OBO ontologies - meaning

[Nico Matentzoglu]

Hey all,

because people I talk to stumble across this all the time. Is there anyone that objects to this:

The term "OBO ontology" means: "An ontology which is accepted into the OBO foundry ontology registry".

It does NOT mean (unless the context demands it):

1. An ontology serialised in OBO format (in particular, OBO ontologies can be serialised in OWL!)

2. An ontology developed in accordance with OBO principles but not in the OBO foundry

3. An open biomedical ontology in general.

I will interpret silence as agreement :)

All best,

Nico

[Melissa Haendel]

Nico I like your definition and description. It would be helpful to have on the website. 

Sent from my iPhone

On Feb 26, 2021, at 3:08 AM, Nico Matentzoglu <nicolas.m...@gmail.com> wrote:



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[Charles Tapley Hoyt]

If you want to mint a recommended terminology for ontologies accepted in the OBO Foundry, I think you also should provide a recommended terminology for the other three points you made (maybe even as a Venn diagram or a flowchart).

Personally, I would assume if someone says "OBO ontology" that it means the ontology stored/serialized in the OBO format, the same as if they say an OWL ontology. Maybe it would be better to say "OBO Foundry ontology" to be completely unambiguous.

[Melissa Haendel]

Hi Charlie, I agree, however this could only work if we could remove the current Foundry distinction. Only 10 ontologies have that distinction of having been reviewed and approved at some point in their history. I have long been an advocate for its removal, I think it makes the OBO community look bad as folks come to me sort of dismissing the Foundry as not having very many “approved” ontologies. If they meet the criteria to be in the OBO library, they are all OBO Foundry ontologies in my mind.

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[Melanie Courtot]

Thanks Nico for proposing this! 

I don't work much with the OBO format, so don't tend to have the OBO vs OWL issue. Which may explain why when I hear OBO ontology I understand "an ontology registered with the OBO Foundry"

However I am not clear with what does "accepted" mean and what is the "OBO foundry ontology registry". I am used to the terms "OBO library" to denote the overall table and all ontologies listed there (i.e. those that have a PURL), and the "OBO Foundry ontologies" for those in the library who have undergone review and been 'stamped' as foundry resources.

Is the "OBO foundry registry" the registry of ontologies registered with the OBO Foundry (i.e., the equivalent of my OBO library")?

Is "accepted" the outcome of the PURL request and attribution, and listing in the overall table?

Second Melissa's point, it would be great to have this somewhere on the website, this would really help with consistency.

Thanks,

Melanie

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[Tiago Lubiana]

Good discussion! 
I was very confused about this when writing about the OBO Foundry on Wikipedia: https://en.wikipedia.org/wiki/OBO_Foundry  and https://en.wikipedia.org/wiki/List_of_OBO_Foundry_ontologies 

Maybe we could craft an ontology of OBO-related concepts and choose preferred aliases for each concept, and then in the process make explicit what is meant by "OBO library", "OBO Foundry ontology" and "accepted", what do you think? :) 

I sketched a rough subclassing system based on the discussion (it might be too simplified) : 



Best,

Tiago

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[Chris Mungall]

Thanks Tiago. This is actually a very clear and coherent distillation of the current situation.

It also illustrates how complicated and confusing we have made things for people. On behalf of everyone in OBO I apologize for this!

It is clear the way the community uses terms like "OBO Foundry" and "OBO Ontology" vastly differs from how some of us intended. I think we have to accept this, rather than continuing to use terms inconsistently.

My experience echoes that of Charles': when interacting with people outside the circles of mostly experts on this list, "OBO Ontology" frequently means "Ontology in OBO Format".

Similarly, the way the community uses "OBO Foundry" is not restricted to the small unrepresentative set that has passed the review process, but broadly encompasses all ontologies in the registry:

https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=%22OBO+Foundry%22&btnG=

I think we need to vastly simplify things in order to stop confusing people. I also think we need to be more transparent about the fact that the review process has stalled, and there are many good ontologies that are not "foundry status", and therefore "foundry designation" is not something meaningful to our community, and its usage as a way of grouping ontologies should be discovered (we will soon have better metrics through the dashboard)

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[Nico Matentzoglu]

I tried to write up a proposal for a terminology here:

https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1448

Feel free to weigh in.

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