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16 changes: 9 additions & 7 deletions _docs/ontology-documentation.md
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Expand Up @@ -37,13 +37,8 @@ Each of the three GO aspects is represented by a separate root ontology term. Mo

----

# The GO hierarchy
The GO is structured as a graph in which each GO term is a *node* and the relationships between the nodes are *edges*. GO is hierarchical, with *child* terms being more specialized than their *parent* terms, but unlike a strict hierarchy, a term may have more than one parent term (note that the parent/child model does not hold true for all types of relations, see the [relations documentation](/docs/ontology-relations/)). For example, the biological process term [hexose biosynthetic process](http://amigo.geneontology.org/amigo/term/GO:0019319){:target="blank"} has two parents, [hexose metabolic process](http://amigo.geneontology.org/amigo/term/GO:0019318){:target="blank"} and [monosaccharide biosynthetic process](http://amigo.geneontology.org/amigo/term/GO:0046364){:target="blank"}. This reflects the fact that *biosynthetic process* is a subtype of *metabolic process* and a *hexose* is a subtype of *monosaccharide*.

<img src="/assets/hexose-biosynthetic-process.png" width="450" height="450" />

# GO term elements
The different elements of a GO term are show in the image below (screen shot from the [AmiGO GO browser](https://amigo.geneontology.org/amigo/landing)).
The different elements of a GO term are show in the image below (screen shot from the [AmiGO GO browser](https://amigo.geneontology.org/amigo/landing)){:target="blank"}.

<img src="/assets/GO_term.png" width="950" height="450" />

Expand All @@ -58,7 +53,7 @@ Denotes which of the three sub-ontologies (MF, CC or BP) the term belongs to. Wr
A textual description of what the term represents, plus reference(s) to the source of the information.

### Relationships to other terms
How the term relates to other terms in the ontology. All terms (other than the root terms representing each aspect, above) have an *is a* sub-class relationship to another term. The Gene Ontology employs a number of other relations; the [relations documentation page](/docs/ontology-relations/) describes the relations used in the ontology.
How the term relates to other terms in the ontology. All terms (other than the root terms representing each aspect, above) have an *is a* sub-class relationship to another term. The Gene Ontology employs a number of other relations; the [relations documentation page](/docs/ontology-relations/) describes the relations used in the ontology. The GO hierarchy (see below) is built from these relations.

## Optional elements
### Secondary IDs (also known as Alternate ID)
Expand Down Expand Up @@ -87,6 +82,13 @@ Boolean value that indicates that the term has been deprecated and should not be

----

# The GO hierarchy
The GO is structured as a graph in which each GO term is a *node* and the relationships between the nodes are *edges*. GO is hierarchical, with *child* terms being more specialized than their *parent* terms, but unlike a strict hierarchy, a term may have more than one parent term (note that the parent/child model does not hold true for all types of relations, see the [relations documentation](/docs/ontology-relations/)). For example, the biological process term [hexose biosynthetic process](http://amigo.geneontology.org/amigo/term/GO:0019319){:target="blank"} has two parents, [hexose metabolic process](http://amigo.geneontology.org/amigo/term/GO:0019318){:target="blank"} and [monosaccharide biosynthetic process](http://amigo.geneontology.org/amigo/term/GO:0046364){:target="blank"}. This reflects the fact that *biosynthetic process* is a subtype of *metabolic process* and a *hexose* is a subtype of *monosaccharide*.

<img src="/assets/hexose-biosynthetic-process.png" width="450" height="450" />

----

# GO is a dynamic ontology
GO aims to represent the current state of knowledge in biology, hence it is constantly revised and expanded as biological knowledge accumulates. Revisions to the ontology are managed by a team of editors with broad biological knowledge and expertise in computational knowledge representation. GO updates are made collaboratively between the GOC ontology team and scientists who request the updates. Most requests come from scientists making GO annotations (these typically impact only a few terms each), and from domain experts in particular areas of biology (these typically revise an entire ‘branch’ of the ontology comprising many terms and relations). Changes to the ontology can be visualized on the [GO statistics](/stats.html) page. We welcome researchers and computational scientists to [submit requests for either new terms, new relations, or any other improvements to the ontology](/docs/contributing-to-go-terms/).

Expand Down