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

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* [[response_to]]
* [[response_to]]
* [[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_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]]
** [[has_input]]
* [[has_output]]
** [[has_output]]
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.  
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==
==Using the Cell Type Ontology to enhance Cellular Component annotations==

Revision as of 09:20, 12 October 2010

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
  • 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'.

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 in a spermatocyte:

 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) 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:0005887) 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:0005887 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 in Purkinje cells(CL:0000121):

 col 5: GO:0006350
 col 16: occurs_in(CL:0000121)
  • Specifying that a particular cell type is involved in a process

For example: If a gene product is involved in cell migration of neural crest cells (CL:0000333):

 col 5: GO:0001755
 col 16: has_output(CL:0000333)

or if a gene product is involved in antigen presentation on a T cell:

 col 5: GO:0002457
 col 16: has_input(CL:0000084)


Use cases

1. 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 occurs_in(CL:0000071)

2. 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)


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.