Obsolete "life cycle temporal boundary" and descendants

[matentzn]

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We have the following branch in Uberon:

• [] UBERON:0000000 ! processual entity "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity."
  • [i] UBERON:0035943 ! life cycle temporal boundary "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity."
    • [i] UBERON:0035946 ! start of neonate stage "A life cycle temporal boundary that marks the start of the neonate stage of the organism."
    • [i] UBERON:0035945 ! start of life cycle "A life cycle temporal boundary that marks the start of the life cycle of the organism."
    • [i] UBERON:0035944 ! life-death temporal boundary "A life cycle temporal boundary that marks the end of the life cycle of the organism."

I would like to suggest to obsolete life cycle temporal boundary from Uberon for the following reasons:

1. The classes are not, themselves, used anywhere in Uberon for formalisation (they are themselves defined in terms of other classes). This suggests that they are part of an incomplete attempt many years ago to model process boundaries in Uberon.
2. There are only three temporal boundaries - which means the list is highly incomplete. In 7 years, there have not been any attempts to flesh out / extend this list.
3. The original creator of Uberon calls them "useless vestiges of the heady days of over-formalization" (cite).

Please file your objects here until end of March, else I will go ahead with the plan. If you can add a like to indicate you agree with the decision, that would make me feel confident that someone at least has seen it.

[sbello]

According to Ontobee there are 2 ontologies using life cycle temporal boundary

• Obstetric and Neonatal Ontology
• Apollo Structured Vocabulary

https://ontobee.org/ontology/UBERON?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0035943 Have you reached out to them? I know nothing about them I was just checking to make sure none of the MGI related ontologies used the terms since they are labeled as being in the mouse subset. As far as I can tell this would not impact MGI, and the reasons you presented above make sense to me, s I have no objection.

[matentzn]

Thank you @sbello for taking the time to answering, much appreciated!

I have reached out to @hoganwr for his opinion (ApolloSV). @FernandaFarinelli can you also take a look if you agree (ONTONEO)?

[gouttegd]

The only use of a 'life cycle temporal boundary' term in ONTONEO that I could find is in the redefinition of EFO’s 'date of birth':

'date of birth' EquivalentTo: 'date' and ('starts' some 'start of life cycle')

Given that 'start of life cycle' is already defined as

'life cycle temporal boundary' and ('starts' some 'life cycle')

I don’t think it makes much sense. Uberon’s “temporal boundaries” are intended as “abstract, instantaneous” entities. How can an “instantaneous“ moment have a starting point?

'date of birth' could simply be defined as:

'date of birth' EquivalentTo: 'date' and ('starts' some 'life cycle')

[hoganwr]

We use life-death temporal boundary a fair amount in Apollo-SV, however, it's trivial to replace. No objection from us to obsoleting it.

[FernandaFarinelli]

I'm taking a look of this.

Fernanda Farinelli

On Tue, Mar 11, 2025, 10:53 Nico Matentzoglu @.***> wrote:

Thank you @sbello https://github.com/sbello for taking the time to answering, much appreciated!

I have reached out to @hoganwr https://github.com/hoganwr for his opinion (ApolloSV). @FernandaFarinelli https://github.com/FernandaFarinelli can you also take a look if you agree (ONTONEO)?

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Thank you @sbello https://github.com/sbello for taking the time to answering, much appreciated!

I have reached out to @hoganwr https://github.com/hoganwr for his opinion (ApolloSV). @FernandaFarinelli https://github.com/FernandaFarinelli can you also take a look if you agree (ONTONEO)?

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[FernandaFarinelli]

Perfect. Thanks for that.

Fernanda Farinelli

On Tue, Mar 11, 2025, 11:51 Damien Goutte-Gattat @.***> wrote:

The only use of a 'life cycle temporal boundary' term in ONTONEO that I could find is in the redefinition of EFO’s 'date of birth http://www.ebi.ac.uk/efo/EFO_0004950':

'date of birth http://www.ebi.ac.uk/efo/EFO_0004950' EquivalentTo: ' date http://purl.obolibrary.org/obo/ONTONEO_00000055' and ('starts http://purl.obolibrary.org/obo/RO_0002223' some 'start of life cycle http://purl.obolibrary.org/obo/UBERON_0035945')

Given that 'start of life cycle http://purl.obolibrary.org/obo/UBERON_0035945' is already defined as

'life cycle temporal boundary http://purl.obolibrary.org/obo/UBERON_0035943' and ('starts http://purl.obolibrary.org/obo/RO_0002223' some 'life cycle http://purl.obolibrary.org/obo/UBERON_0000104')

I don’t think it makes much sense. Uberon’s “temporal boundaries” are intended as “abstract, instantaneous” entities. How can an “instantaneous“ moment have a starting point?

'date of birth http://www.ebi.ac.uk/efo/EFO_0004950' could simply be defined as:

'date of birth http://www.ebi.ac.uk/efo/EFO_0004950' EquivalentTo: ' date http://purl.obolibrary.org/obo/ONTONEO_00000055' and ('starts http://purl.obolibrary.org/obo/RO_0002223' some 'life cycle http://purl.obolibrary.org/obo/UBERON_0000104')

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The only use of a 'life cycle temporal boundary' term in ONTONEO that I could find is in the redefinition of EFO’s 'date of birth http://www.ebi.ac.uk/efo/EFO_0004950':

'date of birth http://www.ebi.ac.uk/efo/EFO_0004950' EquivalentTo: ' date http://purl.obolibrary.org/obo/ONTONEO_00000055' and ('starts http://purl.obolibrary.org/obo/RO_0002223' some 'start of life cycle http://purl.obolibrary.org/obo/UBERON_0035945')

Given that 'start of life cycle http://purl.obolibrary.org/obo/UBERON_0035945' is already defined as

'life cycle temporal boundary http://purl.obolibrary.org/obo/UBERON_0035943' and ('starts http://purl.obolibrary.org/obo/RO_0002223' some 'life cycle http://purl.obolibrary.org/obo/UBERON_0000104')

I don’t think it makes much sense. Uberon’s “temporal boundaries” are intended as “abstract, instantaneous” entities. How can an “instantaneous“ moment have a starting point?

'date of birth http://www.ebi.ac.uk/efo/EFO_0004950' could simply be defined as:

'date of birth http://www.ebi.ac.uk/efo/EFO_0004950' EquivalentTo: ' date http://purl.obolibrary.org/obo/ONTONEO_00000055' and ('starts http://purl.obolibrary.org/obo/RO_0002223' some 'life cycle http://purl.obolibrary.org/obo/UBERON_0000104')

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[tgbugs]

There is some interest on our side and from @lzehl for retaining and expanding these as the basis for defining many of the existing life cycle stages related to the issues discussed in https://github.com/obophenotype/uberon/issues/577.

[matentzn]

There is some interest on our side and from @lzehl for retaining and expanding these as the basis for defining many of the existing life cycle stages related to the issues discussed in https://github.com/obophenotype/uberon/issues/577.

In this case @tgbugs I will of course not obsolete them.. It will make my life a bit harder as now I have deal with upper ontology crazyness and figure out how to get this class into COB.. :D

[gouttegd]

@tgbugs I fail to see how the terms that are proposed for obsoletion here could be of any use for the issue discussed in #577.

expanding these as the basis for defining many of the existing life cycle stages

Are you planning on redefining all the existing life stages in terms of life stage boundaries?

[lzehl]

@tgbugs thanks for bringing up our issue. #577 is though not referring to the temporal boundary cases. We rediscovered those for an update of the BIDS participant information.

To explain the context a bit:

For subject (animal or human) it is helpful to require at least (non-sensitive) age information, namely the life cycle stage of the subject. For this we would like to have non-numerically defined consecutive life cycle stages (for which for example young adult is missing). However there is also the need to define a couple of commonly used life cycle stages which are more fuzzy in their definition (e.g. adolescent). This is discussed in #577

Now in case a subject can be described with its numerical age information (e.g. 5 days) there is the need to also define the age reference point to this numerical information (5 days after birth vs 5 days after fertilization). The most relevant ones (for mammals) would be: start_of_neonate_stage (birth), start_of_embryo_stage (fertilization), start_of_gestational_stage (first day of the mother's last menstrual period), and start_of_death_stage (death). The need is less for defining all life cycle boundaries, but for relevant boundaries that are typically used as non-numerical reference points for a numerical information.

Defining the actual date of birth or other life cycle boundaries is forbidden in public settings for human subjects and also not necessarily preferred in animal studies (because the burden of calculating the age should be on the data providers side not on the data user side).

Does this makes our request clearer?

[dosumis]

@tgbugs - I think not necessary to use the temporal boundary classes to define the terms you need in #577. The relations should be sufficient as they reference start and end temporal boundaries.

[lzehl]

@dosumis please see my last comment for clarification

[tgbugs]

Here is a diagram from @UlrikeS91 that illustrates the use of temporal boundaries for defining life cycle stages. As @lzehl mentions, we have annotation use cases for these boundaries (time points) as species independent references that define different ways of measuring age (e.g. since birth, since conception, from christening, etc.). I can think of some other boundaries that might be relevant anatomically, e.g. those related to the development of teeth.

[cmungall]

I think this can be moved to COB, as it seems you are not using the existing uberon classes, you just have an interest in the generic 'life cycle temporal boundary' (we would never put social boundaries on uberon), so would you be OK with the obsoletions going ahead?

On Tue, Apr 1, 2025 at 10:10 AM Tom Gillespie @.***> wrote:

Here is a diagram from @UlrikeS91 https://github.com/UlrikeS91 that illustrates the use of temporal boundaries for defining life cycle stages. As @lzehl https://github.com/lzehl mentions, we have annotation use cases for these boundaries (time points) as species independent references that define different ways of measuring age (e.g. since birth, since conception, from christening, etc.). I can think of some other boundaries that might be relevant anatomically, e.g. those related to the development of teeth. AgeCategories_Timeline.jpg (view on web) https://github.com/user-attachments/assets/6b81b531-fedf-4cac-a7d0-ec76ee3d8714

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Here is a diagram from @UlrikeS91 https://github.com/UlrikeS91 that illustrates the use of temporal boundaries for defining life cycle stages. As @lzehl https://github.com/lzehl mentions, we have annotation use cases for these boundaries (time points) as species independent references that define different ways of measuring age (e.g. since birth, since conception, from christening, etc.). I can think of some other boundaries that might be relevant anatomically, e.g. those related to the development of teeth. AgeCategories_Timeline.jpg (view on web) https://github.com/user-attachments/assets/6b81b531-fedf-4cac-a7d0-ec76ee3d8714

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[lzehl]

@cmungall I think I don't understand your comment.

The life cycle temporal boundaries we propose (missing fertilization and maybe start of gestation) are not social boundaries but markers for biological/physical events (across mammals) that define the start, end or anchor points of the life cycle stages. So we are not okay if the life cycle temporal boundaries disappear completely.

We are okay if they are updated and more closely linked as start, end or anchor points for the life cycle stages (e.g. through definitions). We already updated in our terminology the respective definitions for all life cycle stages using those boundaries.

In addition (as explained above), some of those boundaries are used as age reference points in various communities (e.g., age from start of gestation, fertilization, birth, or death).

Does this explanation help? Maybe I missed that you are offering an alternative registration of those life cycle boundaries...

[cmungall]

The life cycle temporal boundaries we propose (missing fertilization and maybe start of gestation) are not social boundaries but markers for biological/physical events

my comment was about this one:

from christening,

for your use cases if uberon provides the phases, then others can define boundaries e.g. start-of-X, end-of-X, ... would that work?

otherwise we should go all the way and just precompose all start-of-X and end-of-X in the ontology

missing fertilization

this would go in a phenotype ontology and would reference the stage or GO BP