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Ontodog: A Web-based Ontology Community View Generator

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Ontodog is a web-based ontology community view generator. For the details on how to use the ontodog, please see the tutorial page. This page also shows some examples on how to use the Ontodog output files.

Ontodog data input:

(1) Provide Ontodog input term file (Microsoft Excel file or tab-delimited text file. see help or use tool to generate template file):
Upload: * Required
(2) Select one source ontology: * Required
Or enter your own source ontology and SPARQL endpoint: Example

Settings for Ontodog output files: * Please check at least one file

Output File 1: inSubSet annotation ontology (help)
(1) URI of owl file (e.g.: http://purl.obolibrary.org/obo/FGED_inSubset.owl, optional):
(2) Annotation Property URI (default: http://www.geneontology.org/formats/oboInOwl#inSubset).
(3) Annotation Value (e.g.: SLIM, FGED, IEDB ...):
* Required for output file 1
Output File 2: User preferred annotation ontology (help)
NOTE: This file includes user-preferred label defined in Ontodog input term file (e.g., OBI term 'selective maintained organism' = FGED term 'strain').
(1) URI of owl file (e.g.: http://purl.obolibrary.org/obo/FGED_annotation.owl):
(2) * Required for output file 2
Annotation Property URI (one child term of IAO: alternative term, e.g.: http://purl.obolibrary.org/obo/OBI_9991119)
or label of the Annotation Property if not defined. A new term will be generated.
(3) Language of annotation values used:
Output File 3: Subset of source ontology containing all view terms and related terms/axioms (help)
(1) URI of owl file (e.g.: http://purl.obolibrary.org/obo/obi_FGED.owl)
(2) Include inferred hierarchy?
(3) Include all individuals of a class in the subset?

Please cite the reference: 

Zheng J, Xiang Z, Stoeckert Jr. CJ, He Y. Ontodog: a web-based ontology community view generation tool. Bioinformatics. 2014; doi: 10.1093/bioinformatics/btu008. [PDF]


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