Import Concept dictionary CSV

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Import Concept dictionary CSV

How can import concept dictionary CSV file into my system. 

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Titi T. Tsholofelo
Office Tel:00267- 3632273
Mobile Phone:00267- 72623601


"Psalm 121"


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Darius Jazayeri-3 Darius Jazayeri-3
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Re: Import Concept dictionary CSV

Hi Titi,

As far as I know there is no tool that does this.

I think you would have to either write java code to parse the csv and create concepts via the API, or else do scripting to parse the csv and create concepts via web services.

-Darius

On Fri, Apr 13, 2012 at 6:43 AM, Titi Tsholofelo <[hidden email]> wrote:
How can import concept dictionary CSV file into my system. 

--
Titi T. Tsholofelo
Office Tel:00267- 3632273
Mobile Phone:00267- 72623601


"Psalm 121"


[hidden email] from OpenMRS Implementers' mailing list


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Jonathan Galingan Jonathan Galingan
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Re: Import Concept dictionary CSV

Hi, I made a short python script to insert the icd-10 codes from a csv through mysql. If you're using ubuntu, just download the necessary MySQLdb module for python and run the script while the csv file is in the same directory. Change the parameters as necessary in the script. (The current parameters are set to get the name of the code from the first column of the csv while the code is placed on the second column)

Then update the concept word table by clicking 'Update Concept Index' in the Administration page.

Its quite messy compared to using the webservices. I'll try to fix it once I've gained more knowledge on how to use the webservices.

On Fri, Apr 13, 2012 at 10:44 PM, Darius Jazayeri <[hidden email]> wrote:
Hi Titi,

As far as I know there is no tool that does this.

I think you would have to either write java code to parse the csv and create concepts via the API, or else do scripting to parse the csv and create concepts via web services.

-Darius


On Fri, Apr 13, 2012 at 6:43 AM, Titi Tsholofelo <[hidden email]> wrote:
How can import concept dictionary CSV file into my system. 

--
Titi T. Tsholofelo
Office Tel:00267- 3632273
Mobile Phone:00267- 72623601


"Psalm 121"


[hidden email] from OpenMRS Implementers' mailing list


[hidden email] from OpenMRS Implementers' mailing list



--
Jonathan D. Galingan, MD
Project Manager for Computerization
Philippine General Hospital


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icd-10dump.py (2K) Download Attachment
Tobin Greensweig Tobin Greensweig
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Re: Import Concept dictionary CSV

Hi Jonathan,

This scrip is GREAT, thank you for sharing. I've been needing to make just this for the same purpose and avoiding it!

To get it to work for me I had to set the dilimeter of the csv.reader from 'rb' to 'U'. This may be because my csv file was produced with Excel on mac.  Also, in the last part of your code you have source being specified as "1" which is SNOMED CT in the standard OpenMRS install. You mentioned ICD 10 so you might double check. I ended up using 8.

I think that having sharing a metadata sharing export of all the code-able ICD-10 concepts would be very useful for implementers, does anybody know if this is allowed in terms of WHO licensing etc?


Tobin




On Mon, Apr 16, 2012 at 3:07 AM, Jonathan Galingan <[hidden email]> wrote:
Hi, I made a short python script to insert the icd-10 codes from a csv through mysql. If you're using ubuntu, just download the necessary MySQLdb module for python and run the script while the csv file is in the same directory. Change the parameters as necessary in the script. (The current parameters are set to get the name of the code from the first column of the csv while the code is placed on the second column)

Then update the concept word table by clicking 'Update Concept Index' in the Administration page.

Its quite messy compared to using the webservices. I'll try to fix it once I've gained more knowledge on how to use the webservices.

On Fri, Apr 13, 2012 at 10:44 PM, Darius Jazayeri <[hidden email]> wrote:
Hi Titi,

As far as I know there is no tool that does this.

I think you would have to either write java code to parse the csv and create concepts via the API, or else do scripting to parse the csv and create concepts via web services.

-Darius


On Fri, Apr 13, 2012 at 6:43 AM, Titi Tsholofelo <[hidden email]> wrote:
How can import concept dictionary CSV file into my system. 

--
Titi T. Tsholofelo
Office Tel:00267- 3632273
Mobile Phone:00267- 72623601


"Psalm 121"


[hidden email] from OpenMRS Implementers' mailing list


[hidden email] from OpenMRS Implementers' mailing list



--
Jonathan D. Galingan, MD
Project Manager for Computerization
Philippine General Hospital


[hidden email] from OpenMRS Implementers' mailing list



--
Tobin

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Andrew Kanter Andrew Kanter
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Re: Import Concept dictionary CSV

Folks, I strongly advise not putting ICD-10 in your dictionaries for clinical use. ICD-10 is a classification, administrative terminology and is not designed for front-line clinical use. We (CIEL/MVP) include ICD-10 as mapped terminology but use separate concepts for actual data collection. For example, a patient does not present with "Other disease of blood and blood-forming organs". That can be a classification after the fact, but we should record what the patient actually has. You also have a problem if the text of the code or the code itself changes... that is why it is best to separate this from the actual concepts used in the record. Happy to discuss this more.... but quick and easy is not always best for long term sustainability and interoperability...

Best,
Andy
 
--------------------
Andrew S. Kanter, MD MPH

- Director of Health Information Systems/Medical Informatics
Millennium Villages Project, Earth Institute, Columbia University
- Asst. Prof. of Clinical Biomedical Informatics and Clinical Epidemiology
Columbia University

Email: [hidden email]
Mobile: +1 (646) 469-2421
Office: +1 (212) 305-4842
Skype: akanter-ippnw
Yahoo: andy_kanter


From: Tobin Greensweig <[hidden email]>
To: [hidden email]
Sent: Monday, April 16, 2012 2:25 AM
Subject: Re: [OPENMRS-IMPLEMENTERS] Import Concept dictionary CSV

Hi Jonathan,

This scrip is GREAT, thank you for sharing. I've been needing to make just this for the same purpose and avoiding it!

To get it to work for me I had to set the dilimeter of the csv.reader from 'rb' to 'U'. This may be because my csv file was produced with Excel on mac.  Also, in the last part of your code you have source being specified as "1" which is SNOMED CT in the standard OpenMRS install. You mentioned ICD 10 so you might double check. I ended up using 8.

I think that having sharing a metadata sharing export of all the code-able ICD-10 concepts would be very useful for implementers, does anybody know if this is allowed in terms of WHO licensing etc?


Tobin




On Mon, Apr 16, 2012 at 3:07 AM, Jonathan Galingan <[hidden email]> wrote:
Hi, I made a short python script to insert the icd-10 codes from a csv through mysql. If you're using ubuntu, just download the necessary MySQLdb module for python and run the script while the csv file is in the same directory. Change the parameters as necessary in the script. (The current parameters are set to get the name of the code from the first column of the csv while the code is placed on the second column)

Then update the concept word table by clicking 'Update Concept Index' in the Administration page.

Its quite messy compared to using the webservices. I'll try to fix it once I've gained more knowledge on how to use the webservices.

On Fri, Apr 13, 2012 at 10:44 PM, Darius Jazayeri <[hidden email]> wrote:
Hi Titi,

As far as I know there is no tool that does this.

I think you would have to either write java code to parse the csv and create concepts via the API, or else do scripting to parse the csv and create concepts via web services.

-Darius


On Fri, Apr 13, 2012 at 6:43 AM, Titi Tsholofelo <[hidden email]> wrote:
How can import concept dictionary CSV file into my system. 

--
Titi T. Tsholofelo
Office Tel:00267- 3632273
Mobile Phone:00267- 72623601


"Psalm 121"


[hidden email] from OpenMRS Implementers' mailing list


[hidden email] from OpenMRS Implementers' mailing list



--
Jonathan D. Galingan, MD
Project Manager for Computerization
Philippine General Hospital


[hidden email] from OpenMRS Implementers' mailing list



--
Tobin

[hidden email] from OpenMRS Implementers' mailing list



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Friedman, Roger (CDC/CGH/DGHA) (CTR) Friedman, Roger (CDC/CGH/DGHA) (CTR)
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Re: Import Concept dictionary CSV

In reply to this post by Jonathan Galingan

All the ICD-10 codes are in the MVP-CIE dictionary

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jonathan Galingan
Sent: Sunday, April 15, 2012 8:08 PM
To: [hidden email]
Subject: Re: [OPENMRS-IMPLEMENTERS] Import Concept dictionary CSV

 

Hi, I made a short python script to insert the icd-10 codes from a csv through mysql. If you're using ubuntu, just download the necessary MySQLdb module for python and run the script while the csv file is in the same directory. Change the parameters as necessary in the script. (The current parameters are set to get the name of the code from the first column of the csv while the code is placed on the second column)

 

Then update the concept word table by clicking 'Update Concept Index' in the Administration page.

 

Its quite messy compared to using the webservices. I'll try to fix it once I've gained more knowledge on how to use the webservices.

 

On Fri, Apr 13, 2012 at 10:44 PM, Darius Jazayeri <[hidden email]> wrote:

Hi Titi,

 

As far as I know there is no tool that does this.

 

I think you would have to either write java code to parse the csv and create concepts via the API, or else do scripting to parse the csv and create concepts via web services.

 

-Darius

 

On Fri, Apr 13, 2012 at 6:43 AM, Titi Tsholofelo <[hidden email]> wrote:

How can import concept dictionary CSV file into my system. 

 

--
Titi T. Tsholofelo
Office <a href="Tel:00267-">Tel:00267- 3632273
Mobile Phone:00267- 72623601


"
Psalm 121"

 


[hidden email] from OpenMRS Implementers' mailing list

 


[hidden email] from OpenMRS Implementers' mailing list



 

--
Jonathan D. Galingan, MD

Project Manager for Computerization

Philippine General Hospital

 


[hidden email] from OpenMRS Implementers' mailing list


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Rajib Sengupta Rajib Sengupta
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Re: Import Concept dictionary CSV

In reply to this post by Andrew Kanter
Though I am new in openmrs implementation, this is the same across other EMRs also. I strongly support Andrew on this. Except few instances ICD-10 codes are really not used at the front end of the data collection. At-least, in the oncology implementation, that's what is our experience in last few months
 
Thanks,
Rajib
 
From: Andrew Kanter <[hidden email]>
To: [hidden email]
Sent: Monday, April 16, 2012 8:37 AM
Subject: Re: [OPENMRS-IMPLEMENTERS] Import Concept dictionary CSV

Folks, I strongly advise not putting ICD-10 in your dictionaries for clinical use. ICD-10 is a classification, administrative terminology and is not designed for front-line clinical use. We (CIEL/MVP) include ICD-10 as mapped terminology but use separate concepts for actual data collection. For example, a patient does not present with "Other disease of blood and blood-forming organs". That can be a classification after the fact, but we should record what the patient actually has. You also have a problem if the text of the code or the code itself changes... that is why it is best to separate this from the actual concepts used in the record. Happy to discuss this more.... but quick and easy is not always best for long term sustainability and interoperability...

Best,
Andy
 
--------------------
Andrew S. Kanter, MD MPH

- Director of Health Information Systems/Medical Informatics
Millennium Villages Project, Earth Institute, Columbia University
- Asst. Prof. of Clinical Biomedical Informatics and Clinical Epidemiology
Columbia University

Email: [hidden email]
Mobile: +1 (646) 469-2421
Office: +1 (212) 305-4842
Skype: akanter-ippnw
Yahoo: andy_kanter

From: Tobin Greensweig <[hidden email]>
To: [hidden email]
Sent: Monday, April 16, 2012 2:25 AM
Subject: Re: [OPENMRS-IMPLEMENTERS] Import Concept dictionary CSV

Hi Jonathan,

This scrip is GREAT, thank you for sharing. I've been needing to make just this for the same purpose and avoiding it!

To get it to work for me I had to set the dilimeter of the csv.reader from 'rb' to 'U'. This may be because my csv file was produced with Excel on mac.  Also, in the last part of your code you have source being specified as "1" which is SNOMED CT in the standard OpenMRS install. You mentioned ICD 10 so you might double check. I ended up using 8.

I think that having sharing a metadata sharing export of all the code-able ICD-10 concepts would be very useful for implementers, does anybody know if this is allowed in terms of WHO licensing etc?


Tobin




On Mon, Apr 16, 2012 at 3:07 AM, Jonathan Galingan <[hidden email]> wrote:
Hi, I made a short python script to insert the icd-10 codes from a csv through mysql. If you're using ubuntu, just download the necessary MySQLdb module for python and run the script while the csv file is in the same directory. Change the parameters as necessary in the script. (The current parameters are set to get the name of the code from the first column of the csv while the code is placed on the second column)

Then update the concept word table by clicking 'Update Concept Index' in the Administration page.

Its quite messy compared to using the webservices. I'll try to fix it once I've gained more knowledge on how to use the webservices.

On Fri, Apr 13, 2012 at 10:44 PM, Darius Jazayeri <[hidden email]> wrote:
Hi Titi,

As far as I know there is no tool that does this.

I think you would have to either write java code to parse the csv and create concepts via the API, or else do scripting to parse the csv and create concepts via web services.

-Darius


On Fri, Apr 13, 2012 at 6:43 AM, Titi Tsholofelo <[hidden email]> wrote:
How can import concept dictionary CSV file into my system. 

--
Titi T. Tsholofelo
Office Tel:00267- 3632273
Mobile Phone:00267- 72623601


"Psalm 121"

[hidden email] from OpenMRS Implementers' mailing list

[hidden email] from OpenMRS Implementers' mailing list



--
Jonathan D. Galingan, MD
Project Manager for Computerization
Philippine General Hospital

[hidden email] from OpenMRS Implementers' mailing list



--
Tobin
[hidden email] from OpenMRS Implementers' mailing list


[hidden email] from OpenMRS Implementers' mailing list



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Hannan, Terry J Hannan, Terry J
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Re: Import Concept dictionary CSV

In reply to this post by Andrew Kanter

Andy, this is a wonderful clarification of this issue. I would like to send this to members of our College (ACHI). May I have your permission? Terry

 

Dr Terry J. Hannan MBBS;FRACP;FACHI;FACMI
Consultant Physician
Clinical Associate Professor  School of Human Health Sciences,
University of Tasmania Department of Medicine, Launceston General Hospital
Charles Street Launceston 7250

Past President Australasian College of Health Informatics(2007-9)

Visiting Professor, Universita di Modena, e reggio emelia, Italy (Sept-Nov 2010)

 

Moderator: http://www.ghdonline.org/

 

Ph. 61 3 6348 7578
Mob. 0417 144 881
Fax 61 3 6348 7577
Email <a href="outbind://21-00000000CE6891EA9693784F8369C3F9F842586007004536092D6B1A8140A17AEDB955662848000001418F68000077AB6B1EC4168B4D82A274505EB2163A0001B4192C160000/terry.hannan@dhhs.tas.gov.au" title="blocked::outbind://21-00000000CE6891EA9693784F8369C3F9F842586007004536092D6B1A8140A17AEDB955662848000001418F68000077AB6B1EC4168B4D82A274505EB2163A0001B4192C160000/terry.hannan@dhhs.tas.gov.au&#10;blocked::outbind://21-00000000CE6891EA9693784F8369C3F9F84258600">terry.hannan@...

 

Web/Blog: www.austemrs.com.au

 

Skype: thehannans

 


From: [hidden email] [mailto:[hidden email]] On Behalf Of Andrew Kanter
Sent: Monday, 16 April 2012 10:38 PM
To: [hidden email]
Subject: Re: [OPENMRS-IMPLEMENTERS] Import Concept dictionary CSV

 

Folks, I strongly advise not putting ICD-10 in your dictionaries for clinical use. ICD-10 is a classification, administrative terminology and is not designed for front-line clinical use. We (CIEL/MVP) include ICD-10 as mapped terminology but use separate concepts for actual data collection. For example, a patient does not present with "Other disease of blood and blood-forming organs". That can be a classification after the fact, but we should record what the patient actually has. You also have a problem if the text of the code or the code itself changes... that is why it is best to separate this from the actual concepts used in the record. Happy to discuss this more.... but quick and easy is not always best for long term sustainability and interoperability...

 

Best,

Andy

 

--------------------
Andrew S. Kanter, MD MPH

- Director of Health Information Systems/Medical Informatics

Millennium Villages Project, Earth Institute, Columbia University

- Asst. Prof. of Clinical Biomedical Informatics and Clinical Epidemiology

Columbia University

Email: [hidden email]
Mobile: +1 (646) 469-2421
Office: +1 (212) 305-4842
Skype: akanter-ippnw
Yahoo: andy_kanter

 


From: Tobin Greensweig <[hidden email]>
To: [hidden email]
Sent: Monday, April 16, 2012 2:25 AM
Subject: Re: [OPENMRS-IMPLEMENTERS] Import Concept dictionary CSV



Hi Jonathan,


This scrip is GREAT, thank you for sharing. I've been needing to make just this for the same purpose and avoiding it!

 

To get it to work for me I had to set the dilimeter of the csv.reader from 'rb' to 'U'. This may be because my csv file was produced with Excel on mac.  Also, in the last part of your code you have source being specified as "1" which is SNOMED CT in the standard OpenMRS install. You mentioned ICD 10 so you might double check. I ended up using 8.

 

I think that having sharing a metadata sharing export of all the code-able ICD-10 concepts would be very useful for implementers, does anybody know if this is allowed in terms of WHO licensing etc?

 

 

Tobin



On Mon, Apr 16, 2012 at 3:07 AM, Jonathan Galingan <[hidden email]> wrote:

Hi, I made a short python script to insert the icd-10 codes from a csv through mysql. If you're using ubuntu, just download the necessary MySQLdb module for python and run the script while the csv file is in the same directory. Change the parameters as necessary in the script. (The current parameters are set to get the name of the code from the first column of the csv while the code is placed on the second column)

 

Then update the concept word table by clicking 'Update Concept Index' in the Administration page.

 

Its quite messy compared to using the webservices. I'll try to fix it once I've gained more knowledge on how to use the webservices.

 

On Fri, Apr 13, 2012 at 10:44 PM, Darius Jazayeri <[hidden email]> wrote:

Hi Titi,

 

As far as I know there is no tool that does this.

 

I think you would have to either write java code to parse the csv and create concepts via the API, or else do scripting to parse the csv and create concepts via web services.

 

-Darius

 

On Fri, Apr 13, 2012 at 6:43 AM, Titi Tsholofelo <[hidden email]> wrote:

How can import concept dictionary CSV file into my system. 

 

--
Titi T. Tsholofelo
Office Tel:00267- 3632273
Mobile Phone:00267- 72623601


"
Psalm 121"

 


[hidden email] from OpenMRS Implementers' mailing list

 


[hidden email] from OpenMRS Implementers' mailing list



 

--
Jonathan D. Galingan, MD

Project Manager for Computerization

Philippine General Hospital

 


[hidden email] from OpenMRS Implementers' mailing list



 

--
Tobin


[hidden email] from OpenMRS Implementers' mailing list

 

Want to Get Healthy?

The Tasmanian Government's Get Healthy Information and Coaching Service(R) provides free information and coaching support to Tasmanian adults who would like to learn healthier eating habits, be more active or achieve and maintain a healthy weight. Call 1300 806 258 between 8am and 8pm, Monday to Friday or visit www.gethealthy.tas.gov.au for more information.
"

CONFIDENTIALITY NOTICE AND DISCLAIMER

The information in this transmission may be confidential and/or protected by legal professional privilege, and is intended only for the person or persons to whom it is addressed. If you are not such a person, you are warned that any disclosure, copying or dissemination of the information is unauthorised. If you have received the transmission in error, please immediately contact this office by telephone, fax or email, to inform us of the error and to enable arrangements to be made for the destruction of the transmission, or its return at our cost. No liability is accepted for any unauthorised use of the information contained in this transmission.

If the transmission contains advice, the advice is based on instructions in relation to, and is provided to the addressee in connection with, the matter mentioned above. Responsibility is not accepted for reliance upon it by any other person or for any other purpose.

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Jonathan Galingan Jonathan Galingan
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Re: Import Concept dictionary CSV

Our government requires us to label our patients based on ICD-10 codes so that they may be able to monitor the prevalence of certain diseases such as cholera, dengue, measles, etc. Almost every doctor in our hospital agrees that ICD-10 codes barely cover the diseases in their specialty but we know that this helps our ministry of health allocate their resources to more prevalent diseases. I heard that SNOMED covers more diseases but would require some fee. Nevertheless, I think that the only way that these codes could be tweaked to cover all diseases for better research is if clinicians themselves use it and note the bugs. 

In terms of using the MVP dictionary. I implemented it in one clinic and could only use 10-20 concepts then I had to create around 200 to 300 more which were highly synonymous to existing ones. This prompted to forego the MVP dictionary in this present implementation as it would create a lot of confusion with the employees and developers here.

If integration between OpenMRS implementations would occur, I think it is easier to simply map concepts after than to restrict the creation while the implementation is ongoing.

On Tue, Apr 17, 2012 at 5:22 AM, Hannan, Terry J <[hidden email]> wrote:

Andy, this is a wonderful clarification of this issue. I would like to send this to members of our College (ACHI). May I have your permission? Terry

 

Dr Terry J. Hannan MBBS;FRACP;FACHI;FACMI
Consultant Physician
Clinical Associate Professor  School of Human Health Sciences,
University of Tasmania Department of Medicine, Launceston General Hospital
Charles Street Launceston 7250

Past President Australasian College of Health Informatics(2007-9)

Visiting Professor, Universita di Modena, e reggio emelia, Italy (Sept-Nov 2010)

 

Moderator: http://www.ghdonline.org/

 

Ph. 61 3 6348 7578
Mob. 0417 144 881
Fax 61 3 6348 7577
Email [hidden email]

 

Web/Blog: www.austemrs.com.au

 

Skype: thehannans

 


From: [hidden email] [mailto:[hidden email]] On Behalf Of Andrew Kanter
Sent: Monday, 16 April 2012 10:38 PM
To: [hidden email]


Subject: Re: [OPENMRS-IMPLEMENTERS] Import Concept dictionary CSV

 

Folks, I strongly advise not putting ICD-10 in your dictionaries for clinical use. ICD-10 is a classification, administrative terminology and is not designed for front-line clinical use. We (CIEL/MVP) include ICD-10 as mapped terminology but use separate concepts for actual data collection. For example, a patient does not present with "Other disease of blood and blood-forming organs". That can be a classification after the fact, but we should record what the patient actually has. You also have a problem if the text of the code or the code itself changes... that is why it is best to separate this from the actual concepts used in the record. Happy to discuss this more.... but quick and easy is not always best for long term sustainability and interoperability...

 

Best,

Andy

 

--------------------
Andrew S. Kanter, MD MPH

- Director of Health Information Systems/Medical Informatics

Millennium Villages Project, Earth Institute, Columbia University

- Asst. Prof. of Clinical Biomedical Informatics and Clinical Epidemiology

Columbia University

Email: [hidden email]
Mobile: +1 <a href="tel:%28646%29%20469-2421" value="+16464692421" target="_blank">(646) 469-2421
Office: <a href="tel:%2B1%20%28212%29%20305-4842" value="+12123054842" target="_blank">+1 (212) 305-4842
Skype: akanter-ippnw
Yahoo: andy_kanter

 


From: Tobin Greensweig <[hidden email]>
To: [hidden email]
Sent: Monday, April 16, 2012 2:25 AM
Subject: Re: [OPENMRS-IMPLEMENTERS] Import Concept dictionary CSV



Hi Jonathan,


This scrip is GREAT, thank you for sharing. I've been needing to make just this for the same purpose and avoiding it!

 

To get it to work for me I had to set the dilimeter of the csv.reader from 'rb' to 'U'. This may be because my csv file was produced with Excel on mac.  Also, in the last part of your code you have source being specified as "1" which is SNOMED CT in the standard OpenMRS install. You mentioned ICD 10 so you might double check. I ended up using 8.

 

I think that having sharing a metadata sharing export of all the code-able ICD-10 concepts would be very useful for implementers, does anybody know if this is allowed in terms of WHO licensing etc?

 

 

Tobin



On Mon, Apr 16, 2012 at 3:07 AM, Jonathan Galingan <[hidden email]> wrote:

Hi, I made a short python script to insert the icd-10 codes from a csv through mysql. If you're using ubuntu, just download the necessary MySQLdb module for python and run the script while the csv file is in the same directory. Change the parameters as necessary in the script. (The current parameters are set to get the name of the code from the first column of the csv while the code is placed on the second column)

 

Then update the concept word table by clicking 'Update Concept Index' in the Administration page.

 

Its quite messy compared to using the webservices. I'll try to fix it once I've gained more knowledge on how to use the webservices.

 

On Fri, Apr 13, 2012 at 10:44 PM, Darius Jazayeri <[hidden email]> wrote:

Hi Titi,

 

As far as I know there is no tool that does this.

 

I think you would have to either write java code to parse the csv and create concepts via the API, or else do scripting to parse the csv and create concepts via web services.

 

-Darius

 

On Fri, Apr 13, 2012 at 6:43 AM, Titi Tsholofelo <[hidden email]> wrote:

How can import concept dictionary CSV file into my system. 

 

--
Titi T. Tsholofelo
Office Tel:00267- 3632273
Mobile Phone:00267- 72623601


"
Psalm 121"

 


[hidden email] from OpenMRS Implementers' mailing list

 


[hidden email] from OpenMRS Implementers' mailing list



 

--
Jonathan D. Galingan, MD

Project Manager for Computerization

Philippine General Hospital

 


[hidden email] from OpenMRS Implementers' mailing list



 

--
Tobin


[hidden email] from OpenMRS Implementers' mailing list

 

Want to Get Healthy?

The Tasmanian Government's Get Healthy Information and Coaching Service(R) provides free information and coaching support to Tasmanian adults who would like to learn healthier eating habits, be more active or achieve and maintain a healthy weight. Call 1300 806 258 between 8am and 8pm, Monday to Friday or visit www.gethealthy.tas.gov.au for more information.
"

CONFIDENTIALITY NOTICE AND DISCLAIMER

The information in this transmission may be confidential and/or protected by legal professional privilege, and is intended only for the person or persons to whom it is addressed. If you are not such a person, you are warned that any disclosure, copying or dissemination of the information is unauthorised. If you have received the transmission in error, please immediately contact this office by telephone, fax or email, to inform us of the error and to enable arrangements to be made for the destruction of the transmission, or its return at our cost. No liability is accepted for any unauthorised use of the information contained in this transmission.

If the transmission contains advice, the advice is based on instructions in relation to, and is provided to the addressee in connection with, the matter mentioned above. Responsibility is not accepted for reliance upon it by any other person or for any other purpose.

[hidden email] from OpenMRS Implementers' mailing list
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Jonathan D. Galingan, MD
Project Manager for Computerization
Philippine General Hospital


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Andrew Kanter Andrew Kanter
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Re: Import Concept dictionary CSV

Jonathan,

I am surprised to hear that you tried the MVP dictionary and didn't speak to us at all about it. The purpose of the shared dictionary is NOT to create new concepts which are synonymous. We at CIEL have offered to help sites map their content to existing concepts or if you can't find necessary concepts to request them from us and we will add them (and then everyone benefits). I would appreciate knowing what where the 200-300 concepts you felt you needed to add.

As for disease coverage, I think we cover the vast majority of diseases and map these to ICD-10 and SNOMED CT. Again, if there is something missing, or a map is incorrect, the community would benefit if you would let us know. BTW, how did you get a copy of the MVP/CIEL dictionary? I don't see you on our registration list.

I could go a long way in explaining why it is best not to create concepts on the fly. Maternalconceptlab.com is a great way to search the dictionary and in many cases the concepts already exist.

Thanks for letting us know of your difficulties,
Andy
 
--------------------
Andrew S. Kanter, MD MPH

- Director of Health Information Systems/Medical Informatics
Millennium Villages Project, Earth Institute, Columbia University
- Asst. Prof. of Clinical Biomedical Informatics and Clinical Epidemiology
Columbia University

Email: [hidden email]
Mobile: +1 (646) 469-2421
Office: +1 (212) 305-4842
Skype: akanter-ippnw
Yahoo: andy_kanter


From: Jonathan Galingan <[hidden email]>
To: [hidden email]
Sent: Monday, April 16, 2012 6:48 PM
Subject: Re: [OPENMRS-IMPLEMENTERS] Import Concept dictionary CSV

Our government requires us to label our patients based on ICD-10 codes so that they may be able to monitor the prevalence of certain diseases such as cholera, dengue, measles, etc. Almost every doctor in our hospital agrees that ICD-10 codes barely cover the diseases in their specialty but we know that this helps our ministry of health allocate their resources to more prevalent diseases. I heard that SNOMED covers more diseases but would require some fee. Nevertheless, I think that the only way that these codes could be tweaked to cover all diseases for better research is if clinicians themselves use it and note the bugs. 

In terms of using the MVP dictionary. I implemented it in one clinic and could only use 10-20 concepts then I had to create around 200 to 300 more which were highly synonymous to existing ones. This prompted to forego the MVP dictionary in this present implementation as it would create a lot of confusion with the employees and developers here.

If integration between OpenMRS implementations would occur, I think it is easier to simply map concepts after than to restrict the creation while the implementation is ongoing.

On Tue, Apr 17, 2012 at 5:22 AM, Hannan, Terry J <[hidden email]> wrote:
Andy, this is a wonderful clarification of this issue. I would like to send this to members of our College (ACHI). May I have your permission? Terry
 
Dr Terry J. Hannan MBBS;FRACP;FACHI;FACMI
Consultant Physician
Clinical Associate Professor  School of Human Health Sciences,
University of Tasmania Department of Medicine, Launceston General Hospital
Charles Street Launceston 7250
Past President Australasian College of Health Informatics(2007-9)
Visiting Professor, Universita di Modena, e reggio emelia, Italy (Sept-Nov 2010)
 
 
Ph. 61 3 6348 7578
Mob. 0417 144 881
Fax 61 3 6348 7577
Email [hidden email]
 
 
Skype: thehannans
 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Andrew Kanter
Sent: Monday, 16 April 2012 10:38 PM
To: [hidden email]

Subject: Re: [OPENMRS-IMPLEMENTERS] Import Concept dictionary CSV
 
Folks, I strongly advise not putting ICD-10 in your dictionaries for clinical use. ICD-10 is a classification, administrative terminology and is not designed for front-line clinical use. We (CIEL/MVP) include ICD-10 as mapped terminology but use separate concepts for actual data collection. For example, a patient does not present with "Other disease of blood and blood-forming organs". That can be a classification after the fact, but we should record what the patient actually has. You also have a problem if the text of the code or the code itself changes... that is why it is best to separate this from the actual concepts used in the record. Happy to discuss this more.... but quick and easy is not always best for long term sustainability and interoperability...
 
Best,
Andy
 
--------------------
Andrew S. Kanter, MD MPH

- Director of Health Information Systems/Medical Informatics
Millennium Villages Project, Earth Institute, Columbia University
- Asst. Prof. of Clinical Biomedical Informatics and Clinical Epidemiology
Columbia University

Email: [hidden email]
Mobile: +1 (646) 469-2421
Office: +1 (212) 305-4842
Skype: akanter-ippnw
Yahoo: andy_kanter
 

From: Tobin Greensweig <[hidden email]>
To: [hidden email]
Sent: Monday, April 16, 2012 2:25 AM
Subject: Re: [OPENMRS-IMPLEMENTERS] Import Concept dictionary CSV


Hi Jonathan,

This scrip is GREAT, thank you for sharing. I've been needing to make just this for the same purpose and avoiding it!
 
To get it to work for me I had to set the dilimeter of the csv.reader from 'rb' to 'U'. This may be because my csv file was produced with Excel on mac.  Also, in the last part of your code you have source being specified as "1" which is SNOMED CT in the standard OpenMRS install. You mentioned ICD 10 so you might double check. I ended up using 8.
 
I think that having sharing a metadata sharing export of all the code-able ICD-10 concepts would be very useful for implementers, does anybody know if this is allowed in terms of WHO licensing etc?
 
 
Tobin



On Mon, Apr 16, 2012 at 3:07 AM, Jonathan Galingan <[hidden email]> wrote:
Hi, I made a short python script to insert the icd-10 codes from a csv through mysql. If you're using ubuntu, just download the necessary MySQLdb module for python and run the script while the csv file is in the same directory. Change the parameters as necessary in the script. (The current parameters are set to get the name of the code from the first column of the csv while the code is placed on the second column)
 
Then update the concept word table by clicking 'Update Concept Index' in the Administration page.
 
Its quite messy compared to using the webservices. I'll try to fix it once I've gained more knowledge on how to use the webservices.
 
On Fri, Apr 13, 2012 at 10:44 PM, Darius Jazayeri <[hidden email]> wrote:
Hi Titi,
 
As far as I know there is no tool that does this.
 
I think you would have to either write java code to parse the csv and create concepts via the API, or else do scripting to parse the csv and create concepts via web services.
 
-Darius
 
On Fri, Apr 13, 2012 at 6:43 AM, Titi Tsholofelo <[hidden email]> wrote:
How can import concept dictionary CSV file into my system. 
 
--
Titi T. Tsholofelo
Office Tel:00267- 3632273
Mobile Phone:00267- 72623601

"
Psalm 121"
 

[hidden email] from OpenMRS Implementers' mailing list
 

[hidden email] from OpenMRS Implementers' mailing list


 
--
Jonathan D. Galingan, MD
Project Manager for Computerization
Philippine General Hospital
 

[hidden email] from OpenMRS Implementers' mailing list


 
--
Tobin

[hidden email] from OpenMRS Implementers' mailing list
 
Want to Get Healthy?
The Tasmanian Government's Get Healthy Information and Coaching Service(R) provides free information and coaching support to Tasmanian adults who would like to learn healthier eating habits, be more active or achieve and maintain a healthy weight. Call 1300 806 258 between 8am and 8pm, Monday to Friday or visit www.gethealthy.tas.gov.au for more information.
"
CONFIDENTIALITY NOTICE AND DISCLAIMER
The information in this transmission may be confidential and/or protected by legal professional privilege, and is intended only for the person or persons to whom it is addressed. If you are not such a person, you are warned that any disclosure, copying or dissemination of the information is unauthorised. If you have received the transmission in error, please immediately contact this office by telephone, fax or email, to inform us of the error and to enable arrangements to be made for the destruction of the transmission, or its return at our cost. No liability is accepted for any unauthorised use of the information contained in this transmission.
If the transmission contains advice, the advice is based on instructions in relation to, and is provided to the addressee in connection with, the matter mentioned above. Responsibility is not accepted for reliance upon it by any other person or for any other purpose.

[hidden email] from OpenMRS Implementers' mailing list
[hidden email] from OpenMRS Implementers' mailing list



--
Jonathan D. Galingan, MD
Project Manager for Computerization
Philippine General Hospital


[hidden email] from OpenMRS Implementers' mailing list



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Jonathan Galingan Jonathan Galingan
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Re: Import Concept dictionary CSV

I used to be part of a team with Randy Fernandez. I think he was the one given the MVP dictionary. I was not able to document the changes we put in it but from what I remember, these were highly internal concepts and I sincerely doubt that any other institution would use it. They did not use standards such as LOINC and ICD-10. We used the concept dictionary for the identifiers of their forms and specimens. We gave codes representing employees. The chief complaint was an open-ended textbox. They used a lot of remarks in their forms. Some of these remarks would even be pertaining to certain fields on probable inaccuracies. Some of these concepts are even used to create reports for internal audit.

These are not the best practices but it facilitates the implementation because these are what the employees know and are used to. 

One of our reasons for choosing OpenMRS was its ability to facilitate an evolutionary type of implementation wherein people don't need to assume at once the best practices and simply evolve to it via revision of the concept dictionary and its forms. By doing this, we allow people to immediately feel the benefits of computerization without having to make a lot of changes that could cause rejection. 

I think eventually, when these implementations mature and note inefficiencies with what they do, they will adhere to the best practices. 

On Tuesday, April 17, 2012, Andrew Kanter wrote:
Jonathan,

I am surprised to hear that you tried the MVP dictionary and didn't speak to us at all about it. The purpose of the shared dictionary is NOT to create new concepts which are synonymous. We at CIEL have offered to help sites map their content to existing concepts or if you can't find necessary concepts to request them from us and we will add them (and then everyone benefits). I would appreciate knowing what where the 200-300 concepts you felt you needed to add.

As for disease coverage, I think we cover the vast majority of diseases and map these to ICD-10 and SNOMED CT. Again, if there is something missing, or a map is incorrect, the community would benefit if you would let us know. BTW, how did you get a copy of the MVP/CIEL dictionary? I don't see you on our registration list.

I could go a long way in explaining why it is best not to create concepts on the fly. Maternalconceptlab.com is a great way to search the dictionary and in many cases the concepts already exist.

Thanks for letting us know of your difficulties,
Andy
 
--------------------
Andrew S. Kanter, MD MPH

- Director of Health Information Systems/Medical Informatics
Millennium Villages Project, Earth Institute, Columbia University
- Asst. Prof. of Clinical Biomedical Informatics and Clinical Epidemiology
Columbia University

Email: <a href="javascript:_e({}, &#39;cvml&#39;, &#39;andrew.kanter@dbmi.columbia.edu&#39;);" target="_blank">andrew.kanter@...
Mobile: <a href="tel:%2B1%20%28646%29%20469-2421" value="+16464692421" target="_blank">+1 (646) 469-2421
Office: <a href="tel:%2B1%20%28212%29%20305-4842" value="+12123054842" target="_blank">+1 (212) 305-4842
Skype: akanter-ippnw
Yahoo: andy_kanter


From: Jonathan Galingan <<a href="javascript:_e({}, &#39;cvml&#39;, &#39;galinganmd@GMAIL.COM&#39;);" target="_blank">galinganmd@...>
To: <a href="javascript:_e({}, &#39;cvml&#39;, &#39;openmrs-implement-l@LISTSERV.IUPUI.EDU&#39;);" target="_blank">openmrs-implement-l@...
Sent: Monday, April 16, 2012 6:48 PM
Subject: Re: [OPENMRS-IMPLEMENTERS] Import Concept dictionary CSV

Our government requires us to label our patients based on ICD-10 codes so that they may be able to monitor the prevalence of certain diseases such as cholera, dengue, measles, etc. Almost every doctor in our hospital agrees that ICD-10 codes barely cover the diseases in their specialty but we know that this helps our ministry of health allocate their resources to more prevalent diseases. I heard that SNOMED covers more diseases but would require some fee. Nevertheless, I think that the only way that these codes could be tweaked to cover all diseases for better research is if clinicians themselves use it and note the bugs. 

In terms of using the MVP dictionary. I implemented it in one clinic and could only use 10-20 concepts then I had to create around 200 to 300 more which were highly synonymous to existing ones. This prompted to forego the MVP dictionary in this present implementation as it would create a lot of confusion with the employees and developers here.

If integration between OpenMRS implementations would occur, I think it is easier to simply map concepts after than to restrict the creation while the implementation is ongoing.

On Tue, Apr 17, 2012 at 5:22 AM, Hannan, Terry J <[hidden email]> wrote:
Andy, this is a wonderful clarification of this issue. I would like to send this to members of our College (ACHI). May I have your permission? Terry
 
Dr Terry J. Hannan MBBS;FRACP;FACHI;FACMI
Consultant Physician
Clinical Associate Professor  School of Human Health Sciences,
University of Tasmania Department of Medicine, Launceston General Hospital
Charles Street Launceston 7250
Past President Australasian College of Health Informatics(2007-9)
Visiting Professor, Universita di Modena, e reggio emelia, Italy (Sept-Nov 2010)
 
 
Ph. 61 3 6348 7578
Mob. 0417 144 881
Fax 61 3 6348 7577
Email

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Jonathan D. Galingan, MD
Project Manager for Computerization
Philippine General Hospital


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Dave Thomas Dave Thomas
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Re: Import Concept dictionary CSV

In reply to this post by Jonathan Galingan
Hi.  We have similar requirements in Rwanda, and the way we've dealt with this in pure OpenMRS terms is that we've let the clinical teams drive the clinical concepts that define the way that they deliver care.  Then, we've mapped diagnoses from this process to ICD-10 and directly to the Rwanda HMIS report using the ConcepMap and ConceptSource architecture.  In this model multiple clinical concepts can 'count' toward the same ICD-10 code or report item.  This way, we have a nice separation between the terminologies used in the clinical interface and the back-end reporting requirements.  In terms of HMIS, we've gone so far as to create Rwanda HMIS as a ConceptSource (along with the ICD-10 ConceptSource), and the ConceptMap for a given Concept, if applicable, is the question number on the HMIS report.

We use the maternal concept lab site whenever we get a clinical concept request -- its pretty comprehensive at this point, and an incredibly useful resource.

d

On Mon, Apr 16, 2012 at 3:48 PM, Jonathan Galingan <[hidden email]> wrote:
Our government requires us to label our patients based on ICD-10 codes so that they may be able to monitor the prevalence of certain diseases such as cholera, dengue, measles, etc. Almost every doctor in our hospital agrees that ICD-10 codes barely cover the diseases in their specialty but we know that this helps our ministry of health allocate their resources to more prevalent diseases. I heard that SNOMED covers more diseases but would require some fee. Nevertheless, I think that the only way that these codes could be tweaked to cover all diseases for better research is if clinicians themselves use it and note the bugs. 

In terms of using the MVP dictionary. I implemented it in one clinic and could only use 10-20 concepts then I had to create around 200 to 300 more which were highly synonymous to existing ones. This prompted to forego the MVP dictionary in this present implementation as it would create a lot of confusion with the employees and developers here.

If integration between OpenMRS implementations would occur, I think it is easier to simply map concepts after than to restrict the creation while the implementation is ongoing.

On Tue, Apr 17, 2012 at 5:22 AM, Hannan, Terry J <[hidden email]> wrote:

Andy, this is a wonderful clarification of this issue. I would like to send this to members of our College (ACHI). May I have your permission? Terry

 

Dr Terry J. Hannan MBBS;FRACP;FACHI;FACMI
Consultant Physician
Clinical Associate Professor  School of Human Health Sciences,
University of Tasmania Department of Medicine, Launceston General Hospital
Charles Street Launceston 7250

Past President Australasian College of Health Informatics(2007-9)

Visiting Professor, Universita di Modena, e reggio emelia, Italy (Sept-Nov 2010)

 

Moderator: http://www.ghdonline.org/

 

Ph. 61 3 6348 7578
Mob. 0417 144 881
Fax 61 3 6348 7577
Email [hidden email]

 

Web/Blog: www.austemrs.com.au

 

Skype: thehannans

 


From: [hidden email] [mailto:[hidden email]] On Behalf Of Andrew Kanter
Sent: Monday, 16 April 2012 10:38 PM
To: [hidden email]


Subject: Re: [OPENMRS-IMPLEMENTERS] Import Concept dictionary CSV

 

Folks, I strongly advise not putting ICD-10 in your dictionaries for clinical use. ICD-10 is a classification, administrative terminology and is not designed for front-line clinical use. We (CIEL/MVP) include ICD-10 as mapped terminology but use separate concepts for actual data collection. For example, a patient does not present with "Other disease of blood and blood-forming organs". That can be a classification after the fact, but we should record what the patient actually has. You also have a problem if the text of the code or the code itself changes... that is why it is best to separate this from the actual concepts used in the record. Happy to discuss this more.... but quick and easy is not always best for long term sustainability and interoperability...

 

Best,

Andy

 

--------------------
Andrew S. Kanter, MD MPH

- Director of Health Information Systems/Medical Informatics

Millennium Villages Project, Earth Institute, Columbia University

- Asst. Prof. of Clinical Biomedical Informatics and Clinical Epidemiology

Columbia University

Email: [hidden email]
Mobile: +1 <a href="tel:%28646%29%20469-2421" value="+16464692421" target="_blank">(646) 469-2421
Office: <a href="tel:%2B1%20%28212%29%20305-4842" value="+12123054842" target="_blank">+1 (212) 305-4842
Skype: akanter-ippnw
Yahoo: andy_kanter

 


From: Tobin Greensweig <[hidden email]>
To: [hidden email]
Sent: Monday, April 16, 2012 2:25 AM
Subject: Re: [OPENMRS-IMPLEMENTERS] Import Concept dictionary CSV



Hi Jonathan,


This scrip is GREAT, thank you for sharing. I've been needing to make just this for the same purpose and avoiding it!

 

To get it to work for me I had to set the dilimeter of the csv.reader from 'rb' to 'U'. This may be because my csv file was produced with Excel on mac.  Also, in the last part of your code you have source being specified as "1" which is SNOMED CT in the standard OpenMRS install. You mentioned ICD 10 so you might double check. I ended up using 8.

 

I think that having sharing a metadata sharing export of all the code-able ICD-10 concepts would be very useful for implementers, does anybody know if this is allowed in terms of WHO licensing etc?

 

 

Tobin



On Mon, Apr 16, 2012 at 3:07 AM, Jonathan Galingan <[hidden email]> wrote:

Hi, I made a short python script to insert the icd-10 codes from a csv through mysql. If you're using ubuntu, just download the necessary MySQLdb module for python and run the script while the csv file is in the same directory. Change the parameters as necessary in the script. (The current parameters are set to get the name of the code from the first column of the csv while the code is placed on the second column)

 

Then update the concept word table by clicking 'Update Concept Index' in the Administration page.

 

Its quite messy compared to using the webservices. I'll try to fix it once I've gained more knowledge on how to use the webservices.

 

On Fri, Apr 13, 2012 at 10:44 PM, Darius Jazayeri <[hidden email]> wrote:

Hi Titi,

 

As far as I know there is no tool that does this.

 

I think you would have to either write java code to parse the csv and create concepts via the API, or else do scripting to parse the csv and create concepts via web services.

 

-Darius

 

On Fri, Apr 13, 2012 at 6:43 AM, Titi Tsholofelo <[hidden email]> wrote:

How can import concept dictionary CSV file into my system. 

 

--
Titi T. Tsholofelo
Office Tel:00267- 3632273
Mobile Phone:00267- 72623601


"
Psalm 121"

 


[hidden email] from OpenMRS Implementers' mailing list

 


[hidden email] from OpenMRS Implementers' mailing list



 

--
Jonathan D. Galingan, MD

Project Manager for Computerization

Philippine General Hospital

 


[hidden email] from OpenMRS Implementers' mailing list



 

--
Tobin


[hidden email] from OpenMRS Implementers' mailing list

 

Want to Get Healthy?

The Tasmanian Government's Get Healthy Information and Coaching Service(R) provides free information and coaching support to Tasmanian adults who would like to learn healthier eating habits, be more active or achieve and maintain a healthy weight. Call 1300 806 258 between 8am and 8pm, Monday to Friday or visit www.gethealthy.tas.gov.au for more information.
"

CONFIDENTIALITY NOTICE AND DISCLAIMER

The information in this transmission may be confidential and/or protected by legal professional privilege, and is intended only for the person or persons to whom it is addressed. If you are not such a person, you are warned that any disclosure, copying or dissemination of the information is unauthorised. If you have received the transmission in error, please immediately contact this office by telephone, fax or email, to inform us of the error and to enable arrangements to be made for the destruction of the transmission, or its return at our cost. No liability is accepted for any unauthorised use of the information contained in this transmission.

If the transmission contains advice, the advice is based on instructions in relation to, and is provided to the addressee in connection with, the matter mentioned above. Responsibility is not accepted for reliance upon it by any other person or for any other purpose.

[hidden email] from OpenMRS Implementers' mailing list
[hidden email] from OpenMRS Implementers' mailing list



--
Jonathan D. Galingan, MD
Project Manager for Computerization
Philippine General Hospital


[hidden email] from OpenMRS Implementers' mailing list


[hidden email] from OpenMRS Implementers' mailing list