Open jagadishcs opened 3 years ago
kaiiam
commented
3 years ago @jagadishcs yes something along these lines, see response in https://github.com/EnvironmentOntology/envo/issues/1067.
@pbuttigieg Perhaps we can clarify this in ENVO-annotations-for-MIxS-v5?
wdduncan
commented
3 years ago The Expected value field for env_medium indicates (to me) that terms from other ontologies can serve as values. I posted a ticket in MIxS addressing this:
https://github.com/GenomicsStandardsConsortium/mixs/issues/117
pbuttigieg
commented
3 years ago @wdduncan
The Expected value field for env_medium indicates (to me) that terms from other ontologies can serve as values. I posted a ticket in MIxS addressing this:
Yes, I updated the guidance in our wiki page to make it more clear.
Other terms can be used, as long as they are mass/volume nouns and not discrete, countable entities.
@jagadishcs
I have come across some biosamples, like ice cream and currency notes from which the microbial communities were studied. EnvO terms 'ice cream food product' - FOODON_00001045 for ice cream and 'currency note' - ENVO_00003896 for currency notes were found to be appropriate EnvO terms, but they come under the hierarchy of food material and material entity respectively.
FOODON:00001045 is a FOODON term, not an ENVO term. You can, however, use that in a MIxS annotation as it interoperates with ENVO and is an appropriate env_medium class as it's under environmental material and seems to be a mass/volume noun.
Currency note is appropriate for the env_local field, as it's a countable, discrete entity. It is not appropriate for the env_medium field. The latter would capture the material(s) the note was made out of.
I could not find any other suitable terms from the list of env_medium terms available at environmental material, as suggested in the EnvO General notes and guidance.
Do you need any?
Similar to the above examples, I have used a several such terms from material entity and food material since there were no equivalent terms under environmental material.
I don't understand what you're trying to say.
So, when no appropriate term is found in the hierarchy, environmental material, but present in material entity/food material hierarchies, would it be appropriate to allow such terms to be used for MIxS env_medium field.
The food material branch is under environmental material, so that should be fine (again, always check the definition and ensure that it's a mass/volume noun).
material entity is very high up the tree, and includes environmental materials but also includes things that are not materials and are not valid for the env_medium field. Again, these have to be mass/volume nouns (a portion of "air", "water", "blood", "linen", "paper" etc) not countable things (a "currency note", a "tree", a "table").
@cmungall, @wdduncan, @pbuttigieg, @kaiiam, @TBKReddy
I have come across some biosamples, like ice cream and currency notes from which the microbial communities were studied. EnvO terms 'ice cream food product' - FOODON_00001045 for ice cream and 'currency note' - ENVO_00003896 for currency notes were found to be appropriate EnvO terms, but they come under the hierarchy of food material and material entity respectively. I could not find any other suitable terms from the list of env_medium terms available at environmental material, as suggested in the EnvO General notes and guidance.
Similar to the above examples, I have used a several such terms from material entity and food material since there were no equivalent terms under environmental material.
So, when no appropriate term is found in the hierarchy, environmental material, but present in material entity/food material hierarchies, would it be appropriate to allow such terms to be used for MIxS env_medium field.