How to add markup to Plant resources

More information about the ELIXIR Plant community

This tutorial complements the tutorials how to select the right profile for your resource and how to mark up your own resource with Bioschemas for resources from the plant sciences, so please check these tutorial first.

1. Philosophy for marking-up plant sciences resources with Bioschemas

The main goal of marking-up plant sciences resources with Bioschemas is to improve their Findability on the Web, in accordance with the goal of Bioschemas themselves. Thus, while plant datasets themselves are expected to fully comply with applicable metadata standards, such as MIAPPE, the web pages containing these datasets need only be marked-up with the metadata that are critical for Findability. For this end, and to ensure a consistent use of Bioschemas markup across different types of plant datasets, the plant sciences community established a MIAPPE-Bioschemas mapping, spanning the MIAPPE fields deemed relevant for Findability of plant datasets, namely those that describe the study and its biological material(s). Despite the domain of MIAPPE being plant phenotyping experiments, the metadata fields encompassed by this mapping are generic, and can be used for plant genotyping or omics experiments.

2. Key Bioschemas profiles

• The DataCatalog profile can be used to markup data repositories or any listings of plant datasets.
• Dataset and Study are the central profiles to markup web pages about plant phenotyping, genotyping or omics datasets, as per the MIAPPE-BioSchemas mapping provided below.
• Taxon and BioChemEntity are critical for identifying the biological material(s) used in the dataset, with the former enabling taxonomic identification down to the variety level (if applicable) and the latter identifying a specific germplasm, seed lot or genotype.
• Person and Place should be used to identify the authors and locations of the dataset.
• Molecule-level profiles, such as Gene, RNA or Protein should only be used to markup web pages that describe a specific molecular entity, such as in the case of plant genome portals.
• Likewise, Sample should only be used to markup pages that specifically describe a sample.

3. MIAPPE-Bioschemas mapping

The correspondence between Bioschemas profiles and MIAPPE sections is the following:

The recommended fields within each profile and their correspondence to MIAPPE fields are the following.

Dataset

Study

Note that keywords and studyProcess enable only a flat representation of experimental factors and traits, respectively, but this is enough for Findability. For genotyping or omics datasets, studyProcess can be used accordingly to indicate the types of assays done.

Person

Place

BioChemEntity

Taxon

To enable a flat taxonomic characterization of the biological material, taxonRank should always be “species”, with the “Infraspecific name” provided as a textual value for the childTaxon field.