The Human BAC Ends database includes all non-redundant human BAC end sequences (BESs) generated by The Institute for Genomic Research (TIGR), the University of Washington (UW) and California Institute of Technology (CalTech). It incorporates the available BAC mapping data from different genome centers and the annotation results of each end sequence for the contents of repeats, ESTs and STS mark...

State of the art RDF stores often rely on exhaustive indexing and sequential (self-)joins for SPARQL query processing. However, query execution is dependent on, and often limited by the underlying storage and indexing schemes. Even though RDF can give birth to datasets with loosely defined schemas, it is common for an emerging structure to be present in the data. In this paper we introduce a no...

A central component in many applications is the underlying data management layer. In Data-Web applications, of this layer triple store. It thus evident that finding most adequate store for application to develop crucial importance individual projects as well integration on Data Web general. paper, we propose a generic benchmark creation procedure SPARQL, which apply DBpedia knowledge base. cont...

To gain insights into the microstructure of polyvinylpyrrolidone (PVP), a detailed reaction mechanism is developed, which characterizes polymer along property coordinate chain length, terminal double bonds (TDB), and branching points. For practical purposes, calculations with three coordinates are unfeasible, model reduction needed. Here, reduced only one single without significant loss accurac...

ToxoDB (http://ToxoDB.org) provides a genome resource for the protozoan parasite Toxoplasma gondii. Several sequencing projects devoted to T. gondii have been completed or are in progress: an EST project (http://genome.wustl.edu/est/index.php?toxoplasma=1), a BAC clone end-sequencing project (http://www.sanger.ac.uk/Projects/T_gondii/) and an 8X random shotgun genomic sequencing project (http:/...

We have compared the performance of five non-commercial triple stores, Virtuoso-open source, Jena SDB, Jena TDB, SWIFT-OWLIM and 4Store. We examined three performance aspects: the query execution time, scalability and run-to-run reproducibility. The queries we chose addressed different ontological or biological topics, and we obtained evidence that individual store performance was quite query s...

In this paper, we compare various options for reifying RDF triples. We are motivated by the goal of representing Wikidata as RDF, which would allow legacy Semantic Web languages, techniques and tools – for example, SPARQL engines – to be used for Wikidata. However, Wikidata annotates statements with qualifiers and references, which require some notion of reification to model in RDF. We thus inv...

While genome sequencing projects are advancing rapidly, EST sequencing and analysis remains a primary research tool for the identification and categorization of gene sequences in a wide variety of species and an important resource for annotation of genomic sequence. The TIGR Gene Indices (http://www.tigr.org/tdb/tgi. shtml) are a collection of species-specific databases that use a highly refine...