Guide

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Sample ID and Metadata
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🌿
Sample ID and Metadata
Guide
Here you will find proposed guidelines for standardizing sample metadata to describe interdisciplinary samples within DOE's Environmental Systems Science community.
Most of the sample metadata follows SESAR's metadata guidelines. However, we modified some metadata elements, specific requirements, and vocabularies based on ESS community 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).
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​
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
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
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
​
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
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 |
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]|
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 |[email protected] |