Guide
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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 . 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 , or genomic standards .
We seek any additional feedback, with the goal of making ESS sample information Findable, Accessible, Interoperable, and Reusable (FAIR).
*Required fields are marked with an asterisk, and indicated in detailed tables below.
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ESS-DIVE Proposed Element
objectType Required
Definition
Broad characterization of the nature of a sample or specimen.
Format
Additional Instructions
Provide feedback on additional terms or revisions needed.
Examples
Core; Individual Sample; Organism
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
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
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
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
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
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
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
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
Proposed ESS-DIVE Element
material Required
Definition
Material that the sample consists of.
Format
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
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
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
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.
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
Proposed ESS-DIVE Element
sizeUnit only if Size provided,Required
Definition
Unit for the numerical value provided for ‘size’.
Format
Additional Instructions
Examples
square centimeter; kilogram
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
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
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
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
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
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
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
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.
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
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
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
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
Proposed ESS-DIVE Element
geolocationInstrument Recommended
Definition
Type of geolocation instrument used to obtain geographic coordinates.
Format
Additional Instructions
Provide feedback on additional terms needed.
Examples
GPS; RTK GPS
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
Proposed ESS-DIVE Element
country Required
Definition
Country where the sample was collected.
Format
Additional Instructions
Examples
United States
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
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
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
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
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
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
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
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
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
Additional Instructions
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].
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
Additional Instructions
Examples
shrubland biome [ENVO:01000176]; tropical moist broadleaf forest biome [ENVO:01000228]; estuarine biome [ENVO:01000020]
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
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
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
scientist@lbl.gov
. See for revised terms proposed for ESS-DIVE
See ESS-DIVE's proposed from Environment Ontology (ENVO)
Use any additional unit terms from , and provide feedback.
.
.
Use SESAR list, but may change controlled list to .
. Provide the appropriate term and ENVO identifier - see examples below.
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, .
. Provide the appropriate term and ENVO identifier - see examples below.
We recommend using subclasses of . Use a semi-colon to delimit multiple biomes where needed. If needed, request new terms on the ENVO tracker, .