ConcentrationQualityInOBI

How do we specify solute concentration in OBI using BFO + OBO-RO + PATO

There are typically two ways in which concentration is important to the experimental descriptions OBI will need to support:

1. Concentration of a particular set of solutes is fed into an experiment as a part of an assay or material transformation - e.g.:
   • incubate this set of materials in a saline buffer composed of these solute concentrations
   • set the pH of your electrophysiological recording saline to X

1. Concentration of a particular solute is the output of an assay - e.g.:
   • the concentration of protein in this solution
   • the concentration of glucose in this blood sample

How can we build formal descriptions for capturing concentration both as a description of a planned process/protocol, as well as the information content entity output of an assay?

One of the most difficult requirements of the representational strategy we adopt is it must be able to provide a means to capture the fact that frequently concentration measurement assays will indicate the molecule in question has a concentration outside of the linear range of sensitivity for that assay. When hitting the lower bounds, If present at all, the material is at a concentration that is less than the sensitivity of the assay being used. When reaching the upper bound for the assay (typically the bound beyond which the data transformation used to interpret the information content entity output of the assay no longer provides a predictable linear relation to the concentration being measured). For instance, the standard Coomassie Blue-based Bradford protein assay is only linear in the range of 0.1 mg - 1.5 mg protein/ml. When the data hits the upper bounds, there would likely be an additional assay performed on a diluted sample with the intension of obtaining a determination that falls within the linear range. When one hits the lower bounds (for Bradford, 0.1 mg/ml), one can only state the value is < that lower limit - not that it is zero. One would often then resort to a method whose linear range is more sensitive - e.g., the Micro BCA assay with a sensitivity in the range of 0.5 - 20 micrograms/ml. Additional techniques such as silver stained gels or various immunoassays can provide determination of very specific proteins down in the nanogram range. This variety of techniques is presented in an effort to capture the everyday complexity behind even a simple determination of protein concentration in a sample. This is important for OBI to cover, since the type of assay and its concommittant sensitivity range will provide a means to determine whether two concentration values (information content entities) can actually be compared. When the values are close to the bounds of linear sensitivity of the assay, such comparisons must only be made with a modicum of caution. Some would even say to support a quantitative comparison between concentration values, the same assay should be used.

[problem summary by BB]

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