Architecture

The General Architecture For Representing Metadata in BioPortal

The general architecture of the metadata representation in BioPortal. There are two main components: (1) the BioPortal Metadata ontology defines the types of metadata that BioPortal represents; (2) The BioPortal Metadata knowledge base imports the BioPortal Metadata ontology and contains the instances of its classes corresponding to the specific metadata values.

The set of ontologies and key classes for representing metadata in Bioportal

Metadata instances describing two versions of the FMA and a view of the FMA

We represent all BioPortal metadata as instances in the BioPortal Metadata ontology. The two figures below present the overall architecture and an example of several connected instances in the metadata ontology. When a service or another API call requests metadata information, the implementation queries the BioPortal Metadata ontology for the corresponding instance information.

All the metadata in BioPortal are represented as instances of classes in the BioPortal Metadata Ontology (see the figure). This ontology imports three other OWL ontologies:

1. The Ontology Metadata Vocabulary (OMV) describes most of the metadata for ontologies themselves (e.g., domain, author, version number, ontology language, etc.)
2. The Protégé Changes ontology provides the definitions for generic annotations (the Annotation class) and ontology components that they annotate.
3. The Mappings ontology provides vocabulary for describing one-to-one mappings between concepts and corresponding metadata

The BioPortal Metadata ontology, by importing these three ontologies, can use all the classes and definitions from there and extend these definitions. The specific metadata is represented as instances of corresponding classes.

The BioPortal Metadata Ontology

The following ontologies are available for download and direct access at the Protege web site:

• The BioPortal Metadata ontology
• The Changes ontology
• The Mappings ontology

Classes and properties in the BioPortal Metadata ontology

We will now describe some key classes used to represent metadata.

Representing ontology metadata and provenance information

The metadata about ontologies themselves is represented mostly using the OMV vocabulary (namespace prefix “OMV”). OMV is the ontology developed jointly with the NeON consortium and accounts for much of the ontology metadata, including provenance information, static values (number of classes, etc.), licensing information, and so on.

The class OMV:Ontology

The main class in OMV is OMV:Ontology. It contains a set of metadata for a particular version of the ontology. Some properties of interest, among others, are:

• name
• acronym
• creationDate
• description (range: String)
• documentation (range: URL)
• endorsedBy (range: OMV:Party)
  • one of the instances to fill in this value is OBOFoundry, an instance of OMV:Organisation
• domain
• ontologyLanguage
• keyClasses
• keywords
• ...

We also add some instances for ontology engineering tools and methodologies to account for OBO ontologies (OBO-Edit tool and the DAG ontology structure) and to include the OBO Foundry, caBIG, and others as endorsing organizations.

The class VirtualOntology

A class VirtualOntology collects the information about each virtual ontology in the repository, all its versions and views. There is one instance of the VirtualOntology class for each virtual ontology in BioPortal. Each such instance has the following properties:

• currentVersion (range: OMV:Ontology) is a pointer to the metadata describing the current version of the ontology;
• ontologyName (range: String) provides a name for the ontology (e.g., “NCI Thesaurus); we don’t technically have to have it as we can get it from the current version, but it may be useful to have it here for convenience (but need to remember to update it)
• virtualURI (range: URI) provide a virtual URI for this ontology; it could also be an ontology ID, as used in BioPortal now
• hasViews (range OMV:Ontology) provides a collection of instances of the OMV:Ontology class corresponding to the views of this virtual ontology
• hasVersions (range OMV:Ontology) provides a collection of instances of the OMV:Ontology class corresponding to the versions of this virtual ontology

The class Project

A class Project contains the information about each project. This information is represented as instances of the Project class. Each project has the following properties:

• projectName (range: String)
• description (range: String)
• institution (range: String)
• homepage (range: URL)
• administrator (range: User)
• hasContactInformation (range: String)
• usesOntologies (range: VirtualOntology)

The class BioPortalUser

A class BioPortalUser extends the class OMV:Person and foaf:Person. In addition, each user has the following properties:

• userName (range: String)
• createdReviews (range: Review)
• createdMarginalNotes (range: changes:Annotation)
• createdMappings (range: mappings:Mapping)

Representing marginal notes and reviews

Marginal notes and ontology reviews instances contain the content of the notes and reviews, their types, and the provenance information for them. The Protégé Changes ontology provides several key classes for representing ontology components and annotations and we extend these classes with several classes and properties relevant to BioPortal:

Classes for annotations and objects that can be annotated. Classes in white boxes are imported from the Protégé changes ontology. Classes in grey boxes are added in the BioPortal Metadata ontology.

The classes and properties below describe annotations

The class changes:AnnotatableThing

The class changes:AnnotatableThing represents anything that can be annotated, including ontology components, ontologies themselves, mappings, other annotations, etc. This class has the following key property:

• changes:associatedAnnotations (range: changes:Annotation) links to all annotations that are associates with this object

The subclasses of changes:AnnotatableThing:

• changes:OntologyComponent (represents classes and properties; we will use this class to encapsulate how we address individual classes and properties)
• the class Ontology added in the BioPortal Metadata ontology to represent ontology as a whole as a target of a review
• changes:Annotation, includes marginal notes and reviews.

The class changes:Annotation

Instances of the class changes:Annotation represent reviews and marginal notes, as well as notes on mappings and other reviews. For now, marginal notes will be direct instances of Annotation because we do not distinguish between different types of marginal notes, such as questions or proposals. This class has the following key properties:

• changes:annotates, which is the inverse of the property changes:associatedAnnotations. This property has instances of changes:AnnotatableThing as its value. Thus, it refers to the exact version of a concept or an ontology for which annotation has been created.
• annotatesByVirtualID contains the virtual id for the ontology or the concept that this annotation annotates. We need this property for efficient retrieval so that we can query by the id.

The only subclass of the class Annotation that we will currently use is the class Review that represents the reviews of the ontologies (see below).

The class Review

Representing a single ontology review with several dimensions

A class Review is a subclass of Annotation. This class represents reviews of an ontology as a whole. Each review contains ratings and comments along each of the dimensions specified as the evaluation dimensions (class EvaluationDimension, with two properties: numericRating, textualReview). It has the following properties, in addition to the provenance ones inherited from the Annotation class:

• inTheContextOfProject (range: Project; inverse property: ontologyReviews) indicates that a review was created in the context of a particular project
• the range for the property annotates is restricted to OMV:Ontology
• A property for each of the review dimensions. These properties are all subproperties of the property reviewOnDimension (range: EvaluationDimension (see figure)):
  • digreeOfFormalityReview
  • documentationAndSupportReview
  • usabilityReview
  • domainCoverageReview
  • correctnessReview
  • qualityOfContentReview

This list of properties can be changed or extended, and, thus, other implementations can custom-tailor the dimensions. Each property has an annotation property rdfs:label that contains a string that will be displayed for this dimension (e.g., "Domain coverage"). If the order in which these dimensions appear is important, the developers will need to update the Constant Names.DIMENSIONS in the code.

Representing Mappings

The Mappings ontology represents different types of mappings and the corresponding metadata. More details on the mapping metadata in a separate document. We define the mapping ontology for BioPortal to represent one-to-one mappings. This ontology has the key classes described below.

Mappings and the mapping metadata. Note that we may choose to represent the source and target of mapping as an instance of changes:Ontology_Component to factor out the way that we use to refer to specific versions of concepts

The class mappings:One_to_one_mapping

A class mappings:One_to_one_mapping represents a mapping between any two concepts (usually, from different ontologies) It has the following properties (all in the mappings namespace:

• source (range: URL)
• target (range: URL)
• relation (range: URL)
• mapping_metadata (range: Mapping_Metadata)

The class mappings:Mapping_Metadata

A class mappings:Mapping_Metadata represents the metadata about each mapping:

• applicationContext (range: String)
• authority (range: Authority, a class with two subclasses Authority_Algorithm and Authority_Manual; the former contains the details of the algorithm)
• comment (range: String)
• date (range: date)
• dependency (range: One_to_one_mapping)
• externalReferences (range: String)
• submittedBy (range: undefined)
• verified (range: undefined)

Note that we change the range for mappings:source and mappings:target to be changes:Ontology_Component. Thus, we will re-use whatever solution we choose to represent targets of annotations. Because one can also add comments to mappings, we add changes:AnnotatableThing as another superclass of the class One_To_One_Mapping. Thus, One_To_One_Mapping now has changes:associatedAnnotations as one of its properties.