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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)