Data Standards

EMPHASIS due to its experience and out of its own interest to maximize collaboration across Europe and beyond, will make sure that data is i) discoverable and available in a machine readable format, ii) is tagged with metadata using standard terms and ontologies such that the experiment could be repeated. As EMPHASIS is dealing with plants and their reaction to the environment this comprises a description of the environment as well and is not limited to plant (organ) sampling strategy, sensors and evaluation.

As laid down in our recommendation, EMPHASIS believes that minimal information standards already established are relevant and that these are necessary towards description of phenotyping even though these are mostly geared towards destructive phenotyping (MIAME, MIAPE, MSI, MIxS). We mostly consider plant specific extensions as relevant and necessary to describe any kind of phenotyping experiment, such as MIAME-Plant, CIMR and the MIxS plant environment package. To formalize this we have begun to work on minimal standards for plant phenotyping MIAPPE and link in necessary or (depending on experiment) optional ontologies to be used for a formalized and machine readable description of phenotyping experiments such as plant and crop ontology.

Thus EMPHASIS will work together with these to also shape ontologies for further needs in phenotyping. Also through the EMPHASIS partner’s link into the international plant phenotyping network (IPPN), EMPHASIS will also oversee that standards development is kept abreast with emerging needs of the phenotyping community at the same time not jumping on the all bandwaggons, as to allow continuity and safeguard the merit of legacy data. As fluctuating standards provide no stability for the community that is needed to best profit from data sharing and reuse.

In addition to necessary metadata and ontologies, EMPHASIS will also further its work on suitable data formats for data sharing and will provide extensions to download data in e.g. ISA-Tab. Once again however EMPHASIS will keep abreast to developments and provide additional export/import facilities.

EMPHASIS will also refine APIs to access data using APIs (e.g. RESTful services) that allow retrieving and collecting the data, if the data is stored at the partners.

EMPHASIS emphasizes the need for data stewardship, i.e. also long term availability and potentially adding additional metadata and observations even after experiments have been conducted.

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EMPHASIS is an ESFRI listed project supported by the European Union