ontology: go/go_templates
remark: this file specifies high level templates for GO

!! ----------------------------------------
!! GENERIC DEVELOPMENT
!! ----------------------------------------

[Term]
id: GO:0032502 ! developmental process
relationship: primary_participant_role role:target_state
relationship: additional_participant_role role:initial_state

[Term]
id: GO:0023052 ! signaling
relationship: primary_participant_role role:signal_transmitter
relationship: additional_participant_role role:signal_receiver

[Term]
id: GO:0006810 ! transport
relationship: results_in_transport_of BFO:0000040 ! material entity
relationship: participant_role role:location
relationship: participant_role role:transportation_source
relationship: participant_role role:destination
relationship: participant_role role:cargo
relationship: participant_role role:conduit
relationship: participant_role role:transporter

[Term]
id: GO:0022610 ! biological adhesion
relationship: primary_participant_role role:adherer
relationship: additional_participant_role role:adherer

!! ----------------------------------------
!! CELL TYPES
!! ----------------------------------------

[Term]
id: GO:0055082 ! cellular chemical homeostasis
relationship: primary_cell_participant_role role:location

[Term]
id: GO:0001708 ! cell fate specification
relationship: primary_cell_participant_role role:target_state

[Term]
id: GO:0001709 ! cell fate determination
relationship: primary_cell_participant_role role:target_state

[Term]
id: GO:0045165 ! cell fate commitment
relationship: primary_cell_participant_role role:target_state

[Term]
id: GO:0048468 ! cell development
relationship: primary_cell_participant_role role:target_state

[Term]
id: GO:0030154 ! cell differentiation
relationship: primary_cell_participant_role role:target_state

[Term]
id: GO:0001775 ! cell activation
relationship: primary_cell_participant_role role:activated_state

[Term]
id: GO:0045058 ! T cell selection
relationship: primary_cell_participant_role role:selected_state

[Term]
id: GO:0016049 ! cell growth
relationship: primary_cell_participant_role role:grower

[Term]
id: GO:0032940 ! secretion by cell
comment: not always by a cell - see for example histamine secretion
relationship: primary_cell_participant_role role:secretor

[Term]
id: GO:0012501 ! programmed cell death
relationship: primary_cell_participant_role role:dier

[Term]
id: GO:0001906 ! cell killing
relationship: primary_cell_participant_role role:dier
relationship: additional_participant_role role:agent

[Term]
id: GO:0002507 ! tolerance induction
relationship: primary_cell_participant_role role:acted_upon

[Term]
id: GO:0050896 ! response to stimulus
relationship: primary_cell_participant_role role:acted_upon

[Term]
id: GO:0010496 ! intercellular transport
comment: no unambiguous primary participant

[Term]
id: GO:0046907 ! intracellular transport
relationship: primary_cell_participant_role role:location

[Term]
id: GO:0060326 ! cell chemotaxis
relationship: primary_cell_participant_role role:cargo

[Term]
id: GO:0051301 ! cell division
relationship: primary_cell_participant_role role:parent_state

[Term]
id: GO:0052127 ! movement on or near host
relationship: primary_cell_participant_role role:cargo

[Term]
id: GO:0051674 ! localization of cell
relationship: primary_cell_participant_role role:cargo

[Term]
id: GO:0048469 ! cell maturation
relationship: primary_cell_participant_role role:target_state

[Term]
id: GO:0043697 ! cell dedifferentiation
relationship: primary_cell_participant_role role:initial_state

[Term]
id: GO:0031130 ! creation of an inductive signal
relationship: primary_cell_participant_role role:signal_originator

[Term]
id: GO:0007267 ! cell-cell signaling
relationship: primary_cell_participant_role role:signal_transmitter
relationship: additional_cell_participant_role role:signal_receiver

[Term]
id: GO:0044237 ! cellular metabolic process
relationship: primary_cell_participant_role role:location

[Term]
id: GO:0007155 ! cell adhesion
relationship: primary_cell_participant_role role:adherer

[Term]
id: GO:0007166 ! cell surface receptor linked signaling pathway
relationship: primary_cell_participant_role role:location
relationship: primary_cell_participant_role role:signal_receiver

[Term]
id: GO:0022403 ! cell cycle phase
relationship: primary_cell_participant_role role:location
comment: need a more specific relation..?

[Term]
id: GO:0048870 ! cell motility
relationship: primary_cell_participant_role role:cargo

!! ----------------------------------------
!! GROSS ANATOMICAL STRUCTURES
!! ----------------------------------------

[Term]
id: GO:0048856 ! anatomical structure development
relationship: primary_gross_anatomical_participant_role role:target_state
relationship: additional_participant_role role:initial_state

[Term]
id: GO:0048513 ! organ development
comment: example: MGI annotation for 'mammary gland development' with 'glandular epithelial cell' in c16
relationship: primary_gross_anatomical_participant_role role:target_state
relationship: primary_cell_participant_role role:target_population

[Term]
id: GO:0048731 ! system development
relationship: primary_gross_anatomical_participant_role role:target_state
relationship: primary_cell_participant_role role:target_population

[Term]
id: GO:0048771 ! tissue remodeling
relationship: primary_gross_anatomical_participant_role role:acted_upon

[Term]
id: GO:0048646 ! anatomical structure formation involved in morphogenesis
relationship: primary_gross_anatomical_participant_role role:target_state

[Term]
id: GO:0003008 ! system process
relationship: primary_gross_anatomical_participant_role role:agent

[Term]
id: GO:0007389 ! pattern specification process
relationship: primary_gross_anatomical_participant_role role:target_state

[Term]
id: GO:0065008 ! regulation of biological quality
relationship: primary_gross_anatomical_participant_role role:location

[Term]
id: GO:0007049 ! cell cycle
relationship: primary_gross_anatomical_participant_role role:location

[Term]
id: GO:0048872 ! homeostasis of number of cells
relationship: primary_gross_anatomical_participant_role role:member_of_regulated_population


!! ----------------------------------------
!! CELLULAR COMPONENTS
!! ----------------------------------------

[Term]
id: GO:0071840 ! cellular component organization or biogenesis
relationship: primary_cell_participant_role role:location

!! ----------------------------------------
!! ROLES
!! ----------------------------------------

[Term]
id: role:role

[Term]
id: role:agent
is_a: role:role
def: "The agent is the active participant in a process. In a cellular process, this may be a gene product or complex. The agent is typically unchanged by the process" [GOC:cjm]
xref: occurs_in

[Term]
id: role:acted_upon
is_a: role:role
def: "A participant in a process is acted_upon if it is not an agent and is changed in some way be the process - either structurally, or locationally. Examples: cargo in transportation" [GOC:cjm]
xref: occurs_in
disjoint_from: role:agent

[Term]
id: role:location
is_a: role:role
def: "The process occurs_in the location. The location is necessarily different than the cargo or conduit" [GOC:cjm]
xref: occurs_in
disjoint_from: role:transportation_source
disjoint_from: role:destination
disjoint_from: role:cargo
disjoint_from: role:conduit

[Term]
id: role:transportation_source
is_a: role:role
def: "Each transportation process results in the movement of cargo from some *source*. The source is necessarily different from the cargo or conduit, but in principle it could be the same as the destination (e.g. a circuit). It could also be the same as the agentitive entity (e.g. a cell sending a signal)" [GOC:cjm]
xref: results_in_transport_from
disjoint_from: role:cargo
disjoint_from: role:conduit

[Term]
id: role:destination
is_a: role:role
def: "Each transportation process results in the movement of cargo to some *destination*" [GOC:cjm]
xref: results_in_transport_to
disjoint_from: role:cargo
disjoint_from: role:conduit

[Term]
id: role:cargo
is_a: role:acted_upon
def: "Each transportation process results in the movement of *cargo* to some destination. Note that secreted entities are also considered to play the cargo role. Note that in self-directed movement, the moving entity is considered cargo (we may want a more generic name since it is odd to call this cargo - transportee?)" [GOC:cjm]
xref: results_in_transport_of
disjoint_from: role:conduit

[Term]
id: role:conduit
is_a: role:role
def: "A transportation process may result in the movement of a cargo through or along some *conduit*. Examples: cytoplasm, pore, germline ring canal" [GOC:cjm]
xref: results_in_transport_through

[Term]
id: role:transporter
is_a: role:agent
def: "A transportation process is carried about by some *transporter*" [GOC:cjm]
xref: results_in_transport_through

[Term]
id: role:secretor
is_a: role:role
def: "A secretor releases some cargo during a secretion process." [GOC:cjm]
comment: is this equivalent to or a subtype of transporter? Consider cellular secretion assisted by cell components (channels) and/or gene products.
xref: secreted_by

[Term]
id: role:signal_transmitter
is_a: role:agent
is_a: role:transportation_source
def: "In any signaling process, the initial signal is released by the *signal_transmitter*" [GOC:cjm]
xref: results_in_signalling_from

[Term]
id: role:signal_receiver
is_a: role:destination
def: "In any signaling process, the signal is received by the *signal_receiver*. " [GOC:cjm]
xref: results_in_signalling_to

[Term]
id: role:initial_state
is_a: role:role
def: "A development process has one entity that plays the source state role. This entity is there at the begining of the process, and is changed during the process. It may cease to exist, or it may continue after the process ends, but it is always changed somehow." [GOC:cjm]
xref: has_input

[Term]
id: role:target_state
is_a: role:role
def: "A developmental progress is directed towards the changing participant attaining the target state. For example, in neuron differentiation, the participant with the 'changing' role / source state role is the neuron precursor and the participant with the target_state is the neuron. In cell maturation, the initial_state is the non-fully functional entity, and the target_state is the fully-functional entity. Note that in both these cases, from one perspective these are the same entity at different points in time. Note also that we use participation in a weak inclusive sense, such that the target cell participates in its own specification." [GOC:cjm]
xref: results_in_progression_towards

[Term]
id: role:target_population
is_a: role:role
def: "TBD. See for example the MGI mammary gland development c16 annotations." [GOC:cjm]

[Term]
id: role:parent_state
is_a: role:initial_state
def: "In a process of division or budding, the entity with the parent role is present at the beginning of the process, and is either replaced by two entities, or buds off an additional entity." [GOC:cjm]
xref: results_in_division_of

[Term]
id: role:dier
is_a: role:initial_state
comment: ok, not a great name - think of others?

[Term]
id: role:grower
is_a: role:acted_upon
comment: ok, not a great name - think of others?

[Typedef]
id: participant_role
def: "A relationship between a process and a role that some entity plays in that process" [GOC:cjm]

[Typedef]
id: primary_cell_participant_role
is_a: participant_role
comment: note that every process can have only a single cell as a *primary* cell participant.
functional: true

[Typedef]
id: primary_gross_anatomical_participant_role
is_a: participant_role
comment: note that every process can have only a single gross anatomical entity as a *primary* gross anatomical participant.
functional: true