! This is a list of annotation extension relations, providing friendly
! display text for the extensions themselves and for any reciprocal
! annotations that can be inferred. Not every extension would yield
! sensible reciprocals, so some relations have "N/A" for reciprocal
! display text.

! These don't depend on what the annotated term is, so the same
! display text works for any extension using the relation:

name	display text	reciprocal annotation display text	comment	
activated_by	activated by	N/A	only used with ChEBI IDs; could use 'activates'
coincident_with	at	N/A	(wouldn't apply to SO terms, and hard to craft sensible text for PomBase IDs)
directly_negatively_regulates	directly inhibits	directly inhibited by
directly_positively_regulates	directly activates	directly activated by
during	during	N/A	only used with GO IDs
exists_during	during	N/A	only used with GO IDs
happens_during	during	N/A	only used with GO IDs
has_regulation_target	regulates	regulated by
in_presence_of	in presence of	N/A	only used with CHEBI IDs, for modification annotations
inhibited_by	inhibited by	N/A	only used with ChEBI IDs; could use 'inhibits'
not_during	except during	N/A	only used with GO IDs; deprecated by GO
not_exists_during	except during	N/A	only used with GO IDs; deprecated by GO
not_happens_during	except during	N/A	only used with GO IDs; deprecated by GO
not_occurs_at	not at	N/A	not used with PomBase IDs; mix of GO, SO, CL; deprecated by GO
not_occurs_in	not in	N/A	not used with PomBase IDs; mix of GO, SO, CL; deprecated by GO
occurs_at	at	N/A	not used with PomBase IDs; mix of GO, SO, CL
occurs_in	in	N/A	not used with PomBase IDs; mix of GO, SO, CL
part_of	part of	N/A	only used with GO or CL IDs
required_for	required for	N/A	only used with GO IDs
stabilizes	stabilizes	N/A	not used at present



! For some relations, the best display string depends on term and its
! ancestry. These relations are affected:
!
! GO: has_input, has_direct_input, has_indirect_input
!
! For these, it's a case of "if we're displaying X for the annotation,
! the reciprocal should display Y", i.e.:
!
! relation displayed as	reciprocal displayed as
! has substrate	substrate of
! transports	transported by
! binds	binds
! localizes	localized by

relation	if descendent of	display	reciprocal display
has_input	GO:0003824 catalytic activity	has substrate	substrate of
has_input	GO:0006810 transport	transports	transported by
has_input	GO:0005215 transporter activity	transports	transported by
has_input	GO:0005488 binding	binds	binds
has_input	GO:0051179 localization	localizes	localized by
has_direct_input	GO:0003824 catalytic activity	has substrate	substrate of
has_direct_input	GO:0006810 transport	transports	transported by
has_direct_input	GO:0005215 transporter activity	transports	transported by
has_direct_input	GO:0005488 binding	binds	binds
has_direct_input	GO:0051179 localization	localizes	localized by
has_indirect_input	GO:0003824 catalytic activity	has substrate	substrate of
has_indirect_input	GO:0006810 transport	transports	transported by
has_indirect_input	GO:0005215 transporter activity	transports	transported by
has_indirect_input	GO:0005488 binding	binds	binds
has_indirect_input	GO:0051179 localization	localizes	localized by

! For FYPO, extensions should always be displayed, but reciprocal
! annotations should only be shown for abnormal phenotypes. All
! display text below lumps overexpression/knockdown of wild type with
! sequence-altering mutations for simplicity. 
!
! If we wanted to be fussier, we have a couple of other options: 1) We
! could use a longer, clunkier display text, e.g. 'affected by
! mutation or expression change in'; or 2) The display conversion code
! could do something sophisticated like "if the allele is wild type
! (and therefore expression must be overexpression or knockdown), use
! 'affected by expression change in'; otherwise use 'affected by
! mutation in'"

relation	if is_a descendant of	display	reciprocal display
assayed_using	FYPO:0001985	affecting	affected by mutation in
assayed_enzyme	FYPO:0001985	affecting activity of	activity affected by mutation in
assayed_substrate	FYPO:0001985	affecting	affected by mutation in
assayed_using	FYPO:0000257	affecting	N/A
assayed_enzyme	FYPO:0000257	affecting activity of	N/A
assayed_substrate	FYPO:0000257	affecting	N/A