Column 16: linking GO functions, processes, and components in one annotation: Difference between revisions

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* nuclear translation vs mt translation (or both)
* nuclear translation vs mt translation (or both)
* transport within, to or from cytoplasm or nucleus
* transport within, to or from cytoplasm or nucleus
=== Specifying the location in which a process happens ===
rocess terms can be further specified by subcellular location. For example: ''plastid translational elongation''
At the time of writing this term is not declared in GO. Again we use the occurs_in relation:
  Col 5: GO:0006414
  Col 16: occurs_in(GO:0009536)
Why, you might ask, can we not instead make two annotations to:</strike>
* GO:0032544 ! plastid translation
* GO:0006414 ! translational elongation
The answer is that co-annotation carries less information. Computationally we have no way of knowing these two processes are linked. See the FAQ
Note that the majority of the time, BP x CC cross-products should be pre-composed in the ontology. If the above scenario comes up, consider requesting a new term ''plastid translational elongation'' rather than using col 16.
Also note that when using a GO ID in col 16, a redundant annotation should sometimes be added. See [[#Guidelines]]


=== Functions carried out as part of a process ===
=== Functions carried out as part of a process ===

Revision as of 10:45, 8 May 2012

The identifers used in the annotation extension field need not be external - a GO ID can be used, for example to state that a function F is executed during process P.

Why allow GO IDs in col 16? Can I just co-annotate instead

co-annotation is not sufficient. Important information is lost. For example, if a gene has 4 annotations to

  • mitochondrion
  • nucleus
  • translation
  • transport

We have no way of knowing whether the gene is involved in

  • nuclear translation vs mt translation (or both)
  • transport within, to or from cytoplasm or nucleus

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

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