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==== Using examples (from above) to demonstrate | ==== 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