Annotation Extension: Capturing cell and tissue types

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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 - Indicates a GO Molecular Function or GO Biological Process occurs in response to a specific cell type from the Cell Type (CL) Ontology.
  • 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 - Indicates a specific cell type's presence is required for a GO Molecular Function or GO Biological Process.
    • has_output - Indicates a specific cell type is affected by a GO Molecular Function or GO Biological Process.

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

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)

Specifying that a gene product is involved in a process that also involves a specific cell type

For example: If a gene product is involved in cell migration (GO:0001755 neural crest cell migration) of neural crest cells (CL:0000333):

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

N.B. The relationship here is has_output because the effect on the cell is the result of the process.

or if a gene product is involved in antigen presentation (GO:0002457 T cell antigen processing and presentation) on a T cell (CL:0000084):

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

N.B. The relationship here is has_input because the presence of the cell is necessary for the process to occur. If you are unsure whether the relationship should be has_input or has_output, you may use the generic has_participant which will be correct but less specific.

Specifying that a gene product is involved in a process that occurs in response to a particular cell type

For example: If a gene product is involved in killing (GO:0070947 neutrophil mediated killing of fungus) a fungus (CL:0000521):

 col 5: GO:0070947
 col 16: response_to(CL:0000521)

Use cases

1. 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)


2. 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 has_output(CL:0000071)


3. Mouse Icam1 (MGI:96392) is involved in antigen processing and presentation (GO:0002457) on T lymphocytes (CL:0000084), PMID:2479693

So the annotation would be;

DB (Col 2) Object (Col 3) GO ID (Col 5) Reference (Col 6) Extension (Col 17)
MGI:96392 Icam1 GO:0002457 PMID:2479693 has_input(CL:0000084)

4. Mouse Elane (MGI:2679229) is involved in neutrophil mediated killing of fungus (GO:0070947; CL:0000521), PMID:11907569

So the annotation would be;

DB (Col 2) Object (Col 3) GO ID (Col 5) Reference (Col 6) Extension (Col 17)
MGI:2679229 Elane GO:0070947 PMID:11907569 response_to(CL:0000521)


5. Mouse Ncf1 (MGI:97283) is involved in neutrophil mediated killing of gram-positive bacterium (GO:0070946; CL:0000520), PMID:11907569

So the annotation would be;

DB (Col 2) Object (Col 3) GO ID (Col 5) Reference (Col 6) Extension (Col 17)
MGI:97283 Ncf1 GO:0070946 PMID:11907569 response_to(CL:0000520)

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.