mellybelly
commented
4 years ago My understanding from days of old (dating back to the 2006 F2F in UK) was that the Foundry status indicated that an ontology had been through the review process and had "passed". I am not aware of it being an indication of convergence; in my view that would require computational and content evaluations that have not been done much to my knowledge.
In our current implementation, I think the Foundry status does OBO a disservice. I hear regularly that when people go to the OBO site they only see a few "good" or "community endorsed" ontologies. Of course there are many good ontologies in OBO that have been extensively published upon, reviewed elsewhere, and are in wide use, but are have not been through the OBO review and so do not have Foundry status.
I do believe there should be an effort to have a point of convergence (the principle of orthogonality), but I also believe there should be some flexibility to model overlapping domains in different ways. We just approved the PURL for the Ontology for Nutritional Studies #1198 and prior to that we had our MaXO ontology approved, which has nutritional interventions - there is most definitely overlapping content conceptually, but it is modeled differently. There is also the challenge of determining what is an "application ontology" versus what is canonical and what would be allowed in that context. There are things to consider with resources that "come from outside" or that have been around longer than OBO, such as NCBItaxon, or NCIt (for which we worked hard to get a CC-BY license and to develop OBO axioms for) due to its extensive use and potential for improved translational computation as well as covering a domain not well covered in OBO already.
I personally would vote no on having Foundry status be "points of convergence" because there are not the governance processes nor the criteria in place to determine such things at this time, nor do I see what value it would bring. We can certainly work on governance and on orthogonality and alignment of modeling, but any such determination would likely be a subjective one at this time. I do think the dashboard checks are AWESOME and am excited to see this evolve- this i do find very useful.
To me, joining the OBO library, getting your OBO PURL, and participating in community processes and reusing ontologies from across the OBO community is what makes OBO valuable, including a dedication to adherence to our founding principles. I do not believe we need an additional distinction of "Foundry" nor do i believe we have the computational criteria nor governance structures in place for fairly determining such things.
Finally, I think the goals of OBO should be interoperability, computability, and reuse, and I don't see where a separate Foundry distinction helps us achieve that.
wdduncan
nataled
lschriml
alanruttenberg
BACKGROUND: Strictly speaking, Foundry designation has one real purpose: to indicate which of the (possibly several) ontologies in a given domain should be the point of 'convergence' (that is, reference and reuse by other ontologies). That's it. The manual reviews were meant as a way of selecting these. That's it. Unfortunately, every time we discuss abolishing the distinction between Foundry and Library, the discussion centers around reviews and how many were done and how the process works, and misses the main point. Given the developments around streamlining and automating the review process, I think we need to return to the central question: Do we find any value in selecting specific ontologies as points of convergence? If the answer is "No" then by all means get rid of the distinction completely. If the answer is "Yes" then consider the following proposal:
Decouple Foundry designation from manual review status, except in certain cases (see below). The designation can be given right away to any ontology that covers a completely unique sub-domain (that is, one that doesn't have overlap with another ontology). We would need a consensus on which ontologies meet this criterion. Ontologies that do have overlap with one or more other ontologies will need to be manually selected to get the Foundry designation, and that selection process can include manual reviews. We can decide that such reviews must be done in tandem (that is, the two or more conflicting ontologies get reviewed at once), or we can decide that whichever ontology makes the request gets reviewed, with favorability points given for the decision to be engaged in the process. Any unreviewed ontology with the Foundry designation would have that designation revoked if another ontology within the same sub-domain appears.
The advantage of this approach is that it encourages some of the very things we want to encourage, such as development of non-overlapping ontologies, yet maintains the purpose of the Foundry distinction. I imagine there would be quite a lot of ontologies with this designation using this approach, thus minimizing the issue of "it looks bad not having so many ontologies with Foundry status". Manual reviews can still be performed as insurance against revoking Foundry status.
This proposal addresses how it looks to the outside world AND maintains one of the key reasons why the Foundry exists: "By joining the initiative, the authors of an ontology commit to working with other members to ensure that, for any particular domain, there is convergence on a single ontology." (quote is from the 2007 Foundry paper). Note that this proposal is not mutually exclusive with the idea of a new sortable column (which really doesn't help the "how it looks" issue, it just potentially hides it until the sort is done).
The question then becomes how to ensure that a 'bad' ontology doesn't get Foundry status. For this we should make use of the dashboard.
Gold star (filled) = unique scope confirmed + manually reviewed Gold star (empty) = unique scope confirmed + good dashboard rating Silver star (filled) = unique scope suspected + good dashboard rating Silver star (empty) = needs scope review + good dashboard rating No star = needs scope review + poor dashboard rating
Current 'Foundry' status would be gold-filled. All others would be silver-empty if the dashboard indicates its okay (we'd have to decide what that means--should make a separate ticket if this proposal is accepted in principle). Cursory looks would reveal which silver-empty should get filled.