Merge pull request #678 from geneontology/pgaudet-patch-82

Update ontology-documentation.md

_docs/ontology-documentation.md

@@ -13,7 +13,7 @@ redirect_from:
 ---
 
 # 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/). 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 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. 
 
 ----
 
@@ -38,7 +38,7 @@ 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*.
+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" />
 
@@ -65,17 +65,17 @@ The different elements of a GO term are show in the image below (screen shot fro
   + **Related**: the terms are related in some imprecise way; for e.g. *cytochrome bc1 complex* is a related synonym of *ubiquinol-cytochrome-c reductase activity*; *virulence* is a related synonym of *pathogenesis*.
   + **Custom synonym** types are also used in the ontology. For example, a number of synonyms are designated as systematic synonyms; synonyms of this type are exact synonyms of the term name.
 * **Comment**: Any extra information about the term and its usage.
-* **Chem. react.**: For terms having cross references to the [RHEA database of chemical reactions](https://www.rhea-db.org/), this section lists the reaction paticipants.
-* **Subset**: Indicates that the term belongs to one or more [GO subsets](/docs/go-subset-guide/).
+* **Chem. react.**: For terms having cross references to the [RHEA database of chemical reactions](https://www.rhea-db.org/){:target="blank"}, this section lists the reaction paticipants.
+* **Subset**: Indicates that the term belongs to one or more [GO subsets](/docs/go-subset-guide/){:target="blank"}.
 * **Obsolete tag**: Boolean value that indicates that the term has been deprecated and should not be used. A GO term is obsoleted when it is out of scope, misleadingly named or defined, or describes a concept that would be better represented in another way and needs to be removed from the published ontology. In these cases, the term and ID still persist in the ontology, but the term is tagged as obsolete, and all relationships to other terms are removed. A comment is added to the term detailing the reason for the obsoletion and replacement terms are suggested whenever possible.
-* **[Taxon constraints](/docs/taxon-constraints/)**: Annotations to some GO terms are restricted to specific species; the taxon constraints specify which taxa a term can be applied to. 
-* **[Database cross-references](/docs/download-mappings/)**: Database cross-references, or dbxrefs, refer to identical or very similar objects in other databases. For instance, the molecular function term *[cytosine deaminase activity](http://amigo.geneontology.org/amigo/term/GO:0004131)*{:target="blank"} is cross-referenced to [RHEA:20605](https://www.rhea-db.org/reaction.xhtml?id=20605){:target="blank"}; the biological process term [sulfate assimilation](http://amigo.geneontology.org/amigo/term/GO:0000103){:target="blank"} has the [InterPro](https://www.ebi.ac.uk/interpro/){:target="blank"} cross-reference [Sulphate adenylyltransferase (IPR002650)](https://www.ebi.ac.uk/interpro/entry/IPR002650){:target="blank"}. Database cross-references are visible from the tab at the bottom of the term description (as shown in screenshot below).
+* **[Taxon constraints](/docs/taxon-constraints/){:target="blank"}**: Annotations to some GO terms are restricted to specific species; the taxon constraints specify which taxa a term can be applied to. 
+* **[Database cross-references](/docs/download-mappings/){:target="blank"}**: Database cross-references, or dbxrefs, refer to identical or very similar objects in other databases. For instance, the molecular function term *[cytosine deaminase activity](http://amigo.geneontology.org/amigo/term/GO:0004131)*{:target="blank"} is cross-referenced to [RHEA:20605](https://www.rhea-db.org/reaction.xhtml?id=20605){:target="blank"}; the biological process term [sulfate assimilation](http://amigo.geneontology.org/amigo/term/GO:0000103){:target="blank"} has the [InterPro](https://www.ebi.ac.uk/interpro/){:target="blank"} cross-reference [Sulphate adenylyltransferase (IPR002650)](https://www.ebi.ac.uk/interpro/entry/IPR002650){:target="blank"}. Database cross-references are visible from the tab at the bottom of the term description (as shown in screenshot below).
 <img width="538" alt="fumarate reductase (NADH) activity xrefs" src="https://github.com/user-attachments/assets/aef80afa-2ecd-4225-ad4d-22a07fdd549d">
 
 ----
 
 # 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/).
+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"}.