> For the complete documentation index, see [llms.txt](https://docs.biobox.io/guide/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.biobox.io/guide/data-packages/external-ontologies/gene-ontology.md).

# Gene Ontology

The Gene Ontology (GO) knowledge base is a curated database and ontology of gene function in biological systems. For more information, see [here](https://geneontology.org/docs/introduction-to-go).

The BioBox GO data package is an A-Box transformation of the latest version of GO. Each GO class belongs to 1 of 3 subsets:

* Molecular Function
* Biological Process
* Cellular Component

Each GO class that is included in this data package will become an Object under its corresponding Concept.

For example the GO term for nuclear lamina ([GO:0005652](https://amigo.geneontology.org/amigo/term/GO:0005652)) is a `cellular_component` and is represented in the data packaged as:

```json
{
    "_id": "GO:0005652",
    "labels": ["Object", "CellularComponent"],
    "properties": {
        "uuid": "GO:0005652",
        "displayName": "nuclear lamina",
        ...
    }
}
```

Additionally, we use GO annotations, to connect genes to ontology terms. How they are related depends on the nature of the association and may/may not have semantic meaning. They are represented in the relationships listed on this page.

## Concepts

### Biological Process

**Definition:** A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.

### Cellular Component

**Definition:** A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).

### Molecular Function

**Definition:** A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs

## Relationships

{% hint style="info" %}
Fragments listed below are valid BxQL statements! Copy and search them to see some results.
{% endhint %}

`(Gene)-> enables ->(MolecularFunction)`

`(Gene)-> located in ->(CellularComponent)`

`(Gene)-> involved in ->(BiologicalProcess)`

`(Gene)-> part of ->(CellularComponent)`

`(Gene)-> not enables ->(MolecularFunction)`

`(Gene)-> not involved in ->(BiologicalProcess)`

`(Gene)-> is active in ->(CellularComponent)`

`(Gene)-> not colocalizes with ->(CellularComponent)`

`(Gene)-> acts upstream of or within ->(BiologicalProcess)`

`(Gene)-> contributes to ->(MolecularFunction)`

`(Gene)-> not located in ->(CellularComponent)`

`(Gene)-> not part of ->(CellularComponent)`

`(Gene)-> acts upstream of positive effect ->(BiologicalProcess)`

`(Gene)-> not acts upstream of or within ->(BiologicalProcess)`

`(Gene)-> acts upstream of ->(BiologicalProcess)`

`(Gene)-> acts upstream of negative effect ->(BiologicalProcess)`

`(Gene)-> acts upstream of or within positive effect->(BiologicalProcess)`

`(Gene)-> acts upstream of within negative effect ->(BiologicalProcess)`

`(Gene)-> not contributes to ->(MolecularFunction)`

`(Gene)-> not acts upstream of or within negative effect ->(BiologicalProcess)`

`(Gene)-> not is active in ->(CellularComponent)`


---

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