Table 1 Minimum Information About a Plant Phenotyping Experiment (MIAPPE)

General metadata

Unique identifier*

Title*

Description*

Submission date

Public release date

Publications

Laboratory address and contact details

ISA reporting standard [65]

OBI, Ontology for Biomedical Investigations [66]

CRO, Crop Research Ontology [35]

Timing and location

Timing:

 Start of experiment (date/hour)*

 Duration (hours/days/months/years)*

Experiment location:

 Geographic location*

 Latitude and longitude

 Altitude

 Inclination and aspect

 Habitat

Poorter et al. [26]

Morrison et al. [17]

CIMR [67]: Environmental Analysis Context

OBI, Ontology for Biomedical Investigations [66]

GAZ, Gazetteer [68]

Biosource

Organism (taxon)*

Infraspecific_name*

Infraspecific_rank

Common name

Genotype

Organism age

Life stage

Seed preparation:

 Seed source*

 Pretreatments

 Conservation conditions

MIxS Plant-associated environmetal package [69]

Yilmaz et al. [12]

FAO/Bioversity Multi-Crop Passport Descriptors V.2 (MCPD V.2) [30]

UNIPROT Taxonomy [70]

NCBI Taxonomy [71]

Environment

Growth facility* (growth chamber, GC/greenhouse, GH/open top chamber, OTC/experimental garden/experimental field)

Poorter et al. [26]

Hanneman et al. [27]

XEO, XEML Environment Ontology [36]

ENVO, Ontology of environmental features and habitats [72]

Crop Research Ontology [35]

Aerial conditions*

 CO₂

  For GC and GH:

   Controlled/uncontrolled

  Average CO₂ during the light and dark period (µmol mol⁻¹)

 Air humidity (moisture)*

  Average VPDair during the light period (kPa) or average humidity during the light period (%)

  Average VPDair during the night (kPa) or average humidity during the night (%)

 Daily photon flux (light intensity)*

  Average daily integrated PPFD measured at plant or canopy level (mol m⁻² day⁻¹)

  Average length of the light period (h)

  For GC:

   Light intensity (µmol m⁻² s⁻¹)

   Range in peak light intensity (µmol m⁻² s⁻¹)

  For GH and OTC:

   Fraction of outside light intercepted by growth facility components and surrounding structures

 Light quality:

  For GC and GH:

   Type of lamps used

  R/FR ratio (mol mol⁻¹)

 Temperature (°C)*

  Average day temperature

  Average night temperature

  Change over the course of experiment

Rooting conditions*

 Rooting medium*: aeroponics/hydroponics (water-based, solid-media based)/soil type (sand, peat, clay, mixed, …)

  For greenhouse:

   Container type*

   Volume (L)*

   Height

   Other dimensions*

   Number of plants per container*

  For field:

   Plot size*

   Sowing density*

 pH*

 Frequency and volume of replenishment or addition

 Soil parameters:

  Soil penetration strength (Pa m⁻²)

  Water retention capacity (g g⁻¹ dry weight)

  Organic matter content (%)

  Porosity (%)

 Rooting medium temperature

 Nutrients

  For hydroponics:

   Composition*

   Concentration

  For soil:

   Extractable N content per unit ground area before fertiliser added*

   Type and amount of fertiliser added per container or m²*

   Concentration of P and other nutrients before start of the experiment

   Extractable N content per unit ground area at the end of the experiment

 Watering

   Irrigation type: irrigation from top/bottom/drip irrigation*

   Volume (L) and frequency of water added per container or m²*

  For soil:

   Range in water potential (MPa)

 Salinity

  Concentration of Na, Cl and Mg in the water used for irrigation

  For soils and hydroponics:

   Electrical conductivity (dS m⁻¹)

 Aquatic environment

 If sample was submerged and emerged

  Depth

  Time

 Water temperature

 Tidal phase

 Biotic environment

  Description of interacting organism (pathogens, mutualists, herbivores, endophytes, etc.)

Treatments

Seasonal environment

Air temperature regime

Soil temperature regime

Antibiotic regime

Chemical administration

Disease status

Fertilizer regime

Fungicide regime

Gaseous regime

Gravity

Growth hormone regime

Herbicide regime

Mechanical treatment

Mineral nutrient regime

Humidity regime

Non-mineral nutrient regime

Radiation (light, UV-B, X-ray) regime

Rainfall regime

Salt regime

Watering regime

Water temperature regime

Standing water regime

Pesticide regime

pH regime

Other perturbation

MIxS Plant-associated environmetal package [69]

Yilmaz et al. [12]

XEO, XEML Environment Ontology [36]

CRO, Crop Research Ontology [35]

Experimental design

Spatial coordinates

 Plant ID

 Plot ID

 Plot (x, y) coordinates

Blocking

 Block ID

 Sub-block ID

 Sub-sub-block ID

 Superblock ID

 Row ID

 Column ID

 Other ID

Replication

 Biological replication

 Technical replication

Experimental unit

OBI, Ontology for Biomedical Investigations [66]

STATO, Statistics Ontology [37]

CRO, Crop Research Ontology [35]

Sample collection, processing, management

Plant body of interest (organ)*

Plant product

Organism count

Sample temperature

Oxygenation status of sample

Sample salinity

Sample storage duration

Sample storage location

Sample storage temperature

Sampling time

CIMR [67]: Plant Biology Context

Fiehn et al. [16]

Observed variables

Phenotypic variables

 Trait*

 Method*

 Scale*

Environmental variables

 Trait*

 Method*

 Scale*

Data processing protocols

“Trait/Method/Scale” triplet approach applied by Generation Challenge Program, Crop Ontology [32]

Shrestha et al. [33]

Poorter et al. [26]

Hanneman et al. [27]

PTO, Plant Trait Ontology [73]

PO, Plant Ontology [74]

CO, Crop Ontology [32]

PATO, Phenotypic Quality Ontology [75]

XEO, XEML Environment Ontology [36]