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[bioontology-support] Bioportal API & REDCap

John Graybeal jgraybeal at stanford.edu
Thu Sep 12 09:48:38 PDT 2019


Hello Muriel,

There are ways to achieve what you want, though they will require some additional work. BioPortal does not make older versions of ontologies available in routine operations, unless (as in the case of ICD 9 and 10) the providers choose to register them as different ontologies.

There are two paths, each involving uploading yourself the older versions of CTCAE that you want available. That step in turn implies that the CTCAE license supports this type of use, and that you have access to all the older versions you want. (I see the 4.02 and 4.03 versions are available as downloads on BioPortal, but not anything older than that.)

For maximum control, you could install your own BioPortal service, and connect your REDCap software to that. This would involve maintaining all the ontologies you need locally, and a configuration change to REDCap (or possibly a coding change to REDCap—sorry I am not more conversant with that software).

A more straightforward alternative is that you could install the additional (non-5.0) CTCAE ontologies as private ontologies in BioPortal, and give your REDCap configuration private access to them.  So you would have ontology acronyms like CTCAE403 and CTCAE50, which would make very clear that the term is from that specific ontology.  This is relatively straightforward using the ontology and submission management metadata in BioPortal, we could provide assistance if it isn't obvious how to do this.

(While it is also possible to install these as public ontologies, we would discourage that due to the confusion and term redundancy that would come from the overlap of concepts across the various CTCAE ontology versions.)

I hope this offers you a viable approach, and will contact you offline about more advanced scenarios.

John

On Sep 12, 2019, at 5:35 AM, muriel.helmers at ctu.unibe.ch<mailto:muriel.helmers at ctu.unibe.ch> wrote:

Dear Bioportal

I am contacting you with a request concerning your Bioportal API in combination with REDCap (https://www.project-redcap.org/).

The CTU Bern is the Clinical Trials Unit of the University of Bern, Switzerland. We are supporting clinical researchers of different Swiss institutions, and have been running over 800 clinical studies and registries so far. We are using REDCap for most of our studies and are using the Bioportal API for ontologies.

We recently discovered that the ontology ‘Common Terminology Criteria for Adverse Events’ (CTCAE) was updated from 4.03 to 5.0.
Unfortunately the old Version, 4.03 is not accessible anymore. This is a major problem for us: The clinical research field is very regulated and sponsors of a study have to declare in their study protocol, what version of CTCAE they will be using in their study. This version should not be changed during the study as this would
a) make the analysis of the data very difficult as for some events the old ontology would have been used, for some events the new one
b) the sponsor of the study would have to inform the local ethics committee about the change in CTCAE version.

In summary, it would be of enormous help to us if the different versions of CTCAE would be accessible and also stay accessible, also after the release of a new version. I guess this issue is concerning all REDCap users using CTCAE through the Bioportal API.
If we cannot access the older versions, we will in future probably have to find another solution, e.g. implementing a solution on our own, which would be a real pity.

I would be happy to get feedback from you on the feasibility of our request. If you have any questions, please do not hesitate to contact me anytime.

Best regards,
Muriel Helmers

___________________________
University of Bern
CTU Bern

Muriel Helmers Walker
Head of Data Management
Mittelstrasse 43
3012 Bern
Switzerland
Tel          +41 31 631 34 27
http://www.ctu.unibe.ch<http://www.ctu.unibe.ch/>
___________________________

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bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
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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


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