Figure 7

Location-related ruleforms. The Location Context Attribute ruleform is used to specify what kinds of Attributes a Location in the given context is allowed to have; these can be thought of as defining the internal structure of the Location. In Panel A, four rules specify that Locations in the 18th draft of the human genome must have four coordinates. "Base Sequence" here will refer to a chromosome, but can be used in other Location Contexts to stand for some sequence a Location may be defined on, such as a cloning vector or protein sequence. "Strand" will refer to either the forward or reverse DNA strand, while "Start" and "Stop" refer to the numerical coordinates where the Location will begin and end. This can be seen in Panel B, where the boxed region of the genome shown is represented as rules in the Location and Location Attribute ruleforms. First, a new Location must be defined, named "Genomic Region 100" (it may be anything, so long as it is unique among all Locations). This Location can now have values defined for each coordinate specified in the Location Context Attribute ruleform for an 18th draft genomic region by using Location Attribute rules, as shown. Finally, Panel C illustrates the BioEntity Location ruleform, which is used to define the kinds of Relationships that BioEntities can have with various Locations. In this sense, it is similar to the BioEntity Network ruleform, with the difference that here we relate a BioEntity and Location, not two BioEntities. This ruleform is another example of a Resource-qualified ruleform; it is important to know who says a particular annotation is located at a specific genomic location, just as it is important to allow for the fact that different proteogenomic analysis methods may map the same peptide to several places on the genome.