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[[Category: Annotation]]
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= GO-CAMs and Noctua =
=Summary=
+
*This documentation is presented in two parts:
Noctua is an online system for making extensible GO annotations, which we call "GO-CAM models"Anything from simple annotations to complicated pathways are supported. However, the overall goal should be for a model to represent a unit that roughly corresponds to a biological pathway. This document describes how to make GO-CAM models using Noctua.
+
** GO-CAM Principles
 +
** Noctua Curation Tool
 +
 
 +
== GO-CAM Principles ==
 +
=== Standard GO Annotations and GO-CAM Models ===
 +
==== Standard GO Annotations ====
 +
 
 +
[http://geneontology.org/docs/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 [http://geneontology.org/docs/ontology-documentation/ 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 [http://www.obofoundry.org/ontology/ro.html Relations Ontology (RO)] and a term from GO or an external ontology, e.g. [http://uberon.github.io/ 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 [http://geneontology.org/docs/gocam-overview/ 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.  [[File:GO CAM figure from Google drive.png|thumb|center|Figure 1. GO-CAM Model Specifications|800px]]
 +
 
 +
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.
 +
 
 +
=== Use of GO in GO-CAMs ===
 +
 
 +
==== Molecular Activities in GO-CAMs ====
 +
 
 +
* Wherever possible, curators should strive to select the single most granular GO Molecular Function (MF) term that best describes the overall activity of the gene, gene product, or protein-containing complex being annotated.
 +
 
 +
* If desired, individual "sub-functions" may be captured by using the 'part of' relation between the main MF and its sub-functions.
 +
 
 +
==== Biological Processes in GO-CAMs ====
 +
 
 +
* The ultimate aim of GO-CAMs is to create a suite of Biological Process (BP)-centric models that can be used to interrogate causal effects of molecular activities on one another as part of the execution of a larger BP.
 +
 
 +
* When annotating, curators should always think about the BP they are modeling and what MFs are 'part of' that BP.
 +
 
 +
* Additional relations between MFs and BPs, e.g. 'causally upstream of or within', can be used to capture experimental information that, in the future, will be incorporated into a more complete model of that process.
 +
 
 +
==== Cellular Components in GO-CAMs ====
 +
 
 +
* Cellular component annotations are intended to capture where the MF enabled by a gene, gene product, or protein-containing complex occurs.
 +
 
 +
* Cellular component annotations may be further qualified with cell, tissue, and organismal context if that information is germane to the process being modeled.
 +
 
 +
== Noctua: the Gene Ontology's GO-CAM Annotation Tool ==
 +
[http://noctua.geneontology.org/ Noctua] is a web-based, collaborative [http://geneontology.org/ Gene Ontology (GO)] annotation tool developed by the GO Consortium.  Noctua can be used to create standard GO annotations as well as more expressive models of biological processes, known as [http://geneontology.org/docs/gocam-overview/ GO-CAMs (Gene Ontology Causal Activity Models)].  There are two types of user interface available in Noctua: 1) a form interface and 2) a graph interface.
 +
 
 +
=== System Requirements ===
 +
Noctua is a web-based annotation tool and thus requires only a web browser to access and use. 
 +
 
 +
We have tested Noctua primarily with Chrome on a Mac operating system.   
 +
 
 +
Issues that arise using other browsers and operating systems may be reported on [https://github.com/geneontology/helpdesk/issues go-helpdesk]
 +
 
 +
=== User Account Setup ===
 +
GO-CAMs can be browsed using Noctua, but no annotations can be created or edited unless a user has a registered account.
 +
 +
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]. 
 +
 
 +
Note that to create a Noctua account, you will need an [https://orcid.org/ ORCID] and a [https://github.com/ github account].
 +
 
 +
Please allow 24 hours for your account to be created.
 +
 
 +
If you have any questions about user accounts, please contact help@geneontology.org
 +
 
 +
==Entities and Ontologies for Annotation==
 +
=== Entities for Annotation ===
 +
 
 +
==== Genes and Gene Products ====
 +
 
 +
* The primary nodes in a GO-CAM model are the ACTIVITIES (Molecular Functions (MFs)) of genes, gene products, or protein-containing complexes.  
 +
 
 +
* Every gene, gene product, and protein-containing complex annotated in GO-CAMs must be associated with a stable database identifier and represented either in a GPI (Gene Production Information) file (preferred), in an existing annotation file, e.g. a GAF (Gene Association File), or in the GO Cellular Component aspect.
 +
 
 +
* Curators should strive to annotate activities (MFs) to individual genes or gene products wherever possible.
 +
 
 +
==== Protein-Containing Complexes ====
 +
 
 +
* In GO-CAMs, curators should always try to assign each member of a protein-containing complex its specific activity (e.g. regulatory activity vs catalytic activity).
 +
 
 +
* However, if the main activity of the protein-containing complex cannot be ascribed to a single subunit of the complex (e.g. RNA polymerase II activity), then the activity should be enabled by an appropriate protein-containing complex (e.g. a GO protein-containing complex), with each gene or gene product associated with that protein-containing complex with a 'part of' relation.
 +
 
 +
* Requests to add new entity identifiers to Noctua should be directed to help@geneontology.org
 +
 
 +
=== Ontologies for Annotation ===
 +
 
 +
==== Gene Ontology ====
 +
* The GO is used to annotate:
 +
** Molecular Activities (MF)
 +
** Biological Processes (BP)
 +
** Cellular Component (CC)
 +
 
 +
 
 +
To provide appropriate biological context to a model, additional ontologies may be used. 
 +
 
 +
==== Cell and Anatomy Ontologies ====
 +
* Can be used to describe the location where processes and functions occur.
 +
* Can be used to describe the location of a GO cellular component.
 +
 
 +
==== Biological Phase and Life Stage Ontologies ====
 +
* Can be used to describe the temporal period during which processes and functions occur.
 +
* Can be used to describe the temporal period during which a cellular component or anatomical entity exists.
 +
 
 +
==== Chemical Ontology ====
 +
* Can be used to capture inputs and outputs of processes and functions.
 +
* GO-CAM uses the Chemical Entities of Biological Interest (ChEBI)
 +
 
 +
==== Sequence Ontology ====
 +
 
 +
Requests to add ontologies to Noctua should be sent to help@geneontology.org
 +
 
 +
== GO-CAM 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.
 +
* 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 Users Manual ==
 +
* Noctua is accessed via: http://noctua.geneontology.org/
 +
 
 +
=== Noctua Landing Page ===
 +
* The Noctua landing page is the portal by which curators can browse or search and filter models
 +
* It is also the starting point for curation (when logged in) and where individual GPAD and OWL files for a model can be downloaded.
 +
 
 +
* By default, the Noctua landing page displays models by date, descending order, i.e. the most recently edited models are shown at the top of the list.
 +
 
 +
 
 +
[[File:NLP_home.png|thumb|center|upright=3.00|Noctua Landing Page]]
 +
 
 +
 
 +
==== Filtering Models ====
 +
* There are two ways to filter GO-CAMs on the landing page:
 +
#Click on the magnifying glass icon in the upper left
 +
#Click on the metadata icons to the right of the model title in the table.
 +
 
 +
 
 +
[[File:Filtering options.png|thumb|center|upright=3.00|Filtering Options]]
 +
 
 +
 
 +
===== Filtering with the Magnifying Glass =====
 +
 
 +
Clicking on the magnifying glass opens up the menu of available filter options:
 +
 
 +
#'''Ontology term''' (autocomplete)
 +
#'''Gene product''' (autocomplete)
 +
#'''Reference'''
 +
## If entered as free-text, must be the full reference id, e.g. PMID:31884020 or doi:10.1016/j.ydbio.2019.12.010
 +
## Can also use the drop-down prefix menu (and PMID look-up feature) by clicking on the =+ icon.
 +
## Must press return after entering search string.
 +
#'''Organism''' (drop-down list)
 +
#'''Contributor''' (autocomplete and drop-down list)
 +
#'''Groups''' (autocomplete and drop-down list)
 +
#'''Exact date''' (enter YYYY-MM-DD/return or calendar, select/return)
 +
#'''Date range''' (enter YYYY-MM-DD/return or calendar, select/return)
 +
#'''Title''' (enter/return)
 +
#'''State''' (drop-down list)
  
=Requirements=
+
[[File:Filter options menu.png|thumb|center|upright=3.00|Filtering Options]]
A web browser.  Chrome is recommended.
 
  
=Launching Noctua=
+
=== Noctua Form Editor ===
* Go to http://geneontology.org/cam.
 
  
=Setup=
 
* Before using Noctua to edit or create models, please follow this procedure to request edit access.  You will need a ORCID (https://orcid.org), so you can be uniquely identified.  Each part of a Noctua model is individually attributed to an editor, as well as the project that provided their funding (if applicable).
 
  
=Using Noctua=
 
  
==Login==
 
You can view models without logging in, but you must log in before creating new annotations (by editing an existing model, or creating a new model).  Click on the Login button in the right upper corner of the page.  There are several options for logging in.  We recommend using Github (if you don't already have an account just go to http://github.com).
 
  
==Editing an existing model==
 
Just click on the "Edit" button in the rightmost column of the model list.  The model list can be filtered using the search box just above the list of available models.
 
  
==Starting a new model==
+
=== Noctua Graph Editor ===
Just click on the blue "Create Noctua Model" button.
 
  
==What is a Noctua model?==
+
{| class="wikitable"
===Molecular activity===
+
!colspan="3" | Noctua Users Manual
Each Noctua model consists of at least one MOLECULAR ACTIVITY (FUNCTION), carried out by at least one GENE PRODUCT. Ideally, all of the following “aspects” of the gene product’s function will be specified in the model. However, in cases where some or most of these aspects are unknown, a model may still be constructed with details added as more information becomes available. Users should attempt to specify functions as fully as possible, but partial models are expected and still contribute to the GO knowledgebase. The following aspects are represented in a model:
+
|-
*Molecular function (MF): the molecular activity carried out by a gene product as part of a larger biological process; this is specified by a term from the GO molecular function ontology. MF may be qualified, using defined relations, as follows:
+
!rowspan="2" | Getting started: the Noctua landing page
**If the function acts upon another “target” molecule, this can be specified using a gene product identifier (for a protein or a gene) or term from the ChEBI ontology (for a small molecule)
+
|[[Browsing and searching annotations and models]]
**If the function acts during a particular “biological phase” (e.g. a particular stage in organism development), this can be specified using a term from an appropriate ontology
+
|-
*Cellular component (CC): the location of the gene product when it is carrying out its activity; this is specified by a term from the GO cellular component ontology. CC may be qualified, using defined relations, as follows:
+
|[[Login]]
**If the activity occurs in a specific cell type, this can be specified using a term from a Cell Type or Anatomy Ontology.
+
|-
**If the activity occurs in a specific anatomical structure, this can be specified using a term from the Uberon, or other organismal Anatomy, ontology.
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!colspan="3" |Creating standard GO annotations
*Biological process (BP): the larger “biological program” to which the activity contributes; this is specified by a term from the GO biological process ontology. BP may be qualified, using defined relations, as follows:
+
|-
**If the process is a part of a larger biological program, it can be linked to the larger biological program with another GO biological process term.
+
!rowspan = "3" | Form Editor
All of these aspects together constitute a unit of annotation, which we call an “annoton”. Each annoton is centered on the molecular activity, as this is the most basic description of gene product function.
+
|[http://wiki.geneontology.org/index.php/Noctua_Form_Molecular_Function Molecular Function]
===Molecular activities can be linked by causal relations===
+
|-
Activities can be linked together by relations that describe their causal dependence. The most common relations are “regulates” and “provides input for”, but there are other relations of greater and lesser specificity, depending on what is known. “Regulates” should be used to denote biological control of a downstream activity. “Provides input for” should be used when there is no control, but an upstream function creates a molecular entity that is the target of the downstream function, such as in a metabolic pathway.
+
|[http://wiki.geneontology.org/index.php/Noctua_Form_Biological_Process Biological Process]
 +
|-
 +
|[http://wiki.geneontology.org/index.php/Noctua_Form_Cellular_Component Cellular Component]
 +
|-
 +
!rowspan = "3" | Graph Editor
 +
|[http://wiki.geneontology.org/index.php/Noctua_Graph_Molecular_Function Molecular Function]
 +
|-
 +
|[http://wiki.geneontology.org/index.php/Noctua_Graph_Biological_Process Biological Process]
 +
|-
 +
|[http://wiki.geneontology.org/index.php/Noctua_Graph_Cellular_Component Cellular Component]
 +
|-
 +
!colspan="3" |Adding contextual information (annotation extensions)
 +
|-
 +
!rowspan = "3" | Form Editor
 +
|[http://wiki.geneontology.org/index.php/Noctua_Form_MF_Extensions Molecular Function]
 +
|-
 +
|[http://wiki.geneontology.org/index.php/Noctua_Form_BP_Extensions Biological Process]
 +
|-
 +
|[http://wiki.geneontology.org/index.php/Noctua_Form_CC_Extensions Cellular Component]
 +
|-
 +
!rowspan = "3" | Graph Editor
 +
|[http://wiki.geneontology.org/index.php/Noctua_Graph_MF_Extensions Molecular Function]
 +
|-
 +
|[http://wiki.geneontology.org/index.php/Noctua_Graph_BP_Extensions Biological Process]
 +
|-
 +
|[http://wiki.geneontology.org/index.php/Noctua_Graph_CC_Extensions Cellular Component]
 +
|-
 +
!colspan="2" | Editing annotations
 +
|-
 +
|[http://wiki.geneontology.org/index.php/Noctua_Manual:_Editing_in_form Form Editor]
 +
|-
 +
|[[Graph Editor]]
 +
|-
 +
!colspan="2" | Creating GO-CAMs
 +
|-
 +
!rowspan = "2" | Creating an activity unit
 +
|[http://wiki.geneontology.org/index.php/Noctua_Manual:_Creating_an_Activity_Unit_in_Form Form Editor]
 +
|-
 +
|[[Graph Editor]]
 +
|-
 +
!rowspan = "2" | Linking Activities
 +
|[http://wiki.geneontology.org/index.php/Noctua_Manual:_Linking_Activities_in_Form Form Editor]
 +
|-
 +
|[[Graph Editor]]
 +
|-
 +
!colspan = "2" | Model metadata
 +
|-
 +
!rowspan = "2" | Naming models
 +
|[http://wiki.geneontology.org/index.php/Noctua_Manual:_Naming_Models_in_Form Form Editor]
 +
|-
 +
|[[Graph Editor]]
 +
|-
 +
!rowspan = "2" | Releasing models to production
 +
|[http://wiki.geneontology.org/index.php/Noctua_Manual:_Making_Models_Production_in_Form Form Editor] Form Editor]
 +
|-
 +
|[[Graph Editor]]
 +
|-
 +
!rowspan = "7" | Other tips and tricks
 +
|[http://wiki.geneontology.org/index.php/Noctua_Manual:_Adding_NOT_Qualifer_in_Form Adding a NOT qualifier to an annotation]
 +
|-
 +
|[http://wiki.geneontology.org/index.php/Noctua_Manual:_Importing_existing_annotations Importing existing annotations]
 +
|-
 +
|[http://wiki.geneontology.org/index.php/Noctua_Manual:_Changing_annotation_group Changing annotation group]
 +
|-
 +
|[http://wiki.geneontology.org/index.php/Noctua_Manual:_Model_validation Model validation]
 +
|-
 +
|[http://wiki.geneontology.org/index.php/Noctua_Manual:_Running_the_reasoner Running the reasoner]
 +
|-
 +
|[http://wiki.geneontology.org/index.php/Noctua_Manual:_Viewing_GPAD_export Viewing GPAD export]]
 +
|-
 +
|[http://wiki.geneontology.org/index.php/Noctua_Manual:_Using_templates Using templates]
 +
|-
 +
|}
  
  
==Creating a new activity and its properties==
 
After either selecting an existing model or starting a new one, you will see the graph view by default.  To create new activities, you should use the “Simple annoton editor” tool, available in the Workbench menu:
 
Workbench -> Simple annoton editor
 
[[File:Launch_noctua_activity_form.png|thumb|Fig. 1 Launching the simple annoton editor|400px]]
 
This will launch a new browser tab
 
===Step 1. Fill in the form===
 
Fill in as many fields as possible in the form, by typing in the field, and then selecting from the autocomplete suggestions by moving the mouse over your selection and clicking.  Tips:
 
*The required fields are gene product, molecular function and evidence for the function.  All other fields are optional.
 
*You can annotate a complex instead of a single gene product, by choosing "macromolecular complex" from the drop-down menu
 
*For gene products, you can type in the gene symbol, e.g. Wnt3a.  If necessary to narrow down the choices, type a space after the symbol, and enter the three letter code for the species (first letter from genus and two from species name, e.g. mmu for Mus musculus).  Each entry in the autocomplete will also show the associated unique database identifier or accession, so curators can confirm that they are selecting the appropriate entity for annotation.
 
* In general, enter a space after a complete word, to narrow down the choices.
 
Just as in conventional GO annotation, you must fill in the Evidence and Reference fields for each line of annotation, or an annoton will not be created.
 
We recommend that you fill in as many fields as possible before creating the annoton, as after it is created, you will need to edit it from the graph canvas, which requires more steps to do.
 
===Step 2. Add the new activity to a model===
 
Press the CREATE button.  A new activity will appear on the graph canvas (the main window).  Tips:
 
*Each new activity will appear on the same part of the canvas, so if you add more than one activity you will need to move them around on the canvas (by clicking and dragging) to see the ones underneath.
 
*If the CREATE button is grayed-out, there is some information missing from the form that you still need to fill in.  You can press the "why is the save button disabled?" for a list of missing fields.
 
  
The analogy is to a library.  You will first find and check out (lock) the families you want to curate, and then select a family to curate from your list of locked families. All families now have a curation status (curated, partially curated, uncurated).
 
  
---------
+
[[Category: Annotation]]

Latest revision as of 13:24, 9 November 2020

GO-CAMs and Noctua

  • This documentation is presented in two parts:
    • GO-CAM Principles
    • Noctua Curation Tool

GO-CAM Principles

Standard GO Annotations and GO-CAM Models

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 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.
Figure 1. GO-CAM Model Specifications

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.

Use of GO in GO-CAMs

Molecular Activities in GO-CAMs

  • Wherever possible, curators should strive to select the single most granular GO Molecular Function (MF) term that best describes the overall activity of the gene, gene product, or protein-containing complex being annotated.
  • If desired, individual "sub-functions" may be captured by using the 'part of' relation between the main MF and its sub-functions.

Biological Processes in GO-CAMs

  • The ultimate aim of GO-CAMs is to create a suite of Biological Process (BP)-centric models that can be used to interrogate causal effects of molecular activities on one another as part of the execution of a larger BP.
  • When annotating, curators should always think about the BP they are modeling and what MFs are 'part of' that BP.
  • Additional relations between MFs and BPs, e.g. 'causally upstream of or within', can be used to capture experimental information that, in the future, will be incorporated into a more complete model of that process.

Cellular Components in GO-CAMs

  • Cellular component annotations are intended to capture where the MF enabled by a gene, gene product, or protein-containing complex occurs.
  • Cellular component annotations may be further qualified with cell, tissue, and organismal context if that information is germane to the process being modeled.

Noctua: the Gene Ontology's GO-CAM Annotation Tool

Noctua is a web-based, collaborative Gene Ontology (GO) annotation tool developed by the GO Consortium. Noctua can be used to create standard GO annotations as well as more expressive models of biological processes, known as GO-CAMs (Gene Ontology Causal Activity Models). There are two types of user interface available in Noctua: 1) a form interface and 2) a graph interface.

System Requirements

Noctua is a web-based annotation tool and thus requires only a web browser to access and use.

We have tested Noctua primarily with Chrome on a Mac operating system.

Issues that arise using other browsers and operating systems may be reported on go-helpdesk

User Account Setup

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

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.

Please allow 24 hours for your account to be created.

If you have any questions about user accounts, please contact help@geneontology.org

Entities and Ontologies for Annotation

Entities for Annotation

Genes and Gene Products

  • The primary nodes in a GO-CAM model are the ACTIVITIES (Molecular Functions (MFs)) of genes, gene products, or protein-containing complexes.
  • Every gene, gene product, and protein-containing complex annotated in GO-CAMs must be associated with a stable database identifier and represented either in a GPI (Gene Production Information) file (preferred), in an existing annotation file, e.g. a GAF (Gene Association File), or in the GO Cellular Component aspect.
  • Curators should strive to annotate activities (MFs) to individual genes or gene products wherever possible.

Protein-Containing Complexes

  • In GO-CAMs, curators should always try to assign each member of a protein-containing complex its specific activity (e.g. regulatory activity vs catalytic activity).
  • However, if the main activity of the protein-containing complex cannot be ascribed to a single subunit of the complex (e.g. RNA polymerase II activity), then the activity should be enabled by an appropriate protein-containing complex (e.g. a GO protein-containing complex), with each gene or gene product associated with that protein-containing complex with a 'part of' relation.
  • Requests to add new entity identifiers to Noctua should be directed to help@geneontology.org

Ontologies for Annotation

Gene Ontology

  • The GO is used to annotate:
    • Molecular Activities (MF)
    • Biological Processes (BP)
    • Cellular Component (CC)


To provide appropriate biological context to a model, additional ontologies may be used.

Cell and Anatomy Ontologies

  • Can be used to describe the location where processes and functions occur.
  • Can be used to describe the location of a GO cellular component.

Biological Phase and Life Stage Ontologies

  • Can be used to describe the temporal period during which processes and functions occur.
  • Can be used to describe the temporal period during which a cellular component or anatomical entity exists.

Chemical Ontology

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

Sequence Ontology

Requests to add ontologies to Noctua should be sent to help@geneontology.org

GO-CAM 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.
  • 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 Users Manual

Noctua Landing Page

  • The Noctua landing page is the portal by which curators can browse or search and filter models.
  • It is also the starting point for curation (when logged in) and where individual GPAD and OWL files for a model can be downloaded.
  • By default, the Noctua landing page displays models by date, descending order, i.e. the most recently edited models are shown at the top of the list.


Noctua Landing Page


Filtering Models

  • There are two ways to filter GO-CAMs on the landing page:
  1. Click on the magnifying glass icon in the upper left
  2. Click on the metadata icons to the right of the model title in the table.


Filtering Options


Filtering with the Magnifying Glass

Clicking on the magnifying glass opens up the menu of available filter options:

  1. Ontology term (autocomplete)
  2. Gene product (autocomplete)
  3. Reference
    1. If entered as free-text, must be the full reference id, e.g. PMID:31884020 or doi:10.1016/j.ydbio.2019.12.010
    2. Can also use the drop-down prefix menu (and PMID look-up feature) by clicking on the =+ icon.
    3. Must press return after entering search string.
  4. Organism (drop-down list)
  5. Contributor (autocomplete and drop-down list)
  6. Groups (autocomplete and drop-down list)
  7. Exact date (enter YYYY-MM-DD/return or calendar, select/return)
  8. Date range (enter YYYY-MM-DD/return or calendar, select/return)
  9. Title (enter/return)
  10. State (drop-down list)
Filtering Options

Noctua Form Editor

Noctua Graph Editor

Noctua Users Manual
Getting started: the Noctua landing page Browsing and searching annotations and models
Login
Creating standard GO annotations
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
Naming models 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