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syringe, injection, and injection function #1662

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cmungall opened this issue Feb 28, 2023 · 6 comments
Open

syringe, injection, and injection function #1662

cmungall opened this issue Feb 28, 2023 · 6 comments
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@bpeters42
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domain:material - devices_instruments_reagents Merging issues related to things created to have functions.

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@cmungall
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cmungall commented Feb 28, 2023 •
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OBI frequently has the same concept or closely related concepts distributed across different BFO branches. Sometimes the different aspects are coordinated, and sometimes not:

  1. MATERIAL: syringe - A processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw.
  2. PROCESS: injection injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue.
  3. FUNCTION: injection function The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc.

The function branch doesn't appear to have any connection with the process or material branch, I can't find axioms connecting them. The ascribed function of a syringe doesn't seem to connect to the injection function, only to "transfer" (of course syringes can inject or withdraw, but it would seem to have both functions):

image

over on the process side, there is a connection to an objective branch, which is a 4th BFO branch under information/GDC, this branch seems to have a distinctly function-like aspect. However, while the "objective" of injection is to transform, in contrast to the "injection function", which is to transfer:

image

Is this distinction intentional or does it reflect the fact that the branches are old developed by different people at different times, etc? What is the use case for breaking things down into elemental concepts like transference, transformation?

the material and process branches appear to be a bit more synchronized; there is a complex axiom connecting syringe and injection:

injection EquivalentTo:

I think the intent here overall is to model the two things a syringe does - inject and withdraw. But it seems to require a lot of different branches with lots of abstract concepts (I have read the definition of material to be added role a few times and I am not sure I get it). And there are inconsistencies between the branches, it's not clear if this is intentional reflecting different nuances or just the fact it is hard to coordinate multiple branches.

For example:

  • the textual definition of injection says introducing a compound or a mixture into a material entity (either biological entity or instrument), but the owl says injection must be realized by a syringe which has more restrictive criteria (fluids)
  • the textual definition of injection says it must be injected into a vascular system (which strangely includes machines) or tissues, but syringe is more lenient (any material entity)
  • the textual definition of injection says by means of devices such as syringe or injector connection, but according to the OWL this is restricted to syringes (and what is an injector connection?)

Here is a more zoomed out view:

image

I'm also confused about the duplication between objective and process hierarchies:

image

These seem to partially mirror one another, but with differences. There also don't seem to be linkages between shadow concepts, e.g. material combination and material combination objective.

I realize there is likely a lot of history here, and I appreciate it is hard to retrospectively fix these things. We have been going through a similar process in GO of removing duplication between MF and BP branches, and it takes time. I appreciate it also takes time to add to the existing excellent but limited visual documentation here (https://obi-ontology.org/docs/core-classes/).

However, for long term maintenance, and to simplify things for users I think it would make sense to commit to either documenting some of the duplication patterns, or to start trimming them down. I'm not totally sure why simply having a process and material entity branch wouldn't suffice for most people who want terms for syringes, injection protocols, etc.
@jamesaoverton
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@cmungall and I talked about this a bit on Slack last week. @bpeters42 do you want to raise this issue on Monday's call, when you're chairing?

@bpeters42
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bpeters42 commented Mar 8, 2023 via email

@cmungall
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cmungall commented Mar 9, 2023 via email

@bpeters42
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bpeters42 commented Mar 9, 2023 via email

@bpeters42
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Discussed on call 3/13. The decision was made to follow Chris recommendations and document the use of our design patterns and clean up OBI in the process. The decision was made to do this as part of the OBI to COB migration, which should be used to document the high level classes of OBI in COB for the broader OBO community. 'Planned process' and 'device' would be the favored classes to create named subclasses for in OBI.

@bpeters42 bpeters42 self-assigned this Mar 13, 2023
@bpeters42 bpeters42 added the domain:material - devices_instruments_reagents Merging issues related to things created to have functions. label Mar 20, 2023
@turbomam
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reflection from today's call: if we started using a device template, we could impose consistent modeling

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