1. A method of using a data presentation system including a graphical user interface that displays data to a user and accepts inputs from the user, the method comprising: a) importing at least one ontology into an ontology data storage accessible by the data presentation system, the ontology representing a formal identity of the data describing relationships in common vocabularies for the data, in order to contextualize the data to allow uniform query of the data; b) mapping the at least one ontology onto a presentation layer to provide a reference from data elements to one or more known schemas, which represent dependencies and similarities between data elements, based on meta-data associated with the data elements; c) displaying the presentation layer, the presentation layer comprising a subset workspace of the displayed data and the mapped ontology from the ontology data storage, the subset workspace comprising a set of data elements having a common relationship; d) accepting a first set of inputs from the user, wherein the first set of inputs specify selections of positions within the subset workspace; and e) generating an ontology element comprising at least some of the displayed data, based at least in part on the first set of inputs.