Part of - deprecated: Difference between revisions

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==== Using examples (from above) to demonstrate [Folding_and_Unfolding folding and unfolding] using part_of ====
==== Using examples (from above) to demonstrate [[Folding_and_Unfolding folding and unfolding]] using part_of ====


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Revision as of 06:33, 9 May 2014

Back to Annotation usage examples for each annotation extension relation

Definition

Identifies the cell, tissue, anatomical entity, biological process or developmental stage in which the molecular function or biological process occurs or the cellular component exists.

Child terms

  • None

Scope of use

Domain

BFO:0000001 ! entity (Biological Process, Molecular Function or Cellular Component)

Range

ENTITY_UNION:0000008 ! cell, anatomy, cellular component, biological process and developmental stage

Annotation Extension Usage Examples

Enhancing Cell Component Annotations

Localization

Specifying that a gene product is located in a cellular component of a specific cell or tissue type

1. Toll-like receptor 4 (TLR4) (O00206) is located intracellularly in the perinuclear region (GO:0048471 perinuclear region of cytoplasm) only in dendritic cells (CL:0000451), PMID:15027902

So the annotation would be;

DB (Col 2) Object (Col 3) GO ID (Col 5) Reference (Col 6) Extension (Col 16)
O00206 TLR4 GO:0048471 PMID:15027902 part_of(CL:0000451)


2. TLR4 is located on the cell surface (GO:0009986) in monocytes (CL:0000576), PMID:15027902

So the annotation would be;

DB (Col 2) Object (Col 3) GO ID (Col 5) Reference (Col 6) Extension (Col 16)
O00206 TLR4 GO:0009986 PMID:15027902 part_of(CL:0000576)


Further examples of these usages of part_of can be found on the documentation page for Column_16:_Cell_Type

Enhancing Molecular Function and Biological Process Annotations

Specifying the developmental stage at which a process occurs

We can use a developmental stage ontology and the part_of relation. part_of is used because both the process/function and the developmental stages are things with temporal parts (they are occurrents in bfo-speak).

For example, apoptosis during Segmentation:1-4 somites in zebrafish

 col5: GO:0006915
 col16: part_of(ZFS:0000023)

Functions carried out as part of a process

We use the part_of relation to link function and process (this relation is already used for the inter-ontology links)

For example, if a gene product is observed to have GTPase activity as a part of the nerve growth factor receptor signaling pathway, you would annotate:

 col5: GO:0003924
 col16: part_of(GO:0048011)

Note you should also include a separate annotation in which GO:0048011 is in col5, so that people who are not using col 16 will not be worse off than they are now. See guidelines.

Note that you would not say something like this:

 col5: GO:0016301
 col16: part_of(GO:0016310)
  • GO:0016301 - kinase activity
  • GO:0016310 - phosphorylation

This is harmless but pointless, because we know that kinase activity is part_of phosphorylation from gene_ontology_ext

Function-Process-Component threesomes

 col5: GO Function ID
 col16: part_of(GO PROCESS ID),occurs_in(GO CC ID)

Also include 2 redundant annotation lines


Using examples (from above) to demonstrate Folding_and_Unfolding folding and unfolding using part_of



Back to Annotation usage examples for each annotation extension relation