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