Guide

Here you will find proposed guidelines for standardizing sample metadata to describe interdisciplinary samples within DOE's Environmental Systems Science research.

Most of the sample metadata follows SESAR's metadata guidelines. However, we modified some metadata elements, specific requirements, and vocabularies based on ESS researcher needs. This includes additional fields, which mostly come from biodiversity standards Darwin Core, or genomic standards Minimum Information about any Sequence (MIxS).

We seek any additional feedback, with the goal of making ESS sample information Findable, Accessible, Interoperable, and Reusable (FAIR).

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Sample Metadata Content - Link to More Details

*Required fields are marked with an asterisk, and indicated in detailed tables below.

Header Rows: Object Type* |User Code*

Sample IDs and Related Identifiers: Sample Name* |Other names |IGSN |Parent IGSN |Collection ID |Event ID |Location ID

Sample Description: Material* |Field name informal classification |Sample Description |Purpose |Size |Size unit |Filter Size |Filter Size Unit |Scientific Name |Sample Remarks

Sample Collection Details: Collector Chief Scientist* |Collection Date* |Collection Time |Collection Method Description* |Sample Processing |Field Program or Project Name*

Location: Latitude Coordinate system WGS 84* |Longitude Coordinate system WGS 84* |Navigation Type |Location Description |Country |Elevation start |Elevation end |Elevation unit |Minimum Depth in Meters |Maximum Depth in Meters |Depth scale |Minimum Distance above Surface in Meters |Maximum Distance above Surface in Meters |

Environmental Context: Physiographic feature* |Biome

Sample Access: Release Date* |Current Archive |Current Archive Contact

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Header Rows

Object Type

ESS-DIVE Proposed Element	objectType Required
Definition	Broad characterization of the nature of a sample or specimen.
Format	SESAR Controlled List. See object type list for revised terms proposed for ESS-DIVE
Additional Instructions	Provide feedback on additional terms or revisions needed.
Examples	Core; Individual Sample; Organism

User Code

ESS-DIVE Proposed Element	userCode Required
Definition	Globally unique IGSN code that will be used as a prefix for IGSNs in the submitted batch template.
Format	Five-letter code
Additional Instructions	User codes should be unique to an individual or large project managed by a team; avoid creating multiple user codes. If assigning IGSNs in the IGSN column, the user code must match the user code in the IGSNs. For example, if the user specifies IEMEG is the user code, any user-specified IGSNs must begin with IEMEG. If you do not specify the user code to be used, a default user code belonging to the registrant will be used.
Examples	IEMEG, IEJDE

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Sample IDs and Related Identifiers

Sample Name

ESS-DIVE Proposed Element	sampleName Required
Definition	Collector's project-specific sample name, which must be unique for each sample that you are submitting.
Format	free text, unique
Additional Instructions	You can develop a sample ID that has meaning to you and may help in your internal, project sample management.
Examples	001-ER18-FO

Other names

ESS-DIVE Proposed Element	otherName Optional
Definition	Other sample name(s) that have been used in the past.
Format	free text
Additional Instructions	Use a semi-colon to delimit multiple names where needed.
Examples	001ER18FO; 001ER18-FO

IGSN

ESS-DIVE Proposed Element	IGSN Recommended
Definition	Globally unique and persistent identifier for the sample. Leave blank if you want SESAR to assign the IGSN, which is recommended.
Format	semi-opaque, alphanumeric characters (9 recommended)
Additional Instructions	For split samples/subsamples, you can assign your own 1-2 character extensions from the Parent IGSN, and submit your own IGSNs for registering these child samples. This is not required, but is an option if desired. For assigning your own IGSNS, you must use upper-case alpha-numeric characters.
Examples	IEWER7214, IEMEG0215

Parent IGSN

Proposed ESS-DIVE Element	parentIGSN if relevant,Required
Definition	The larger sample from which a child sample was derived. For example, a core section may be the parent of a series of subsamples or split samples. Parent and child samples are linked in the SESAR catalog. Sibling samples are inferred from parent-child relationships and are linked on the landing page for a sample.
Format	semi-opaque, alphanumeric characters (9 recommended)
Additional Instructions	Leave blank if a parent IGSN does not exist.
Examples	IEMEG0002

Collection ID

Not a SESAR Field

Proposed ESS-DIVE Element	collectionID Optional
Definition	A unique identifier for the set of information associated with a collection of samples; collections may be organized around a particular project, data set, field season, region, site, etc.
Format	free text, unique
Additional Instructions	Must be unique within the data package (project-assigned, and does not need to be globally unique). See link to diagram that demonstrates linking related collection, site, event, and sample IDs. A collection identifier can be used to link a set of samples together, and/or to enable efficient entry of metadata that is the same across all samples in a "sample collection."
Examples	WSFA_June2019

Event ID

Not a SESAR Field

Proposed ESS-DIVE Element	eventID Optional
Definition	A unique identifier for the set of information associated with an Event (something that occurs at a place and time).
Format	free text, unique
Additional Instructions	Must be unique within the data package (project-assigned, and does not need to be globally unique). See link to diagram that demonstrates linking related collection, site, event, and sample IDs. An event identifier can be used to link a set of samples collected on a specific date, and/or to enable efficient entry of metadata that is the same across these samples.
Examples	WSFA_20191023

Location ID

Not a SESAR Field

Proposed ESS-DIVE Element	locationID Optional
Definition	A unique identifier for the set of location information. May be a global unique identifier or an identifier specific to the data set.
Format	free text, unique
Additional Instructions	Must be unique within the data package (project-assigned, and does not need to be globally unique). See link to diagram that demonstrates linking related collection, site, event, and sample IDs. A site identifier can be used to link a set of samples collected from a specific site, and/or to enable efficient entry of metadata that is the same across these samples.
Examples	CoyoteRiver_D22

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Sample Description

Material

Proposed ESS-DIVE Element	material Required
Definition	Material that the sample consists of.
Format	SESAR controlled list.See ESS-DIVE's proposed material terms from Environment Ontology (ENVO)
Additional Instructions	Use a semi-colon to delimit multiple materials where needed. Please provide feedback on any other terms needed.
Examples	Soil; Sediment; Gas; Liquid>aqueous

Field name informal classification

Proposed ESS-DIVE Element	classification, or remove Optional
Definition	Informal classification of sample
Format	free text
Additional Instructions	Here you can add additional material classifications that are not in the current SESAR IGSN controlled fields.
Examples	leaf, root, surface water, groundwater

Sample Description

Proposed ESS-DIVE Element	sampleDescription Recommended
Definition	Description of sample features, such as its components, texture, color, shape, treatments, plot ID from which the sample was taken, etc.
Format	free-text
Additional Instructions
Examples	Example 1) Day 223 core section from unheated control plot 1C of a deep soil warming experiment; Example 2) Filter used for filtered surface water samples

Purpose

Proposed ESS-DIVE Element	purpose Recommended
Definition	The scientific purpose for collecting the sample.
Format	free text
Additional Instructions	Purpose may often be the same across a series/collection of samples; To avoid entering the same information across numerous samples, you can create a separate file with metadata to describe a sample collection, which contains a "collectionID", and any associated metadata fields (e.g. "collectionMethodDescription", "Purpose", "Chief Scientist", etc.).
Examples	Characterize the biogeochemistry, geochemistry and microbiology of soils associated with trees and shrubs.

Size

Proposed ESS-DIVE Element	size Optional
Definition	Size of the registered object, such as the surface area, length of a core, weight, or volume
Format	Number
Additional Instructions	Must be associated with Size unit.
Examples	4; 6.8

Size unit

Proposed ESS-DIVE Element	sizeUnit only if Size provided,Required
Definition	Unit for the numerical value provided for ‘size’.
Format	Controlled List
Additional Instructions	Use any additional unit terms from Units Ontology, and provide feedback.
Examples	square centimeter; kilogram

Filter Size

Not a SESAR Field

Proposed ESS-DIVE Element	filterSize only if object type is "fitrate" or "material captured in filter",Required
Definition	Filtering pore size used in sample preparation (filter size value range). Filter size value range.
Format	Number range (float-float)
Additional Instructions
Examples	0-0.22

Filter Size Unit

Not a SESAR Field

Proposed ESS-DIVE Element	filterSizeUnit only if object type is "fitrate" or "material captured in filter",Required
Definition	Filtering pore size unit.
Format	unit (float-float unit)
Additional Instructions
Examples	micrometer

Scientific Name

Not a SESAR Field

Proposed ESS-DIVE Element	scientificName only if object type is Organism, Required
Definition	The full scientific name, with authorship and date information if known. When forming part of an Identification, this should be the name in lowest level taxonomic rank that can be determined.
Format
Additional Instructions
Examples	Vochysia ferruginea; Miconia borealis; Terminalia amazonia

Sample Remarks

Not a SESAR Field

Proposed ESS-DIVE Element	sampleRemarks Optional
Definition	Comments or notes about the sample.
Format	free text
Additional Instructions	You can include weather descriptions here, if relevant.
Examples

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Sample Collection Details

Collector Chief Scientist

Proposed ESS-DIVE Element	collector Required
Definition	Name of the person(s) who collected the sample.
Format
Additional Instructions	You can enter multiple collectors/sampling team for large sampling efforts, separated with a semi-colon. If the collector(s) of the sample(s) is/are not known, enter name of the person responsible for the sample.
Examples	John Smith; Jane Johnson

Collection Date

Proposed ESS-DIVE Element	collectionDate Required
Definition	Date when the sample was collected.
Format	YYYY-MM-DD
Additional Instructions	All dates and times must be reported in Coordinated Universal Time (UTC) and follow the ISO 8601 standard (RFC 3339). Temporal data using different standards can be provided as a separate variable (column) in addition to UTC format.
Examples	2019-08-14

Collection Time

Proposed ESS-DIVE Element	collectionTime Optional
Definition	Time when the sample was collected.
Format	HH:MM:SSZ
Additional Instructions	All dates and times must be reported in Coordinated Universal Time (UTC) and follow the ISO 8601 standard (RFC 3339). Temporal data using different standards can be provided as a separate variable (column) in addition to UTC format.
Examples	12:05:03Z

Collection Method Description

Proposed ESS-DIVE Element	collectionMethodDescription Required
Definition	Description of the collection method for the sample. Include any important terms and details for potential users to understand how your sample was collected.
Format
Additional Instructions	Collection methods may often be the same across a series/collection of samples; there are two options for providing collection method details at a higher level. Option 1: Create a separate file with metadata to describe a sample collection, which contains a "collectionID", and any associated metadata fields (e.g. "collectionMethodDescription", "Purpose", "Chief Scientist", etc.). Option 2: Create a methods file, with a series of methods descriptions that are each associated with a "methodID" and an associated "methodDescription."
Examples	Example 1) Collect soil samples from top 10 cm using 2-3 cores from with meadow plot or under the bulk of tree/shrub canopies. Example 2) Excised branch. Example 3) Pumped water at specific depths using tubing connected to CTD.

Sample Processing

Not a SESAR Field

Proposed ESS-DIVE Element	sampleProcessing if relevant, Recommended
Definition	Any processing applied to the sample during or after retrieving the sample from the environment. Can provide a list of preparations and preservation methods for the sample.
Format
Additional Instructions	Sample processing may often be the same across a series/collection of samples. To avoid entering the same information across numerous samples, you can create a separate file with metadata to describe a sample collection, which contains a "collectionID", and any associated metadata fields (e.g. "sampleProcessing", "collectionMethodDescription", "Purpose", "Chief Scientist", etc.). Separate multiple sample processing methods with a semi-colon.
Examples	filter water; store samples in ethanol

Field Program or Project Name

SESAR name is "Field Program/Cruise"

Proposed ESS-DIVE Element	projectName Required
Definition	Enter the name of the DOE project to associate with this/these sample(s).
Format	free text
Additional Instructions	Required at dataset level, but want to associate with samples for data search and integration. Project details may often be the same across a series/collection of samples; To avoid entering the same information across numerous samples, you can create a separate file with metadata to describe a project or sample collection, which contains a "collectionID" or "Field Program/Cruise", and any associated metadata fields (e.g. "Collection Method Description", "Purpose", "Chief Scientist"...
Examples	Next Generation Ecosystem Experiments (NGEE) Tropics; LBNL Watershed Function SFA

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Location

Latitude Coordinate system WGS 84

Proposed ESS-DIVE Element	decimalLatitude if relevant, Required
Definition	Latitude of the location where the sample was collected, entered in decimal degrees. Negative values for South latitudes.
Format	Decimal degrees, coordinate system: WGS 84
Additional Instructions	Please supply no more than 6 decimal places (meter scale resolution) in the actual number (not just display format.) No letters are allowed.
Examples	5.89634

Longitude Coordinate system WGS 84

Proposed ESS-DIVE Element	decimalLongitude if relevant, Required
Definition	Longitude of the location where the sample was collected. Negative values for ‘West’ longitudes.
Format	Decimal degrees, coordinate system: WGS 84
Additional Instructions	Please supply no more than 6 decimal places (meter scale resolution) in the actual number (not just display format.) No letters are allowed.
Examples	-103.785

Navigation Type

Proposed ESS-DIVE Element	geolocationInstrument Recommended
Definition	Type of geolocation instrument used to obtain geographic coordinates.
Format	Controlled list.
Additional Instructions	Provide feedback on additional terms needed.
Examples	GPS; RTK GPS

Location Description

Proposed ESS-DIVE Element	locationDescription Recommended
Definition	Free text description of the location.
Format
Additional Instructions	You can also include details here about the location type, e.g. whether it is an absolute or reference location, plot ID and description.
Examples	300 year old low-land tropical rainforest in Parque Natural San Lorenzo, Panama

Country

Proposed ESS-DIVE Element	country Required
Definition	Country where the sample was collected.
Format	SESAR controlled list.
Additional Instructions	Use SESAR list, but may change controlled list to GAZ ontology.
Examples	United States

Elevation start

Proposed ESS-DIVE Element	minimumElevationInMeters Optional
Definition	Elevation at which a sample was collected. Minimum elevation value, if elevation taken over a range.
Format	Number
Additional Instructions	Provide elevation in meters where possible.
Examples	678.5

Elevation end

Proposed ESS-DIVE Element	maximumElevationInMeters Optional
Definition	Maximum elevation at which a sample was collected, if elevation was taken over a range.
Format	Number
Additional Instructions	Leave blank if elevation is a single value and not range. Provide elevation in meters where possible.
Examples	689.2

Elevation unit

Proposed ESS-DIVE Element	elevationUnit (recommend meters) if relevant, Required
Definition	Unit that elevation start and/or end are provided in.
Format	Recommend meters.
Additional Instructions	This will be removed when elevation field is changed to specify meters.
Examples	meters

Minimum Depth in Meters

Note that SESAR field is "Depth in Core (min)"

Proposed ESS-DIVE Element	minimumDepthInMeters if relevant, Required
Definition	Depth, or minimum depth (if taken over a range) at which a sample was collected, below ground or under water.
Format	Number
Additional Instructions	Recommend using meters.
Examples	0.001

Maximum Depth in Meters

Note that SESAR field is "Depth in Core (max)"

Proposed ESS-DIVE Element	maximumDepthInMeters if relevant, Required
Format	Number
Definition	Maximum depth at which a sample was collected, below ground or under water.
Additional Instructions	Recommend using meters.
Examples	0.003

Depth scale

Proposed ESS-DIVE Element	depthUnit (recommend meters) if relevant, Required
Format	Recommend meters.
Definition	Unit in which the depth is provided, should be meters.
Additional Instructions	This field will be deleted when we change the depth field to be required in meters.
Examples	meters

Minimum Distance above Surface in Meters

Not a SESAR Field

Proposed ESS-DIVE Element	minimumDistanceAboveSurfaceInMeters Optional
Definition	Minimum height above the ground surface, in meters. If no range of values collected, provide height measurement here.
Format	Number
Additional Instructions
Examples	4.2

Maximum Distance above Surface in Meters

Not a SESAR Field

Proposed ESS-DIVE Element	maximumDistanceAboveSurfaceInMeters Optional
Definition	Maximum height above the ground surface, in meters.
Format	Number
Additional Instructions
Examples	7.2

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Environmental Context

Physiographic feature

Proposed ESS-DIVE Element	localEnvironmentalContext Recommended
Definition	Entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen.
Format	Terms from Environment Ontology (ENVO). Provide the appropriate term and ENVO identifier - see examples below.
Additional Instructions	Choose environmental context that is a smaller spatial grain than your entry for biome. Delimit multiple values using semi-colon. If needed, request new terms on the ENVO tracker, identified here.
Examples	river [ENVO:00000022]; pond [ENVO:00000033]; wet meadow ecosystem [ENVO:01000449]; mountain [ENVO:00000081] For annotating a pooled sample taken from various vegetation layers in a forest, consider: canopy [ENVO:00000047]; herb and fern layer [ENVO:01000337]; litter layer [ENVO:01000338]; understory [01000335]; shrub layer [ENVO:01000336].

Biome

Not a SESAR Field

Proposed ESS-DIVE Element	biome Recommended
Definition	Major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?).
Format	Terms from Environment Ontology (ENVO). Provide the appropriate term and ENVO identifier - see examples below.
Additional Instructions	We recommend using subclasses of ENVO’s biome class. Use a semi-colon to delimit multiple biomes where needed. If needed, request new terms on the ENVO tracker, identified here.
Examples	shrubland biome [ENVO:01000176]; tropical moist broadleaf forest biome [ENVO:01000228]; estuarine biome [ENVO:01000020]

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Sample Access

Release Date

Proposed ESS-DIVE Element	releaseDate Required
Definition	Date when sample metadata should be publicly accessible and searchable. If null , defaults to date of registration in SESAR (recommended).
Format	YYYY-MM-DD
Additional Instructions	SESAR recommends that sample metadata become public within 2 years of sample registration.
Examples	2018-03-15

Current Archive

Proposed ESS-DIVE Element	currentArchive Optional
Definition	Name of institution, museum, or repository where the sample is currently stored.
Format
Additional Instructions	Only applies to physical samples that are archived in a collection for some period of time.
Examples	Geosciences and Environmental Change Science Center, USGS Federal Center, Lakewood, CO

Current Archive Contact

Proposed ESS-DIVE Element	currentArchiveContact Optional
Definition	Address and/or email of the person who should be contacted for information about or access to the sample.
Format	free text
Additional Instructions	Email is not mandatory, but helps with communication about samples.
Examples	[e-mail]