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

From: Measures for interoperability of phenotypic data: minimum information requirements and formatting

Checklist section Attributes Source list/biosharing ID/reference Recommended ontologies
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]
  1. Attributes (concepts, subconcepts—in terms of ontology) marked by asterisk (*) are essential for a description of experiment (e.g. by Poorter et al. [26]); the rest forms an extended description. For some attributes possible values are listed (after colon)