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EnvironmentOntology / envo

A community-driven ontology for the representation of environments
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NTRs: radiation #255

Open cmungall opened 9 years ago

cmungall commented 9 years ago

Add as a process. Add subclasses for different wavelengths.

This may well belong in a physics ontology, but we can incubate for now

ENVO would only store the process. Various other experimental condition ontologies like ZECO EO would use this as a base to define treatment/exposure etc to radiation. Presumably of interest to SDG-like projects too? E.g. MDG-7 is about ozone depletion.

     is_a EO:0007151 ! radiation treatment *** 
      is_a EO:0001039 ! radiation mutagen treatment *** 
      is_a EO:0007152 ! radiation intensity regimen *** 
       is_a EO:0007224 ! light intensity regimen *** 
      is_a EO:0007153 ! radiation quantity regimen *** 
       is_a EO:0007078 ! light quantity regimen *** 
      is_a EO:0007154 ! radiation quality treatment *** 
       is_a EO:0001022 ! gamma radiation treatment *** 
       is_a EO:0007196 ! light regimen
        is_a EO:0007222 ! UV light regimen *** 
         is_a EO:0007001 ! UV-B light regimen *** 
         is_a EO:0007002 ! UV-A light regimen *** 
         is_a EO:0007129 ! UV-C light regimen *** 
       is_a EO:0007615 ! Bevatron irradiation *** 
       is_a EO:0007616 ! deuteron irradiation *** 
       is_a EO:0007628 ! X-ray ***

and

   is_a ZECO:0000128 ! experimental conditions
    is_a ZECO:0000145 ! electromagnetic radiation experimental conditions *** 
     is_a ZECO:0000146 ! magnetic field
     is_a ZECO:0000147 ! electric field
     is_a ZECO:0000148 ! ionizing radiation *** 
      is_a ZECO:0000149 ! gamma ray
      is_a ZECO:0000150 ! xray
      is_a ZECO:0000151 ! ionizing uv radiation *** 
     is_a ZECO:0000152 ! non-ionizing radiation *** 
      is_a ZECO:0000153 ! visible light
      is_a ZECO:0000154 ! non-ionizing uv
      is_a ZECO:0000155 ! infrared
cmungall commented 8 years ago

See linked ticket for comment on NPO tracker

NPO models radiation, waves and energy in what appears to be a very sensible manner. It's not clear if all of these are required to be imported in ENVO, but I can see this being useful in a variety of contexts. Energy is obviously an important concept when looking at some of the wider ENVO use cases.

See this figure for an example of R/W/E in NPO (subclasses denoted by containment):

rad

cmungall commented 8 years ago

Note: NPO radiation seems to be taken directly from NCIt

cmungall commented 8 years ago

XCO:

  is_a XCO:0000038 ! radiation exposure
   is_a XCO:0000039 ! ionizing radiation exposure
    is_a XCO:0000040 ! gamma ray exposure
    is_a XCO:0000041 ! radon exposure
    is_a XCO:0000043 ! X-ray exposure
    is_a XCO:0000179 ! ionizing ultraviolet radiation exposure
   is_a XCO:0000044 ! non-ionizing radiation exposure
    is_a XCO:0000046 ! infrared radiation exposure
    is_a XCO:0000180 ! non-ionizing ultraviolet radiation exposure
   is_a XCO:0000045 ! electromagnetic radiation exposure
    is_a XCO:0000040 ! gamma ray exposure
    is_a XCO:0000042 ! ultraviolet ray exposure
     is_a XCO:0000179 ! ionizing ultraviolet radiation exposure
     is_a XCO:0000180 ! non-ionizing ultraviolet radiation exposure
    is_a XCO:0000043 ! X-ray exposure
    is_a XCO:0000046 ! infrared radiation exposure
    is_a XCO:0000284 ! controlled visible light exposure
     is_a XCO:0000182 ! controlled exposure to ambient light
     is_a XCO:0000283 ! visible light stimulus
     is_a XCO:0000459 ! controlled light/dark cycle
      is_a XCO:0000462 ! light phase of controlled light/dark cycle
      is_a XCO:0000463 ! dark phase of controlled light/dark cycle
cmungall commented 7 years ago

Any further thoughts on this? Just adopt NCIt here?

pbuttigieg commented 7 years ago

I've made a few ENVO radiation classes, but I agree that we should reuse, especially as we have to get used to importing out of the OBO world in the future. Can we reinstate this import?

I'm a little unsure about energy as a realisable entity, but the way the realisation works through waves makes sense. I wonder if we can do this with other forms of energy (heat via vibration etc)

pbuttigieg commented 7 years ago

xref: https://github.com/OBOFoundry/purl.obolibrary.org/pull/346

cmungall commented 7 years ago

I think the ultimate best home way be a physics ontology. I'm wondering if ENVO may be a better incubator for now. I'm involved in the linked efforts above and the emphasis is really on bringing cancer-specific knowledge from NCIT into OBO.

pbuttigieg commented 7 years ago

We can incubate, it will help us axiomatise quite a few processes. Is the NCIT import the same as any other? I notice that some radiation PURLs aren't being resolved by ontobee.

On 11 Aug 2017 17:42, "Chris Mungall" notifications@github.com wrote:

I think the ultimate best home way be a physics ontology. I'm wondering if ENVO may be a better incubator for now. I'm involved in the linked efforts above and the emphasis is really on bringing cancer-specific knowledge from NCIT into OBO.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/EnvironmentOntology/envo/issues/255#issuecomment-321847695, or mute the thread https://github.com/notifications/unsubscribe-auth/ACK7Mjx-2Jlu0Ec1C__MHXCDVk_ZmKkEks5sXHZsgaJpZM4GEKb1 .

cmungall commented 7 years ago

It should be the same now NCIT is in OBO. It will look slightly odd as there are still different conventions, e.g. capitalization. But I guess that is a somewhat weak reason for doing a separate incubation.

On 11 Aug 2017, at 19:08, Pier Luigi Buttigieg wrote:

We can incubate, it will help us axiomatise quite a few processes. Is the NCIT import the same as any other? I notice that some radiation PURLs aren't being resolved by ontobee.

On 11 Aug 2017 17:42, "Chris Mungall" notifications@github.com wrote:

I think the ultimate best home way be a physics ontology. I'm wondering if ENVO may be a better incubator for now. I'm involved in the linked efforts above and the emphasis is really on bringing cancer-specific knowledge from NCIT into OBO.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/EnvironmentOntology/envo/issues/255#issuecomment-321847695, or mute the thread https://github.com/notifications/unsubscribe-auth/ACK7Mjx-2Jlu0Ec1C__MHXCDVk_ZmKkEks5sXHZsgaJpZM4GEKb1 .

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cmungall commented 7 years ago

Actually it would be slightly different. We would have to 'lop off' the top of the ontology - normally we import to root.

But we'll need to be able to stitch on specific subclasses to e.g. http://purl.obolibrary.org/obo/ENVO_01001026 EM radiation

On 11 Aug 2017, at 19:08, Pier Luigi Buttigieg wrote:

We can incubate, it will help us axiomatise quite a few processes. Is the NCIT import the same as any other? I notice that some radiation PURLs aren't being resolved by ontobee.

On 11 Aug 2017 17:42, "Chris Mungall" notifications@github.com wrote:

I think the ultimate best home way be a physics ontology. I'm wondering if ENVO may be a better incubator for now. I'm involved in the linked efforts above and the emphasis is really on bringing cancer-specific knowledge from NCIT into OBO.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/EnvironmentOntology/envo/issues/255#issuecomment-321847695, or mute the thread https://github.com/notifications/unsubscribe-auth/ACK7Mjx-2Jlu0Ec1C__MHXCDVk_ZmKkEks5sXHZsgaJpZM4GEKb1 .

-- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: https://github.com/EnvironmentOntology/envo/issues/255#issuecomment-321950866

pbuttigieg commented 7 years ago

I suppose we'll need to get used to this as we reuse (always preferable if possible) more resources outside OBO) . Perhaps that would be a cool robot extension : specify where to stop the import and where to stitch it into the host.

On 11 Aug 2017 22:41, "Chris Mungall" notifications@github.com wrote:

Actually it would be slightly different. We would have to 'lop off' the top of the ontology - normally we import to root.

But we'll need to be able to stitch on specific subclasses to e.g. http://purl.obolibrary.org/obo/ENVO_01001026 EM radiation

On 11 Aug 2017, at 19:08, Pier Luigi Buttigieg wrote:

We can incubate, it will help us axiomatise quite a few processes. Is the NCIT import the same as any other? I notice that some radiation PURLs aren't being resolved by ontobee.

On 11 Aug 2017 17:42, "Chris Mungall" notifications@github.com wrote:

I think the ultimate best home way be a physics ontology. I'm wondering if ENVO may be a better incubator for now. I'm involved in the linked efforts above and the emphasis is really on bringing cancer-specific knowledge from NCIT into OBO.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/EnvironmentOntology/envo/issues/255#issuecomment- 321847695, or mute the thread https://github.com/notifications/unsubscribe-auth/ACK7Mjx-2Jlu0Ec1C__ MHXCDVk_ZmKkEks5sXHZsgaJpZM4GEKb1 .

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pbuttigieg commented 7 years ago

There's some bandwidth to tackle adding radiation and energy classes into ENVO

@kaiiam will try to add the NPO classes via our standard import process, but may need some support in adapting the import to the OBO top levels.

If this doesn't work out, he will add many of these classes directly to ENVO, cross-referencing the NCIT and NPO classes where appropriate.

diatomsRcool commented 4 years ago

Can this please be prioritized? Thanks! @kaiiam

kaiiam commented 4 years ago

@diatomsRcool I'm pretty swamped ATM, but if you can help the process by identifying what you need and where they should go aka drafting those terms of high priority to you, I can make the PR for you.

diatomsRcool commented 4 years ago

ultrasound radiation: should be equivalent to http://purl.bioontology.org/ontology/npo#NPO_1744 subclass of http://purl.obolibrary.org/obo/ENVO_01001027

mid-infrared: should be equivalent to http://purl.bioontology.org/ontology/npo#NPO_1739 subclass of http://purl.obolibrary.org/obo/ENVO_21001214

near-infrared: should be equivalent to http://purl.bioontology.org/ontology/npo#NPO_1740 subclass of http://purl.obolibrary.org/obo/ENVO_21001214

far-infrared: should be equivalent to http://purl.bioontology.org/ontology/npo#NPO_1738 subclass of http://purl.obolibrary.org/obo/ENVO_21001214

cmungall commented 4 years ago

Hmm, looks like this ticket should have been closed a year ago, as we have the basic terms in there:

image

it's probably best to start new tickets for new terms (sorry, ticket pedant)

...or @diatomsRcool do you want to just go ahead and make a PR for these?

diatomsRcool commented 4 years ago

heh - yes, I noticed there were some there. I'll do the PR.