Computational protocol: OntoQuery: easy-to-use web-based OWL querying

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Protocol publication

[…] The implementation is based on two existing APIs: the OWLTools API (http://code.google.com/p/owltools/) and the JFact API (http://sourceforge.net/projects/jfact/). On the server side, the ontology is loaded, inferences are pre-computed and then query functionality is exposed to the client via a web service. Performance is comparable with query execution in the Protégé tool, once loading and reasoning have been completed. The ontology may be reloaded via an administrator URL as needed.Queries are sent to the server for syntax checks while they are being typed as well as when the query is submitted. The translation of labels to IDs and the parsing of the query to OWL Manchester syntax are performed on the server. Parsing errors are translated into a user-friendly informative format. The client-side JavaScript is responsible for most of the functionality of the input box, i.e. determining the possible type of the next token for suggestion, ranking of the suggestions’ relevance and syntax coloring. However, it is the server that returns fixed length lists of class names matching the introduced pattern for auto-suggestion. For the syntax-aware auto suggestion, we have implemented our own simple automaton, and for the ranking of suggestions, we use a custom-made metric. We use the Levenshtein distance and the position of the first match, assigning a bigger weight to the match position. Usability testing was conducted using ChEBI curators, who are trained chemists and not software or logic experts.Although the tool was initially developed for ChEBI, it is applicable to any ontology. Installation for another ontology requires specifying the online ontology file and setting a few installation variables. A default result view lays out the results with IDs, labels and the term Uniform Resource Identifier (URI) as the hyperlink.The tool has been tested on Firefox version 22 and on Google Chrome version 28. […]

Pipeline specifications

Software tools OWLTools, Protégé
Databases ChEBI
Application Ontology generation
Organisms Homo sapiens