Design Patterns for Lab Values

Design Patterns for Lab Values

Urine levels

The concentration of X in the urine, normalized for urine concentration, is below the lower limit of normal. The concentration of X in the urine, normalized for urine concentration, is above the upper limit of normal.

Logical design patterns

We are still working out the optimal design patterns to computationally define lab values. In essence, there are two main ways of referring to the items that are being measured by lab tests.

1. Activity (e.g., GO:0070186 ! growth hormone activity)
2. A molecular entity (e.g., growth hormone). Here, the PRO andthe ChEBI ontologies offer many terms

There are a number of abnormalities that are measured by lab tests that are represented in the HPO, including

• increased/decreased level of X
• increased/decreased secretion of X
• increased/decreased response of X level to stimulus
• abnormal modification of X (e.g., addition of a sugar group to a protein, e.g., HbA1c)
• presence of a molecule that is not normally present in the body

This page should be used to develop guidelines for the computational definitions of these molecules.

Design patterns for metabolic abnormalities

The following design pattern is recommended for phenotypes that represent an increased or decreased concentration of some metabolite or ion in a bodily fluid. For instance, oligosacchariduria (HP_0010471) is defined as

'has part' some 
    ('increased amount'
     and ('inheres in' some 
        (oligosaccharide
         and ('part of' some urine)))
     and ('has modifier' some abnormal))

Note that the HPO previously has used a different design pattern, e.g., for hyperglycemia (HP_0003074):

 'has part' some 
    ('increased amount'
     and ('inheres in' some blood)
     and (towards some glucose)
     and ('has modifier' some abnormal)
     and ('has modifier' some pathological))

This pattern is deprecated, and the definitions will be migrated to the preferred pattern.

Hormones

We have used hormone in a logical def. But hormone is a biological role in ChEBI.

It is possible possible to model something like: 'molecular entity' and ('has role' some 'hormone')

(Note: this issue is still unresolved).