorie count and has had an average intake of 1100 calories. She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.
She agrees with the plan and has my number for further assessment. May want a Metabolic Rate as well. She takes Codeine a day for knee and stomach pain.
Original entities and concepts are identified such as "Hyperlidemia" , "knee","pain". However concepts associated with addition to the text are not identified such as "Aphasia", "blood pressure", "stomach". Also "metabolic rate" is not identified. Does anyone know why this is?
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
RE: concept identification query
Posted by "Rooney, Niall" <nf...@ulster.ac.uk>.
Pei,
I don't have a UMLS license yet but thanks for looking into this.
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: 12 April 2013 15:10
To: <us...@ctakes.apache.org>
Subject: Re: concept identification query
Thanks Tim for confirming...
AggregatePlaintextUMLSProcessor.xmlshould pick up stomach and aphasia etc.
Sent from my iPhone
On Apr 12, 2013, at 9:25 AM, "Tim Miller" <ti...@childrens.harvard.edu>> wrote:
Niall,
I'm sure Pei will get back to you soon, but just wanted to let you know, many of those entities will be found by the standard ctakes installation. I get aphasia and stomach. It does not get blood pressure, I think because this is filtered out by UMLS semantic class - I think it is categorized as a "measurement," and cTAKES will find things like disease/disorder, signs/symptoms, and a few others, which this does not fit into exactly. It may be worth thinking about how to include it if it will be useful. In this example it looks like it's linked to some assessment "HB +20%", I assume that is some measurement that would be useful to extract?
Tim
On 04/12/2013 07:05 AM, Rooney, Niall wrote:
Hi,
I have question concerning concept identification. I have modifying the example text given in the installation instructions to demonstrate the use of CAS Visual Debugger.
My text is:
Dr. Nutritious
Medical Nutrition Therapy for Hyperlipidemia and Aphasia
Referral from: Julie Tester, RD, LD, CNSD
Phone contact: (555) 555-1212
Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
Diet: General
Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity and blood pressure.
Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
Pt has been on a 3-day calorie count and has had an average intake of 1100 calories. She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.
She agrees with the plan and has my number for further assessment. May want a Metabolic Rate as well. She takes Codeine a day for knee and stomach pain.
Original entities and concepts are identified such as "Hyperlidemia" , "knee","pain". However concepts associated with addition to the text are not identified such as "Aphasia", "blood pressure", "stomach". Also "metabolic rate" is not identified. Does anyone know why this is?
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
________________________________
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Re: concept identification query
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Thanks Tim for confirming...
AggregatePlaintextUMLSProcessor.xmlshould pick up stomach and aphasia etc.
Sent from my iPhone
On Apr 12, 2013, at 9:25 AM, "Tim Miller" <ti...@childrens.harvard.edu>> wrote:
Niall,
I'm sure Pei will get back to you soon, but just wanted to let you know, many of those entities will be found by the standard ctakes installation. I get aphasia and stomach. It does not get blood pressure, I think because this is filtered out by UMLS semantic class - I think it is categorized as a "measurement," and cTAKES will find things like disease/disorder, signs/symptoms, and a few others, which this does not fit into exactly. It may be worth thinking about how to include it if it will be useful. In this example it looks like it's linked to some assessment "HB +20%", I assume that is some measurement that would be useful to extract?
Tim
On 04/12/2013 07:05 AM, Rooney, Niall wrote:
Hi,
I have question concerning concept identification. I have modifying the example text given in the installation instructions to demonstrate the use of CAS Visual Debugger.
My text is:
Dr. Nutritious
Medical Nutrition Therapy for Hyperlipidemia and Aphasia
Referral from: Julie Tester, RD, LD, CNSD
Phone contact: (555) 555-1212
Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
Diet: General
Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity and blood pressure.
Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
Pt has been on a 3-day calorie count and has had an average intake of 1100 calories. She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.
She agrees with the plan and has my number for further assessment. May want a Metabolic Rate as well. She takes Codeine a day for knee and stomach pain.
Original entities and concepts are identified such as “Hyperlidemia” , “knee”,“pain”. However concepts associated with addition to the text are not identified such as “Aphasia”, “blood pressure”, “stomach”. Also “metabolic rate” is not identified. Does anyone know why this is?
________________________________
This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster@ulster.ac.uk<ma...@ulster.ac.uk> and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA
Re: concept identification query
Posted by Tim Miller <ti...@childrens.harvard.edu>.
Niall,
I'm sure Pei will get back to you soon, but just wanted to let you know,
many of those entities will be found by the standard ctakes
installation. I get aphasia and stomach. It does not get blood
pressure, I think because this is filtered out by UMLS semantic class -
I think it is categorized as a "measurement," and cTAKES will find
things like disease/disorder, signs/symptoms, and a few others, which
this does not fit into exactly. It may be worth thinking about how to
include it if it will be useful. In this example it looks like it's
linked to some assessment "HB +20%", I assume that is some measurement
that would be useful to extract?
Tim
On 04/12/2013 07:05 AM, Rooney, Niall wrote:
>
> Hi,
>
> I have question concerning concept identification. I have modifying
> the example text given in the installation instructions to demonstrate
> the use of CAS Visual Debugger.
>
> My text is:
>
> Dr. Nutritious
>
> Medical Nutrition Therapy for Hyperlipidemia and Aphasia
>
> Referral from: Julie Tester, RD, LD, CNSD
>
> Phone contact: (555) 555-1212
>
> Height: 144 cm Current Weight: 45 kg Date of current weight:
> 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
>
> Diet: General
>
> Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for
> activity and blood pressure.
>
> Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
>
> Pt has been on a 3-day calorie count and has had an average intake of
> 1100 calories. She was instructed to drink 2-3 cans of liquid
> supplement to help promote weight gain.
>
> She agrees with the plan and has my number for further assessment.
> May want a Metabolic Rate as well. She takes Codeine a day for knee
> and stomach pain.
>
> Original entities and concepts are identified such as "Hyperlidemia" ,
> "knee","pain". However concepts associated with addition to the text
> are not identified such as "Aphasia", "blood pressure", "stomach".
> Also "metabolic rate" is not identified. Does anyone know why this is?
>
>
> ------------------------------------------------------------------------
>
> This email and any attachments are confidential and intended solely
> for the use of the addressee and may contain information which is
> covered by legal, professional or other privilege. If you have
> received this email in error please notify the system manager at
> postmaster@ulster.ac.uk and delete this email immediately. Any views
> or opinions expressed are solely those of the author and do not
> necessarily represent those of the University of Ulster. The
> University's computer systems may be monitored and communications
> carried out on them may be recorded to secure the effective operation
> of the system and for other lawful purposes. The University of Ulster
> does not guarantee that this email or any attachments are free from
> viruses or 100% secure. Unless expressly stated in the body of a
> separate attachment, the text of email is not intended to form a
> binding contract. Correspondence to and from the University may be
> subject to requests for disclosure by 3rd parties under relevant
> legislation. The University of Ulster was founded by Royal Charter in
> 1984 and is registered with company number RC000726 and VAT registered
> number GB672390524.The primary contact address for the University of
> Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry
> BT52 1SA