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'''p occurs_in c if and only if all of the participants of p are part_of c.''' | '''p occurs_in c if and only if all of the participants of p are part_of c.''' | ||
==Child terms== | |||
* None. | * None. | ||
==Annotation Examples== | |||
== Enhancing Molecular Function and Biological Process Annotations == | === Enhancing Molecular Function and Biological Process Annotations === | ||
=== Specifying the cell or tissue type in which a process happens === | ==== Specifying the cell or tissue type in which a process happens ==== | ||
Examples of this usage of occurs_in can be found on the documentation page for [[Column_16:_Cell_Type]] | Examples of this usage of occurs_in can be found on the documentation page for [[Column_16:_Cell_Type]] | ||
=== Specifying the subcellular location in which a process happens === | ==== Specifying the subcellular location in which a process happens ==== | ||
Biological process terms can be further specified by subcellular location. For example: ''plastid translational elongation'' | Biological process terms can be further specified by subcellular location. For example: ''plastid translational elongation'' | ||
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Also note that when using a GO ID in col 16, a redundant annotation should sometimes be added. See [[Annotation_Cross_Products#Guidelines]] | Also note that when using a GO ID in col 16, a redundant annotation should sometimes be added. See [[Annotation_Cross_Products#Guidelines]] | ||
== Function-Process-Component threesomes == | === Function-Process-Component threesomes === | ||
col5: GO Function ID | col5: GO Function ID | ||
Revision as of 06:36, 3 May 2012
Definition
p occurs_in c if and only if all of the participants of p are part_of c.
Child terms
- None.
Annotation Examples
Enhancing Molecular Function and Biological Process Annotations
Specifying the cell or tissue type in which a process happens
Examples of this usage of occurs_in can be found on the documentation page for Column_16:_Cell_Type
Specifying the subcellular location in which a process happens
Biological process 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. We should 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.
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 Annotation_Cross_Products#Guidelines
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