Tripal within the Arabidopsis Information Portal

The Arabidopsis Information Portal (https://www.araport.org, Araport) is an NSF and BBSRC funded project aimed at providing users with an interface to access a wide variety of Arabidopsis data by leveraging powerful web services. The portal includes an instance of InterMine based query interface to the data (which is currently rebuilt periodically from data derived from multiple sources), called ThaleMine. As part of its mandate, Araport inherited from TAIR the responsibility to provide the community with open access to up-to-date Col-0 data. Towards this end, we have been involved in the migration of data from TAIR’s database a custom-built schema in Oracle) to Araport into a Chado-backed data warehouse, fronted by Tripal. This serves as our core database, used to track multiple versions of genome annotation (TAIR10, Araport11, etc.), evidentiary data (used by our annotation update pipeline), metadata such as publications collated from multiple sources like TAIR, NCBI PubMed and UniProtKB (curated and unreviewed), stock/germplasm data linked to AGI loci via their associated polymorphisms. On top of this database, we intend to deploy a community curation layer that will track user contributions to gene structure and function modifications via an implementation of WebApollo. We also plan to leverage the Tripal API platform to expose RESTful web services, powered by Drupal modules (called “Services” and “REST”). These can be consumed both by community resources (such as the ABRC and NASC stock centers) and by users (who wish to work with the latest annotation datasets), giving them access to up-to-date data.