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pato-ontology / pato

PATO - the Phenotype And Trait Ontology
https://pato-ontology.github.io/pato/
BSD 3-Clause "New" or "Revised" License
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deprecate PATO_0001744 Radiation exposure and replace #485

Closed PaulNSchofield closed 2 years ago

PaulNSchofield commented 2 years ago

Radiation exposure is a process and does not conform to the definition given. This would best be deprecated and replaced with

Label: Irradiated Definition: A quality inhering in a bearer by virtue of the bearer being exposed to electromagnetic, usually ionising, radiation. Parent: PATO_0001241 Physical object quality Comments: Irradiation may be external or in the case of an organism, internal from ingested or otherwise absorbed radioactive material.

shawntanzk commented 2 years ago

assigning myself for now as part of triage - will return to this when I am able to

shawntanzk commented 2 years ago

Hi @PaulNSchofield would you suggest that the child nodes under radiation exposure be moved to child of irradiated too? From the definition you have given, could I suggest that instead of depercating radiation exposure, we move it to a physical object quality, change the label to irradiated, and use radiation exposure as a related synonym? I would think that most people refer to irradiated when using radiation exposure (correct me if im wrong, I'm not in the field and all) Thanks

PaulNSchofield commented 2 years ago

Sorry for being slow on this. Radiation exposure is incorrectly defined, so...we can either redefine and move to being a child of "process" or change the label to "irradiated" when it becomes a property of a physical object. Neither are great and Id suggest deprecating and generating two new classes. One: "Irradiated" which can be a child of "quality of a substance". Irradiation can generate altered physical qualities of a substance either temporarily or permanently through the deposition of energy. Two: Radiation exposure - child of "process" and defined as the planned or incidental exposure of an entity to electromagnetic radiation. We do have Radiation exposure in RBO - RBO:00002000 but I think that under the circumstances rather than import it from RBO Id leave it in PATO and assert equivalence.

The dose children of "radiation exposure" currently PATO:0001745, PATO:0001747, PATO:0001746 should be deprecated as these are not qualities. They are defined in RBO and are measurement data. A dose may have a quality but is not a quality in itself.

Once these changes are made we will review RBO as at the moment we draw "radiation quality" from PATO and we will need to correct this bit of RBO.

shawntanzk commented 2 years ago

Ah ok, got it. Happy to make the changes, but given I know just about nothing about radiation, would be good if you could provide me the following: 1) Names, definitions (and associated references), synonyms, superclass (which you have already provided) of the two terms to be added 2) for deprecation of PATO:0001745, PATO:0001747, PATO:0001746, it would be good if I could get their relevant replacements in RBO so I can add a replaced_by or consider axiom there for anyone coming across it to be redirected to RBO Thanks

PaulNSchofield commented 2 years ago

Will discuss this with the RBO team tomorrow and send in class details. Hopefully all done by Friday @shawntanzk !

PaulNSchofield commented 2 years ago

We are agreed on the suggestions above:

  1. add a new class "Irradiated" with a synonym "radiation exposed". Definition: "A quality of a substance currently or previously exposed to electromagnetic radiation" Comments: " This may refer to incident external irradiation or internal radiation from an ingested or otherwise internal source" Reference: Radiobiology for the Radiologist ( 2018) Eric J. Hall DPhil, DSc, FACR, FRCR, Amato J. Giaccia, SBN/ISSN:
  2. Wolters/Kluwer .

  3. Add new class : Radiation exposure - child of "process" Defined as: "The planned or incidental exposure of an entity to electromagnetic radiation" Comments: This refers to the planned or unplanned process by which an entity is exposed to radiation either externally or from an internalised source. Reference: same as above. These are very basic concepts.

    We do have Radiation exposure in RBO - RBO:00002000 but I think that under the circumstances rather than import it from RBO Id leave it in PATO and assert equivalence. You could DXRef.

The three children should be deprecated and suggest using:

PATO:0001745 : RBO:00005010 PATO:0001747: RBO:00000014 PATO:0001746: RBO:00000023 Hope this all makes sense!

shawntanzk commented 2 years ago

Hi @PaulNSchofield I'm looking at the definition of radiation exposure and it is similar to that of irradiated, I've hence opted to keep the ID but change the label, axioms, and def accordingly, hope that is alright

shawntanzk commented 2 years ago

I'm also not sure what the difference between irradiated and quality of interaction of a substance with electromagnetic radiation is?

shawntanzk commented 2 years ago

Add new class : Radiation exposure - child of "process"

I'm not 100% sure PATO deals with actual processes, rather just quality of the process.

PaulNSchofield commented 2 years ago

@shawntanzk you are correct! My internal BFO is getting confused. Radiation exposure should not be in PATO as its a process and not a quality. We now have "Irradiated" which of course is a quality.. I think we should deprecate and recommend using RBO_00002000 Radiation exposure. Im so sorry that this has all been very confusing....combination of dealing with two ontologies at a time and looking at the consequences of taking classes aout and moving them around. Entirely my fault.