EnvironmentOntology / environmental-exposure-ontology

Modular environmental exposures ontology
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exposure to chemical elements #14

Open cmungall opened 7 years ago

cmungall commented 7 years ago

When we say exposure to {caesium, lead, mercury, copper, ...} do we mean

etc

it seems safest to opt for the most general (X molecular entity), and if we need more specific subforms, add more specific classes.

some examples:

    is_a CHEBI:33676 ! d-block molecular entity
     is_a CHEBI:33673 ! zinc group molecular entity
      is_a CHEBI:25196 ! mercury molecular entity ***
       is_a CHEBI:25706 ! organomercury compound
        is_a CHEBI:22648 ! arylmercury compound
        is_a CHEBI:25193 ! mercuribenzoate
        is_a CHEBI:25194 ! mercuribenzoic acid
        is_a CHEBI:33255 ! alkylmercury compound
        is_a CHEBI:39152 ! mercury difulminate
        is_a CHEBI:59445 ! chlormerodrin
       is_a CHEBI:35113 ! elemental mercury
        is_a CHEBI:16170 ! mercury(0)
        is_a CHEBI:25197 ! mercury cation
       is_a CHEBI:36561 ! mercury coordination entity
        is_a CHEBI:28216 ! methylmercury chloride
        is_a CHEBI:31823 ! mercury dichloride
        is_a CHEBI:33050 ! dimercury dichloride
        is_a CHEBI:33210 ! dimercury diacetate
        is_a CHEBI:33211 ! mercury diacetate
        is_a CHEBI:36569 ! triiodomercurate(1-)
        is_a CHEBI:36573 ! mercury dicyanide
        is_a CHEBI:36574 ! diamminemercury(2+)
        is_a CHEBI:36576 ! tetraiodomercurate(2-)
        is_a CHEBI:36577 ! tetrakis(thiocyanato)mercurate(2-)
        is_a CHEBI:49639 ! mercury dibromide
        is_a CHEBI:49659 ! mercury diiodide
        is_a CHEBI:49727 ! (acetyloxy)mercury(1+)
    is_a CHEBI:33674 ! s-block molecular entity
     is_a CHEBI:33296 ! alkali metal molecular entity
      is_a CHEBI:37128 ! caesium molecular entity ***
       is_a CHEBI:33988 ! caesium hydroxide
       is_a CHEBI:37130 ! caeside
       is_a CHEBI:60270 ! caesium ion
        is_a CHEBI:49547 ! caesium(1+)
       is_a CHEBI:63039 ! caesium chloride

may not be sufficient to classify radioactive isotopes

cmungall commented 7 years ago

hmm, CHEBI doesn't seem very consistent here; lithium ME only has one direct subclass; ions are in a different branch

     is_a CHEBI:33296 ! alkali metal molecular entity
      is_a CHEBI:33298 ! lithium molecular entity *** 
       is_a CHEBI:35478 ! lithium salt
        is_a CHEBI:30142 ! lithium tetrahydroaluminate
        is_a CHEBI:30525 ! lithium nitride
        is_a CHEBI:48607 ! lithium chloride
        is_a CHEBI:51753 ! Alexa Fluor 480
        is_a CHEBI:52661 ! Alexa Fluor 488
         is_a CHEBI:52662 ! Alexa Fluor 488 para-isomer
         is_a CHEBI:52663 ! Alexa Fluor 488 meta-isomer
        is_a CHEBI:63042 ! lithium bromide
        is_a CHEBI:63315 ! lithium nitrate
        is_a CHEBI:64735 ! lithium citrate (anhydrous)
        is_a CHEBI:6504 ! lithium carbonate

Filed a ticket for these: https://github.com/ebi-chebi/ChEBI/issues/3336