Annotation Extension: Capturing cell and tissue types: Difference between revisions

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This page describes the guidelines for using the [http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell 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.
This page describes the guidelines for using the [http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell 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.


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!GO ID (Col 5)
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!GO ID (Col 5)
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!Reference (Col 6)
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!GO ID (Col 5)
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!Reference (Col 6)
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!GO ID (Col 5)
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Revision as of 07:13, 11 November 2010

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 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

So the annotation would be;

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: 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 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

So the annotation would be;

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), 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 16)
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.