Parameters & Concentrations Ontology

Summary

Suggestion from Ramona Walls to have OBO ontology for common parameters, measurements and concentrations.

First use case RDF version of MIxS.

Launch using the BerkelyBop ontology development kit 'ODK'. Would almost exclusively use design patterns, having a variety of yaml patterns similar to the ENVO chemical_concentration patterns see example csv and yaml files from ENVO.

Concentration of x chemical entity in predetermined material patterns:

concentration of and (inheres in some (X and (part of some ENV_MAT)))

Where ENV_MAT includes:

• ENVO:soil (for MIxS Soil)
• ENVO:liquid water (for MIxS Water)
• ENVO:air (for MIxS Air)
• ENVO:sediment (for MIxS Sediment)
• ENVO:sludge (for MIxS Wastewater/sludge)
• ENVO:biofilm (for MIxS Microbial mat/biofilm)
• ENVO:microbial mat (for MIxS Microbial mat/biofilm)
• UBERON:blood
• UBERON:feces
• UBERON:urine
• UBERON:milk
• PO:plant anatomical entity (for MIxS Plant-associated)
• PO:root
• PO:leaf
• FOODON:food product type

physical quality design patterns (all PATO)

QUALITY and (inheres in some X (environmental material))

Where QUALITY includes:

• acidity
• depth
• electrical conductivity
• elevation
• fluorescence
• height
• humidity
• luminance? (in units of lux)
• mass density
• mass
• pressure
• temperature
• texture
• [alkalinity](missing from PATO)
• [altitude](missing from PATO)
• [reduction potential](missing from PATO)
• [salinity](missing from PATO) ...

Current examples: temperature of soil, temperature of water, pressure of water, humidity of soil, acidity of soil, fluorescence of water

rates?

For example: MIxS aminopeptidase activity could use GO:aminopeptidase activity PATO:rate

ratio?

For example: MIxS carbon/nitrogen ratio could use PATO:proportionality to some (carbon atom and nitrogen atom)

flux?

For example: MIxS photon flux could use PATO:flux and photon

Ontology Imports

• PATO
• ENVO
• UBERON
• PO