MaastrichtU-IDS / MaastrichtU-IDS/semanticscience

is chemical entity intended to cover macroscopic entities like organism

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Description

SIO splits material entity into chemical entity and specialized chemical entity

![image](https://user-images.githubusercontent.com/50745/110053864-f518f600-7d0e-11eb-9e37-c8919919a98a.png)

all kinds of large objects like humans, telephones are classified under chemical entity, as are waves:

![image](https://user-images.githubusercontent.com/50745/110054096-56d96000-7d0f-11eb-8833-17053aac0422.png)

According to #20 this is intentional. This makes sense from a reductionist viewpoint, we are all made of chemicals, hence chemical entities. But the problem here is that

1. this is not consistent with the definition of chemical entity "A chemical entity is a material entity that *pertains* to chemistry."
2. it poses the question of what is the difference between a material entity and a chemical entity. Do we need both? Are thre MEs that are not CEs?

To partially answer 2, ME has another subclass

![image](https://user-images.githubusercontent.com/50745/110054303-b6377000-7d0f-11eb-9eaa-72220520ad2e.png)

but things here also seem like chemical entities...

I see a few solutions:

1. respect the current definition of chemical entity (pertaining to chemistry, which I interpret roughly to be something we can ascribe chemical properties such as charge to) and create a new home for larger objects like telephones, sibling to chemical entity
2. keep the current structure except collapse CE, ME, SCE, retaining ME as the name
3. keep the current structure and somehow dive CE and SCE new definitions that both reflects their subclasses and tells us how they differ from MEs

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First steps

  1. Read the whole issue, then the project's contributing guide.
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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Review the SIO material entity, chemical entity, specialized chemical entity, and related subclass hierarchy described in the issue, along with issue #20. A decision is needed on the intended definitions and hierarchy; the work is done when the chosen structure consistently distinguishes macroscopic entities, material entities, and chemical entities.

Written by the indexing model from the issue text.

Assessment

Domain
data
Issue type
Refactor
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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