[bioontology-support] Why is CPT being removed?

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[bioontology-support] Why is CPT being removed?

Vining,David

I am curious – why is the CPT ontology being removed from BioPortal? Licensing issues?

 

Thank you,

 

David

 

David J. Vining, MD

Professor, Department of Abdominal Imaging

MD Anderson Cancer Center

 

Disclosures as required by 2019 MDACC COI Management Plan:

VisionSR, Majority owner and CEO, multimedia structured reporting for use in advancing medical research

Bracco Diagnostics, Inventor, virtual colonoscopy-related products for colorectal cancer imaging

 

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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Re: [bioontology-support] Why is CPT being removed?

John Graybeal-2
Hi David,

Simply put, it is being removed because their lawyers asked us to. 

While the UMLS + CPT licenses may have some room for interpretation, we are eager to support the interpretation CPT wants us to follow. It's obviously been a popular ontology in BioPortal and hopefully someday there will be a path by which we can add it again.

As with several other ontologies, individuals have the ability to download UMLS and use the umls2rdf conversion software to work with it in their own OntoPortal repository for their own purposes, while remaining in accordance with the UMLS and CPT licenses. Hopefully this will provide a useful workaround for some individuals.

John

On Sep 20, 2020, at 7:48 AM, Vining,David <[hidden email]> wrote:

I am curious – why is the CPT ontology being removed from BioPortal? Licensing issues?
 
Thank you,
 
David
 
David J. Vining, MD
Professor, Department of Abdominal Imaging
MD Anderson Cancer Center
 
Disclosures as required by 2019 MDACC COI Management Plan:
VisionSR, Majority owner and CEO, multimedia structured reporting for use in advancing medical research
Bracco Diagnostics, Inventor, virtual colonoscopy-related products for colorectal cancer imaging
 
The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.
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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360




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Re: [bioontology-support] Why is CPT being removed?

Mark A Musen
Hi David,

Thanks for your support.  If you think it would be helpful, you could write to the AMA to let them know your feelings about their position.

As John says, there is a workaround by installing your own virtual appliance for BioPortal, but then you’d have to maintain the ontologies yourself in your local system.

Regards,

Mark
____________________________
Mark A. Musen, M.D., Ph.D.
Director, Stanford Center for Biomedical Informatics Research
Professor of Medicine (Biomedical Informatics) and Biomedical Data Science
Stanford University School of Medicine
1265 Welch Road, Room X-271
Stanford, CA. 94305-5479

+1 (650) 725-3390
[hidden email]



On Sep 21, 2020, at 8:57 AM, John Graybeal <[hidden email]> wrote:

Hi David,

Simply put, it is being removed because their lawyers asked us to. 

While the UMLS + CPT licenses may have some room for interpretation, we are eager to support the interpretation CPT wants us to follow. It's obviously been a popular ontology in BioPortal and hopefully someday there will be a path by which we can add it again.

As with several other ontologies, individuals have the ability to download UMLS and use the umls2rdf conversion software to work with it in their own OntoPortal repository for their own purposes, while remaining in accordance with the UMLS and CPT licenses. Hopefully this will provide a useful workaround for some individuals.

John

On Sep 20, 2020, at 7:48 AM, Vining,David <[hidden email]> wrote:

I am curious – why is the CPT ontology being removed from BioPortal? Licensing issues?
 
Thank you,
 
David
 
David J. Vining, MD
Professor, Department of Abdominal Imaging
MD Anderson Cancer Center
 
Disclosures as required by 2019 MDACC COI Management Plan:
VisionSR, Majority owner and CEO, multimedia structured reporting for use in advancing medical research
Bracco Diagnostics, Inventor, virtual colonoscopy-related products for colorectal cancer imaging
 
The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.
_______________________________________________
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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360





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Re: [bioontology-support] Why is CPT being removed?

Vining,David
In reply to this post by John Graybeal-2

John,

 

Thanks! I figured as much! For the cost of licensing CPT I found it interesting that it would be available on BioPortal.

 

By the way, I really like BioPortal a lot! I think that it is an awesome resource! I have been developing a multimedia structured reporting system for diagnostic radiology which has subsequently expanded to other medical disciplines.  We employ an ontological structure similar to the now antiquated American College of Radiology Index for Radiological Diagnoses, akin to being a Dewey Decimal system with a hierarchy of anatomy terms with each having a hierarchy of pathology terms and associated common data elements. However, we cross-reference our elements to SNOMED, RadLex, ICD-X, LOINC, etc. where those references exist. Our approach is a little different but it provides for great versatility.  We’ve used this concept to map and relate treatments (surgery, radiation, drugs), labs, and signs/symptoms of disease to the anatomical-pathology hierarchies.  We have used BioPortal extensively in accomplishing this task.

 

I’ll heed Mark’s recommendation of writing to the AMA, but I suspect that they are motivated to keep selling their coding books LOL!

 

David

 

David J. Vining, MD

Professor, Department of Abdominal Imaging

MD Anderson Cancer Center

 

Disclosures as required by 2019 MDACC COI Management Plan:

VisionSR, Majority owner and CEO, multimedia structured reporting for use in advancing medical research

Bracco Diagnostics, Inventor, virtual colonoscopy-related products for colorectal cancer imaging

 

From: John Graybeal <[hidden email]>
Sent: Monday, September 21, 2020 10:57 AM
To: Vining,David <[hidden email]>
Cc: [hidden email]
Subject: [EXT] Re: [bioontology-support] Why is CPT being removed?

 

WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.

 

Hi David,

 

Simply put, it is being removed because their lawyers asked us to. 

 

While the UMLS + CPT licenses may have some room for interpretation, we are eager to support the interpretation CPT wants us to follow. It's obviously been a popular ontology in BioPortal and hopefully someday there will be a path by which we can add it again.

 

As with several other ontologies, individuals have the ability to download UMLS and use the umls2rdf conversion software to work with it in their own OntoPortal repository for their own purposes, while remaining in accordance with the UMLS and CPT licenses. Hopefully this will provide a useful workaround for some individuals.

 

John



On Sep 20, 2020, at 7:48 AM, Vining,David <[hidden email]> wrote:

 

I am curious – why is the CPT ontology being removed from BioPortal? Licensing issues?

 

Thank you,

 

David

 

David J. Vining, MD

Professor, Department of Abdominal Imaging

MD Anderson Cancer Center

 

Disclosures as required by 2019 MDACC COI Management Plan:

VisionSR, Majority owner and CEO, multimedia structured reporting for use in advancing medical research

Bracco Diagnostics, Inventor, virtual colonoscopy-related products for colorectal cancer imaging

 

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

========================

John Graybeal

Technical Program Manager

Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal

Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360

 

 

 

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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