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Table 1 Basic information about the syntactic ontologies and their mapping rules with the core ontology.

From: Annotation of SBML models through rule-based semantic integration

Data Source

Data Format

Classes

Object Properties

Data Properties

DL Expressivity

Rules

UniProtKB

UniProtKB XML

27

24

34

ALEN (D)

11

BioGRID

PSI-MIF

26

24

15

ALEN (D)

17

SBML

SBML

516

56

44

SHOIN (D)

14*

Pathway Commons

BioPAX

41

33

37

ALCHN (D)

11

  1. Pathway Commons differs from the other sources as its format, BioPAX, is already represented in OWL. The ''Rules'' column lists the number of SWRL mapping statements used to link each syntactic ontology with the core ontology. For the SBML syntactic ontology, the numbers are combined totals of the imported Systems Biology Ontology and MFO. MFO was used for export only, and therefore its rules are marked with "*'' to show that these are export rules. Statistics generated using Protégé 4 (http://protege.stanford.edu/).
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Journal of Biomedical Semantics

ISSN: 2041-1480