Annotation: Column 16: Cell Type Annotation Extensions
This page gives guidelines for using cell type information, for example from the Cell Type Ontology or the Plant Ontology, in annotation extensions (column 16) of the gene association file format 2.0. It is a subset of the guidelines laid out in the GO wiki document Annotation Cross Products. The use of annotation extensions will be incremental, with cell type is the first vocabulary to be employed.
More general information on annotation can be found in the GO annotation guide.
Usage notes
- When including cell type information in column 16, no judgment is made as to whether a gene product is involved in a particular process in just a particular cell type or in all cell types. In other words, curators simply annotate all available data in a paper.
It is incorrect to assume that a gene product used in a GO annotation that has a cell type identifier in column 16 is involved in the curated process only in that annotated cell type. Similarly, it would be a mistake to conclude that lack of a cell type identifier in column 16 indicates that a given gene product is involved in a process in all cell types where it is found. The only correct interpretation of a GO annotation with a cell type identifier in column 16 is that in one particular experiment a given gene product was found to be involved in a particular process in a particular cell line. - An annotation cannot differ solely in the contents of column 16. This is because it will be optional for users to process this field. Therefore all information should be added to one line, and separate statements in column 16 should be separated by pipes (|). See multiple annotation extensions for cell type.
- Cell type location should not be inferred from investigations that use immortalized cell lines. Such cell lines should be treated as an experimental tool rather than an indication of the biological context of function. As the process of immortalization is known to involve multiple genetic changes a curator should never assume that the studied process is carried out in the equivalent normal cell type.
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
Annotations that specify the location of a gene product within a cell of a specific type are constructed by putting the part of relationship and the cell type ID in column 16, the annotation extension column. For example, a gene product located in the mitochondrial membrane (GO:0031966) in a spermatocyte (CL:0000017)
GO term: mitochondrial membrane ; GO:0031966
column 16: part of(CL:0000017)
Or a gene product is located to the cell hair (GO:0070451) of a plant root hair cell (PO:0000256):
GO term: cell hair ; GO:0070451
column 16: part of(PO:0000256)
Use cases
1. Toll-like receptor 4 (TLR4; UniProt:O00206) is located intracellularly in the perinuclear region of cytoplasm (GO:0048471) only in dendritic cells (CL:0000451), PMID:15027902
| DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Extension (Col 16) |
|---|---|---|---|---|
| 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
| DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Extension (Col 16) |
|---|---|---|---|---|
| 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, a gene product is involved in transcription (GO:0006350) in Purkinje cells (CL:0000121):
GO term: transcription ; GO:0006350
column 16: part of(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
| DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Extension (Col 16) |
|---|---|---|---|---|
| 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
| DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Extension (Col 16) |
|---|---|---|---|---|
| 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), where CL:0000056 is myoblast cell. This would indicate that the commitment to become a myoblast cell is occurring in the myoblast cell (CL:0000056); in fact, the commitment process occurs in a stem cell.
Multiple annotation extensions for cell type
For example, a publication describes 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
| DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Extension (Col 16) |
|---|---|---|---|---|
| 1234 | Theo | GO:0031966 | PMID:54321 | part of(CL:0000121)|part of(CL:0000103) |
Nb: there is no meaning attached to the order of identifiers in column 16.
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 or, for plant cell types, on the Plant Ontology SourceForge tracker.