PROVA: Rule-Based Java-Scripting for a Bioinformatics Semantic Web

Abstract

Abstract. Transparent information integration across distributed and heterogeneous data sources and computational tools is a prime concern for bioinformatics. Recently, there have been proposals for a semantic web addressing these requirements. A promising approach for such a semantic web are the integration of rules to specify and implement workflows and object-orientation to cater for computational aspects. We present PROVA, a Java-based rule-engine, which realises this integration. It enables one to separate a declarative description of information workflows from any implementation details and thus easily create and maintain code. We show how PROVA is used to compose an information and computation workflow involving -rules for specifying the workflow, -rules for reasoning over the data, -rules for accessing flat files, databases, and other services, and -rules involving heavy-duty computations. The resulting code is very compact and re-usable. We give a detailed account of PROVA and document its use with a example of a system, PSIMAP, which derives domain-domain interactions from multidomain structures in the PDB using the SCOP domain and superfamily definitions. PSIMAP is a typical bioinformatics application in that it integrates disparate information resources in different formats (flat files (PDB) and database (SCOP)) requiring additional computations. PROVA is available at comas.soi.city.ac.uk/prova

Conceptual knowledge-based modeling of interactive 3D content

“…SCM, SMM as well as semantic content representations have been implemented using the semantic web standards (RDF, RDFS and OWL), which express facts as semantic statements, as well as the Prova declarative language [24], which expresses semantic rules as horn clauses. The restrictive use of the formally specified semantic web standardsthe Resource Description Framework (RDF), the Resource Description Framework Schema (RDFS) and the Web Ontology Language (OWL)-in SEMIC is preferred over the use of other concepts (in particular rules, which have high semantic expressiveness) because of the following two reasons: First, the semantic web standards provide concepts, which are widely accepted on the web and can be processed using well-established tools, such as editors and reasoners.…”

“…Mapping the other classes of the application-specific ontology to PO classes has been performed in a similar fashion (19)(20)(21). Moreover, two basic shapes (the rm:Box and the rm:Cylinder) are designed (23)(24)(25)(26)(27)(28)(29)(30)(31)(32) and assembled into the aso:Stool PO class (33)(34)(35)(36)(37)(38)(39)(40). Every rm:Box and rm:Cylinder included in a aso:Stool have dimensions and relative positions specified (41-52).…”

“…In line 20, a cut-off and a negation-as-failure are used to determine a stool, for which no x coordinate has been specified. Next, in one declaration all artifacts are assigned to stools (23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33). Finally, all artifacts and stools are incorporated in the cpr:granary (35-38).…”

“…The cpr:paintedWoman and its material are created in a similar way (18)(19)(20)(21)(22). Furthermore, for every artifact (24), an mlscm:TouchSensor is generated (27)(28)(29)(30). Every mlscm:TouchSensor activates an mlscm:RotatingInterpolator (32-37), which is controlled by an mlscm:TimeSensor (39-41).…”

“…For every artifact, a Transform node with a position indicated by the translation attribute is generated (e.g., [8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24]. It includes a Shape node with a material and an optional texture.…”