Annotation Guidelines: Difference between revisions
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==Noctua: the Gene Ontology's GO Annotation Tool Suite== | ==Noctua: the Gene Ontology's GO Annotation Tool Suite== | ||
[http://noctua.geneontology.org/ Noctua] is a web-based, collaborative annotation tool developed by the GO Consortium. Noctua can be used to create standard GO annotations as well as [http://geneontology.org/docs/gocam-overview/ GO-CAMs (Gene Ontology Causal Activity Models)] | [http://noctua.geneontology.org/ Noctua] is a web-based, collaborative annotation tool developed by the GO Consortium. Noctua can be used to create standard GO annotations as well as [http://geneontology.org/docs/gocam-overview/ GO-CAMs (Gene Ontology Causal Activity Models)]. | ||
===Getting started with Noctua=== | ===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 ==== | ==== User Account Setup ==== | ||
* To create a new account, please email help@geneontology.org or enter a ticket on the [https://github.com/geneontology/helpdesk helpdesk repo in github]. | * To create a new account, please email help@geneontology.org or enter a ticket on the [https://github.com/geneontology/helpdesk helpdesk repo in github]. |
Revision as of 05:11, 22 September 2022
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 annotation 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.
Noctua: the Gene Ontology's GO Annotation Tool Suite
Noctua is a web-based, collaborative 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).
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.
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.
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.
Getting started | ||
---|---|---|
Topic | Status | Last reviewed |
Noctua Landing Page | Draft | |
Browsing and searching annotations and models | Draft | |
Login | Current | 2022-05-13 |
Model titles | ||
Getting started | ||
Topic | Status | Last reviewed |
Noctua Visual Editor (VPE) | Current | 2022-05-05 |
Noctua Form | Draft | |
Noctua 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 | |
Form Editor | ||
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]
Review Status
Draft: 2021-02-28 Patrick Masson, Pascale Gaudet