In this project we are develping scientific workflow tools that will enable end-user composed semantic web-services to increase the interoperability of the growing array of web-based scientific databases and analysis
tools. These workflow tools are built from available and emerging open-source, open-standards technology.
The prototype problem domain that will guide this project, the phylogenomics of the plastid, will include genomic, transcriptomic, and proteomic data. Plastids are the descendants of cyanobacterial ancestors captured
by eukaryote hosts. As more cyanobacterial and plastid genomes are sequenced, information accumulates that could shed light on plastid genomics and phylogeny. One of the major plagues of humankind, malaria, is
caused by a parasite with a plastid: Plasmodium falciparum. A drug that disrupts the function of this plastid (the apicoplast) might be harmless to humans, who, like all animals, have no plastids.
Examination of the genes, the linear order of the genes, the proteins, and the temporal order of protein expression of related organisms can suggest possible apicoplast functions. The problem is the accurate
identification of relatives or even closely related plastid genes of known function. At present, the phylogeny of the apicoplast is not clear. A phylogenomics approach requires the extraction and analysis of genomic
information from diverse scientific disciplines: plant, algal and cyanobacterial systematics, plant biochemistry, animal parasitology, genetics and cell biology. This phylogenomics investigation will provide
software design use-cases, testing, and evaluation of scientific workflow composition tools and technology.