Part of - deprecated: Difference between revisions
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==Definition== | |||
A [[part_of]] B means that ''every'' A is [[part_of]] ''some'' B. | |||
For example: nucleus [[part_of]] cell | For example: nucleus [[part_of]] cell | ||
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[[Category:Reasoning]] | [[Category:Reasoning]] | ||
==Annotation Examples== | |||
== Enhancing Cell Component Annotations == | === Enhancing Cell Component Annotations === | ||
=== Localization === | ==== Localization ==== | ||
===Specifying that a gene product is located in a cellular component of a specific cell type=== | ====Specifying that a gene product is located in a cellular component of a specific cell type==== | ||
Examples of these usages of part_of can be found on the documentation page for [[Column_16:_Cell_Type]] | 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 == | === Enhancing Molecular Function and Biological Process Annotations === | ||
=== Specifying the developmental stage at which a process occurs === | ==== 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). | 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). | ||
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col16: part_of(ZFS:0000023) | col16: part_of(ZFS:0000023) | ||
=== Functions carried out as part of a process === | ==== 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) | We use the [[part_of]] relation to link function and process (this relation is already used for the inter-ontology links) | ||
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This is harmless but pointless, because we know that kinase activity is part_of phosphorylation from gene_ontology_ext | This is harmless but pointless, because we know that kinase activity is part_of phosphorylation from gene_ontology_ext | ||
== Function-Process-Component threesomes == | === Function-Process-Component threesomes === | ||
col5: GO Function ID | col5: GO Function ID | ||
Revision as of 07:24, 3 May 2012
Definition
A part_of B means that every A is part_of some B.
For example: nucleus part_of cell
Contrast with has_part
Annotation Examples
Enhancing Cell Component Annotations
Localization
Specifying that a gene product is located in a cellular component of a specific cell type
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