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] |