- 1 Summary
- 2 Requirements
- 3 Launching Noctua
- 4 Setup
- 5 Using Noctua
- 5.1 Login
- 5.2 Editing an existing model
- 5.3 Starting a new model
- 5.4 Creating a new activity and its properties
- 5.5 Specifying the causal ordering of the activities
- 5.6 Subfunctions: specifying more detail about molecular activities
- 5.7 Editing the model
- 5.8 Making "traditional" (single aspect) GO annotations using Noctua
- 5.9 Naming your Model and Saving your Work
- 5.10 How to Make a Model Public
- 6 Providing Feedback
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.
What is a GO-CAM model?
A GO-CAM model is a generalization of a GO annotation, that specifies how different "traditional" GO annotations can be combined into a more complex annotation ("model"). It must contain at least one ACTIVITY (a GENE PRODUCT performing a molecular process). An activity can have an CAUSAL EFFECT on another activity (traditional GO "regulation of molecular function" annotations). In general, a Noctua model will contain multiple activities with causal relations linking them together into a pathway.
An ACTIVITY is represented by a GO Molecular Function term, and additional "aspects" that describe when and where the ACTIVITY occurs. An ACTIVITY is a molecular process, so it is performed by a population of gene product molecules, and can be regulated (controlled). Ideally, all of the following “aspects” of the gene product’s activity 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 type of 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:
- 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)
- 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:
- 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.
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.
Activities can be linked together by relations that describe their causal dependence. The most common relations are “directly (positively/negatively) 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.
A web browser. Chrome is recommended.
- Go to http://geneontology.org/cam.
Before using Noctua to edit or create models, you need to have three things:
If you don't already have a GitHub or ORCID account, please obtain these before continuing (note that in exceptional circumstances, it is possible to use Noctua without these). The most important step is to get your information properly into the users' metadata file. The easiest way to do this is to fill out the online new user form and contact sjcarbon at lbl dot gov once complete. Propagating the metadata information may take a little time, so please do this as early as possible. To fill out this form, you will need your name, organization, and GitHub and ORCID account information.
Click on the Login button in the upper right corner, and choose "Log in with Github." When you have logged in, press the "return" button to return to the previous page, now with edit permission.
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
Just click on the blue "Create Noctua Model" button.
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 (Fig. 1)
This will launch a new browser tab with the Simple annoton editor form (Fig. 2)
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.
Tip: In the autocomplete, enter a space after a complete word, to narrow down the choices.
1.a. Enter gene product or macromolecular complex to be annotated
By default, the form allows you to enter a single gene product. Start typing, choices will appear, and then select the gene product.
Tip: 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.
You can annotate a complex instead of a single gene product, by choosing "macromolecular complex" from the drop-down menu on the right of the section header instead of "single gene product". When annotating a complex, you will need to specify the GO macromolecular complex term (use "macromolecular complex" if you don't have a more specific term), and ideally also specify the gene products in the complex.
Tip: Whenever possible, an annoton should have a single gene product. A complex should be used only when the function has been characterized for the entire complex, and it cannot be adequately described in terms of the functions of its component parts (or these functions are unknown). For instance, the ribosome would be represented as a complex, but a calcium-dependent protein kinase would be represented as two different activities (annotons), a calcium sensor activity enabled by the regulatory subunit, and a protein kinase activity enabled by the catalytic subunit.
1.b. Enter the molecular function and evidence
These fields are required. If the molecular function is not specified, enter "molecular_function".
1.c. Enter other fields (optional)
If you fill in the first field of a line, you will need to add evidence. Otherwise any field can be left blank.
We recommend that you fill in as many fields as possible before creating the activity, 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: 1. 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. 2. 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.
Specifying the causal ordering of the activities
Once you have created at least two activities, you can specify the causal relations between them. This is done on the graph canvas, by dragging from the blue circle of the upstream activity box, onto the downstream activity box (Fig. 3). You can then select the relation. Relations that are “direct” mean that there is a physical interaction mediating the effect on the downstream activity.
Choosing the right causal relation between activities/annotons
- If the upstream activity regulates the downstream activity through direct binding or by covalent modification, use the “directly (positively/negatively) regulates” relation. Examples:
- Receptor ligand activity enabled by Wnt1 directly positively regulates receptor activity enabled by Fzd1 (Wnt1 binds to the Fzd1 receptor and activates it).
- Protein kinase activity enabled by MAP3K1 directly positively regulates protein kinase activity enabled by MAP2K1 (MAP3K1 phosphorylates MAP2K1 and activates it)
- If an upstream activity creates a molecule that is acted upon by the downstream activity, use “provides direct input for” relation. Examples:
- Glucose-6-phosphate dehydrogenase activity of GAPDH provides direct input for phosphofructokinase activity of PFK2 (the small molecule output from the GAPDH activity is acted upon by PFK2 as the next step in the metabolism of glucose).
- (X phosphorylates Y, creating a molecule that is then acted upon by Z)
Indirect but proximal causal mechanisms
- Regulation via a small molecule intermediate. Create an instance of the small molecule (an instance of a CHEBI term), using the "Add Individual" item on the left of the graph canvas. Connect the upstream activity to the small molecule with "directly increases/decreases concentration of", and the small molecule to the downstream activity with "directly positively/negatively regulates". Examples:
- ADCYA1 creates cAMP, which directly binds to PKC1 and activates it
- ADCHE1 breaks down acetylcholine, which directly binds to ACHR1 and activates it.
- Transcriptional regulation. Create an instance of the transcriptional process, using the "Add Process" item on the left of the graph canvas. Connect the upstream activity to the transcriptional process with "directly positively regulates", and the transcriptional process to the downstream activity with "causally upstream of".
Indirect and unknown causal mechanisms
- If the mechanism of the causal relation is not known, use the more general “causally upstream of” relations (these can include a positive/negative effect, if known).
Subfunctions: specifying more detail about molecular activities
Sometimes, molecular activities are composed of distinct subfunctions, and those subfunctions may even be carried out in distinct locations, or by distinct subunits of a complex. For example you may want to specify “hormone binding” in the “cytosol” as a subfunction of a nuclear receptor, that then activates (directly positively regulates) “transcription factor activity” in the “nucleus”. To specify subfunctions, you will create new activities and link them to an activity that you have previously created that describes the overall function of the gene product (e.g. “nuclear receptor activity”). Subfunctions (e.g. “hormone binding”) can be created using the simple annoton editor, but do not fill in the biological process field as it is the same as for the overall function. Once the new annoton is created, link it to the overall molecular function you created earlier, by dragging (on the graph canvas) from the subfunction annoton (blue circle) to the overall activity, and selecting the “part of” relation. You will then need to add evidence by clicking on the "part of" edge; a box will pop up; fill in the evidence fields and press the "Add" button.
Editing the model
Editing can currently be performed only on the graph canvas (the simple annoton editor form does not pick up any operations you have performed on the graph canvas).
Note that only one edit operation can be done at a time. To change something on the canvas, you will need to first ADD the correct part, and then DELETE the incorrect part, as separate operations. We recommend that you add first, so that you can transfer evidence from the incorrect part if necessary, by using the “clone other” operation.
Relations can be removed by dragging the end of the relation arrow away from the box it connects to, into an empty part of the canvas. Relations can be added by clicking on the blue circle inside the upstream box, and dragging to the downstream box. Evidence for a relation can be edited by clicking on the relation arrow.
Editing the type/label on a graph node
To edit a simple box on the graph (no colored bars indicating that it has multiple parts folded together for easy viewing), just click on the green square. To change it, first add the new term by filling in the field under “add type”, and clicking add. Then reopen the box again and delete the old term by clicking on the red “x” next to it.
Editing types/labels that are inside a graph node
- To edit properties of an activity that are “folded” into the molecular activity box on the canvas, click on the green box in the corner of a box. Note that only one edit operation can be done at a time, so do not make more than one edit before pressing a button to save the edit. To change part of the annoton, you will need to first ADD the corrected part, and then DELETE the incorrect part, as separate operations.
- To remove a property of the annoton, click the “x” next to it.
- To edit the evidence, click on the “E” next to the part for which you want to edit evidence (e.g., the “E” next to enabled by is the evidence that the molecular function is enabled by the gene product).
Making "traditional" (single aspect) GO annotations using Noctua
Molecular function annotation
- Fill in the gene product field
- Fill in the molecular function field, including evidence
- Optionally, the following "extensions" can be added:
- has_input(molecule): fill in the "has input" field and evidence
- happens_during(biological phase): fill in the "happens during" field and evidence
- occurs_in(cellular component): fill in the "cellular component" field and evidence
- part_of(biological_process): fill in the "biological process" field and evidence
Cellular component annotation
- Use the "Component only" version of the form. This is still under development.
Biological process annotation
- Fill in the gene product field.
- Fill in the molecular function field with "molecular_function" if unknown. Fill in the evidence with the same evidence code and PMID that you will use for biological process.
- Fill in the biological process field with the desired GO term, and evidence.
- Optionally, the following "extensions" can be added:
- part_of(larger biological process): fill in the "part of biological process" field. Other extensions should be added to the molecular function
Naming your Model and Saving your Work
While you create or edit your model, you will see an asterisk appear around the "Untitled" text in your browser tab. The asterisk indicates that your work is not yet saved, and the "Untitled" indicates that you have not yet named your model. To name your model and save your work, click on the drop-down menu under the Model heading and select the "Edit Annotations" option. In the "Title" section, add a title for your model. The beginning of the title will now appear in the browser tab. To save your work, click on the Model heading again and select the "Save" option. Your work is now saved and the asterisk in the tab will disappear. Save your work often while editing!
Tip: If your model already has a name, you will need to delete the name first, before you can rename it. Follow the same instructions above, but press the Delete button next to the name instead
How to Make a Model Public
GO-CAM models can exist in different curation states, depending upon whether the curator(s) wish to make the model public. This allows curators to work on a model over a period of time, perhaps review them with colleagues or experts in the field, and then publish them to the GO or other web sites.
By default, new models are treated as if they are under development, but curators have the ability to explicitly label the production status of their model. To do this, click on the Model drop down menu and select "Edit Annotations" from the list. Under the "Annotation state" section, select from one of five options:
- Production - model will be available from viewing on the GO web site and annotation files available on Jenkins (see below)
- Development - model is still being curated and is not available for viewing on the GO web site; annotations cannot be retrieved from Jenkins (see below)
Curators should send bug reports and requests for new features on the Noctua issue tracker. Be sure to search the tracker to see if the request has not already been reported!