Merge pull request #688 from geneontology/suzialeksander-patch-254024

Update ontology-documentation.md

_docs/ontology-documentation.md

@@ -17,32 +17,33 @@ redirect_from:
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 # Gene Ontology overview
-The Gene Ontology (GO) is a structured, standardized representation of biological knowledge. GO descibes concepts (also known as terms, or formally, *classes*) that are connected to each other via formally defined [relations](/docs/ontology-relations/){:target="blank"}. The GO is designed to be species-agnostic, to enable the annotation of gene products across the entire tree of life. The computational framework of the GO enables consistent genes annotation, comparison of functions across organisms, and integration of knowledge across diverse biological databases. 
+The Gene Ontology (GO) is a structured, standardized representation of biological knowledge. GO describes concepts (also known as terms, or formally, *classes*) that are connected to each other via formally defined [relations](/docs/ontology-relations/){:target="blank"}. The GO is designed to be species-agnostic to enable the annotation of gene products across the entire tree of life. The computational framework of the GO enables consistent gene annotation, comparison of functions across organisms, and integration of knowledge across diverse biological databases. 
 
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 # GO aspects
-The GO is organized in three *aspects*, Molecular Function (MF), Cellular Component (CC) and Biological Process (BP). 
+The GO is organized in three *aspects*: Molecular Function (MF), Cellular Component (CC), and Biological Process (BP). 
 ### Molecular Function
-MF represent molecular-level activities performed by gene products, such as "catalysis" or "transcription regulator activity". MFs correspond to activities that can be performed by individual gene products (*i.e.* a protein or RNA), but some activities are performed by molecular complexes composed of multiple gene products, when the activity cannot be ascribed to a single gene product of the complex. Examples of broad functional terms are *[catalytic activity](http://amigo.geneontology.org/amigo/term/GO:0003824){:target="blank"}* and *[transporter activity](http://amigo.geneontology.org/amigo/term/GO:0005215){:target="blank"}*; examples of narrower functional terms are *[adenylate cyclase activity](http://amigo.geneontology.org/amigo/term/GO:0004016){:target="blank"}* or *[insulin receptor activity](http://amigo.geneontology.org/amigo/term/GO:0005009){:target="blank"}*. 
+MFs represent molecular-level activities performed by gene products, such as "catalysis" or "transcription regulator activity". MFs correspond to activities that can be performed by individual gene products (*i.e.* a protein or RNA), but some activities are performed by molecular complexes composed of multiple gene products, when the activity cannot be ascribed to a single gene product of the complex. Examples of broad functional terms are *[catalytic activity](http://amigo.geneontology.org/amigo/term/GO:0003824){:target="blank"}* and *[transporter activity](http://amigo.geneontology.org/amigo/term/GO:0005215){:target="blank"}*; examples of more specific functional terms are *[adenylate cyclase activity](http://amigo.geneontology.org/amigo/term/GO:0004016){:target="blank"}* or *[insulin receptor activity](http://amigo.geneontology.org/amigo/term/GO:0005009){:target="blank"}*. 
 
-Note that GO MF terms represent *activities* and not the *entities* that perform the actions. To avoid confusion between gene product names and their molecular activities, GO MFs are appended with the word "activity" (a *protein kinase* would have the GO MF *protein kinase activity*). Finally, MFs do not specify where, when, or in what context the action takes place. 
+GO MF terms represent *activities* and not the *entities* that perform the actions. To avoid confusion between gene product names and their molecular activities, GO MFs are appended with the word "activity" (a *protein kinase* would have the GO MF *protein kinase activity*). Finally, MFs do not specify where, when, or in what context the action takes place. 
 
 ### Cellular Component
-CC serves to capture the cellular location where a molecular function takes place. It includes: 
-+ *[cellular anatomical structures](http://amigo.geneontology.org/amigo/term/GO:0110165){:target="blank"}*, emcompassing cellular entities such as the *[plasma membrane](http://amigo.geneontology.org/amigo/term/GO:0005886){:target="blank"}* and the *[cytoskeleton](http://amigo.geneontology.org/amigo/term/GO:0005856){:target="blank"}*, as well as membrane-enclosed cellular compartments such as the *[mitochondrion](http://amigo.geneontology.org/amigo/term/GO:0005739){:target="blank"}*.  
+CC serves to capture the cellular location where a molecular function takes place. CCs include: 
++ *[cellular anatomical structures](http://amigo.geneontology.org/amigo/term/GO:0110165){:target="blank"}*, encompassing cellular entities such as the *[plasma membrane](http://amigo.geneontology.org/amigo/term/GO:0005886){:target="blank"}* and the *[cytoskeleton](http://amigo.geneontology.org/amigo/term/GO:0005856){:target="blank"}*, as well as membrane-enclosed cellular compartments such as the *[mitochondrion](http://amigo.geneontology.org/amigo/term/GO:0005739){:target="blank"}*.  
 + stable *[protein-containing complexes](http://amigo.geneontology.org/amigo/term/GO:0032991){:target="blank"}* of which they are parts. 
 + *[virion components](http://amigo.geneontology.org/amigo/term/GO:0044423){:target="blank"}*, classified separately because viruses are not cellular organisms. Examples include *[viral capsid](http://amigo.geneontology.org/amigo/term/GO:0019028){:target="blank"}* and *[viral envelope](http://amigo.geneontology.org/amigo/term/GO:0019031){:target="blank"}*.
 
 ### Biological Process
 BPs are the larger processes or ‘biological programs’ accomplished by the concerted action of multiple molecular activities. Examples of broad BP terms are *[DNA repair](http://amigo.geneontology.org/amigo/term/GO:0006281){:target="blank"}* or *[signal transduction](http://amigo.geneontology.org/amigo/term/GO:0007165){:target="blank"}*. Examples of more specific terms are *[cytosine biosynthetic process](http://amigo.geneontology.org/amigo/term/GO:0046089){:target="blank"}* or *[D-glucose transmembrane transport](http://amigo.geneontology.org/amigo/term/GO:1904659){:target="blank"}*. 
 
+## Root Terms
 Each of the three GO aspects is represented by a separate root ontology term. Moreover, the three GO aspects are *is a disjoint*, meaning that no *is a* relation exists between terms from the different ontology aspects. However, other relationships such as *part of* and *occurs in* can operate between terms from different GO aspects. For example, the MF term *[cyclin-dependent protein kinase activity](http://amigo.geneontology.org/amigo/term/GO:0097472){:target="blank"}* is *part of* the BP *[regulation of cell cycle](http://amigo.geneontology.org/amigo/term/GO:0051726){:target="blank"}*.
 
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 # 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/){:target="blank"}). 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*.
+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/){:target="blank"}). 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" />
 
@@ -80,6 +81,3 @@ The different elements of a GO term are show in the image below (screen shot fro
 
 # 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){:target="blank"} 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/){:target="blank"}.
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