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Table 1 Francisella data sets combined in RDF with load times (elapsed time) into a Sesame Native repository with index structure [SPOC, POSC, POSC].

From: Francisella tularensis novicida proteomic and transcriptomic data integration and annotation based on semantic web technologies

Resource Source file name Triples load time
Genome data sources and annotations
Integrated Microbial Genome Data francisella.rdf2.nt 10,434 2.37 min
Fn genome data from The integrated microbial genomes (IMG) system
http://genome.jgi-psf.org/mic_home.html
Francisella NCBI RefSeq Data NC_008601.nt 12,781 0.69 min
Fn annotation data from Refseq Database
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=118496615
KEGG genome annotation Pathway*.nt 113,700 3.97 min
Fn genome annotation from KEGG downloaded from PathCase
http://nashua.case.edu/PathwaysKegg/Web/
Superfamily Annotation francisellaSUPERFAMILY.nt 16,110 0.27 min
Fn data from SUPERFAMILY Database
http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/gen_list.cgi?genome=0b
Proteomics Data
Proteomics Experimental Data Membranes.nt 416,086 10.43 min
University of Washington MglA protein abundance data sets from biological samples
Membranes Fraction    
Proteomics Experimental Data WholeCell.nt 184,221 8.36 min
University of Washington MglA protein abundance data sets from biological samples
WholeCell Fraction    
Proteomics Experimental Data Soluble.nt 580,873 4.33 min
University of Washington MglA protein abundance data sets from biological samples
Soluble Fraction    
Francisella (novicida U112) Proteome   248,647 4.79 min
University of Washington Fn peptide data
Francisella(novicida U112) Proteome interact-prot.nt 20,682 0.6 min
University of Washington Fn protein identification data
Francisella (novicida U112) genome FnU112Version3.nt 56,754 1.4 min
University of Washington Fn genome data
Proteome Identifier mapping to Genome Mgla_search_db.fasta.blastp4_ypURL.nt 1,719 0.03 min
Proteomics Identifier mapping to Genome from BLAST comparison
GO genome annotation Ft_novicida_U112_go.nt 135,345 2.2 min
Fn genome annotation from Gene Ontology Database
Transcriptomic Data
Transcriptomics Experimental Data GSE5468_family.soft_2.SERIES._rdf 45 0.01 min
GEO Ac GSE5468 MglA transcript abundance data set SERIES data
Transcriptomics Experimental Data GSE5468_family.soft_2.Platform._rdf 33,797 0.53
GEO Ac GSE5468 MglA transcript abundance data set PLATFORM data
Transcriptomics Experimental Data GSE5468_family.soft_2.SAMPLE._rdf 223,539 12.5 min
GEO Ac GSE5468 MglA transcript abundance data set SAMPLE data
Transcriptomics Experimental Data GSE5468_arrays_metadata.txt.nt 170 0.03 min
GEO Ac GSE5468 MglA transcript abundance data set SAMPLE metadata
Transcriptomics Experimental Data FTN2FTSA.nt 3,626 0.27 min
Blast Mapping of SchuS4 locus tag to U112 locus tag