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 cell type information, e.g. the [http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell cell ontology] or the [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co plant 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== | ==Allowable relations for cell type annotation extensions== | ||
* [[part_of]] - Indicates a GO Cellular Component is part_of a specific cell type from | * [[part_of]] - Indicates a GO Cellular Component is part_of a specific cell type from a cell type ontology. | ||
* [[occurs_in]] - Indicates a GO Biological Process occurs_in a specific cell type from | * [[occurs_in]] - Indicates a GO Biological Process occurs_in a specific cell type from a cell type ontology. | ||
==Using | ==Using cell type ontologies to enhance Cellular Component annotations== | ||
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col 5: GO:0031966 | col 5: GO:0031966 | ||
col 16: part_of(CL:0000017) | col 16: part_of(CL:0000017) | ||
Or, if a gene product is located to the cell hair (GO:0070451) of a root hair cell (PO:0000256): | |||
col 5: GO:0070451 | |||
col 16: part_of(PO:0000256) | |||
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==Using | ==Using cell type ontologies to enhance Molecular Function and Biological Process annotations== | ||
===Specifying that a gene product is involved in a process in a specific cell type=== | ===Specifying that a gene product is involved in a process in a specific cell type=== | ||
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==Requesting new | ==Requesting new cell type ontology terms== | ||
If the cell type term you require does not exist, you can make a request on the [http://sourceforge.net/tracker/?group_id=76834&atid=925065 Cell Type Ontology SourceForge tracker]. | If the cell type term you require does not exist, you can make a request on the [http://sourceforge.net/tracker/?group_id=76834&atid=925065 Cell Type Ontology SourceForge tracker], or for plant cell types, on the [http://sourceforge.net/tracker/?group_id=76834&atid=835555 Plant Ontology SourceForge tracker]. |
Revision as of 07:24, 8 December 2010
This page describes the guidelines for using cell type information, e.g. the cell ontology or the plant 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 a cell type ontology.
- occurs_in - Indicates a GO Biological Process occurs_in a specific cell type from a cell type ontology.
Using cell type ontologies 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)
Or, if a gene product is located to the cell hair (GO:0070451) of a root hair cell (PO:0000256):
col 5: GO:0070451 col 16: part_of(PO:0000256)
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 cell type ontologies 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, or for plant cell types, on the Plant Ontology SourceForge tracker.