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[bioontology-support] Why is CPT being removed?

Mark A Musen musen at stanford.edu
Mon Sep 21 09:04:35 PDT 2020


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
musen at stanford.edu<mailto:musen at stanford.edu>


[cid:image002.jpg at 01D5C6C9.9687DC70]

On Sep 21, 2020, at 8:57 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> 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 <DVining at mdanderson.org<mailto:DVining at mdanderson.org>> 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

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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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