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<table style='border-collapse:collapse'>
<tr><th>Section</th><th>Attributes</th><th>Source list</th><th>Recommended ontologies</th></tr>
<tr style='border-bottom: 1px solid #ddd;'>
<td>General metadata</td>
<td style='padding-top: 15px'><ul>
<li>Unique identifier* <i><small></small></i></li>
<li>Title* <i><small></small></i></li>
<li>Description* <i><small></small></i></li>
<li>Submission date <i><small></small></i></li>
<li>Public release date <i><small></small></i></li>
<li>Publications <i><small></small></i></li>
<li>Laboratory address and contact details <i><small></small></i></li>
</ul></td><td><ul><li><a href="http://www.biosharing.org/bsg-000078">ISA reporting guideline</a></li>
</ul></td>
<td><ul><li><a href="http://obi-ontology.org">Ontology for Biomedical Investigations, OBI</a></li>
<li><a href="http://cropontology.org/ontology/CO_715/Crop%20Research">Crop Research Ontology, CRO</a></li>
</ul></td>
</tr>
<tr style='border-bottom: 1px solid #ddd;'>
<td>Timing and location</td>
<td style='padding-top: 15px'><ul>
<li>Timing <i><small></small></i>
<ul>
<li>
Start of experiment (date/hour)* <i><small></small></i></li>
<li>
Duration (years/months/days/hours) <i><small></small></i></li>
</ul></li>
<li>Experiment location <i><small></small></i>
<ul>
<li>
Geographic location* <i><small></small></i></li>
<li>
Latitude and longitude <i><small></small></i></li>
<li>
Altitude <i><small></small></i></li>
<li>
Inclination and aspect <i><small></small></i></li>
<li>
Habitat <i><small></small></i></li>
</ul></li>
</ul></td><td><ul><li><a href="None">Poorter et al.</a></li>
<li><a href="None">Morrison et al.</a></li>
<li><a href="http://msi-workgroups.sourceforge.net/bio-metadata/reporting/env/reporting-requirements/ECWSG_reporting_requirements_v1.rtf">CIMR, Environmental Analysis Context</a></li>
</ul></td>
<td><ul><li><a href="http://obi-ontology.org">Ontology for Biomedical Investigations, OBI</a></li>
<li><a href="http://purl.bioontology.org/ontology/GAZ">Gazetteer, GAZ</a></li>
</ul></td>
</tr>
<tr style='border-bottom: 1px solid #ddd;'>
<td>Biosource</td>
<td style='padding-top: 15px'><ul>
<li>Organism (taxon)* <i><small></small></i></li>
<li>Infraspecific name* <i><small></small></i></li>
<li>Infraspecific rank <i><small></small></i></li>
<li>Common name <i><small></small></i></li>
<li>Genotype <i><small></small></i></li>
<li>Organism age <i><small></small></i></li>
<li>Life stage <i><small></small></i></li>
<li>Seed preparation <i><small></small></i>
<ul>
<li>
Seed source* <i><small></small></i></li>
<li>
Pretreatments <i><small></small></i></li>
<li>
Conservation conditions <i><small></small></i></li>
</ul></li>
</ul></td><td><ul><li><a href="http://www.biosharing.org/bsg-000518">MIxS Plant-associated environmetal package</a></li>
<li><a href="None">Yilmaz et al.</a></li>
<li><a href="http://www.bioversityinternational.org/e-library/publications/detail/faobioversity-multi-crop-passport-descriptors-v2-mcpd-v2">FAO/Bioversity Multi-Crop Passport Descriptors</a></li>
</ul></td>
<td><ul><li><a href="http://www.uniprot.org/taxonomy">UNIPROT Taxonomy</a></li>
<li><a href="http://www.ncbi.nlm.nih.gov/taxonomy">NCBI Taxonomy</a></li>
</ul></td>
</tr>
<tr style='border-bottom: 1px solid #ddd;'>
<td>Environment</td>
<td style='padding-top: 15px'><ul>
<li>Growth facility (growth chamber, GC / greenhouse, GH / open top chamber, OTC / experimental garden, EG / experimental field, EF)* <i><small></small></i></li>
<li>Aerial conditions* <i><small></small></i>
<ul>
<li>
CO2 <i><small></small></i>
<ul>
<li>
CO2 controlled/uncontrolled <i><small> specific for GC, GH</small></i></li>
<li>
Average CO2 during the light and dark period (umol mol-1) <i><small></small></i></li>
</ul></li>
<li>
Average humidity (moisture)* <i><small></small></i>
<ul>
<li>
Average VPDair during the light period (kPa) or Average humidity during the light period (%) <i><small></small></i></li>
<li>
Average VPDair during the night (kPa) or Average humidity during the night (%) <i><small></small></i></li>
</ul></li>
<li>
Daily photon flux (light intensity)* <i><small></small></i>
<ul>
<li>
Average daily integrated PPFD measured at plant or canopy level (mol m-2 day-1) <i><small></small></i></li>
<li>
Average length of the light period (h) <i><small></small></i></li>
<li>
Light intensity (umol m-2 s-1) <i><small> specific for GC</small></i></li>
<li>
Range in peak light intensity (umol m-2 s-1) <i><small> specific for GC</small></i></li>
<li>
Fraction of outside light intercepted by growth facility components and surrounding structures <i><small> specific for GH, OTC</small></i></li>
</ul></li>
<li>
Light quality <i><small></small></i>
<ul>
<li>
Type of lamps used <i><small> specific for GC, GH</small></i></li>
<li>
R/FR ratio (mol mol-1) <i><small></small></i></li>
</ul></li>
<li>
Temperature (C)* <i><small></small></i>
<ul>
<li>
Average day temperature <i><small></small></i></li>
<li>
Average night temperature <i><small></small></i></li>
<li>
Change over the course of experiment <i><small></small></i></li>
</ul></li>
</ul></li>
<li>Rooting conditions* <i><small></small></i>
<ul>
<li>
Rooting medium: aeroponics / hydroponics (water-based, solid-media based) / soil type (sand, peat, clay, mixed, ...)* <i><small></small></i></li>
<li>
Container type* <i><small> specific for GH</small></i></li>
<li>
Volume (l)* <i><small> specific for GH</small></i></li>
<li>
Height <i><small> specific for GH</small></i></li>
<li>
Other dimensions* <i><small> specific for GH</small></i></li>
<li>
Number of plants per container* <i><small> specific for GH</small></i></li>
<li>
Plot size* <i><small> specific for EF</small></i></li>
<li>
Sowing density* <i><small> specific for EF</small></i></li>
<li>
pH* <i><small></small></i></li>
<li>
Frequency and volume of replenishment or addition <i><small></small></i></li>
<li>
Soil parameters <i><small></small></i>
<ul>
<li>
Soil penetration strength (Pa m-2) <i><small></small></i></li>
<li>
Water retention capacity (g g-1 dry weight) <i><small></small></i></li>
<li>
Organic matter content (%) <i><small></small></i></li>
<li>
Porosity (%) <i><small></small></i></li>
</ul></li>
<li>
Rooting medium temperature <i><small></small></i></li>
</ul></li>
<li>Nutrients <i><small></small></i>
<ul>
<li>
Composition* <i><small> specific for hydroponics</small></i></li>
<li>
Concentration <i><small> specific for hydroponics</small></i></li>
<li>
Extractable N content per unit ground area before fertiliser added* <i><small> specific for soil</small></i></li>
<li>
Type and amount of fertiliser added per container or m2* <i><small> specific for soil</small></i></li>
<li>
Concentration of P and other nutrients before start of the experiment <i><small> specific for soil</small></i></li>
<li>
Extractable N content per unit ground area at the end of the experiment <i><small> specific for soil</small></i></li>
</ul></li>
<li>Watering <i><small></small></i>
<ul>
<li>
Irrigation type: irrigation from top/bottom/drip irrigation* <i><small></small></i></li>
<li>
Volume (L) and frequency of water added per container or m2* <i><small></small></i></li>
<li>
Range in water potential (MPa) <i><small> specific for soil</small></i></li>
</ul></li>
<li>Salinity <i><small></small></i>
<ul>
<li>
Concentration of Na, Cl and Mg in the water used for irrigation <i><small></small></i></li>
<li>
Electrical conductivity (dS m-1) <i><small> specific for soil, hydroponics</small></i></li>
</ul></li>
<li>Aquatic environment <i><small></small></i>
<ul>
<li>
Water temperature <i><small></small></i></li>
<li>
Tidal phase <i><small></small></i></li>
<li>
Depth <i><small> specific for sample submerged and emerged</small></i></li>
<li>
Time <i><small> specific for sample submerged and emerged</small></i></li>
</ul></li>
<li>Biotic environment <i><small></small></i>
<ul>
<li>
Interacting organism (pathogens, mutualists, herbivores, endophytes, etc.) <i><small></small></i></li>
</ul></li>
</ul></td><td><ul><li><a href="None">Poorter et al.</a></li>
<li><a href="None">Hanneman et al.</a></li>
</ul></td>
<td><ul><li><a href="http://purl.bioontology.org/ontology/XEO">XEML Environment Ontology, XEO</a></li>
<li><a href="http://purl.bioontology.org/ontology/ENVO">Ontology of environmental features and habitats, ENVO</a></li>
<li><a href="http://cropontology.org/ontology/CO_715/Crop%20Research">Crop Research Ontology, CRO</a></li>
</ul></td>
</tr>
<tr style='border-bottom: 1px solid #ddd;'>
<td>Treatments</td>
<td style='padding-top: 15px'><ul>
<li>Seasonal environment <i><small></small></i></li>
<li>Air temperature regime <i><small></small></i></li>
<li>Soil temperature regime <i><small></small></i></li>
<li>Antibiotic regime <i><small></small></i></li>
<li>Chemical administration <i><small></small></i></li>
<li>Disease status <i><small></small></i></li>
<li>Fertilizer regime <i><small></small></i></li>
<li>Fungicide regime <i><small></small></i></li>
<li>Gaseous regime <i><small></small></i></li>
<li>Gravity <i><small></small></i></li>
<li>Growth hormone regime <i><small></small></i></li>
<li>Herbicide regime <i><small></small></i></li>
<li>Mechanical treatment <i><small></small></i></li>
<li>Mineral nutrient regime <i><small></small></i></li>
<li>Humidity regime <i><small></small></i></li>
<li>Non-mineral nutrient regime <i><small></small></i></li>
<li>Radiation (light, UV-B, X-ray) regime <i><small></small></i>
<ul>
<li>
light regime <i><small></small></i></li>
<li>
UV-B regime <i><small></small></i></li>
<li>
X-ray regime <i><small></small></i></li>
</ul></li>
<li>Rainfall regime <i><small></small></i></li>
<li>Salt regime <i><small></small></i></li>
<li>Watering regime <i><small></small></i></li>
<li>Water temperature regime <i><small></small></i></li>
<li>Standing water regime <i><small></small></i></li>
<li>Pesticide regime <i><small></small></i></li>
<li>pH regime <i><small></small></i></li>
<li>Other perturbation <i><small></small></i></li>
</ul></td><td><ul><li><a href="http://www.biosharing.org/bsg-000518">MIxS Plant-associated environmetal package</a></li>
<li><a href="None">Yilmaz et al.</a></li>
</ul></td>
<td><ul><li><a href="http://purl.bioontology.org/ontology/XEO">XEML Environment Ontology, XEO</a></li>
<li><a href="http://cropontology.org/ontology/CO_715/Crop%20Research">Crop Research Ontology, CRO</a></li>
</ul></td>
</tr>
<tr style='border-bottom: 1px solid #ddd;'>
<td>Experimental design</td>
<td style='padding-top: 15px'><ul>
<li>Spatial coordinates <i><small></small></i>
<ul>
<li>
Plant ID <i><small></small></i></li>
<li>
Plot ID <i><small></small></i></li>
<li>
Plot (x, y) coordinates <i><small></small></i></li>
</ul></li>
<li>Time coordinates <i><small></small></i>
<ul>
<li>
Day <i><small></small></i></li>
<li>
Time <i><small></small></i></li>
</ul></li>
<li>Blocking <i><small></small></i>
<ul>
<li>
Block ID <i><small></small></i></li>
<li>
Sub-block ID <i><small></small></i></li>
<li>
Sub-sub-block ID <i><small></small></i></li>
<li>
Superblock ID <i><small></small></i></li>
<li>
Row ID <i><small></small></i></li>
<li>
Column ID <i><small></small></i></li>
<li>
Other ID <i><small></small></i></li>
</ul></li>
<li>Replication <i><small></small></i>
<ul>
<li>
Biological replication <i><small></small></i></li>
<li>
Technical replication <i><small></small></i></li>
</ul></li>
<li>Experimental unit <i><small></small></i></li>
</ul></td><td><ul><li><a href="None">None</a></li>
</ul></td>
<td><ul><li><a href="http://obi-ontology.org">Ontology for Biomedical Investigations, OBI</a></li>
<li><a href="http://bioportal.bioontology.org/ontologies/STATO">Statistics Ontology, STATO</a></li>
<li><a href="http://cropontology.org/ontology/CO_715/Crop%20Research">Crop Research Ontology, CRO</a></li>
</ul></td>
</tr>
<tr style='border-bottom: 1px solid #ddd;'>
<td>Sample collection, processing, management</td>
<td style='padding-top: 15px'><ul>
<li>Plant body of interest (organ)* <i><small></small></i></li>
<li>Plant product <i><small></small></i></li>
<li>Organism count <i><small></small></i></li>
<li>Sample temperature <i><small></small></i></li>
<li>Oxygenation status of sample <i><small></small></i></li>
<li>Sample salinity <i><small></small></i></li>
<li>Sample storage duration <i><small></small></i></li>
<li>Sample storage location <i><small></small></i></li>
<li>Sample storage temperature <i><small></small></i></li>
<li>Sampling time <i><small></small></i></li>
</ul></td><td><ul><li><a href="http://msi-workgroups.sourceforge.net/bio-metadata/reporting/pbc/doc.rtf">CIMR: Plant Biology Context</a></li>
<li><a href="None">Fiehn et al.</a></li>
<li><a href="None">List exist for assays in CIMR, MIAPE, MIMARKS (ISA-Tab configurations) + new attributes for phenotypic assays</a></li>
</ul></td>
<td><ul><li><a href="None">None</a></li>
</ul></td>
</tr>
<tr style='border-bottom: 1px solid #ddd;'>
<td>Observed variables</td>
<td style='padding-top: 15px'><ul>
<li>Phenotypic variables <i><small></small></i>
<ul>
<li>
Trait* <i><small></small></i></li>
<li>
Method* <i><small></small></i></li>
<li>
Scale* <i><small></small></i></li>
</ul></li>
<li>Environmental variables <i><small></small></i>
<ul>
<li>
Trait* <i><small></small></i></li>
<li>
Method* <i><small></small></i></li>
<li>
Scale* <i><small></small></i></li>
</ul></li>
<li>Data processing protocols <i><small></small></i></li>
</ul></td><td><ul><li><a href="http://www.cropontology.org">Trait/Method/Scale triplet approach applied by Generation Challenge Program, Crop Ontology</a></li>
<li><a href="None">Shrestha et al.</a></li>
<li><a href="None">Poorter et al.</a></li>
<li><a href="None">Hanneman et al.</a></li>
</ul></td>
<td><ul><li><a href="https://bioportal.bioontology.org/ontologies/PTO">Plant Trait Ontology, PTO</a></li>
<li><a href="http://www.plantontology.org">Plant Ontology, PO</a></li>
<li><a href="http://www.cropontology.org">Crop Ontology, CO</a></li>
<li><a href="http://purl.bioontology.org/ontology/PATO">Phenotypic Quality Ontology, PATO</a></li>
<li><a href="http://purl.bioontology.org/ontology/XEO">XEML Environment Ontology, XEO</a></li>
</ul></td>
</tr>
</table>