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OBOFoundry / COB

An experimental ontology containing key terms from Open Biological and Biomedical Ontologies (OBO)
https://obofoundry.github.io/COB
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Add annotation property to distinguish CORE terms from examples #32

Open beckyjackson opened 5 years ago

beckyjackson commented 5 years ago

We have many example subclasses to help show how OBO Core can be used. These should be annotated to show that they will not be included in the final OBO Core. We can use this annotation to remove any of these examples during the eventual release process.

e.g., 'nickel atom' is a subclass of atom. Atom is a proposed core term, but 'nickel atom' is just an example subclass.

Ideas for the name of this property:

cmungall commented 5 years ago

I suggest we also just use OBO URIs, e.g. CHEBI for these, as it could get confusing using CORE IDs that are not deprecated and will not see the light of day.

Should we use a subset for these?

bpeters42 commented 5 years ago

+1 on using OBO iris

On Wed, Jul 31, 2019, 10:36 AM Chris Mungall notifications@github.com wrote:

I suggest we also just use OBO URIs, e.g. CHEBI for these, as it could get confusing using CORE IDs that are not deprecated and will not see the light of day.

Should we use a subset for these?

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beckyjackson commented 5 years ago

I'm working on changing the IRIs for the example terms, so far I have:

* we also have an 'instrument' term, which I think is very similar to device. Maybe we get rid of the 'instrument' example?

Example terms that don't have corresponding OBO foundry terms:

* @cstoeckert pointed out that there's some ongoing discussion about neoplasm as a material entity vs. as a disease disposition and that this might not be the best example to use here.

And I believe these are intended to be in CORE, but some of these might be example terms:

bpeters42 commented 5 years ago

Instrument is probably my fault, and should go. Device is much better (there was a decade on back and forth on how to define instrument, which could never be settled, and everyone ended up being fine with device instead).

Core:"uncharged nickel atom" should actually be what is called "Nickel atom" in Chebi (CHEBI:28112) Core:"Nickel atom" should be ("Nickel atom" or "Nickel ion") in Chebi, with the ion being CHEBI:60248

I am not sure if all of the ones you have in the tree at the bottom will be possible to get into the Core, but they probably all eventually should.

On Wed, Jul 31, 2019 at 1:52 PM Becky Jackson notifications@github.com wrote:

I'm working on changing the IRIs for the example terms, so far I have:

  • nickel atom (CHEBI:28112)
  • nickel ion (CHEBI:60248)
  • tidal pool (ENVO:00000317)
  • mountain (ENVO:00000081)
  • lung (UBERON:0002048)
  • RNA polymer (CHEBI:83400)
  • DNA polymer (CHEBI:83828)
  • salicylic acid (CHEBI:16914)
  • nucleotide (CHEBI:36976)
  • guanine (CHEBI:16235)
  • adenine (CHEBI:16708)
  • human (Homo sapiens - NCBITaxon:9606)
  • vaccine (VO:0000001)
  • reagent (OBI:0001879)
  • device (OBI:0400002) *
  • plasma membrane (GO:0005886)
  • informed consent process (OBI:0000810)
  • study design (OBI:0500000)
  • we also have an 'instrument' term, which I think is very similar to device. Maybe we get rid of the 'instrument' example?

Example terms that don't have corresponding OBO foundry terms:

  • uncharged nickel atom
  • tumor (possibly 'neoplasm' - HP:0002664)
  • glycosylated protein (possibly 'glycoprotein' - PR:000037069)
  • drug product (possibly 'drug' - CHEBI:23888)

And I believe these are intended to be in CORE, but some of these might be example terms:

  • planned process children:
    • assay
    • data transformation
    • investigation
    • material processing
  • elementary charge (subclass of charge)
  • macromolecular entity children:
    • gene product
    • nucleic acid polymer
    • protein
    • protein-containing macromolecular complex
  • subcellular structure children:
    • cell nucleus
    • cellular membrane
  • information children:
    • conclusion based on data
    • data item
    • directive information entity
      • objective specification
      • plan specification
    • disease diagnosis
    • document
    • phenotypic finding

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beckyjackson commented 5 years ago

Instrument is probably my fault, and should go. Device is much better (there was a decade on back and forth on how to define instrument, which could never be settled, and everyone ended up being fine with device instead).

Great - I'll just remove instrument.

Core:"uncharged nickel atom" should actually be what is called "Nickel atom" in Chebi (CHEBI:28112) Core:"Nickel atom" should be ("Nickel atom" or "Nickel ion") in Chebi, with the ion being CHEBI:60248

OK, changed that. I'm just using a CORE_ex namespace for anything that doesn't have an exact match, so I put 'nickel atom' (CORE_ex:1) in that namespace with the equivalence axiom:

'nickel ion' or 'uncharged nickel atom'

On another note, since nobody is using these IDs yet, do we want to shift all the IDs to fill in blanks? For example, we're missing terms for IDs between 27-30, 39-41, 50-54, 80-100, etc...