Annotation Guidelines: Difference between revisions
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==The three aspects of GO: Molecular Function, Biological Process and Cellular Component== | ==The three aspects of GO: Molecular Function, Biological Process and Cellular Component== | ||
http://geneontology.org/docs/ontology-documentation/ | |||
Each gene should be annotated to at least one of each aspect. 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. | Each gene should be annotated to at least one of each aspect. 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. | ||
==Standard annotations and Causal activity Models (GO-CAMs)== | ==Standard annotations and Causal activity Models (GO-CAMs)== |
Revision as of 04:38, 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 GO annotation is available on the GO website.
The three aspects of GO: Molecular Function, Biological Process and Cellular Component
http://geneontology.org/docs/ontology-documentation/
Each gene should be annotated to at least one of each aspect. 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.
Standard annotations and Causal activity Models (GO-CAMs)
To replace 'general' part of http://wiki.geneontology.org/index.php/Noctua Tracked version is here: https://docs.google.com/document/d/1ENeVLFs4y3gzZS6Icwt0VfK0clL8j-gNDt-qgwrsMXI/edit
Standard GO Annotations
GO annotations have been a key component of GO since its inception. Standard 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. 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.
GO-CAM Models
While standard GO annotations are very useful for discerning basic information about genes, they provide only a partial view of each gene's role in a larger biological context. To provide more comprehensive annotation of genes and link their activities in a causal framework, the GO developed Causal Activity Models (GO-CAMs). Using 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 on the left, 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.
GO-CAM annotation workflow
Modified from http://wiki.geneontology.org/index.php/Noctua#GO-CAM_Workflow
Merge with merge with http://wiki.geneontology.org/index.php/Tips_to_Produce_High_Quality_Annotations ?
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. 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 GO-CAM Editors
Noctua has four curation interfaces:
- The Noctua Visual Editor (VPE) is designed for curating GO-CAM models, i.e. models that include at least two activities/MFs linked by causal relations.
- The Noctua Form is a structured annotation form that is recommended for creating 'standard' GO annotations.
- The Noctua Graph Editor is best suited for linking standard annotations together to create a causal model (GO-CAM).
- The Annotation Review tool
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