S3DB core: a framework for RDF generation and management in bioinformatics infrastructures

BMC Bioinformatics

Table 1 Minimal description of the core 12 relationships and 1 operator between the 7 s3db entities, using notation 3 (N3).

(s3db:deployment s3db:project s3db:collection s3db:item s3db:rule s3db:statement s3db:user) rdfs:subClassOf s3db:entity.
(s3db:DP s3db:PC s3db:PR s3db:CI s3db:CI s3db:Rsubject s3db:Robject s3db:Rpredicate s3db:Ssubject s3db:Sobject s3db:Spredicate) rdfs:subClassOf s3db:relationship.
1. s3db:DP rdfs:domain s3db:deployment; rdfs:range s3db:project.
2. s3db:PC rdfs:domain s3db:project; rdfs:range s3db:collection.
3. s3db:PR rdfs:domain s3db:project; rdfs:range s3db:rule.
4. s3db:CI rdfs:domain s3db:collection; rdfs:range s3db:item.
5. s3db:Rsubject owl:inverseOf rdf:subject; rdfs:domain s3db:collection; rdfs:range s3db:rule.
6. s3db:Robject owl:inverseOf rdf:object; rdfs:domain s3db:collection; rdfs:range s3db:rule.
7. s3db:Rpredicate owl:inverseOf rdf:predicate; rdfs:domain s3db:item; rdfs:range s3db:rule.
8. s3db:Spredicate owl:inverseOf rdf:predicate; rdfs:domain
s3db:rule; rdfs:range s3db:statement.
9. s3db:Ssubject owl:inverseOf rdf:subject; rdfs:domain s3db:item; rdfs:range s3db:statement.
10. s3db:Sobject owl:inverseOf rdf:object; rdfs:domain s3db:item; rdfs:range s3db:statement.
11. s3db:DU rdfs:domain s3db:deployment; rdfs:range s3db:user.
12. s3db:UU rdfs:domain s3db:user; rdfs:range s3db:user.
s3db:user s3db:operator s3db:entity.

All relationships except for s3db:operator (last row) are s3db:relationship (first row). The inversion of RDF subject, predicate and object in relations 5-10 may appear capricious at this point but it will simplify the identification of automata for the propagation of s3db:operator states in the next section. Specifically, it will allow the definition of Equation 3 such that the direction of the arrows in Figure 2 is the same as the propagation of s3db:operator states.

ISSN: 1471-2105