TermGenie - a web-application for pattern-based ontology class generation

Abstract

Background: Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes.

Results: TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 new classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes.

Conclusion: TermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.

Keywords: Class generation; Ontology.

Figure 1

Conventional ontology class request workflow. General workflow for ontology class requests using a traditional issue tracker. A simple class request may take several days, for complex cases even longer.

Figure 2

Overview of TermGenie Components and Workflow. (1) Retrieve existing templates for user selection; (2) Term generation processing and validation; (2a) Generate textual data and OWL axioms; (2b) Use reasoning to check for existing classes and new or changed relations; (3) Review of generated classes by the user in the web interface; (4) After review, assign permanent identifiers to the new classes; (5) Add the new classes into the queue for review; (6) Senior ontology developers review the classes: accept, modify, obsolete; (7) Commit the changes to the ontology; (8) Send confirmation e-mail to the user.

Figure 3

Example template and configuration for TermGenie. (top-left) XML-based example template configuration for the Gene Ontology template chemical_export. Includes declarations for required and optional input fields and corresponding JavaScript file; (top-right) Javascript snippet from the JavaScript file. for generating a class and OWL axioms; (bottom) Screenshot of the generated TermGenie input fields. Also shows autocompletion on ChEBI classes.

Figure 4

Inferences for a class using a standard OWL reasoner. Reasoning example for a genus + differentia pattern for camptothecin catabolism in the GeneOntology. The class is defined by its genus ‘catabolic process’ (GO:0009045) and differentia ‘has_input camptothecin’ (CHEBI:27656). Following that definition, the class is a subclass of catabolic process. Using the additional axioms from ChEBI and the GeneOntology, a standard OWL reasoner can infer the more specific superclass ‘alkaloid catabolic process’ (GO:0009822).

Figure 5

TermGenie user workflow. To create a class in TermGenie, Biocurators go to the TermGenie website and select the relevant template for their request. The template consists of a set of required and optional input fields. TermGenie provides autocompletion for appropriate input fields. After passing some quick checks, the request is sent to the server, where generation and reasoning are executed. The results are send back and the users have the chance to review the proposed classes. The next step is the submission of the generated classes for review. As part of this process, a new permanent identifier is generated using a customizable identifier pattern and range. Furthermore, the request is added to the review queue for final approval by the ontology developers.

Figure 6

TermGenie workflow during a submitted class review by an ontology developer. After a user has submitted their generated class requests, the requests are put into a queue for review by an ontology developer. During the review the ontology developer has the following three choices: approve, modify, or obsolete. For the commit, the server uses the version control adapter to create a clean checkout. From there TermGenie loads the ontology as a separate instance and applies the relevant changes. After writing the changed ontology as a file, TermGenie tries to commit the updated file into the version control. After a successful commit the queue is updated and a confirmation e-mail is sent to the requester.