Annotation Extension: Capturing cell and tissue types
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.