Ontorat

Ontorat: Ontology Representation of Axioms using Templates and Design Patterns

Ontorat is a web server that automatically generates and annotates ontology terms and axioms based on user-provided templates and specific design patterns. The development of Ontorat is inspired by the OBI project QTT (Quick Term Templates) and supported by the Ontology Design Patterns (ODPs) engineering. Ontorat implements the QTT procedure. Ontorat is relatively easy to use through an interactive web interface.

Example (licensed animal vaccines): Example page (Note: using this target ontology (VO), the input Excel template file (or input text file), and the settings design pattern file; after Ontorat execution, getting this output OWL file).

Manually generate Ontorat settings from web form:

(1) Specify target OWL file (RDF/XML format):

Online URL:

Or: File upload:

(2) Specify input data file (Only Excel file (.xls, .xlsx) or tab-delimited text file (.txt) is accepted):

Online URL:

Or: File upload:

Actual data starts from row:

(3) Purpose: New axioms will be used to:

(4) Annotations (use comma to separate annotations):

as
Note: All the listed annotation terms will be recognized in Ontorat, so no need to add them to Section 7 again.

(5) Equivalent classes (use comma to separate classes):

(6) Superclasses (use comma to separate classes):

(7) Terms used to define anntoations, equivalent classes, and superclasses (one line per term):

Examples: rdfs:label, iao:preferredTerm, iao:definition, iao:alternative term.

has URI

(8) Term URIs:

Start with:

(9) Auto-generated term ID:

Prefix: , number of digits: , start from:

Please cite the reference: Xiang Z, Zheng J, Lin Y, He Y. Ontorat: Automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. Journal of Biomedical Semantics. 2015, 6:4 doi:10.1186/2041-1480-6-4. PMID: 25785185.