has_agent.md

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has_agent

• OWL ID: RO_0002218
• label: has active participant
• synonyms []

Definition

x has participant y if and only if x realizes some active role that inheres in y

Usage

Use this relation to link a process to an entity that carries out that process. The entity may be a cellular component, a cell type or an anatomical structure. Examples include recording a vesicle type that mediates a transport process, a cell type that is the agent of a secretion process or a cell adhesion process. Do not use this to extend a molecular function: The agents of molecular functions are gene products and complexes. Use of this relation with a molecular function therefore consistutes reverse annotation.

Comment

Example of use: an annotation of gene X to cytokine production with has_agent of CL:0000057 (fibroblast) means that the fibroblast is producing the cytokine.

Subsets

[valid_for_annotation_extension, ro-eco, AE_cell_or_anatomical, AE_cellular_component, display_for_curators]

##local domain {u'GO:0008150': u'biological_process'}

local range

{u'CL:0000000': u'cell', u'GO:0005575': u'cellular_component', u'UBERON:0001062': u'anatomical entity', u'PO:0025131': u'plant anatomical entity', u'WBbt:0004017': u'Cell', u'WBbt:0005766': u'Anatomy'}

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Annotation Extension Usage Examples

1. Recording the cell type that is the agent in a secretion process

Gene Name (col 2)	GO ID (col 5)	Reference (col 6)	Evidence (col 7)	With (col 8)	Annotation Extension (col 16)
A2A7Q8	GO:0072643 interferon-gamma secretion		ECO:0000315		has_agent(CL:0000623) natural killer cell

2. Recording the agent involved in a transport process

Gene Name (col 2)	GO ID (col 5)	Reference (col 6)	Evidence (col 7)	With (col 8)	Annotation Extension (col 16)
F1PRN2	GO:0061502 early endosome to recycling endosome transport		ECO:0000314		has_agent(GO:0005884) actin filament

Using examples to demonstrate Folding_and_Unfolding using the relationship has_agent

Folded/unfolded	DB (Col 2)	Object (Col 3)	GO ID (Col 5)	Reference (Col 6)	Extension (Col 16)	Parent terms for new folded GO term
Unfolded		A2A7Q8	GO:0072643 interferon-gamma secretion		has_agent(CL:0000623 natural killer cell)
Folded		A2A7Q8	New GO term: interferon-gamma secretion via natural killer cell			is_a GO:0002370 natural killer cell cytokine production

OWL class expression:

interferon-gamma secretion and has_agent some 'natural killer cell'

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