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Figure 3 | BioData Mining

Figure 3

From: Genomic analyses with biofilter 2.0: knowledge driven filtering, annotation, and model development

Figure 3

The simulated knowledge database for exploration of Biofilter functionality. Biofilter has a simulated knowledge database so that researchers can try features of the software and see the results, with the ability to track what happened in the process. The above schematic shows that the database contains three fictitious database sources: “light”, “paint” and “spectrum”. The sources are connected to eleven groups via lines: “red”, “green”, “blue”, “gray”, “cyan”, “magenta”, “yellow”, “gray”, “orange”, “indigo”, and “violet”. These sources/groups contain group members (blue ovals) that are linked to gene aliases (brown boxes). These gene aliases then link to 13 genes (orange hexagons), and three chromosomes (grey bars) with 21 SNPs (yellow diamonds). The gene aliases provide examples of ambiguous gene identifiers. Groups cannot presently be connected to more than one source, however groups may have more than one name provided by the source that defines them. For example, in the real source of KEGG, each KEGG pathway (group) has both a numeric ID number as well as a textual pathway name. In the schematic, the two nodes labeled “gray” are intended to depict two separate groups (provided by two separate sources) which happen to share the “gray” identifier, but which each also have another name which is distinct (“white” and “black”). Additional file 1 contains example commands used with this simulated database, along with the resultant output.

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