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Overview
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The Cell Ontology (CL) is a structured controlled vocabulary that describes a broad range of canonical biological cell types. The CL is not organism-specific, covering cell types from prokaryotes to mammals, but excludes plant cell types. The Cell Ontology is an OBO Foundry ontology and is available at: https://obofoundry.org/ontology/cl.html
The Cell Ontology Browser can be used to find and view descriptions of cell types, and to retrieve expression data associated with those cell types.
This help document answers the following questions about the Browser:
How is the Cell Ontology organized?
The CL organizes cell type classes into a directed acyclic graph (DAG) composed exclusively of a "is a" relationships.
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What can I find in the Cell Ontology Browser?
Use the Browser to find standardized vocabulary terms for cell types found in animals.
You can either browse or search for cell type terms from the Cell Ontology Browser entry page.
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How do I browse the vocabulary?
To browse the vocabulary, click on terms in the Cell Ontology Tree View on the Cell Ontology Browser page. This shows a term's place in the hierarchy, and updates the Cell Ontology Term Detail section of the page with the selected term's parent terms and ID. Click on cell type terms to navigate progressively through the ontology in order to locate specific terms. In the Cell Ontology Tree View, a black triangle at the beginning of a term indicates the term has subterms. You can expand branches by clicking on a term or its preceding triangle. If you click on a term, this also updates the Term Detail section. You can collapse branches by clicking on the downward-pointing triangle. You can click on the triangles to navigate the branches without updating the Term Detail section.
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How do I search the vocabulary?
The Cell Ontology Search field accepts any text string and searches for all terms containing that string plus any synonyms.
You can search by cell type to find a particular cell type in the Cell Ontology and to see, in the Tree View section, the cell type hierarchy. To do this:
- Begin typing a cell type of interest and an autocomplete list activates on the second character.
- The list shows all the cell type terms and their synonyms that match your search characters.
- You can type the beginnings of multiple terms to narrow the list (example: emb fib will limit the list to embryonic fibroblast).
- You must select a term. There is no free text searching in this field.
- You can only select one term.
- Enter a search term or CL accession identifier in the Search field.
- As you type, an autocomplete will display a list of terms matching the text string you have entered. You can select a term from the autocomplete list or continue entering text.
- Use the return/enter key on your keyboard to activate a search. The search finds all terms that contain any of your search terms and displays a list of those cell types.
- If you are uncertain which terms to use for the most effective searching, browse the ontology to see the standardized terms.
Select a term in your search results to automatically update the Cell Ontology Term Detail and Cell Ontology Tree View sections on the right. Use the Clear button to start a new search.
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How do I interpret the results?
| Cell Type Search |
The search finds all cell types with names containing any of your search terms and displays a ranked list of those cell type terms. Click on a term to update the Term Detail and Tree View sections of the page with the selected term highlighted in gold. |
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| Cell Type Term Detail |
| Term |
The selected cell type term is highlighted in gold. If you accessed this page by following a link on another page, the appropriate cell type is highlighted. Otherwise, before you initiate a search or browse, the default term 'cell' which is at the top of the hierarchy is highlighted. |
| Synonyms |
Alternative term(s) used to represent the cell type, provided by Cell Ontology editors. |
| Definition |
Textual description for the selected cell type provided by the Cell Ontology editors. |
| Parent Terms |
Immediate parent terms for the selected cell type. Since the Cell Ontology is built on a DAG framework, a term may have more than one parent term. |
| ID |
Unique accession ID for the selected cell type term. |
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| Cell Type Tree View |
The selected term is presented in the context of a classification hierarchy. You can collapse or expand branches by clicking on a term. A black triangle at the beginning of a term indicates the term has subterms. When you select a new term, it is highlighted in gold and the Term Detail section is updated.
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How do I interpret the gene expression results of my search?
When you click on the number of expression results in the Cell Type Tree View, a search returns all gene expression data, images and assay details annotated to the selected structure. See Interpreting Gene Expression Data Query Results for more information about the results.
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Using the Cell Ontology Browser