kaiiam
commented
3 years ago Hey @ramonawalls if possible I'd like to coordinate on this or perhaps diagram it out with some examples. BCODMO has some good examples of multi-step data processing, the annotation/representation of which might be made possible following the model here (if I understand it correctly).
As an example, BCODMO has parameters like Mg concentrations that are associated with a variety of datasets, one of which being a dataset that measured Stable isotopes in reactive silica pools of Mississippi River plume sediments.
If I'm understand your model as described in your BCO paper then we could describe the above with something like the following:
1) An initial OBI:material sampling process that took as input some ENVO:sediment and results in output of some sediment specimen, which we'd model as some type of OBI:specimen?
2) Then later they took that sediment specimen and performed some stable isotopic incubation experiments (the details of which I'm not an expert on but would be something like those describe here), which involve chemically [separating the] silica into operationally defined [reactive] pools based on kinetics, reaction conditions, and reaction sequence [into ...] (Si‐HCl, Si‐Alk, Si‐NaOH, and T‐bSiO2). This I presume would be modeled by again applying another OBI:material sampling process class that took as input the sediment specimen, and has various outputs, being vials corresponding to the different reactive silica pools.
3) Finally (I presume) they measured the concentration of Mg in the aforementioned reactive silica pools based off an aliquot of each using something like a spectrophotometer. I presume this would again be modeled with a final OBI:material sampling process that took the reactive silica pool specimens as inputs and outputs the aliquots thereof. Then they would have taken those reactive silica pool aliquot specimens and subjected them to an OBI:assay, which would output an IAO:data item (about the material entity in question).
Sorry for the long winded message, but I just wanted to clarify 1) if I'm understanding this correctly, and 2) if this data model could be used to annotate complex parameters (such as described here) within an RDF context. Thanks!
These terms ultimately belong in COB, but I want to test out the hierarchy here. We need these classes for several use cases, including iSamples.
For a longer discussion, see obi-ontology/obi#969