Here are some examples of ways in which administration of chemicals are modeled in mixs:
drug_usage: Lipitor;2/day
chem_administration: agar [CHEBI:2509];2018-05-11T20:00Z
chem_treatment: ACCENT 1125;DOW;2010-11-17
biocide: ALPHA 1427;Baker Hughes;2008-01-23
biocide_used: commercial name of biocide, active ingredient in biocide or class of biocide
biocide_admin_method; 150 mg/l; weekly; 4 hr; 3 days
In some cases, this is split over multiple fields; in some cases syntactic separators are used. Sometimes IDs are used, sometimes names. Sometimes unit abbreviations are used, sometimes they are spelled out. Sometimes ISO non-timezone dates are used, sometimes date-times.
Overall MIxS needs to separate modeling and serialization. Some kind of existing standard should be adopted for the data model for chemical . Here are some candidates:
Even though these are both human the structures are generalizable to other animals or even other organisms like plants.
These data models have the following good characteristics:
normalization and nesting
clear use of ontologies in the appropriate places
use of standards for dates
ability to specify at the necessary level of granularity
MIxS should adopt a data model like this as core. It would still be possible to support various serializations and deserializations for legacy applications and spreadsheets.
Here are some examples of ways in which administration of chemicals are modeled in mixs:
drug_usage: Lipitor;2/day chem_administration: agar [CHEBI:2509];2018-05-11T20:00Z chem_treatment: ACCENT 1125;DOW;2010-11-17 biocide: ALPHA 1427;Baker Hughes;2008-01-23 biocide_used: commercial name of biocide, active ingredient in biocide or class of biocide biocide_admin_method; 150 mg/l; weekly; 4 hr; 3 days
In some cases, this is split over multiple fields; in some cases syntactic separators are used. Sometimes IDs are used, sometimes names. Sometimes unit abbreviations are used, sometimes they are spelled out. Sometimes ISO non-timezone dates are used, sometimes date-times.
Overall MIxS needs to separate modeling and serialization. Some kind of existing standard should be adopted for the data model for chemical . Here are some candidates:
https://phenopacket-schema.readthedocs.io/en/latest/dose-interval.html https://build.fhir.org/dosage.html
Even though these are both human the structures are generalizable to other animals or even other organisms like plants.
These data models have the following good characteristics:
MIxS should adopt a data model like this as core. It would still be possible to support various serializations and deserializations for legacy applications and spreadsheets.