]> This is the "application ontology" of the HGT-DB case study, i.e., the DL-Lite version of the ORM conceptual data model (the latter was developed by Maria Keet and Santiago Garcia-Vallve). It being an "application ontology" with the base material a conceptual data model, it contains several design decisions, such as the naming of relations and inclusion of many data types. new object property for the sole purpose of approximating the reification see also the annotation in "contains" one could argue this is redundant and this info can be obtained through a path in the ontology, but that's not really doable, and easier to make the constraint explicit with the simple relation added gene x adjacent to another gene y if there is no other gene z between x and y actually, this is not "contains" but should be locates (which sounds odd), or that the strict clusters are located in the flexible ones, but then we have a problem on reading the label vs directionality, and on representing the functional and mandatory constraints. A strict cluster is in at most one FlexibleHGTgenecluster gene x nearby another gene y given some threshold value in number of basepairs given that the flexible clusters are built up from combining strict clusters that have a max gap of 1 gene, one could have, say, a flexible cluster that contains, say, 5 strict clusters (with four gaps thus), but there are obviously also "subclusters" of that (say, the concatenation of the first three strict clusters) that one may be interested in, or you do not want a totally perforated flexible cluster and combine a max of, say, 4 strict clusters (because else it may be a 'false positive' and not be a cluster at all) this is to say if "cluster" can also be a single hgt gene instead of at least 2 adjacent genes (or whichever size of the cluster). this is useful for dealing with the flexible clusters see annotation of class PATHway clusters the StrictHGTGeneClusters (= one or more genes with prediction 'hgt' that are adjacent to each other) where there is allowed to be a gap of max 1 gene between the strict clusters ( if >1 gene betweent any two strict clusters, it is another strict/flexible cluster) 1 the grouping of genes on a genome by some criterion, which is specified in its subclasses reification (sort of) of Gene nearby Gene so as to relate Threshold to it is a cluster of genes (not necessarily located adjecent to each other on the genome) whose KEGG codes all participate in the same PATHway one or more genes on a genome with prediction 'hgt' that are adjacent to each other 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 see annotation of class KEGG the values in the database are "though of" as types, not instances; i.e., some gene instance (the id) is in the database and the KEGG code is the categorisation of the gene product, such as 'DNA Polymerase'. 1 1 1 1 1 1 1 1 1 1 1 1 the values in the database are "thought of" as types, not instances; i.e., some gene instance (the id) is in the database and the PATH code is the type of pathway that the gene product (with some KEGG code) participates in.