Merge pull request #642 from geneontology/pgaudet-patch-58

Update go-annotations.md

_docs/go-annotations.md

@@ -23,11 +23,11 @@ redirect_from:
 + How to access GO annotation data
   + [Download GO annotation files](#go-annotation-files)
   + [GO annotation file formats](#GO-annotation-file-formats)
+
 ---
-
 # Introduction to GO annotations
 
-GO annotations come in two flavors: **standard GO annotations** and **GO-CAM Models**.
+GO annotations come in two flavors: **[standard GO annotations](#standard-go-annotations)** and **[GO-CAM Models](#go-causal-activity-models)**.
 
 ### Standard GO annotations
 + A standard GO annotation is a statement that links a gene product and a GO term via a relation from the [Relations Ontology (RO)](https://www.ebi.ac.uk/ols4/ontologies/ro){:target="blank"}. In standard GO annotations, each statement is independent; this is a key difference between standard annotations and [GO-CAMs](#go-causal-activity-models). 
@@ -49,8 +49,8 @@ GO annotations come in two flavors: **standard GO annotations** and **GO-CAM Mod
 + GO adopts an open-world model, meaning that the absence of an annotation for a specific class does not imply that the gene product lacks that function, is not localized to that cellular component, or is uninvolved in that biological process. Moreover, if a gene product is unannotated, it does not mean that its role is unknown. Genes for which no role has been demonstrated are annotated to the root term (*molecular_function, biological_process, cellular_component*) with the evidence code ND ([No Biological Data available](https://wiki.geneontology.org/index.php/No_biological_Data_available_(ND)_evidence_code)).
 
 ---
-### Gene product to term relations
-+ Gene product to term ('gp2term') relations link gene products to GO terms in standard annotations via a relation from the [Relations Ontology (RO)](https://www.ebi.ac.uk/ols4/ontologies/ro){:target="blank"}..
+### Gene product to GO term relations
++ Gene product to GO term ('gp2term') relations explicitly link gene products to GO terms in standard annotations via a relation from the [Relations Ontology (RO)](https://www.ebi.ac.uk/ols4/ontologies/ro){:target="blank"}. 
 + Any of the relations can be associated with the modifer *NOT*. For the full list of permitted gp2term relations, see the [GO wiki](https://wiki.geneontology.org/Annotation_Relations#Standard_Annotation_Relations){:target="blank"}. The most common relations are:
 #### Relations between a gene product and a Molecular Function: 
  + *enables* links a gene product to a Molecular Function it executes. 
@@ -84,13 +84,16 @@ Contrary to positive annotations, *NOT* statements propagate *down* the ontology
 
 
 #### GO-CAM data model
-The primary unit of biological modeling in GO-CAM is a molecular activity, e.g. protein kinase activity, of a specific gene product or complex. A molecular activity is an activity carried out at the molecular level by a gene product; this is specified by a term from the GO MF ontology. GO-CAM models are thus connections of GO MF annotations enriched by providing the appropriate context in which that function occurs. All connections in a GO-CAM model, e.g. between a gene product and activity, two activities, or an activity and additional contextual information, are made using clearly defined semantic relations from the [Relations Ontology](https://obofoundry.org/ontology/ro.html){:target="blank"}. A more complete dscription of GO-CAM can be found in [Thomas & al 2019](https://www.ncbi.nlm.nih.gov/pubmed/31548717){:target="blank"}.
+
+The primary unit of biological modeling in GO-CAM is the **Activity Unit**, which consists of a molecular activity represented by a molecular function, the gene product that enables it, plus the context under which it occurs. This context includes the specific cellular component in which the molecular function takes place, in which larger biological process (biological program) that activity occurs, which in turn, can be nested inside an even larger biological process, and other biological context such as cell types and life cycle stages.
+
+Activity Units are connected to each other by **causal relations**, made using clearly defined semantic relations from the [Relations Ontology](https://obofoundry.org/ontology/ro.html){:target="blank"}. A more complete dscription of GO-CAM can be found in [Thomas & al 2019](https://www.ncbi.nlm.nih.gov/pubmed/31548717){:target="blank"}.
 
 #### Browsing and visualizing GO-CAMs
 GO-CAMs can be browsed and visualized at [http://geneontology.org/go-cam](https://geneontology.org/go-cam){:target="blank"}.
 
 ### Annotation Quality Control
-The GOC runs a number of [GO rules](https://github.com/geneontology/go-site/blob/master/metadata/rules/README.md) to ensure data integrity (for example, identifiers must be valid) that the annotations meet the GO curation guidelines. 
+The GOC runs a number of [GO rules](https://github.com/geneontology/go-site/blob/master/metadata/rules/README.md) to ensure data integrity and compliance with GO curation guidelines. For example, all identifiers must be valid; each annotation muct have an evidence and a references. 
 
 ---
 ### GO as a dynamic source of biological knowledge
@@ -101,17 +104,17 @@ GO aims to represent the current state of knowledge in biology, hence it is cons
 Overall [GO statistics](https://geneontology.org/stats.html) and [detailed statistics](https://current.geneontology.org/release_stats/index.html) are available. The statistics are also [achived](https://release.geneontology.org/).
 
 ---
-### GO annotation files
+### Downloading GO annotation files
 * Download [GO annotations by species](/docs/download-go-annotations/)
+<! --
 * Download [GO-CAM models](https://geneontology.org/go-cam){:target="blank"}
+-->
 
 ---
 ### GO annotation file formats
 * [Gene association file (GAF) 2.2](/docs/go-annotation-file-gaf-format-2.2/)
 * [Gene Product Association Data (GPAD) 2.0 files](/docs/gene-product-association-data-gpad-format-2.0/) + [Gene Product Information (GPI) 2.0 files](/docs/gene-product-information-gpi-format-2.0/): companion files
 
-* *(Deprecated)* [Gene association file (GAF) 2.1](/docs/go-annotation-file-gaf-format-2.1/)
-* *(Deprecated)* [Gene association file (GAF) 2.0](/docs/go-annotation-file-gaf-format-2.0/)
-* *(Currently being deprecated)* [Gene Product Association Data (GPAD) 1.1/1.2 files](/docs/gene-product-association-data-gpad-format-1.1/) + [Gene Product Information (GPI) 1.2 files](/docs/gene-product-information-gpi-format/): companion files
+* For older file formats, see [GO archives](/docs/go-archives.md#Deprecated-Annotation-formats)