Annotation Extension: Capturing cell and tissue types: Difference between revisions
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* [[response_to]] | * [[response_to]] | ||
* [[has_participant]] - Indicates a specific cell type participates in a GO Molecular Function or GO Biological Process. 'has_participant' is the parent of 'has_input' and 'has_output'. | * [[has_participant]] - Indicates a specific cell type participates in a GO Molecular Function or GO Biological Process. 'has_participant' is the parent of 'has_input' and 'has_output'. | ||
* [[has_input]] | ** [[has_input]] | ||
* [[has_output]] | ** [[has_output]] | ||
N.B. If in doubt about which relation (has_input, has_output) to use, it is always possible to use the most generic relation, has_participant. Of course, this does not carry as much information but at least should be correct. | N.B. If in doubt about which relation (has_input, has_output) to use, it is always possible to use the most generic relation, has_participant. Of course, this does not carry as much information but at least should be correct. | ||
==Using the Cell Type Ontology to enhance Cellular Component annotations== | ==Using the Cell Type Ontology to enhance Cellular Component annotations== |
Revision as of 09:20, 12 October 2010
This page is under construction!
This page describes the guidelines for using the cell ontology in Column 16 (Annotation Extension) of the Gene Association File. It is a subset of the guidelines laid out in Annotation_Cross_Products. The use of Column 16 will be incremental, cell type is the first vocabulary to be rolled out.
Allowable relations for cell type annotation extensions
- part_of - Indicates a GO Cellular Component is part_of a specific cell type from the Cell Type (CL) Ontology.
- occurs_in - Indicates a GO Biological Process occurs_in a specific cell type from the Cell Type (CL) Ontology.
- response_to
- has_participant - Indicates a specific cell type participates in a GO Molecular Function or GO Biological Process. 'has_participant' is the parent of 'has_input' and 'has_output'.
N.B. If in doubt about which relation (has_input, has_output) to use, it is always possible to use the most generic relation, has_participant. Of course, this does not carry as much information but at least should be correct.
Using the Cell Type Ontology to enhance Cellular Component annotations
- Localization annotations can be enhanced by specifying the cell type which that cell component is part of
For example: If a gene product is located to the mitochondrial membrane in a spermatocyte:
col 5: GO:0031966 col 16: part_of(CL:0000017)
Use cases
1. Toll-like receptor 4 (TLR4) (O00206) is located intracellularly in the perinuclear region (GO:0048471) 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 17) |
---|---|---|---|---|
O00206 | TLR4 | GO:0048471 | PMID:15027902 | part_of(CL:0000451) |
2. TLR4 is located on the cell surface (GO:0005887) 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 17) |
---|---|---|---|---|
O00206 | TLR4 | GO:0005887 | PMID:15027902 | part_of(CL:0000576) |
Using the cell type ontology to enhance Molecular Function and Biological Process annotations
- Specifying the location in which a process happens
For example: If a gene product is involved in transcription in Purkinje cells(CL:0000121):
col 5: GO:0006350 col 16: occurs_in(CL:0000121)
- Specifying that a particular cell type is involved in a process
For example: If a gene product is involved in cell migration of neural crest cells (CL:0000333):
col 5: GO:0001755 col 16: has_output(CL:0000333)
or if a gene product is involved in antigen presentation on a T cell:
col 5: GO:0002457 col 16: has_input(CL:0000084)
Use cases
1. Human angiopoietin-1 (Q15389) is involved in positive chemotaxis (GO:0050918) in blood vessel endothelial cells (CL:0000071), PMID:19424712
So the annotation would be;
DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Extension (Col 17) |
---|---|---|---|---|
Q15389 | ANGPT1 | GO:0050918 | PMID:19424712 | occurs_in(CL:0000071) |
2. Human SLC22A5 (O76082) is involved in quorum sensing involved in interaction with host (GO:0052106) in colonic epithelial cells (CL:0000066), PMID:18005709
So the annotation would be;
DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Extension (Col 17) |
---|---|---|---|---|
O76082 | SLC22A5 | GO:0052106 | PMID:18005709 | occurs_in(CL:0000066) |
Multiple annotation extensions for cell type
The publication may describe the localization of a gene product in two or more distinct cell types
For example: Theoretical gene 1234 is located in the mitochondrial membrane (GO:0031966) of Purkinje cells (CL:0000121) and bipolar neurons (CL:0000103), PMID:54321
So the annotation would be;
DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Extension (Col 17) |
---|---|---|---|---|
1234 | Theo | GO:0031966 | PMID:54321 | part_of(CL:0000121)|part_of(CL:0000103) |
Requesting new Cell Type Ontology terms
If the cell type term you require does not exist, you can make a request on the Cell Type Ontology SourceForge tracker.