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[bioontology-support] [BioPortal] Feedback from David Rogers

John Graybeal jgraybeal at
Fri May 11 16:17:10 PDT 2018

If you have access to the version 4 ontology—I'm not sure if the version on BioPortal is the right format  but you could download it and look—getting it into BioPortal under a new acronym should be pretty straightforward. At least people do it fairly often, and you know the ontology should be working OK. Maybe under an hour, plus some waiting time for BioPortal to parse and all. (Plus also your REDCap setup time, and the training of the users if they have access to multiple ontologies.)

If you can ask the project owner, that's definitely the best way to learn about differences, plus it will help make sure they aren't unpleasantly surprised to find it there.

If you do that, the custom ontology will definitely be accessible to your API key. If you set it to PRIVATE, only you and the administrators (and the REDHat that's using your API key) could access it, or even know it's in BioPortal.


On May 11, 2018, at 8:53 AM, Rogers, David W <drogers at<mailto:drogers at>> wrote:

Thank you, John! I was thinking of using the old version number as a suffix, as in, “CTCAE_V4”. This would require all of the project owners who want to stay on that version to reconfigure, but presumably they would be happy to have this capability for such a small effort.

I have not compared the two versions. I think I will go back to the project owner and get their  take on the differences. Perhaps this is one of those cases where a knee-jerk reaction to a user request is the wrong way to go.

These ontologies are black boxes to me so I appreciate your analysis of my possible chances of success. Do you have any idea how much time it would take a neophyte to complete this approach? (I have to bill them for my time – a factor that usually increases their thoughtfulness quite a bit…)

As for a magic wand, you can’t be serious! A simple time-stretching device such as the “Give Me Just a Little More Time” model 1970 would suffice. ☺

Thanks again for your thoughts!
David W. Rogers
Software Developer / Collaborative Data Services / 206.667.7089 / drogers<mailto:drogers at>@<mailto:drogers at><mailto:drogers at> / Fred Hutch / Cures Start Here

General CDS help: CdsHelp at<mailto:CdsHelp at> or REDCap-specific help: REDCapHelp at<mailto:REDCapHelp at>

From: John Graybeal <jgraybeal at<mailto:jgraybeal at>>
Sent: Thursday, May 10, 2018 7:17 PM
To: Rogers, David W <drogers at<mailto:drogers at>>
Cc: support at<mailto:support at>
Subject: Re: [bioontology-support] [BioPortal] Feedback from David Rogers


If I may add a few thoughts.

Note that the older version you add would have to have a different acronym than CTCAE (so your REDCAP system and/or users would have to know to use that ontology acronym, not the CTCAE one).

Something else that might be useful: if you make the ontology private, you could give access privileges to the BioPortal users that need to use it. (For example, if it's all served by a single REDCap installation, just the user that owns that API. If it is multiple installations with different user API, that would be harder.)  Then you and your users would be the only ones seeing the older ontology.

It appears that the identifiers in the CTCAE ontology are defined in the ontology. This is good—it means that REDCap is likely to use the same identifiers from your version of the ontology, as the ones originally provided by CTCAE (then the previous version) to your users. So the data would likely be annotated exactly the same way.

One other thought, before you go to that trouble: Have you compared the two versions? It may turn out that the ontology does varies little between them, and you might be able to get away with using the new one.

I hope our contributions have been helpful, I know this is an annoying situation.  If I could wave the wand I would love versions to be configurable in BioPortal, but that would require way more magic than any wand I can wave, sorry!


On May 10, 2018, at 5:17 PM, Jennifer Leigh Vendetti <vendetti at<mailto:vendetti at>> wrote:

Hi David,

On May 10, 2018, at 3:40 PM, Rogers, David W <drogers at<mailto:drogers at>> wrote:

We have numerous projects which use REDCap to select CTCAE ontologies provided through BioPortal. Much like ICD codes, one doesn’t normally switch to a different version (e.g., ICD9 –> ICD10) in the middle of a research study. My request is for you guys to do the same thing with CTCAE as you have done with ICD codes – provide multiple versions – at least the most recent prior version as well as the current version in the api.

I wanted to offer some clarification with regard to ICD. Roughly 5 years ago, we started doing twice annual imports of the ontologies that are part of the National Library of Medicine’s UMLS [1]. The UMLS includes copies of both ICD9 and ICD10, which is why you see both in BioPortal. In other words, there was no internal decision to offer multiple versions of ICD. This is simply a product of what’s available to import from the UMLS.

Generally speaking, we provide the software infrastructure for publishing biomedical ontologies into our repository. In most cases, we aren’t the authors, and/or maintainers of these ontologies and don’t put restrictions on when ontology authors are allowed to publish new versions. The contact information for CTCAE in BioPortal indicates that it’s maintained by NCI.

So I would see CTCAE and CTCAE4 in the list of available ontologies.

If you’re doing a research study that requires access to a particular version of an ontology, you’re welcome to create a new entry in BioPortal. As the owner/administrator of that entry, you’d be able to ensure that no modifications are made for the duration of your study. To add an entry for an older version of CTCAE in BioPortal, you would need to create an account [2], then navigate to the Tools -> Ontology Browser page, and click the Submit New Ontology button.

Kind regards,


bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research

John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research

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