SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services

<p>Abstract</p> <p>Background</p> <p>SSWAP (<b>S</b>imple <b>S</b>emantic <b>W</b>eb <b>A</b>rchitecture and <b>P</b>rotocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP was developed as a hybrid semantic web services technology to overcome limitations found in both pure web service technologies and pure semantic web technologies.</p> <p>Results</p> <p>There are currently over 2400 resources published in SSWAP. Approximately two dozen are custom-written services for QTL (Quantitative Trait Loci) and mapping data for legumes and grasses (grains). The remaining are wrappers to Nucleic Acids Research Database and Web Server entries. As an architecture, SSWAP establishes how clients (users of data, services, and ontologies), providers (suppliers of data, services, and ontologies), and discovery servers (semantic search engines) interact to allow for the description, querying, discovery, invocation, and response of semantic web services. As a protocol, SSWAP provides the vocabulary and semantics to allow clients, providers, and discovery servers to engage in semantic web services. The protocol is based on the W3C-sanctioned first-order description logic language OWL DL. As an open source platform, a discovery server running at <url>http://sswap.info</url> (as in to "swap info") uses the description logic reasoner Pellet to integrate semantic resources. The platform hosts an interactive guide to the protocol at <url>http://sswap.info/protocol.jsp</url>, developer tools at <url>http://sswap.info/developer.jsp</url>, and a portal to third-party ontologies at <url>http://sswapmeet.sswap.info</url> (a "swap meet").</p> <p>Conclusion</p> <p>SSWAP addresses the three basic requirements of a semantic web services architecture (<it>i.e</it>., a common syntax, shared semantic, and semantic discovery) while addressing three technology limitations common in distributed service systems: <it>i.e</it>., <it>i</it>) the fatal mutability of traditional interfaces, <it>ii</it>) the rigidity and fragility of static subsumption hierarchies, and <it>iii</it>) the confounding of content, structure, and presentation. SSWAP is novel by establishing the concept of a canonical yet mutable OWL DL graph that allows data and service providers to describe their resources, to allow discovery servers to offer semantically rich search engines, to allow clients to discover and invoke those resources, and to allow providers to respond with semantically tagged data. SSWAP allows for a mix-and-match of terms from both new and legacy third-party ontologies in these graphs.</p

Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration

<p>Abstract</p> <p>Background</p> <p>Scientific data integration and computational service discovery are challenges for the bioinformatic community. This process is made more difficult by the separate and independent construction of biological databases, which makes the exchange of data between information resources difficult and labor intensive. A recently described semantic web protocol, the Simple Semantic Web Architecture and Protocol (SSWAP; pronounced "swap") offers the ability to describe data and services in a semantically meaningful way. We report how three major information resources (Gramene, SoyBase and the Legume Information System [LIS]) used SSWAP to semantically describe selected data and web services.</p> <p>Methods</p> <p>We selected high-priority Quantitative Trait Locus (QTL), genomic mapping, trait, phenotypic, and sequence data and associated services such as BLAST for publication, data retrieval, and service invocation via semantic web services. Data and services were mapped to concepts and categories as implemented in legacy and <it>de novo </it>community ontologies. We used SSWAP to express these offerings in OWL Web Ontology Language (OWL), Resource Description Framework (RDF) and eXtensible Markup Language (XML) documents, which are appropriate for their semantic discovery and retrieval. We implemented SSWAP services to respond to web queries and return data. These services are registered with the SSWAP Discovery Server and are available for semantic discovery at <url>http://sswap.info</url>.</p> <p>Results</p> <p>A total of ten services delivering QTL information from Gramene were created. From SoyBase, we created six services delivering information about soybean QTLs, and seven services delivering genetic locus information. For LIS we constructed three services, two of which allow the retrieval of DNA and RNA FASTA sequences with the third service providing nucleic acid sequence comparison capability (BLAST).</p> <p>Conclusions</p> <p>The need for semantic integration technologies has preceded available solutions. We report the feasibility of mapping high priority data from local, independent, idiosyncratic data schemas to common shared concepts as implemented in web-accessible ontologies. These mappings are then amenable for use in semantic web services. Our implementation of approximately two dozen services means that biological data at three large information resources (Gramene, SoyBase, and LIS) is available for programmatic access, semantic searching, and enhanced interaction between the separate missions of these resources.</p