Infrastructure and standards for publishing research data in the plant sciences

The aim of open science is to make scientific research accessible, facilitating experimental reproducibility and transparency. Mechanisms exist for preserving and publishing research objects in plant science within the “omics” fields. However, researchers are often hindered by:
(i) complicated and time-consuming procedures for repository deposition;
(ii) a lack of interoperability between disparate information sources and mechanisms;
(iii) sub-optimal search and retrieval facilities across data repositories; (iv) a lack of public awareness of existing services.

To address these issues, we are developing COPO (Collaborative Open Plant Omics), a brokering service which enables aggregation and publishing of research outputs by plant scientists, and provides access to data repository services across disparate sources of information via web interfaces. COPO comprises a novel intuitive wizard-enabled web front-end, data grid infrastructure, and a number of Application Programming Interfaces (APIs),  which facilitate the creation and management of logical profiles containing heterogeneous but related research objects representing a body of work. COPO leverages the Investigation Study/Assay (ISA) formats and ISA software suite (http://www.isa-tools.org) to enable experimental metadata attribution and conversion between metadata formats.

As research objects annotated and deposited through COPO will be accompanied by rich metadata implemented in JSON-LD (http://www.json-ld.org), cutting edge technologies such as MongoDB (http://www.mongodb.org) and neo4J (http://www.neo4j.org) are being used to create a web of linked semantic knowledge, allowing for user customised suggestions for future avenues of investigation.