BEP-0007 - Numeric Annotations

[ncatlett]

Numeric annotations - BEP7

closes #15

[cthoyt]

Does it make sense to associate units separately from the values that are being measured? I had written BEL like this before:

SET Citation = {"PubMed", "23484434"}

############
# Figure 4 #
############

# Disambiguation: TAGI is short for "tau aggregation inhibitors"
SET Evidence = "Redox cycling of methylene blue and TAGI potencies. Upper 
panel (black): Reduced leuco form 2 and structural overlap with inactive 
phenothiazines 3, 4, and 5.  Lower panel (blue): Structural overlap between 
oxidized form 1 and azure A (6), reduced anthraquinone, 8, and 9, showing 
the extended π-conjugated system (ND: not determined)."
SET Page = "D"
SET Figure = "4"

# Disambiguation: CHEBI:22580 label "anthraquinone"
# Disambiguation: HBP00006 label "Tau aggregates"
SET ArticleCompoundNumber = "7"
SET MeasurementType = "IC50"
SET MeasurementUnits = "μM"
SET MeasurementRelation = "~"
SET MeasurementValue = "2"
a(CHEBI:"22580") -| a(HBP:HBP00006)
UNSET {ArticleCompoundNumber, MeasurementType, MeasurementUnits, \
   MeasurementRelation, MeasurementValue}

Or what about when there's a numerical range, like in:

# Disambiguation: CHEBI:6872 label "methylene blue"
# Disambiguation: HBP00006 label "Tau aggregates"
SET ArticleCompoundNumber = "1"
SET MeasurementType = "IC50"
SET MeasurementUnits = "μM"
SET MeasurementRelation = "="
SET MeasurementRangeLower = "1.9"
SET MeasurementRangeUpper = "31"
a(CHEBI:"6872") -| a(HBP:HBP00006)

UNSET {ArticleCompoundNumber, MeasurementType, MeasurementUnits, \
   MeasurementRelation, MeasurementRangeLower, MeasurementRangeUpper}

[johnbachman]

How would measurement units be specified where there are multiple values being specified? E.g., there could be numeric annotations associated with the dose of a drug or ligand used in a treatment, as well as the change in an output variable (fold change, amount of cytokine secreted, etc.)

[ncatlett]

I would not separate the units from a numeric annotation. Ideally, the units would be included as part of the annotation, e.g., "2 hours"

[cthoyt]

Discussion Notes

• John brought up a discussion on Pathway Logic (http://pl.csl.sri.com/datumkb.html)
• William mentioned: LOINC (https://loinc.org/get-started/loinc-term-basics/)

For a given annotation, is it a namespace annotation, or a numeric one? Could we also have more complicated objects with exotic schemata?