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Goals

  • Move activity types to a namespace
    • enable addition of new activity types without requiring language change
    • enable use of external vocabularies (e.g., GO Molecular Function)
  • Improve consistency of activity representation
    • Expert external knowledge is required to determine the appropriate specific BEL activity function
    • Evidence text from scientific papers often indicate that a protein is activated/inactivated, but not the type of activity
    • Citation annotation applies to the implied actIn statement, even though the type of activity may not be indicated in the text

BEL v1.0 activity syntax

10 distinct activity functions are supported in BEL v1.0. See Activities

Short Form

Long Form

cat()

catalyticActivity()

chap()

chaperoneActivity()

gtp()

gtpBoundActivity()

kin()

kinaseActivity()

act()

molecularActivity()

pep()

peptidaseActivity()

phos()

phosphataseActivity()

ribo()

ribosylaseActivity()

tscript()

transcriptionalActivity()

tport()

transportActivity()

kin(p(HGNC:AKT1)) =| tscript(p(HGNC:FOXO1))

The above statement indicates that the kinase activity of AKT1 directly decreases the transcriptional activity of FOXO1.

Activity terms are expanded by the compiler to link them to their root abundance term:

Proposed representation:

  • Simplify BEL activity functions by merging all to act()
    • Simply distinguish activity vs. abundance
  • Modify activity terms with specific molecular function
    • Requires new BEL function/entity type: molecularActivity(); ma()
    • Specified using  a namespace:value
  • Provide BEL v1.0 activity functions in "default" namespace
    • A 'default' namespace does not require designation with a prefix, and can be re-configured by the user
    • Namespace values can be equivalenced (or collapsed) to meet needs of user

Examples

BEL Statement without specific molecular functions

act(p(HGNC:AKT1)) =| act(p(HGNC:FOXO1))

If the specific molecular function is not known, the activity can be used without a molecular function modifier. The above statement indicates that the activity of AKT1 decreases the activity of FOXO1, but neither activity type is specified.

BEL Statement with specific molecular functions attached to activities; default BEL namespace

act(p(HGNC:AKT1), ma(kin)) =| act(p(HGNC:FOXO1), ma(tscript))

The above statement indicates that the kinase activity of AKT1 directly decreases the transcriptional activity of FOXO1. Default BEL namespace is used, so no prefix is required for inner ma() term.

BEL Statement with specific molecular functions attached to activities; external namespace

act(p(HGNC:AKT1), ma(GO:"kinase activity")) =| act(p(HGNC:FOXO1), ma(GO:"nucleic acid
binding transcription factor activity"))

The above statement uses GO Molecular Function terms for kinase and transcriptional activity.



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