Using ricordo refui
Reference User Interface consists of three web applications:
- query application for querying across data and model metadata
- composite editor for creating composites that conforms to the underlying grammar
- annotation editor for annotating data and models with ontological concepts
An example instance is running at http://wwwdev.ebi.ac.uk/ricordo-refui/Ricordo.html#ricordoapp. This documentation uses screenshots from the example instance.
Figure 1 shows the main page of the Reference User Interface listing the three applications. Each application can be accessed by clicking on the load buttons. The following sections describe each of these applications in detail.
The query service application is developed to allow users to search across annotated data repositories. This application allows users to find ontological concepts that are of interest and to search across the meta-data to find data and models that have mappings to the selected concepts.
Figure 2 shows the main page of the query application. Queries are constructed using the Manchester OWL syntax. The Manchester OWL syntax is derived from OWL Abstract Syntax but is less verbose and allows non-logicians to write and understand OWL descriptions. As shown in the figure, if the user is familiar with the syntax, users can type in the Manchester query directly. We also provide help in creating Manchester queries using a set of templates.
Selecting Use template as shown in Figure 2 provides some support for building Manchester queries. This is done by providing a set of templates. Figure 3 shows the interface that allows users to select the type of Manchester query they would like to construct which we refer to as templates.
Each template has a particular form to specify the query terms and relations (see Figure 4). Currently we support the following templates: – the Term template allows users to query the RDF store for data and model resources directly related to the selected term or one of its specializations (i.e. subclasses). For example, if the selected is Cardiac Atrium from the FMA, the query application will return all VPHDM resources bearing annotations to this ontological term or one of its specializations. For example, it will return also VPHM resources annotated to the (FMA's) Left Atrium. some – some AND some – and some ( some ) – and some -
Selecting a particular Manchester query type will generate fields to construct a Manchester query where users can type in terms and relations to build the ontological concept they are interested in. These fields also support auto completion of ontological terms and relations. Figure 5 illustrates the selection of plasma membrane. It may take a few seconds for auto complete terms to appear as we are searching across several large ontologies.
When the selection is complete, this creates the relevant Manchester query (Figure 6). Once the Manchester query is constructed users can click on the Select button. Search results are explained in Interpreting query results section.
Figure 7 illustrates a construction of a complex query using a template. Each reference to term and relation requires an ontological concept and a relation to be filled in, respectively. We have selected the Term and relation some (relation some term) template. In this case, the complex query formed binds the first term of the template to the ontological term volume from PATO, representing volumes, and the second term of the template to the ontological term heart, representing hearts. The query 'volume and inheres-in some (part_of some heart)' will return data and model resources annotated with PATO volume, or one of its specializations (i.e. subclasses), that are volumes of some part of the heart or the heart itself.
Selecting the query takes the user back to the main query page and automatically starts searching the annotations. The search will return a list of all the data and models that have annotations to the ontological concept. Figure 8 shows the search results for all data and models that have references to left atrium. It lists the model URL and the frequency of annotations.
The results table in Figure 8 can be further explored to find out individual elements with the annotations. Figure 9 lists the individual annotations and shows the variable URL, the property (biological qualifier) and the MIRIAM url which is associated with the term.
Composite editor allows users to integrate biological ontological terms to create complex ontological concepts. Similar to the query service application Manchester query syntax is used to search and construct ontological concepts. As shown in Figure 10, composite field allows users to type in the composite using the Manchester query syntax.
Use templates provides support for constructing Manchester queries. It takes the user to the page shown in Figure 4 where they can choose templates to create Manchester queries. Figure 11 shows construction of the composite volume and inheres-in some heart.
Selecting this composite created using Manchester query syntax takes the user back to the main composite editor page (Figure 12).
The composite is then created by clicking on the Create Composite button. This action will assign a RICORDO ID to the composite and save it into the knowledge base. Figure 13 shows the composite that has been created including its RICORDO identifier as well as the status.
If you try to create a composite that is already in the knowledge base, the tool will list the composite as an existing composite and will prevent you from adding it. As this search looks for equivalence classes the tool may list multiple composites.
The annotation editor provides an interface to annotate data and model resources with ontological concepts. The editor provides functionality to find relevant ontological terms which can be assigned to data and model resources. The output of the tool is an RDF statement which is stored in the meta-data repository. Figure 15 shows the main page of the annotation editor.
Model url field allows users to type in the URL of the resource they wish to annotate (Figure 16). In this example we have selected http://www.ebi.ac.uk/ricordo/toolbox/sbmlo#BIOMD0000000101 model.
Pressing the Search button lists the variables of the selected model.
Users can select the variable they wish to annotate from the list. This will take the user to a page where they can add annotations to variables. Figure 18 shows the output page when http://www.ebi.ac.uk/ricordo/toolbox/sbmlo#BIOMD0000000101_PM is selected. The page shows the variable identifier that the user is about to annotate and a list of existing annotations including the relationship and MIRIAM url of the biological annotations.
Qualifier field allows users to select the relation between the variable and the biological annotation. Term ID field allows users to type in the ID of the biological concept that they wish to annotate.
Find term ID button allows users to query for term identifiers using Manchester queries. In this example we have selected plasma membrane from FMA (Figure 19).
Pressing the Select button in Figure 19 will take the user back to the add annotation page. As shown in Figure 20 ID of the plasma membrane from FMA is added to the term ID field
Selecting Add annotation adds the new annotation to the RDF store. As shown in Figure 21 the new annotation is added to the list of annotations. Cancel takes the user back to the variable list.
