Annotation Extension: Capturing cell and tissue types
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.
Using the Cell Type Ontology to enhance Cellular Component annotations
Specifying that a gene product is located in a cellular component of a specific cell type
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 that a gene product is involved in a process in a specific cell type
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)
Use cases
1. Human SLC22A5 (UniProtKB: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 Wnt7a (UniProtKB:O00755) is involved in positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054) in corneal epithelial cells (CL:0000575), PMID:15802269
So the annotation would be;
DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Extension (Col 17) |
---|---|---|---|---|
O00755 | Wnt7a | GO:0060054 | PMID:15802269 | occurs_in(CL:0000575) |
Exception
One exception to using the occurs_in relationship for enhancing Biological Process annotations is when annotating a gene product to terms such as '<X> cell fate commitment'. The commitment actually occurs in a stem cell before 'X cell' forms. For example, an annotation to 'myoblast cell fate commitment' should not have the annotation extension: occurs_in(CL:0000056), which indicates that the commitment to become a myoblast cell is occuring in the myoblast cell (CL:0000056) as, in fact, it is occuring in a stem cell.
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.