Scaling success: Linking public breeding with private enterprise

<p>The known Downstream Promoter Element and Initiator site motifs are shown in boldface.</p

Additional file 1: of SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases

List of SPARQL shortcuts with example usages. (PDF 71 kb

Additional file 3: of SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases

Example SPANG commands compared with the corresponding plain SPARQL queries. (PDF 70 kb

List of the datasets available at the MBGD SPARQL endpoint.

<p>List of the datasets available at the MBGD SPARQL endpoint.</p

Retrieval of phylogenetic patterns of orthologs related to a specific function.

<p>(A) Schematic diagram of the RDF graph structure related to the queries in B and C. (B) SPARQL query to get MBGD clusters including members related to the GO term GO:0009288 (bacterial-type flagellum). (C) SPARQL query to obtain organisms that contain members of an ortholog group. (D) Search results of the query shown in B. (E) The results obtained from the queries shown in B and C visualized using R (the R source code is included in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122802#pone.0122802.s005" target="_blank">S1 Dataset</a>). The number of target organisms in each phylum is shown in parenthesis. After obtaining the output from R, the phyla containing gram-positive bacteria (+) and genes functioning in the flagellar export system (*) are marked, and the blue line was added to represent clusters with relatively wide organismal distribution (in at least 16 phyla).</p

Retrieval of ortholog information of a specific protein.

<p>(A) Schematic diagram of the RDF graph structure related to the query in B. The elliptical nodes represent resources. Specifically, the shaded elliptical nodes where classes are shown in italics represent the instances of the classes. In the unshaded elliptical node, the URI of the resource is directly shown. (B) SPARQL query to get GO annotation of an ortholog group. The prefix declarations are omitted for readability; the full description of the SPARQL query is included in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122802#pone.0122802.s005" target="_blank">S1 Dataset</a>. (C) Search results of the query shown in B.</p

RDF model of ortholog information based on OrthO.

<p>(A) Hierarchical structure of classes and properties in OrthO. OrthO includes 12 classes (<i>owl</i>:<i>Class</i>) and 20 properties (15 of <i>owl</i>:<i>ObjectProperty</i> and 5 of <i>owl</i>:<i>DatatypeProperty</i>). (B) Schematic representation of RDF graph structure of ortholog information described using OrthO. The elliptical nodes represent instances of classes. The directed edges represent properties. The dotted lines represent possible links to other resources.</p

Comparison of ortholog information from different data sources.

<p>(A) Schematic diagram of the RDF graph structure related to the query in B. The elliptical nodes represent instances of classes. The rectangular nodes represent literals (integers in this example). (B) SPARQL query to compare orthologs between MBGD and eggNOG. The first line enables the inference based on sub-class and sub-property relations (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122802#sec012" target="_blank">Methods</a>). (C) Search results of the query shown in B.</p

The portal page of MBGD SPARQL Search.

<p>The portal page of MBGD SPARQL Search.</p

Time required for executing SPARQL queries.

<p>Time required for executing SPARQL queries.</p