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Figure 9 | BMC Bioinformatics

Figure 9

From: Ultra-Structure database design methodology for managing systems biology data and analyses

Figure 9

Location-finding interface. This interface for querying Locations in our Ultra-Structure system is generated based on the contents of the rulebase and user input. Here, the user has a region of the genome that has been mapped as the source of a peptide detected by MS/MS analysis and she wishes to see what other annotations contain this mapped region. Initially, only panel A is shown. The region the user has is the "query location"; in the top selection box, the user indicates that it comes from the 18th draft of the human genome. The user indicates she is interested in other annotations from the same draft with the drop-down box labeled "Target Context". Finally, based on the relationships the system knows that can exist between the given Query Context and Target Context (defined by rules), the user selects a Relationship; here, she chooses "overlap-contained-by" to indicate that she wants all Locations that fully contain her query location. Upon selecting the Query Context, the interface in Panel B appears, requesting details pertinent to a Location of the chosen Context. Since the user has a genomic location, the system asks for details such as "Base Sequence" (e.g., a chromosome), and "Strand". When the user enters this information and presses the "Fetch BioEntities" button, the system reads the rules that govern the "overlap-contained-by" Relationship between Locations from the 18th draft of the human genome, finds all the Locations that satisfy that Relationship, and returns a list of all BioEntities that are associated with those Locations. In this scenario, six such BioEntities are returned, along with detailed Location information. The two rows indicated by the arrows represent annotated introns (suggesting heretofore unknown translational activity), while the other four represent annotations that themselves contain the introns (and, by extension, the user's query Location).

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