GenopageOrganism is the concrete entity for E.coli from Genopage, MetabolicPathway is the abstract entity for metabolic pathway, GenopageCDS are the concrete entities for neighboring genes and GenopageProtein is the concrete entity for the proteins encoded by the genes.
For example, GenopageProtein is the concrete entity mapped with the abstract entity Protein, for which instances can be found in the database Genopage.
With each concrete entity is associated a query in its underlying database, which expresses how to retrieve instances of the concrete entity in the database (e.g. v1 for C11 in Fig. 1).
A second kind of link is the association between the concrete entities and their properties.
The abstract entities are CDS (linked to the property name) and Organism (linked to the property speciesname), whereas the concrete entities are PareoProtein and PareoBiochemicalReaction (linked to the property EC_number).
The concrete entities level is represented by a directed graph, the graph of concrete entities (Figs 1 and 2. Its vertices are of three kinds: (1) concrete entities such as ProseProtein (circles in the bottom panel of Fig. 2), (2) properties of these entities such as length or amino acid sequence (data not shown) and (3) link entities, such as ProteinLink, which represent the links tables.
Since biological entities can be considered at two degrees of abstraction, we distinguish the abstract entities level and the concrete entities level.
The quantum vacuum is a concrete entity (in the sense described in sections 4 and 7) and so is in the philosopher's domain of discourse.
Then, we add associations between concrete entities that are not in the same source, (thin black lines in Fig. 5) in order to link the concrete entities between the sources (e.g. Proseprotein and GenopageProtein).
Alternative paths are high-level paths (containing only abstract entities), that take into account the mapping between the biological links in the concrete entities level and the paths in the abstract entities level defined in Section 3.2.
