Planteome Noctua (Beta) quick-start-guide

Getting Started With Noctua and GO-CAM Curation

What is GO-CAM?

GO-CAM (Gene Ontology Causal Activity Models) is a formalism for constructing models of biological pathways or processes using Gene Ontology (GO) annotations, contextual information (e.g., cell and tissue types) and defined semantic relations from the Relations Ontology (RO).

For more details see the GO-CAM Curation Guide.

What is Noctua?

Noctua (http://noctua.berkeleybop.org) is the web-based collaborative editing system used to create GO-CAM models. Noctua can also be used to create simpler, conventional GO annotations that may be incorporated into GO-CAM models.

Creating a GO-CAM Model

Login

To create or edit a GO-CAM model using Noctua, you currently need to have three things: an account on GitHub, an ORCID, and to be properly registered as a Noctua user in the GO users' metadata. If you are already a registered GO curator and have a GitHub account, you can login to Noctua by following the steps after clicking [Login] on any page and be clicking [Return] once a token has been issued.

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.

Accessing the Graph Editor

Once you've logged into Noctua, click on the [Create Noctua Model] button at the top of the home page to create a new model using graphical editing interface. If you want to edit an existing model, click on the "Edit" button to the right of that model in the list at the bottom of the page.

Creating an Individual

The core graphical view of a statement in GO-CAM is called an "individual". To create a new individual, you can click on either of the four options on the left side of the editor: [Add individual], [Add annoton], [Add function], [Add process]. Simply fill in the the autocomplete fields in one of the options and hit the appropriate "add" button. The core unit of annotation for a GO-CAM model is the annoton. Annotons represent linked statements about the function of a gene product, where the function occurs at a cellular level and the process in which the function is executed.

Add text and screenshot for each.

Adding Contextual Information

Information about an individual, for example a statement that a Molecular Function is enabled by a given entity, can be refined by adding additional contextual information such as input for the Molecular Function. To add contextual information to an individual, click on the green box in the individual and in the resulting pop-up window go to the section entitled "Add edge & class expression" and enter the appropriate relation and entity in each of the two respective fields.

Adding Evidence

Every assertion in a GO-CAM model should be supported by evidence. To add evidence to an individual, click on the empty box in the upper right corner of each colored box that illustrates a relation and an entity. In the resulting pop-up window, go to the "Evidence" section and add an Evidence Code from the Evidence Code Ontology (ECO), a supporting reference (either PMID, doi, or GO_REF), and where appropriate an entry in the With/From field.

Linking Individuals with Relations

Individuals in GO-CAM models are linked with semantically appropriate relations from the RO. To link two individuals, click on the blue circle in the box of the individual that is the "subject" of the relation and drag the cursor from that individual to the individual that is the "object" of the relation. The "object" individual will be highlighted when you've made the connection and then a pop-up window will open displaying a list of RO relations. Click on the radio button for the relation you want to use and then save your selection. The evidence pop-up window is searchable in the standard ways for searching a web page.

To add evidence to a relation, click on the box containing the relation name and you will be taken to a pop-window where you can add an Evidence Code, reference, and With/From entry, as described above.

To delete a relation, drag the blue circle off of the "object" individual and onto the background canvas. The relation will automatically be deleted from your model.

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!

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:

Incorporating GO-CAM Annotations into your Workflow

GO annotations created in Noctua can be downloaded in three different annotation file formats: GAF, GPAD, and OWL.  Note that the OWL representation of GO-CAM models is the semantically correct representation, and that GAF and GPAD file formats are the closest representation of the OWL-based GO-CAM model that can be made using these legacy annotations file formats.

From Noctua, annotation files for a specific model can be viewed and downloaded by clicking on the Model drop down and then selecting the appropriate Export option from the list. Resulting annotation files will appear in the browser and can be downloaded from there.

Alternatively, GO-CAM annotations files can be retrieved from Jenkins. Currently there is a repository for legacy file formats that are marked production here.

OWL models may be retrieved here:

TBD.

Providing Feedback

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!