Supporting Complexes and Family members via Famplex

[jvwong]

To include grounding support for Famplex complexes and family members in grounding-search may involve updates herein. In particular:

• Curation tool support for Famplex types:

  1. protein (aka 'family')
  2. complex namedComplex

• Updates to the BioPAX export to handle the Famplex entity types

  1. protein (aka 'family')
  2. *complex namedComplex

• *BioPAX and Complexes:

  • BioPAX L3 does not specify an EntityReference for a complex, merely it's components
  • A Complex may have 0 components aka "black-box"
  • A complex may declare an Xref (e.g. UnificationXref)

[jvwong]

Some more considerations around FamPlex complexes:

• Type
  • A Biofactoid Complex is created within the editor via drag and drop (top-down)
  • No (clear) way to swap a Biofactoid Entity for a Complex when a grounding search top hit is a FamPlex 'complex' (bottom-up).
    • Although, the latter would be more extensible (e.g. adding GO terms to grounding search )
• Nesting
  • Should we (dis)allow a (compound) complex to have a (FamPlex) complex entity inside it?