Column 16: linking GO functions, processes, and components in one annotation
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
Specifying the stage at which a localization is observed
Cellular component annotations can be enhanced by specifying that localization is observed during a cell cycle or developmental stage, or in the context of a specific biological process.
If a gene product is localized to the nuclear periphery in S phase, G2, and mitosis (S. pombe Ulp1; PMID:11884512):
col 5: GO:0034399 ! nuclear periphery col 16: exists_during(GO:0000084)|exists_during(GO:0000085)|exists_during(GO:0007067) ! S phase of mitotic cell cycle, G2 phase of mitotic cell cycle, and mitosis respectively
If a gene product is localized to the spindle pole body (SPB) and nucleolus in interphase and to the actin contractile ring, the mitotic spindle, and kinetochores during mitosis (S. pombe Clp1; PMID:16085490):
col 5: GO:0005816 ! spindle pole body col 16: exists_during(GO:0051329) ! interphase of mitotic cell cycle
col 5: GO:0005730 ! nucleolus col 16: exists_during(GO:0051329) ! interphase of mitotic cell cycle
col5: GO:0005826 ! actomyosin contractile ring col 16: exists_during(GO:0007067) ! mitosis
col5: GO:0005819 ! spindle col 16: exists_during(GO:0007067) ! mitosis
col5: GO:0000777 ! condensed chromosome kinetochore col 16: exists_during(GO:0007067) ! mitosis
Note that an experiment that supports 'CC exists_during BP' may also support an annotation of the 'BP occurs_in CC' pattern.
Also see the go-discuss mailing list for more information.
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:
- 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
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