Brain is a Java library facilitating the interaction with OWL2 EL ontologies. The library aims at bridging the gap between graphical user interfaces such as Protege and the OWL-API: It provides a series of convenience methods to create and query knowledge bases using the Manchester syntax. The library is useful to develop web applications and particularly suited for the biomedical domain. Brain relies on ELK for reasoning tasks. The open source project is available at https://github.com/loopasam/Brain.
1.1
OWL2 EL
The second version of the Web Ontology Language (OWL2) introduces a series of
pro les: OWL2 EL, RL and QL [
The biomedical domain is particularly interesting for the OWL community
because of the richness and variety of the ontologies it contains. The majority of
resources such as the Gene Ontology [
The rest of the document will present the core features of the library as well as
an example of axiom implementation. The main idea behind Brain is to prevent
ambiguous situations to happen while manipulating an ontology and to simplify
the interaction with biomedical knowledge bases. Brain is implemented following
a pattern facade: It wraps the interaction with the OWL-API and the ELK
reasoner [
The source code of the library is open and freely available [
The interaction with Brain resolves only to the Manchester syntax [
One of the core design decision behind the library was to enforce the users to work with only one ontology. This simpli cation helps to focus on one knowledge base at the time and remove any ambiguity that could be present while dealing with scattered entities. It is yet possible to import and load external ontologies and entities, but Brain merge any new axioms into one single knowledge base. 2.4
Brain also enforces OWL entities to have a unique short form name. This choice was made in order to prevent ambiguity while using the Manchester syntax to formulate OWL expressions. For instance the short forms of the OWL entities http://example.org/Cat and http://semanticweb.org/Cat will be the same: Cat. The string \Cat" is ambiguous in this case and could present problems later on when this short form is used for a query. This issue is prevented by Brain and an exception is thrown when a potentially dangerous situation such as this one occurs. This choice is not exactly in line with some of the Semantic Web philosophy, but it seems likely to work in the biomedical domain, where entity identi ers are most of the time preceded by a unique pre x anyway. For example the short form names of the Open Biomedical Ontology (OBO) classes all start with a pre x uniquely identifying the biomedical resource. All Gene Ontology concepts start with the pre x "GO ". Note that this design is not against the unique name assumption: It is still possible for di erent names to refer to the same entities. 2.5
Brain enforces some constraints in order to keep the OWL ontology as robust and straightforward as possible. A lot of di erent types of errors can be thrown in order to alert the user that a problem exists in the underlying ontology. A special care had also to be put when interacting with expressions entered as strings. Problems encountered when creating or querying the ontology are made explicit to the developer in order to preserve the consistency of the knowledge base. Errors handling is also helpful to route requests and redirect users in a web application scenario. 2.6
A common use-case for OWL ontologies is to run queries in order to retrieve some implicit information. An OWL query is a standard OWL class expression in the context of Brain. The ELK reasoner is handling the classi cation and query tasks. The classi cation of the ontology is triggered only when absolutely needed and transparent to the user (lazy initialization). Queries are also formulated using the Manchester syntax and it is possible to use the label (rdfs:label) of OWL entities to enter the query expression, as featured in Protege. Queries are thread-safe: For instance the simultaneous queries of two users will be correctly handled by Brain. This characteristic is important in a concurrent web server setting. 2.7
The methods present in the library are only ful lling requirements from users. However some important features are still missing: Individuals are not currently supported for example. Despite not being oriented towards OWL individuals, OWL2 EL ontologies are yet sometimes using them. This drawback will be addressed in a coming release. 3
The easiest way to understand the interaction with Brain is probably by
looking at a concrete example. This section will present the implementation of a
biomedical axiom using the library. The features discussed before are illustrated
in Figure 1. The interested reader can nd more examples on the wiki page [
Brain is a Java library leveraging the interaction with the OWL-API and the ELK reasoner. The library is dedicated to OWL2 EL ontologies and provide an interface to manipulate and query biomedical knowledge bases. The library has been designed to build web applications and to perform new type of biomedical analysis relying heavily on an OWL reasoner. Some features will be added in future releases, such as individual support. New functionalities are also currently implemented, such as the generation of scalable vector graphics (SVG) representing the OWL class taxonomies from the underlying ontology. Brain is already stably used in some real life biomedical applications and new use-cases from the community will guide the further development of this library. //Creation of a fresh Brain instance. //All the operations will be done on this object.
Brain brain = new Brain(); //Add some OWL classes to the ontology. //Short forms or full URIs can be used, but //the short forms have to be unique. brain.addClass("Nucleus"); brain.addClass("http://example.org/Cell"); //Add an OWL object property to the ontology brain.addObjectProperty("part-of"); //Declare a complex axiom (partial existential restriction). //Note that OWL expressions using the //Manchester syntax can be used directly for the axiom //assertion. If the entities used in the expression were //missing, an error will be thrown (not shown here). brain.subClassOf("Nucleus", "part-of some Cell"); //Integrate the content of an external knowledge base //with the current ontology. brain.learn("http://example.org/bar.owl"); //Query the knowledge base for indirect subclasses //with the help of the ELK reasoner. //Note that the classification initialization is //transparent to the user.
List<String> subClasses =
brain.getSubClasses("part-of some Cell", false); //Free the resources used by the reasoner. brain.sleep(); //Save the ontology as a file //using the Manchester syntax. brain.save("your/path/to/ontology.owl"); using Brain; the axiom expressed in natural language: A nucleus is part of some cells. Same axiom described in OWL using the Manchester syntax: Nucleus subClassOf partof some Cell.