PLAIN – A Computational API for Plant Genomic Data

The Arabidopsis Information Resource (TAIR) provides foundational data and services to the plant biology research community, including the Arabidopsis thaliana reference genome and its functional and structural annotation. The current web site makes the data available through search pages and graphical genome browser displays. The PLAIN project adds several open-source computational application programming interfaces (APIs) to the TAIR tool set to enable computational biologists to access TAIR data easily and efficiently. Based on a completely new object-oriented data warehouse design, PLAIN provides SOAP and REST web services for common data sets, available through the TAIR web site, and the ability to develop customized web services using Model Driven Architecture (MDA) and the Unified Modeling Language (UML). PLAIN bases its queries on Plant/SQL, a version of the ANSI SQL 200x SELECT statement standard, extended with special-purpose expressions to handle queries that are difficult or impossible to express in basic SQL: ontology tree queries, polymorphism-between-variant queries, and polymorphism range queries. PLAIN implements a reference query tool, the TAIR Query Builder, which integrates these technologies in a simple web-based interface. All PLAIN software will be available through github as open source software.