Noctua

Noctua: the Gene Ontology's Annotation Tool

Noctua is a web-based GO annotation tool developed and maintained by the GO Consortium. Noctua is used to create standard GO annotations as well as GO-CAMs (Gene Ontology Causal Activity Models) that link multiple GO annotations into integrated models of biological systems.

Using Noctua

User Accounts

• To use Noctua, you must have a registered account.
• To create an account, fill out the New Member Onboarding form. If you need assistance with the form, please email help@geneontology.org.
• Once you have filled out the New Member Onboarding form, please allow 24 hours for your account to be created.

Training

• New Noctua users will need to complete a training session with a member of the GO Consortium.
• Once you have filled out the New Member Onboarding form, you will be contacted to set up the training session.

Editorial Permissions

• Noctua allows users to add to, or edit, any existing GO-CAM model or set of standard GO annotations.
• As a matter of best practices, though, we strongly encourage curators to only modify models made by their annotation group, e.g. a model organism database, UniProt, etc.

Meetings

• The GO Consortium holds regular meetings to discuss annotation practices and Noctua development. These meetings are:
  • General GO annotation meeting - first Tuesday of each month at 8am Pacific time.
  • GO-CAM meeting - 2nd and 4th Thursdays of each month at 8:15am Pacific time. This meeting is held only when there are agenda items.
  • Noctua development - Thursdays at 1pm Pacific time. This meeting is primarily for developers.
• All meetings are on the GO's Google calendar with links to the Zoom URL.

Bug reports, feature requests, maintenance outages

• To report a bug, or request a new feature or enhancement, please create a ticket on the Noctua issue tracker.
• Routine Noctua maintenance is performed on the 2nd and 4th Thursdays of each month, from ~4-6pm Pacific time. During this time, Noctua is not available for use. More specific information about each Noctua maintenance outage can be found in the corresponding issue on the Noctua issue tracker.
  • During these maintenance outages the following tasks are typically performed:
    • Ontology updates:
      • All ontologies are updated with the most recent versions
    • Entity updates:
      • All annotatable entities as specified by contributing groups are updated (see below)
    • Model updates:
      • Obsolete ontology terms are automatically updated if there is a corresponding 'replaced by' value
      • When applicable and possible, ontology terms are updated if there are new usage guidelines
      • Models marked for deletion are removed
    • Software updates:
      • Incorporate bug fixes
      • Add new features
• Noctua maintenance outage reminders are sent out on the go-consortium mailing list ~48 hrs. prior to the outage.

Making Annotations in Noctua

Noctua Landing Page

• The Noctua landing page is the starting point for all Noctua functionality. Briefly, it contains:
  • A table listing all models and functionality to browse and search them.
  • Links to curation workbenches.
  • Model metadata, model copy functionality, and links to file downloads (GPAD and OWL).

Noctua Workbenches

Noctua has several annotation workbenches, customized for the type of annotation curators need to do.

Standard Annotation Workbenches

• For creating standard GO annotations, curators can use:
  • The Standard Annotations Editor is the newest Noctua workbench and the preferred workbench for creating standard GO annotations.
  • The Form Editor is an older implementation of a form for creating standard GO annotations. Note: the Form Editor will be replaced by the Standard Annotations Editor in the fall of 2024.
  • The Annotation Review Tool can be used to edit entities and ontology terms in bulk.

GO-CAM Workbenches

• For creating GO-CAMs, curators can use:
  • The Pathway Editor (VPE), is a graphical curation interface that guides curators through the process of creating causal models.
  • The Graph Editor is an older implementation of a causal modeling curation interface and is not recommended for current use.

Entities

Genes and Gene Products

• In Noctua, GO annotations may be assigned to genes, gene products, and protein-containing complexes.
• Every gene, gene product, and protein-containing complex must be associated with a stable database identifier sourced from:
  • A GPI (Gene Production Information) file submitted by the authoritative group for a species (preferred)
  • An existing annotation file, e.g. a GAF (Gene Association File) submitted by the authoritative group for a species
  • The protein-containing complex branch of the GO Cellular Component ontology.
• To request adding new entity identifiers, please create a ticket in the Noctua issue tracker.

Ontologies for Annotation

• Noctua uses a number of different ontologies to create standard annotations and GO-CAMs.
• To request adding a new ontology to Noctua, please create a ticket in the Noctua issue tracker.

Gene Ontology (GO)

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

Relations Ontology (RO)

• RO is used in standard annotations to:
  • Link gene products to GO terms
  • Provide additional context to GO terms with annotation extensions
• RO is used in GO-CAMs to:
  • Link molecular activities in a causal chain
  • Link molecular activities to biological processes and cellular components
  • Provide additional context to GO terms
• RO relations and their usage in GO are described more fully in the Annotation Relations page.

Cell and Anatomy Ontologies

• Cell and anatomy ontologies can be used to annotate:
  • The location where processes and functions occur
  • The location of a GO cellular component
• Cell and anatomy ontologies currently available in Noctua are:
  • C. elegans gross anatomy ontology (WBbt)
  • Cell Ontology (CL)
  • Dicty anatomy ontology (DDANAT)
  • Drosophila anatomy ontology (FBbt)
  • Mouse anatomy ontology (EMAPA)
  • Uberon
  • Xenopus anatomy ontology (XAO)
  • Zebrafish anatomical ontology (ZFA)

Biological Phase and Life Stage Ontologies

• Biological phase and life stage ontologies can be used to annotate:
  • The temporal period during which processes and functions occur
  • The temporal period during which a cellular component or anatomical entity exists
• Biological phase and life stage ontologies currently available in Noctua are:
  • GO BP (GO:0044848 biological phase and children)
  • C. elegans development ontology
  • Drosophila developmental ontology
  • Mouse anatomy ontology (EMAPA)

Chemical Ontology (ChEBI)

• Chemicals can be used to annotate:
  • Primary inputs and outputs of processes and functions
  • Small molecule regulators of functions
• GO uses the Chemical Entities of Biological Interest (ChEBI) ontology

Sequence Ontology (SO)

• Not imported yet

GO-CAM Modeling Guidelines

• Documentation for how to annotate specific functions and processes in GO-CAMs is available in the GO-CAM Modeling Guidelines folder
• Documentation on relations used in GO-CAMs may be accessed on the wiki here.

Other information - to be transferred to, or linked from, Google docs

Creating standard GO annotations
Form Editor - annotation	Molecular Function
	Biological Process
	Cellular Component
Form Editor - annotation extensions	Molecular Function
	Biological Process
	Cellular Component
Editing annotations
Form Editor
Model metadata
Model titles	General Guidelines
Other tips and tricks	Adding a NOT qualifier to an annotation
	Importing existing annotations
	Changing annotation group
	Running the reasoner
	Viewing GPAD export