What is the activity function's return type?

OpenBEL / language

Specification for the Biological Expression Language

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What is the activity function's return type? #8

Closed abargnesi closed 8 years ago

abargnesi commented 8 years ago

BEL 1.0 declared abundance as the return type for specific activity types (e.g. kinaseActivity). This implies that the following is semantically valid:

complex( kin( p(HGNC:JAK2) ) )

Given the following function signatures of kinaseActivity and complexAbundance:

kinaseActivity(F:proteinAbundance)abundance
complexAbundance(F:abundance...)abundance

Does this hold true for BEL 2.0's general-purpose activity function?

@ncatlett

ncatlett commented 8 years ago

complex( kin( p(HGNC:JAK2) ) ) should NOT be semantically valid. Maybe this is a mistake in the BEL 1.0 implementation?

abargnesi commented 8 years ago

Yeah it looks that way. Here was my experience running this through the BelCheck tool.

Thanks for the clarification. We will make sure to correct the semantics in BEL 1.0 & 2.0 implemented in OpenBEL/parsers.

We may want to consider a patch to OpenBEL Framework.

abargnesi commented 8 years ago

Added OpenBEL/openbel-framework#67