NBO Review

[DitchingIt]

Judging by the lack of responses to my recent issues #122 and #123, and the many open issues, it looks like the NBO needs CPR. Without pretending to own it, but seeing that no-one else seems to lay claim, I would like to offer to facilitate finding a path forward. If someone else is better placed, I'd be happy to defer to them. Failing that, I suggest anyone interested join in this discussion about reviewing and maybe rebooting the NBO. I am working on a list of core items to discuss and drafting a couple of documents to contribute. It might be that a workshop online at some point would help. Meanwhile contributions welcome and I will work on those documents.

[matentzn]

I apologise about the responses. I read your analyses and definitions, and I am super happy someone is looking at this. I have the following suggestion:

We have a regular meeting for phenotype ontologies, cc @sbello. NBO plays a big role for the representation of behaviours. What about this:

For the next 4 meetings, we carve out a 20 minute slot (each time) for NBO where you come an present architectural changes (not to verify this with the phenotype team). So for example, you say: I want to ditch the phenotype branch. Objections? then the people there (one or two are experts in behavior) will yay/nay your suggestions. You then proceed to implement the suggestion the way you see fit. I will find a reviewer for you for each pull request.

What do you think?

[DitchingIt]

Thanks @matentzn I appreciate your positive words. I also appreciate your offering to bring me into the meetings to discuss changes to NBO. Something like that would be great. I'd rather do issues ad hoc however, as I don't know when any particular issue will be ready and I hope to encourage more input from others before venturing big changes. There is also the question of timing: I work full time in the UK, and I don't know when the meetings are. Can we feel our way forward until I feel more familiar with things?
In the mean time, would it help me to have write access to behavior-ontology and a stock of blank class numbers?

[sbello]

@DitchingIt I post a reminder the day before the calls with a call for agenda items on the UPheno slack in the general channel. Feel free to add items whenever you are ready to discuss. The calls are every other Thursday at noon Eastern time. If you are not on the UPheno slack @matentzn or I can send you a link to join. We met this week so the next call is Thursday, January 26th.

[matentzn]

I invited you @DitchingIt - its super informal, small group, and you can learn a lot about phenotypes and ontology curation! Dont worry you don't have to ever present anything - but this is the best way for you to get any feedback.. the issues are unlikely to get any responses in my experience.

[DitchingIt]

Opportunities

Moving forward constructively with the NBO, I suggest the following needs present significant opportunities. Feel free to suggest more, and to break these out into individual issues if you want to focus discussion:

• 1. It needs clearer ownership, even if it is operating in an open way, or it will be difficult to track accountability and make decisions.

• 2. It needs to develop and uniformly implement a reasonably comprehensive style and convention guide, rooted in OBO principles and guidelines.
  NBO Styles and Conventions #122 for further discussion

• 3. It needs a model structure potentially incorporating all behaviour processes, which makes biological sense even if there is not a full consensus, but is consistent with an axiomatic approach.

• 4. It needs to refocus, because its two branches (processes and phenotypes) are pulling strongly in different directions.
  grouping pathological behaviors (interesting discussion) #120 for further discussion

• 5. It needs a consistent rewrite of many labels, definitions and annotations.
  NBO Styles and Conventions #122 for further discussion

• 6. It needs a much more fully saturated set of terminal (leaf) classes.

• 7. It needs a valid cross-referencing system.

• 8. It needs a revamp of its logical axioms.

[matentzn]

re ownership, lets use the same model we use in many other community-managed OBO ontologies.

1. Define a core team (to start with, @pmidford @sbello @DitchingIt @dosumis @matentzn and then anyone who wants to join)
2. Define a CONTRIBUTING.md which states how PRs are merged. (Needs at least one review from another core team member)

The rest of the details we can sort out. I will be responsible for managing versioning and releases, and will occasionally drop some issues in the tracker.

[DitchingIt]

re ownership, lets use the same model we use in many other community-managed OBO ontologies.

1. Define a core team (to start with, @pmidford @sbello @DitchingIt @dosumis @matentzn and then anyone who wants to join)

2. Define a CONTRIBUTING.md which states how PRs are merged. (Needs at least one review from another core team member)

The rest of the details we can sort out. I will be responsible for managing versioning and releases, and will occasionally drop some issues in the tracker.

Sounds good to me. Not sure what point 2 means so someone else needs to lead on that.

[matentzn]

I made a team here: https://github.com/orgs/obo-behavior/teams/behavior-ontologies

but @pmidford has to manage it (I don't have access to the org).

[DitchingIt]

I made a team here: https://github.com/orgs/obo-behavior/teams/behavior-ontologies

but @pmidford has to manage it (I don't have access to the org).

I'm getting a Jedi giving me a 404 message: have I clicked the link wrong?

[DitchingIt]

re ownership, lets use the same model we use in many other community-managed OBO ontologies.

1. Define a core team (to start with, @pmidford @sbello @DitchingIt @dosumis @matentzn and then anyone who wants to join)

@aclark-binghamton-edu would you like to join this community-managed group? I think you, me and @pmidford represent users of an ontology which focused on ethology. @matentzn agrees with me that the phenotype branch would be better incorporated by another ontology. It is also becoming hard to know how to deal with potentially out of scope terms - see #109 - and my suggestion would be to limit ourselves not only to "observable" behaviours, but to those which have an actual or potential animal analogue.

There is a suggestion in #126 by @cmungall that, "This ontology is functionally inactive, and I think it should be declared as such on the OBO site to be fully transparent... There simply seems to be a lack of people willing commit effort to this project, and no funding on the horizon... I would say that any revamp of NBO should driven as much by requirements than by theory... I do think that with any ontology, legacy or otherwise, and incremental approach often works best... Or it may be the case that you think a more radical overhaul is necessary -- in which case I would encourage you to go for it!

I think that this debate and pinning key issues at the top is open enough to do justice for now; Chris won't be aware of how commited I am to making this ontology fly again, so I wouldn't want to call it inactive just yet. But I do think a refocus onto things which were important when the ABO got started is our best way forward.

[aclark-binghamton-edu]

Yes, @DitchingIt, I would be interested in being part of a core team of caring people! The difficulties of finding the coherent ABO section of the larger NBO has, I think, sidelined the use cases that the ABO/Ethosource group originally imagined. I agree with the "observable in animals, not just human animals" and would add "not requiring a human internal perspective to appreciate the meaning" (as I take #109 "Hiking behavior" to require). There will be fine lines, but if there is a human behavior ontology, much the better place where there are questions. As @pmidford knows, I am not a Protege or ontology expert, but ethograms are foundational.

…

On Fri, Jan 20, 2023 at 1:24 PM Ditch Townsend ***@***.***> wrote: re ownership, lets use the same model we use in many other community-managed OBO ontologies. 1. Define a core team (to start with, @pmidford @sbello @DitchingIt @dosumis @matentzn and then anyone who wants to join) @aclark-binghamton-edu <https://github.com/aclark-binghamton-edu> would you like to join this community-managed group? I think you, me and @pmidford <https://github.com/pmidford> represent users of an ontology which focused on ethology. @matentzn <https://github.com/matentzn> agrees with me that the phenotype branch would be better incorporated by another ontology. It is also becoming hard to know how to deal with potentially out of scope terms - see #109 <#109> - and my suggestion would be to limit ourselves not only to "observable" behaviours, but to those which have an actual or potential animal analogue. There is a suggestion in #126 <#126> by @cmungall <https://github.com/cmungall> that, "This ontology is functionally inactive, and I think it should be declared as such on the OBO site to be fully transparent... There simply seems to be a lack of people willing commit effort to this project, and no funding on the horizon... I would say that any revamp of NBO should driven as much by requirements than by theory... I do think that with any ontology, legacy or otherwise, and incremental approach often works best... Or it may be the case that you think a more radical overhaul is necessary -- in which case I would encourage you to go for it! I think that this debate and pinning key issues at the top is open enough to do justice for now; Chris won't be aware of how commited I am to making this ontology fly again, so I wouldn't want to call it inactive just yet. But I do think a refocus onto things which were important when the ABO got started is our best way forward. — Reply to this email directly, view it on GitHub <#124 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADUXTFWZFE6IFFVDQYDRPMDWTLJ5PANCNFSM6AAAAAAT2EEKOY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Anne B. Clark, Ph.D. Biological Sciences Binghamton University Binghamton, NY 13902-6000 (607) 222-0905 (cell) (607) 777-6521 (fax-Dept office) (607) 777-2438 (Biol Sci office)

[DitchingIt]

I made a team here: https://github.com/orgs/obo-behavior/teams/behavior-ontologies
but @pmidford has to manage it (I don't have access to the org).

I'm getting a Jedi giving me a 404 message: have I clicked the link wrong?

Got it now, thanks. Can you also add @aclark-binghamton-edu ?

[DitchingIt]

re ownership, lets use the same model we use in many other community-managed OBO ontologies.

1. Define a core team (to start with, @pmidford @sbello @DitchingIt @dosumis @matentzn and then anyone who wants to join)

@matentzn can you please add @aclark-binghamton-edu to the core team - see our dialogue just now. Thanks

[matentzn]

Someome seems to have already added @aclark-binghamton-edu!

[DitchingIt]

I've closed #126 as I think it needs a different approach.

[DitchingIt]

Issue #123 is closed as it is subsumed into #122, so I have edited the discussion link in Opportunity 5 above.

[DitchingIt]

My attempts over the last year to change the NBO have not made enough progress to justify pursuing it further. I have removed the most recent unmerged commits to reduce confusion in future, since they are dependent on wholesale changes throughout NBO and cannot realistically stand alone.

Unlike anatomy or biochemistry, I doubt behaviour above the morpho-physiological level will (in the near future at least) be more than a set of more or less disputed opinions, although doubtless there will be individuals or 'schools' who believe in the universality of their own systematics.

Perhaps a more viable approach to cataloguing behaviour would be to map these opinions as a knowledge graph of behavioural ssertions (something I have already begun to explore) rather than to think there is a universally acceptable set of fixed behavioural entities which can be pinned down in a fixed ontology.

Even if I am wrong, at the very least, involvement, let alone consensus, has virtually disappeared over the last 12 years from the construction of the NBO. I now support @cmungall in his suggestion that the NBO be labelled functionally inactive, and declared as such on the OBO site (see#126).