Plants

CorkOakDB

CorkOakDB integrates knowledge generated from fundamental and applied studies about Quercus suber, with a focus on genetics. It features the first draft genome of Quercus suber, released in 2018 by the GENOSUBER consortium, and allows genome browsing and gene search. It also incorporates other types of data from cork oak scientific research, including gene expression data from publicly available datasets.

Plant Experimental Assay Ontology (PEAO)

The Plant domain has been the subject of several attempts to structure and formally define terms and corresponding relations, such as their anatomical features, developmental stages, and the application of particular experimental procedures to a biological problem. However, a focus on experimental assays in order to describe the whole experimental procedure, to the best of our knowledge, has only been attempted in the context of a very general description based on classical views of the scientific method.

Plant Data Hackathon

During the Barcelona all hands meeting we have committed to prepare a procedure and example on how to use Google Spreadsheets to record and standardise data in WP7. Our idea is to guide the ateendees in the procedure that we have devised, and enable them to work on their data using a tool (OntoMaton) to facilitate searching for terms in Bioportal Ontologies. The procedure attempts to provide standardisation to both column names and the data within their rows. This should facilitate the access to ISA-tools and to publishing standardised data sets in repositories.

Plant Phenotyping-Genotyping Data Management Workshop

Plant phenotyping research has gone through a data revolution with the automation of plant phenotyping platforms, making it critical to adopt good data management practices in order the exploit the torrent of data to its full potential. Concretely, data should be published in a Findable, Accessible, Interoperable and Reusable (FAIR) way in order to enable the integration of data from disparate sources and the discovery of new knowledge. Yet, this is one of the more challenging domains to standardize, as it is extremely heterogeneous in terms of experimental settings and types of data.