Proposal Github repository ownership transfer

[sherwoodf]

Hi,

I'm an engineer/ontologist working on the BioImage Archive: https://www.ebi.ac.uk/bioimage-archive/. We rely on FBBI to classify submissions, but would like to add more terms to the ontology. Both a number of options in the near future, but also to regularly update as new imaging methods are developed.

Because of this semi-frequent update pattern, and that the ontology development is currently inactive (based off of #1), we would like to propose taking ownership of the GitHub repository, so that we don't have to bother you with pull requests in the future. Is this something CRBS/the cell imaging project would be open to?

Best,
Francois

[cthoyt]

@sherwoodf I'd suggest reaching out by email. Contact information for Willy is listed on the OBO page: https://obofoundry.org/ontology/fbbi.html

[joshmoore]

@cthoyt: any thoughts on what recourse there is after having received no response?

[cthoyt]

We could coordinate with OBO Foundry and talk about doing a hard fork of this repo, then updating their PURL configuration to point to a new place. I don't know if there is any precedent for this happening without the consent of the original repository owner, but this is sort of the nice draw of the open data/open science world.

@joshmoore would you be willing to write a short summary (no more than a paragraph or two) of the situation on the OBO Foundry issue tracker (https://github.com/OBOFoundry/OBOFoundry.github.io/issues) and ask for the advice of the OBO Operations Committee?

Maybe the first step is to petition OBO to write that this repository has been abandoned, then there are a few ways it can go:

1. Make a fork (this time, probably in a place with more than 1 person)
2. Make a new repo that has IDs that supersede fbbi IDs. I would not prefer this but it requires asking for less permission.

[joshmoore]

Thanks, @cthoyt! @sherwoodf and I will take this on board along with the others from the project.

[cthoyt]

@joshmoore one other possibility - try and figure out who are the owners of https://github.com/CRBS and see if you can contact them. I just did a quick look in the other repos in this org, and it seems they're all more or less abandoned.

Last suggestion - if you go the hard fork route, make sure that you offer to make an OBO person an extra "owner" of the new ontology. Nico Matentzoglu has been a very good steward in these situations before, when people had to abandon their things

[gouttegd]

Hi, FlyBase ontology editor here. Just a bit of context (I already sent an email to @sherwoodf with those informations, but since there is a public discussion already, I think this context should be part of the public record):

FBbi was initially created and maintained by FlyBase (hence the FBxx name and prefix), back in the early 2000s. The last version edited by us is dated from August 2005 and is available here. We have not been maintaining it since then, as we are no longer doing image curation.

As far as I and other FlyBase curators/ontology editors know, the version of FBbi available on this repository has nothing to do with us, beyond the fact that it was obviously built upon “our” version.

Now as the editors of the original 2005 version of FBbi, we at FlyBase would have no objection whatsoever to the BioImage Archive team taking over its maintenance.

But we have no particular rights over the version in this repository, which has changed significantly compared to our last version (in particular, it has grown from ~250 terms in our last version to ~650 terms in this repository).

For what it’s worth, after 8 months without a reply from any repository owner, I personally agree with @cthoyt that making a “hard fork” would be justified.

[lubianat]

As a note, me and @gouttegd are now (well, in 6 days) working for German BioImaging with @joshmoore, so there are more ontology people that will have FBbi on their radar. It could be a good time for sorting out the ownership/maintenance here.

It has been used experimentally in OME in the past (https://ome.github.io/ome2024-ngff-challenge/) and may be used again in the future, by the way.

[lubianat]

Also, I just noticed https://github.com/Imaging-semantics/fbbi, not sure with the relation between both repos

[gouttegd]

Given the complete absence of a reply from the owners here, the FoundingGIDE project (which several of the people who participated in the above discussion are part of, through either German BioImaging or the EBI BioImage Archive) has forked this repository and will now coordinate the maintenance and evolution of the FBbi ontology, which will live at https://github.com/foundingGIDE/fbbi.

[cthoyt]

@gouttegd let's try and update the appropriate metadata in OBO Foundry and link back to this issue too

[gouttegd]

@cthoyt There are two things to update on the OBO Foundry side.

(A) The first one is the configuration of the purl.obolibrary.org server so that http://purl.obolibrary.org/obo/fbbi.owl redirects to the release artefacts in the new repository.

That one should be hopefully uncontroversial (and I was planning to do that right now). There were seemingly no objections in 2019 for changing the redirection so that it would point to the Imaging-Semantics version, so I don’t see why there should be objections today (especially since we are taking over with David’s blessing).

(B) The second one are the metadata shown on https://obofoundry.org/ontology/fbbi.html. Those were not updated in 2019 when David took over, and they still point to this repository.

For that one, I am assuming the OBO Foundry folks will want more than a mere “declaration of intent”, and that forking the repository and saying “we’ll take of it from now on” will not be enough until they can see that we are actively maintaining it. Therefore I was planning to wait for a bit before submitting a request to update the OBO Foundry page.

[gouttegd]

Part (A) is here: OBOFoundry/purl.obolibrary.org#1085

[gouttegd]

And here is part (B): OBOFoundry/OBOFoundry.github.io#2874