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[bioontology-support] AFO Error Diff

Jennifer Leigh Vendetti vendetti at
Wed Oct 27 14:09:03 PDT 2021

Hi Karin,

Apologies for the late reply.

I manually regenerated a diff file in our system for your last two submissions (both uploaded on Oct. 14th) and reset some statuses. I think the system is in a state now where the diffs should succeed going forward. If possible, please let me know the next time you upload a new version if you experience issues again.

The diff file I generated shows no class changes / additions / deletions. Does this seem correct to you? I noticed that the last two uploads have the same version number of "REC/2021/09”.

Kind regards,

On Oct 11, 2021, at 5:45 PM, Jennifer Leigh Vendetti <vendetti at<mailto:vendetti at>> wrote:

Hi Karin,

On Oct 11, 2021, at 10:01 AM, Karin Colsman <karin.colsman.contractor at<mailto:karin.colsman.contractor at>> wrote:

 Hi Jennifer,

we are still having problems with getting the AFO to conform to the BioPortal tooling – the upload result says “ Error Diff”. I am experimenting with using a newer OWL API version in our tooling, but it’s not giving us any errors.

Are you using any Open Source tools on your end that are producing the error? If so, it would be of great help to us to know which ones they are, so that I can try to reproduce the problem.

We use a 3rd party Java library to perform the diffs called Bubastis:

It’s unfortunately somewhat of an outdated library. We’ve discussed moving to ROBOT instead:

… but haven’t been able to find the resources for that yet.

I’ve entered an issue in our tracker for the failing diff for AFO so that we can investigate:

At first glance, I don’t know if the error is in our code or from Bubastis.

Kind regards,

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