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Update go-annotations.md
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@@ -21,7 +21,7 @@ redirect_from:
GO annotations come in two flavors: **standard GO annotations** and **GO-CAM 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)](http://www.obofoundry.org/ontology/ro.html){: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).
+ 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).
+ A standard GO annotation minimally contains:
+ a gene product; may be a protein, an miRNA, a tRNA, etc.
+ a [GO term](/docs/ontology-documentation/)
@@ -35,13 +35,13 @@ GO annotations come in two flavors: **standard GO annotations** and **GO-CAM Mod
+ **Molecular Function**: the *normal* molecular activity of a gene product; mutants and roles in disease are outside the scope for GO
+ **Biological Process**: the pathways and larger processes to which the gene product's activity contributes
+ **Cellular Component**: where the gene product is located when the activity occurs
+ By the transitivity principle, an annotation to a GO term implies annotation to all its parents (also known as superclasses).
+ By the transitivity principle, an annotation to a GO term implies annotation to all its *is a* and *part of* parents (also known as superclasses). Details about the ontology structure can be found on the [Gene Ontology overview page](/docs/ontology-documentation/).
+ GO annotations are meant to reflect the most up-to-date understanding of a gene product's role. As biological knowledge advances, annotations for a particular gene product may be updated to align with new insights or adjustments in the ontology.
+ 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 relations
+ Gene product to term relations ('gp2term') relations link gene products to GO terms in standard annotations.
+ 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"}..
+ 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.
@@ -61,7 +61,7 @@ The *NOT* statement indicates that the gene product *does NOT* enable a Molecula

Both positive and NOT statements can be used between a single gene product and a GO term when there is unresolved conflicting experimental findings in the literature. If an isoform has a different function from the main isoform represented by the gene-centric entity, a NOT annotation can be captured together with the isoform identifier.

Contrary to positive annotations, *NOT* statements propagate *down* the ontology to more specific terms, such that the annotation `gene product` `NOT|enables` `protein kinase activity` means that the gene product does not enable `protein kinase activity`, and neither does it enable and more specific functions, such as protein serine/threonine kinase activity and protein tyrosine kinase activity.
Contrary to positive annotations, *NOT* statements propagate *down* the ontology to more specific terms, such that the annotation *gene product* *NOT|enables* *protein kinase activity* means that the gene product does not enable *protein kinase activity`* and neither does it enable more specific functions, such as p*rotein serine/threonine kinase activity* and *protein tyrosine kinase activity*.

---
### GO-Causal Activity Models
@@ -71,14 +71,17 @@ Contrary to positive annotations, *NOT* statements propagate *down* the ontology
+ **Molecular Function**: substrates ("input"), products ("output"), activators, inhibitors
+ **Biological Process**: the broader process that the molecular function helps accomplish: cell cycle transition, transcription, signaling pathways, etc. Processes can be nested, i. e., a biological process can be part of another biological process. For example, a signaling pathway can be part of a developmental process, like the [Wnt signaling pathway](https://amigo.geneontology.org/amigo/term/GO:0016055){:target="blank"} is part of [dorsal/ventral pattern formation](https://amigo.geneontology.org/amigo/term/GO:0009953){:target="blank"}.
+ **Cellular Component**: the cellular component, cell, and/or tissue the function/process take place.
+ See the [GO-CAM example](http://model.geneontology.org/5323da1800000002){:target="blank"} for an illustration.
+ See the [GO-CAM example]([http://model.geneontology.org/](https://model.geneontology.org/5323da1800000002){:target="blank"} for an illustration.

#### 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"}.

#### 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.

---
### GO as a dynamic source of biological knowledge
GO aims to represent the current state of knowledge in biology, hence it is constantly revised and expanded as biological knowledge accumulates. With the ever-increasing number of published articles, experiments and methods, covering all biology with the latest annotations is always challenging. We therefore invite researchers and computational scientists to [submit requests for missing, erroneous or out-of-date annotations to improve the GO database](/docs/contributing-to-go/).

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