Annotation Extension: Capturing cell and tissue types: Difference between revisions
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col 16: has_input(CL:0000084) | col 16: has_input(CL:0000084) | ||
N.B. The relationship here is has_input because the presence of the cell is necessary for the process to occur. | N.B. The relationship here is has_input because the presence of the cell is necessary for the process to occur. If you are unsure whether the relationship should be has_input or has_output, you may use the generic has_participant which will be correct but less specific. | ||
* Specifying that a process or function occurs in response to a particular cell type. | * Specifying that a process or function occurs in response to a particular cell type. |
Revision as of 06:05, 14 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 - Indicates a GO Molecular Function or GO Biological Process occurs in response to a specific cell type from the Cell Type (CL) Ontology.
- 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 - Indicates a specific cell type's presence is required for a GO Molecular Function or GO Biological Process.
- has_output - Indicates a specific cell type is affected by a GO Molecular Function or GO Biological Process.
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 (GO:0031966) in a spermatocyte (CL:0000017):
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 perinuclear region of cytoplasm) 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:0009986) 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:0009986 | 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 (GO:0006350) in Purkinje cells (CL:0000121):
col 5: GO:0006350 col 16: occurs_in(CL:0000121)
- Specifying that a particular cell type participates in a process
For example: If a gene product is involved in cell migration (GO:0001755 neural crest cell migration) of neural crest cells (CL:0000333):
col 5: GO:0001755 col 16: has_output(CL:0000333)
N.B. The relationship here is has_output because the effect on the cell is the result of the process.
or if a gene product is involved in antigen presentation (GO:0002457 T cell antigen processing and presentation) on a T cell (CL:0000084):
col 5: GO:0002457 col 16: has_input(CL:0000084)
N.B. The relationship here is has_input because the presence of the cell is necessary for the process to occur. If you are unsure whether the relationship should be has_input or has_output, you may use the generic has_participant which will be correct but less specific.
- Specifying that a process or function occurs in response to a particular cell type.
For example: If a gene product is involved in killing (GO:0070947 neutrophil mediated killing of fungus) a fungus (CL:0000521):
col 5: GO:0070947 col 16: response_to(CL:0000521)
Use cases
1. 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) |
2. 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 | has_output(CL:0000071) |
3. Mouse Icam1 (MGI:96392) is involved in antigen processing and presentation (GO:0002457) on T lymphocytes (CL:0000084), PMID:2479693
So the annotation would be;
DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Extension (Col 17) |
---|---|---|---|---|
MGI:96392 | Icam1 | GO:0002457 | PMID:2479693 | has_input(CL:0000084) |
4. Mouse Elane (MGI:2679229) is involved in neutrophil mediated killing of fungus (GO:0070947; CL:0000521), PMID:11907569
So the annotation would be;
DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Extension (Col 17) |
---|---|---|---|---|
MGI:2679229 | Elane | GO:0070947 | PMID:11907569 | response_to(CL:0000521) |
5. Mouse Ncf1 (MGI:97283) is involved in neutrophil mediated killing of gram-positive bacterium (GO:0070946; CL:0000520), PMID:11907569
So the annotation would be;
DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Extension (Col 17) |
---|---|---|---|---|
MGI:97283 | Ncf1 | GO:0070946 | PMID:11907569 | response_to(CL:0000520) |
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.