Annotation Extension Relation:part of

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Definition

"This relation has two uses in annotation extension. It may be used to relate a cellular component to some cellular component, cell or anatomical structure that it is part of. It may also be used to relate a molecular function or biological process to a biological process or developmental stage of which it is a part. It may not be used to relate cellular components to functions, processes or stages, or to relate processes or functions to cellular components, cells or anatomical structures."

Comment

Consider using TermGenie to create a new biological process GO term. Only use this term when the role of the gene product in the process is clearly known to be involved, not just occurring during the process. Consider the use of the relationship happens_during if the process is not definitely part of the biological process

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  	GTPase activity
 col16: part_of(GO:0048011 neurotrophin TRK receptor signaling pathway)

AND the additional annotation col5: GO:0048011 neurotrophin TRK receptor signaling pathway)

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 using the relationship part_of

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

Folded/unfolded DB (Col 2) Object (Col 3) GO ID (Col 5) Reference (Col 6) Extension (Col 16) Parent terms of new folded GO term
Unfolded O00206 TLR4 GO:0048471 perinuclear region of cytoplasm PMID:15027902 part_of(CL:0000451 dendritic cell)
Folded O00206 TLR4 New GO ID dendritic cell perinuclear region of cytoplasm PMID:15027902 is_a GO:0048471 perinuclear region of cytoplasm

OWL class expression: GO:0060070 perinuclear region of cytoplasm AND part_of SOME CL:0000451 dendritic cell

2. Specifying the developmental process which a more specific process is involved in No usage examples for this currently exist

Folded/unfolded DB (Col 2) Object (Col 3) GO ID (Col 5) Reference (Col 6) Extension (Col 16) Parent terms of new folded GO term
Unfolded ID Protein A GO:0060070 canonical Wnt signaling pathway PMID: ID part_of(GO:0035108 limb morphogenesis)
Additional annotation ID Protein A GO:0035108 limb morphogenesis PMID: ID
Folded ID Protein A New GO term canonical Wnt signaling pathway involved in limb morphogenesis PMID: ID is_a GO:0060070 canonical Wnt signaling pathway AND part_of GO:0035108 limb morphogenesis

OWL class expression: GO:0060070 canonical Wnt signaling pathway AND part_of SOME GO:0035108 limb morphogenesis


3. Functions carried out as part of a process No usage examples for this currently exist NOTE Wnt-activated receptor activity is already part_of Wnt signaling pathway. Here we are making a more specific statement that the Wnt-activated receptor activity is part_of a CANONICAL Wnt signaling pathway

Folded/unfolded DB (Col 2) Object (Col 3) GO ID (Col 5) Reference (Col 6) Extension (Col 16) Parent terms of new folded GO term
Unfolded ID Protein B GO:0042813 Wnt-activated receptor activity PMID: ID part_of(GO:0060070 canonical Wnt signaling pathway)
Additional annotation ID Protein B GO:0060070 canonical Wnt signaling pathway PMID: ID
Folded ID Protein B New GO term Wnt-activated receptor activity involved in canonical Wnt signaling pathway PMID: ID is_a GO:0042813 Wnt-activated receptor activity AND part_of GO:0060070 canonical Wnt signaling pathway


OWL class expression: is_a GO:0042813 Wnt-activated receptor activity AND part_of SOME GO:0060070 canonical Wnt signaling pathway



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