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Project 22: Plant data exchange and standard interoperability

Abstract

This project will improve the integration of Plant data standards with important interoperability technologies. Indeed, some interoperability technologies have already been established with BrAPI, MIAPPE and ISA (Tab/JSON) for Phenotyping data, but the link between phenotype and omics data needs to be improved. The latter can rather be well described using bioschemas and therefore it will be useful for plant researchers to build a graph dataset embedding both MIAPPE and Bioschemas annotated data. We will enable plant researchers' friendly data archive by embedding the main plant standards (MIAPPE, BrAPI, ISA) in RO Crate. To link with the current activities of the plant communities, and to ease the integration of more diverse data types, a bridge with Bioschemas will be set up by finalizing the MIAPPE Bioschemas mapping initiated during the 2021 biohackathon. To demonstrate the interest of this, real data will be converted from existing sources (BrAPI, ISA Tab, MIAPPE databases) to RO Crate and Bioschemas to sketch some proof-of-concept use case (eg, showing phenotyping network on a map, showing the link between expression and phenotype data, …).

Topics

Bioschemas Interoperability Platform Plant Sciences Tools Platform

Project Number: 22

Lead(s)

Cyril Pommier [email protected] ; Marco Brandizi [email protected]

Expected outcomes

  1. Alignment of Bioschemas and MIAPPE, with a fully fledged how-to-use guide for embedding Bioschemas markup for MIAPPE compliant web resources
  2. RO Crate containing plant standards (MIAPPE, BrAPI, ISA (tab or JSON))
  3. Use case study with at least one dataset
  4. RO Crate fully usable by plant researchers for their data integration and exchange, including loading into visualization and analysis tools.
  5. RO Crate used for submission in data repositories such as dataverse.
  6. Documentation and training on the use of RO Crate
  7. Reviewed patterns allowed in RO (i.e. does RO work with ontology other than sdo), and updates to API (RO-crate API, BRAPI (?) , ISA-API?)
  8. Eased knowledge extraction from plant integrative graph using tools such as Knetminer.

Expected audience

Experts critical for the success of the project: Stian Soiland-Reyes - The University of Manchester - [email protected] Philippe Rocca-Serra - Oxford e-Research Centre - [email protected]

The project is open to any person that would like to join in this effort. We are especially encouraging people familiar with RO Crate, Bioschemas, ISA.

Number of expected hacking days: 4