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Importing multiple terms from multiple external ontologies
One of the major principle in ontology design is reuse terms defined in other ontologies. To comply with this good practice, we started reusing terms already existing in other ontologies and we focused on the IAO ontology for terms related to model description and on SBO for terms describing model parameters. To import terms from another ontology, you have two main possible options: 1- importing the whole external ontology or 2- importing selected terms from this ontology. Although the option 1 seems to be the easiest, importing large ontologies into CNO could be troublesome and would add up terms that are not necessary in the context of CNO. Therefore we decided to import selected terms.
For this purpose, the Minimum Information to Reference an External Ontology Term or MIREOT format has been proposed. To support such method of importing terms, a web interface, [Ontofox] (http://ontofox.hegroup.org/) has been designed to export selected terms using the MIREOT format.
We used Ontofox to extract the terms of interest from SBO and IAO (Xiang et al., 2010). For this, we created an input file with the support of the [tutorial] (http://ontofox.hegroup.org/tutorial/index.php). This file has been build to import multiple terms ( for information regarding merging OntoFox input files for different source ontologies, see [here] (http://ontofox.hegroup.org/tutorial/index.php#merge)) from SBO, IAO and OBI.
The input file is then submitted to the Ontofox web service, which then gather the requested information using dedicated SPARQL queries and concatenate the result into an owl file.
The output owl file containing the imported terms has been added in the folder /external_import and was named external.owl.
In order to keep track of the import, we also added the input file used to generate the owl file in the folder /external_import.
To include the external.owl ontology into CNO, we used a simple ontology import in Protégé.
To add new terms from other ontologies, we just need to add the necessary information into the input file and generate a new owl file.