Ontology Request Broker

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In the process of annotating data files, curators may encounter terms in the data that have not yet been added to an appropriate ontology. Requesting a new ontology term and adding it to the ontology may take several days or weeks when it involves discussion with other ontology editors and requires a new production release of the ontology. For this reason we have developed the Ontology Request Broker (ORB) for use with Phenex. Using ORB, when an appropriate ontology term cannot be found during annotation, the curator simply requests a new term, providing a suggested label and description, using a special interface within Phenex. A provisional term is immediately created in the Bioportal provisional term database and added to the Phenex session for use by the curator. Independently, this term can be provided with a permanent ID after the ontology editing and release process are complete, and Phenex will automatically replace references to the provisional term with the permanent ID.

Components

Phenex term request interface

Phenex term request panel

During annotation in Phenex, curators can use the term request panel to obtain provisional terms. See the Phenex documenation for more details on usage. Phenex interacts with the Bioportal provisional term services to create provisional terms and also to query their properties and status. At launch time Phenex loads all provisional terms previously created by Phenoscape curators into its ontology session, making them available for use in annotation.

Bioportal provisional term services

The NCBO Bioportal provides web services for creating, and querying and updating the properties of, provisional terms. Provisional terms are created with a UUID-based IRI such as http://purl.bioontology.org/ontology/provisional/064dfc58-8143-491f-ab74-374507502f35 (they currently do not dereference to anything useful). All Phenex requests to the Bioportal services use a common Phenoscape user ID so that curators can use any provisional term created by project members.

Phenoscape provisional term management interface

Using the web-based provisional term management interface, Phenoscape ontology editors can review the requested terms, independently of data annotation work. After adding a term to an appropriate ontology, or deciding that an appropriate term already exists, the management interface can be used to apply the preferred permanent ID to the provisional term. The management interface, like Phenex, makes use of Bioportal web services to interact with the provisional terms database.

When Phenex opens a data file containing provisional terms, it checks to see if any have been assigned permanent IDs. If so, the data is updated to reference the permanent IDs.