Case Study: TreeGenes Uses SSWAP To Serve Semantic Data To Existing Web Applications, New Web Applications, and Semantic Pipelines

Simple Semantic Web Architecture and Protocol (SSWAP), developed at the iPlant Collaborative, enables easy communication with other semantic web services by facilitating data marshaling, implementing data ontologies for self describing documents, and performing semantic matching.  The TreeGenes database has implemented 11 SSWAP semantic web services to serve out genomic and associated data from the database.  Currently, the following SSWAP services are available: a Contig service, Contig Keyword service, Amplicon Service, Alignment service, Tree Sample service, Region Sample service, AmeriFlux service, EST service, Primer service, SNP service, and MultiFasta service.  These semantic web services allow bioinformaticians to select a TreeGenes data set of interest, submit it to the SSWAP pipeline, and process it through any number of downstream services.  SSWAP has been further utilized by TreeGenes in conjunction with a new GIS-enabled web application called CartograTree. Through the SSWAP Tree Sample service, a user is able to submit a variety of input data types (contigs, amplicons, alignments, etc) and view originating Tree Samples within CartograTree's map interface.  Also, other helper table views built into CartograTree allow other web services to be launched from within CartograTree to bring selected data back into the pipeline for downstream analysis.  Likewise, CartograTree enables users to push data selected within its interface to the SSWAP pipeline for downstream analysis.  For more information visit the project websites: SSWAP (http://sswap.info), DiversiTree (http://dendrome.ucdavis.edu/DiversiTree), and CartograTree (http://dendrome.ucdavis.edu/cartogratree).