Methods metadata guide

This page provides guidelines and expectations for completion of the methods metadata template. Note that while defined vocabulary terms are suggested, most variables may be complete with free text entries if required.
The main purpose of this metadata collection will be to aid data search with some common discriminators. It is not meant to be a substitute for a complete experimental description. Additional information should be included as methods supplements tables, or in a methods text file.
Methods Metadata Content - Click links below for more details
* indicate required content
​dataType* | additionalDataIncluded* | instrumentOutputStatus*​
​plantType* | leafType* | requiredProtocols*​
​mesophyllConductanceType | leafStatus* | leafAreaBasis*​
​leafAreaMethod* | kineticConstants | growthEnvironment*​
​experimentalManipulation* | plantAge* | leafAge*​
​canopyPosition* | canopyHeight* | lightExposure*​
dataType
Metadata Element
dataType
Required Recommended Optional
required
Description
Enter data type described by this methods metadata file. Refer to data types in documentation for definitions.
Format
Controlled vocabulary or free text
Additional Instructions
​
Controlled vocabulary terms
Refer to data types table for list.
additionalDataIncluded
Metadata Element
additionalDataIncluded
Required Recommended Optional
required
Description
Indicate if additional data collected in-line during gas exchange is included. e.g. fluorescence, isotopic discrimination
Format
Controlled vocabulary
Additional Instructions
​
Controlled vocabulary terms
yes; no
instrumentOutputStatus
Metadata Element
instrumentOutputStatus
Required Recommended Optional
required
Description
Indicate the highest quality status of complete instrument output included in the data package. Multiple versions may be included.
Format
Controlled vocabulary
Additional Instructions
0 = data not available. 1 = direct instrument download, minimal quality control. 2 = complete quality control, files are verified to only contain valid data, or, invalid data is flagged. Measurement values are reasonable and within expected range. Area corrections are made where required. Time and dates verified as correct. User input errors corrected.
Controlled vocabulary terms
0; 1; 2
plantType
Metadata Element
plantType
Required, Recommended, or Optional
required
Description
Photosynthetic pathway of measured plants.
Format
Controlled vocabulary or free text
Additional instructions
List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms
C3; C4; CAM
leafType
Metadata Element
leafType
Required, Recommended, or Optional
required
Description
Describe the leaf type(s) measured.
Format
Controlled vocabulary or free text
Additional instructions
List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms
broadleaf; graminoid; needleleaf; phyllode
requiredProtocols
Metadata Element
requiredProtocols
Required, Recommended, or Optional
required
Description
Details of measurement protocols. Refer to requiredProtocols for each data type for required protocol information. Can cite reference or other source if this information is recorded elsewhere.
Format
Free text
Additional instructions
​
Controlled vocabulary terms
​
mesophyllConductanceType
Metadata Element
mesophyllConductanceType
Required, Recommended, or Optional
optional
Description
Describe assumption or measurement of mesophyll conductance. Infinite mesophyll conductance assumes intercellular CO2 concentration (Ci) is equal to the CO2 concentration at the site of carboxylation inside the chloroplast (Cc).
Format
Controlled vocabulary
Additional instructions
​
Controlled vocabulary terms
assumed infinite; measured
leafStatus
Metadata Element
leafStatus
Required, Recommended, or Optional
required
Description
Describe the leaf status during gas exchange measurement.
Format
Controlled vocabulary or free text
Additional instructions
List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms
attached leaf; attached leaf on excised branch; excised leaf
leafAreaBasis
Metadata Element
leafAreaBasis
Required, Recommended, or Optional
required
Description
Describe the basis for measurement of leaf area. The default is "one-sided leaf area" which is typical for regular leaf types but there are several other alternatives, including in rare circumstances the use of mass or volume.
Format
Controlled vocabulary or free text
Additional instructions
List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms
one-sided area; hemi-surface area; projected area; total area; dry mass; volume
leafAreaMethod
Metadata Element
leafAreaMethod
Required, Recommended, or Optional
required
Description
Describe the methods used for measurement of leaf area.
Format
Controlled vocabulary or free text
Additional instructions
List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms
single leaf fills chamber of known area; multiple leaves fill chamber of known area; geometrically determined; calculated using imaging software; measured using leaf area meter
kineticConstants
Metadata Element
kineticConstants
Required, Recommended, or Optional
optional
Description
Citations and values for kinetic constants, and their temperature dependance.
Format
Free text
Additional instructions
​
Controlled vocabulary terms
​
growthEnvironment
Metadata Element
growthEnvironment
Required, Recommended, or Optional
required
Description
Describe the plant growth environment. Provide details in Methods.
Format
Controlled vocabulary or free text
Additional instructions
List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms
natural in ground; cultivated in ground; potted; glasshouse; controlled environment chamber; other chamber type; hydroponic
experimentalManipulation
Metadata Element
experimentalManipulation
Required, Recommended, or Optional
required
Description
Indicate if any samples were subject to a manipulation. For naturally grown plants, or cultivated plants with standard fertilizer and pesticide application across all samples, select "none". Provide further treatment details in methodsSupplements tables.
Format
Controlled vocabulary or free text
Additional instructions
List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms
none; atmosphere; genetic; growth media; pesticide; light; nutrients; salinity; soil modification; source-sink; temperature; water availability
plantAge
Metadata Element
plantAge
Required, Recommended, or Optional
required
Description
Age in appropriate units (days, months, years) or relative age category (e.g. seedling, germling, sapling, mature) or other classification relevant to experiment.
Format
Controlled vocabulary or free text
Additional instructions
List all that apply, use a semi-colon to delimit multiple terms. Include a methods supplements table if required.
Controlled vocabulary terms
unknown; seedling; germling; sapling; mature
leafAge
Metadata Element
leafAge
Required, Recommended, or Optional
required
Description
Age in appropriate units (days, months, years) or relative age category (e.g. young, mature, old) or other classification (e.g. most recent fully expanded, physiologically mature leaf; LPI classification).
Format
Controlled vocabulary or free text
Additional instructions
List all that apply, use a semi-colon to delimit multiple terms. Include a methods supplements table if required.
Controlled vocabulary terms
young; mature; old; unknown; multiple ages
canopyPosition
Metadata Element
canopyPosition
Required, Recommended, or Optional
required
Description
Position of leaf samples within canopy.
Format
Controlled vocabulary or free text
Additional instructions
List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms
top of canopy; within canopy
canopyHeight
Metadata Element
canopyHeight
Required, Recommended, or Optional
required
Description
Sample canopy position and canopy height or LAI recorded.
Format
Controlled vocabulary
Additional instructions
If yes, provide details in metadata supplements and/or data tables.
Controlled vocabulary terms
yes; no
lightExposure
Metadata Element
lightExposure
Required, Recommended, or Optional
required
Description
Light environment of leaf samples.
Format
Controlled vocabulary or free text
Additional instructions
List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms
sunlit; shade

Instructions

Guide to data types and required protocol details

Last modified 1yr ago

Metadata Element	dataType
Required Recommended Optional	`required`
Description	Enter data type described by this methods metadata file. Refer to data types in documentation for definitions.
Format	Controlled vocabulary or free text
Additional Instructions
Controlled vocabulary terms	Refer to data types table for list.

Metadata Element	additionalDataIncluded
Required Recommended Optional	`required`
Description	Indicate if additional data collected in-line during gas exchange is included. e.g. fluorescence, isotopic discrimination
Format	Controlled vocabulary
Additional Instructions
Controlled vocabulary terms	yes; no

Metadata Element	instrumentOutputStatus
Required Recommended Optional	`required`
Description	Indicate the highest quality status of complete instrument output included in the data package. Multiple versions may be included.
Format	Controlled vocabulary
Additional Instructions	0 = data not available. 1 = direct instrument download, minimal quality control. 2 = complete quality control, files are verified to only contain valid data, or, invalid data is flagged. Measurement values are reasonable and within expected range. Area corrections are made where required. Time and dates verified as correct. User input errors corrected.
Controlled vocabulary terms	0; 1; 2

Metadata Element	requiredProtocols
Required, Recommended, or Optional	`required`
Description	Details of measurement protocols. Refer to requiredProtocols for each data type for required protocol information. Can cite reference or other source if this information is recorded elsewhere.
Format	Free text
Additional instructions
Controlled vocabulary terms

Metadata Element	mesophyllConductanceType
Required, Recommended, or Optional	`optional`
Description	Describe assumption or measurement of mesophyll conductance. Infinite mesophyll conductance assumes intercellular CO2 concentration (Ci) is equal to the CO2 concentration at the site of carboxylation inside the chloroplast (Cc).
Format	Controlled vocabulary
Additional instructions
Controlled vocabulary terms	assumed infinite; measured

Metadata Element	plantType
Required, Recommended, or Optional	`required`
Description	Photosynthetic pathway of measured plants.
Format	Controlled vocabulary or free text
Additional instructions	List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms	C3; C4; CAM

Metadata Element	leafType
Required, Recommended, or Optional	`required`
Description	Describe the leaf type(s) measured.
Format	Controlled vocabulary or free text
Additional instructions	List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms	broadleaf; graminoid; needleleaf; phyllode

Metadata Element	leafStatus
Required, Recommended, or Optional	`required`
Description	Describe the leaf status during gas exchange measurement.
Format	Controlled vocabulary or free text
Additional instructions	List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms	attached leaf; attached leaf on excised branch; excised leaf

Metadata Element	leafAreaBasis
Required, Recommended, or Optional	`required`
Description	Describe the basis for measurement of leaf area. The default is "one-sided leaf area" which is typical for regular leaf types but there are several other alternatives, including in rare circumstances the use of mass or volume.
Format	Controlled vocabulary or free text
Additional instructions	List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms	one-sided area; hemi-surface area; projected area; total area; dry mass; volume

Metadata Element	leafAreaMethod
Required, Recommended, or Optional	`required`
Description	Describe the methods used for measurement of leaf area.
Format	Controlled vocabulary or free text
Additional instructions	List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms	single leaf fills chamber of known area; multiple leaves fill chamber of known area; geometrically determined; calculated using imaging software; measured using leaf area meter

Metadata Element	kineticConstants
Required, Recommended, or Optional	`optional`
Description	Citations and values for kinetic constants, and their temperature dependance.
Format	Free text
Additional instructions
Controlled vocabulary terms

Metadata Element	growthEnvironment
Required, Recommended, or Optional	`required`
Description	Describe the plant growth environment. Provide details in Methods.
Format	Controlled vocabulary or free text
Additional instructions	List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms	natural in ground; cultivated in ground; potted; glasshouse; controlled environment chamber; other chamber type; hydroponic

Metadata Element	experimentalManipulation
Required, Recommended, or Optional	`required`
Description	Indicate if any samples were subject to a manipulation. For naturally grown plants, or cultivated plants with standard fertilizer and pesticide application across all samples, select "none". Provide further treatment details in methodsSupplements tables.
Format	Controlled vocabulary or free text
Additional instructions	List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms	none; atmosphere; genetic; growth media; pesticide; light; nutrients; salinity; soil modification; source-sink; temperature; water availability

Metadata Element	plantAge
Required, Recommended, or Optional	`required`
Description	Age in appropriate units (days, months, years) or relative age category (e.g. seedling, germling, sapling, mature) or other classification relevant to experiment.
Format	Controlled vocabulary or free text
Additional instructions	List all that apply, use a semi-colon to delimit multiple terms. Include a methods supplements table if required.
Controlled vocabulary terms	unknown; seedling; germling; sapling; mature

Metadata Element	leafAge
Required, Recommended, or Optional	`required`
Description	Age in appropriate units (days, months, years) or relative age category (e.g. young, mature, old) or other classification (e.g. most recent fully expanded, physiologically mature leaf; LPI classification).
Format	Controlled vocabulary or free text
Additional instructions	List all that apply, use a semi-colon to delimit multiple terms. Include a methods supplements table if required.
Controlled vocabulary terms	young; mature; old; unknown; multiple ages

Metadata Element	canopyPosition
Required, Recommended, or Optional	`required`
Description	Position of leaf samples within canopy.
Format	Controlled vocabulary or free text
Additional instructions	List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms	top of canopy; within canopy

Metadata Element	canopyHeight
Required, Recommended, or Optional	`required`
Description	Sample canopy position and canopy height or LAI recorded.
Format	Controlled vocabulary
Additional instructions	If yes, provide details in metadata supplements and/or data tables.
Controlled vocabulary terms	yes; no

Metadata Element	lightExposure
Required, Recommended, or Optional	`required`
Description	Light environment of leaf samples.
Format	Controlled vocabulary or free text
Additional instructions	List all that apply, use a semi-colon to delimit multiple terms.
Controlled vocabulary terms	sunlit; shade