Annotation Guidelines

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 This is the new Annotation Guidelines page (to be completed & reviewed)

New proposed index page: https://docs.google.com/document/d/1UlAsmGOrEbpOaKlCApzdbvt48D_EMgA5gho5ptfTSvE/edit#

Need to include this information: https://docs.google.com/document/d/1DS2ObQc1EVcQKAHjKNt-0jzFCSSVLDQ4Osm-1dsTwdA/edit

General introduction to GO annotation

A general introduction to the Gene Ontology and [GO annotations is available on the GO website.  

Standard GO annotations are defined as an association between a gene and a biological concept from one of the three GO aspects: Molecular Function (MF), Biological Process (BP), and Cellular Component (CC). Standard annotations always contain a reference (either a published, peer-reviewed paper or internal GO reference) and an  Evidence Code that indicates the type of experiment or method used to make the assertion.

  • Annotation extensions. Standard GO annotations may further be qualified using annotation extensions that provide additional biological context to a GO term using a relation from the Relations Ontology (RO) and a term from GO or an external ontology, e.g. UBERON.
  • Unknown MF, BP, CC. If any aspect is unknown, an annotation should be made to the root term. This means that the gene has some molecular function, that is part of some biological process that occurs in some cellular component, but one or more of these aspects may not be known.

Causal Activity Models (GO-CAM Models) provide link activities performed by gene products in a causal framework, using relations from the Relations Ontology RO relations. GO-CAMs link GO annotations together with biological entities and external ontology terms to model how a gene functions in the broader context of a biological process or pathway. GO-CAMS thus provide structured descriptions of biological systems and allow for interrogation of causal events in biology through use of clearly defined, and consistently applied, semantics. A summary of the GO-CAM model specifications is presented in Figure 1.

  • Activity Unit. The basic unit of a GO-CAM model is the Activity Unit, outlined in Figure 1, which represents a set of standard GO annotations with select annotation extensions, e.g. the inputs and outputs of a molecular function. GO-CAM models are constructed by filling in as many pieces of relevant information in an Activity Unit as possible and then linking different Activity Units in a causal chain to model a biological process. Thus, GO-CAM models use standard GO annotations as the foundation on which to build more comprehensive representations of biology.
Figure 1. GO-CAM Model Specifications

Noctua: the Gene Ontology's GO Annotation Tool Suite

THIS SECTION TO BE MOVED TO Noctua documentation from Help in Noctua Editor

Noctua is a web-based annotation tool developed by the GO Consortium. Noctua can be used to create standard GO annotations as well as GO-CAMs (Gene Ontology Causal Activity Models) in a collaborative manner, i. e. multiple users can work on the same model at the same time.

Getting started with Noctua

GO-CAMs can be browsed using Noctua, but no annotations can be created or edited unless a user is logged in with a registered account.

User Account Setup

  • To create a new account, please email help@geneontology.org or enter a ticket on the helpdesk repo in github.
  • Note that to create a Noctua account, you will need an ORCID and a github account.
  • If you have any questions about user accounts, please contact help@geneontology.org

Login

  • To log in, click on the Login button in the upper right corner of the landing page.
  • On the resulting page click on "Sign in with Github."
  • When your identity has been authenticated, press the "Return" button to return to the Noctua landing page.

Noctua Curation interfaces

Noctua has four curation interfaces suited for

  • The Pathway Editor is designed for curating GO-CAM models, i.e. models that include at least two activities/MFs linked by causal relations.
  • The Form Editor is a structured annotation form that is recommended for creating 'standard' GO annotations.
  • The Graph Editor is a generic tool to link individual annotations and is only recommended for advanced uses.
  • The Annotation Review tool serves to do bulk updates on annotations.


Accessing, browsing and searching GO-CAMs
Topic Status Last reviewed
Browsing and searching annotations and models To be reviewed
Noctua Curation interfaces
Visual Editor Current 2022-05-05
Form Editor Draft
Graph Editor Draft
Annotation Review Tool Current 2021-05-26
Form Editor Molecular Function
Biological Process
Cellular Component
Graph Editor Molecular Function
Biological Process
Cellular Component
Adding contextual information (annotation extensions)
Form Editor Molecular Function
Biological Process
Cellular Component
Graph Editor Molecular Function
Biological Process
Cellular Component
Editing annotations
Form Editor
Graph Editor
Creating GO-CAMs
Creating an activity unit Form Editor
Graph Editor
Linking Activities Form Editor
Graph Editor
Model metadata
Model titles General Guidelines
Graph Editor
Releasing models to production Form Editor Form Editor]
Graph Editor
Other tips and tricks Adding a NOT qualifier to an annotation
Importing existing annotations
Changing annotation group
Model validation
Running the reasoner
Viewing GPAD export]
Using templates

External ontologies for annotation

 from http://wiki.geneontology.org/index.php/Noctua#Ontologies_for_Annotation
  • To provide appropriate biological context to an annotation or an activity unit, additional ontologies may be used either in GO-CAM or in annotation extensions [link].

Cell and Anatomy Ontologies

  • Describes the location where processes and functions occur.
  • Describes the location of a GO cellular component.
  • Add list

Biological Phase and Life Stage Ontologies

  • Describes the temporal period during which processes and functions occur.
  • Describes the temporal period during which a cellular component or anatomical entity exists.
  • Add list

Chemical Ontology (ChEBI) [link]

  • Can be used to capture inputs and outputs of processes and functions.
  • GO-CAM uses the Chemical Entities of Biological Interest (ChEBI)
  • Sequence Ontology [link]


 TO INCLUDE SOMEWHERE (1)
[Noctua_Manual:_General_Guidelines_for_Model_Titles]



 TO INCLUDE SOMEWHERE (2)
GO-CAM annotation workflow
 The ultimate goal for GO-CAMs is to create a knowledge graph whereby users can use the GO to traverse a causal representation of a biological system. To that end, curators should try, as much as possible, to make individual annotations in the context of the overall process being modeled. See also Tips_to_Produce_High_Quality_Annotations.
 It can be very helpful to refer to a summary figure from a recent research article or review to help visualize a potential GO-CAM.
 When making a GO-CAM model, we suggesting these steps:
 * What are the main activities (MFs) of each of the gene products in a model?
 * How do those activities relate, in a causal chain, to each other?
 * What processes are those activities involved in?
 * Where do the activities occur?
 Even when annotating a single paper, try to incorporate as much of this workflow as possible. This will make it easier, in the future, to build on existing models with new curation.

Review Status

Draft: 2021-02-28 Patrick Masson, Pascale Gaudet

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