BioData


Quick Links

Child pages
  • Invertebrate Data Upload Files

Retrieve Data
About
Support Home
Contact Us
Login
USGS Home
Contact USGS
Search USGS
Skip to end of metadata
Go to start of metadata

Invertebrate Upload File Specifications

Invertebrate Data Domain Values

Key Points

  • One tab-delimited data file is uploaded at a time
  • The file can contain data for
    • more than one Lab Order (this is typical)
    • more than one project (this is permitted but not recommended)
  • Use Unicode (UTF-8, UTF-16, or UTF-32) to preserve accented and international characters (see help tip - Saving files in a Unicode file format for international character support)
  • Do NOT release ANY of the data for a lab order until ALL of the data for the lab order are ready and included in the file.
  • Put ALL of the data for a lab order into the same data upload file

We recommend releasing data for different projects in separate data upload files.

Example Tab-delimited Text Data Files

To download files, right-click 'example' and choose 'Save Link As'

Examples for invertebrate qualitative analyses:

  • This example contains only the required fields for the upload.
  • This example contains only the required fields plus taxa reference examples.
  • This example illustrates how to handle multiple containers per sample (e.g. field large/rare components).
  • This example gives data entry examples for all fields of the upload.

Examples for invertebrate quantitative analyses:

  • This example contains only the required fields for the upload.
  • This example contains only the required fields plus taxa reference examples.
  • This example illustrates how to handle multiple containers per sample (e.g. field large/rare components).
  • This example gives data entry examples for all fields of the upload.

Invert Data Upload File Column Definitions (Return to Top of Page)

See BioData Taxonomy Downloads for allowable combinations of BenchTaxonName and BenchTaxonNameReferenceCode

See also the Invertebrate Data Domain Values - for allowable values of ResultComponent, LifeStage, UniqueTaxonFlag, TargetLevelNotReachedReason, ParameterCode, and Artifact.

Attribute

Required?

Description For Lab

LabOrderID

Yes

BioData-generated integer (identifier) that is assigned to a Lab Order

  • Obtained by the lab in the downloaded Lab Order files.
  • A Lab Order is comprised of the one or more containers that are processed according to requested procedures.

LabRecordID

Yes

LabRecordID is generated and provided by the Lab to uniquely identifying each record within within a set of records for a Lab Order

  • The combination of LabOrderID and LabRecordID must be unique.

ContainerID

No

BioData-generated integer (identifier) that is assigned to each container assigned to a Lab Order

  • obtained by the lab in the downloaded Lab Order files.

ResultComponent

Yes

Lab processing component in the context OFR 02-150

  • "main" is used in the context of OFR 02-150 (page 43) as a surrogate for "main-body", and should be used to indicate any comparable component of a sample in other field protocols. It is obtained by the lab in the downloaded Lab Order files.
  • "field large/rare" is used in the context of OFR 02-150 (page 43) as a surrogate for "large-rare", and should be used to indicate any comparable component of a sample in other field protocols. It is obtained by the lab in the downloaded Lab Order files.
  • "lab large/rare" is used in the context of OFR 00-212 (page 16) as a surrogate for "large-rare", and should be used to indicate any comparable component of a sample in other protocols. When appropriate in the results for a procedure it replaces "main" as the Result Component.

BenchTaxonName

Yes

The term that is communicated between a Lab and the BioData System about a Taxon's identity

BenchTaxonNameReferenceCode

Conditional

The term that is communicated between a Lab and the BioData System as a link to a full citation of the reference used to apply the BenchTaxonName to the specimen(s)

LifeStage

Conditional

A code indicating the life stage of the specimen(s) associated with the BenchTaxonName for the given record

  • LifeStage must be Null for a TaxonName that is NOT a member of the Subclass Pterygota 
  • If present, and the TaxonName is in any of the following Orders: Ephemeroptera, Odonata, Plecoptera, Orthoptera, or Hemiptera, LifeStage must be L or A
  • If present, and the TaxonName is in any of the following Orders: Megaloptera, Neuroptera, Trichoptera, Lepidoptera, Coleoptera, or Diptera, LifeStage must be L, A, or P

UniqueTaxonFlag

No

Flag indicating a taxon's uniqueness within the results for a single LabOrderID - not uniqueness within the entire result set.

  • "Yes" indicates uniqueness within the set of results for the lab order
  • When parent and child taxa (e.g. Baetidae, Baetis, and Baetis tricaudatus) are included in the same result set for a LabOrderID and they are "known" by the lab not to be the same as other taxa in the sample, the flag may be set. For example, if Baetidae (Epehemerptera) and Baetis (Epehemeroptera: Baetidae) are in the results for the same LabOrderID, Baetidae may be unique, but is not identifiable to Genus, so the flag might be set to "Yes" for Baetidae, but is not needed for Baetis
  • When two identical TaxonNames are included in the same result set for a LabOrderID and they are "known" not to be the same taxon by the Lab, the flag may be set. For example, if Baetis (Epehemerptera: Baetidae) and Baetis (Epehemeroptera: Baetidae) are in the results for the same LabOrderID, they may be different from one another, but not identifiable to Species, so the flag might be set to "Yes"
  • A BenchComment may be appropriate whenever the flag is used

TargetLevelNotReachedReason

Conditional

Standardized codes indicating the condition of a specimen that limited the ability of the lab to identify the specimen(s) to the requested level.

  • When more than one reason applies, the codes describing the reasons should be separated with semicolons; alternatively, results may be reported in different rows with single unique codes for the reasons
  • "TargetLevelNotReachedReason" is used in the context Table 8 in OFR 00-212 (page 23) as a surrogate for identification interferences, and should be used to indicate any comparable reason in other protocols.

ParameterCode

Yes

A code indicating whether the sample was processed quantitatively or qualitatively

  • "RawCount" should be entered if the individuals represented by the TaxonName are enumerated (e.g. a quantitative analysis sorting and identifying >= 500 organisms)
  • "Presence" should be entered if the specimens associated with the TaxonName are only presented as a list of TaxonNames (e.g. a qualitative analysis to solely determine richness).

Value

Conditional

The number of individuals counted for a particular taxon

  • Not corrected for laboratory or field subsampling
  • Must be a positive integer when the ParameterCode equals "RawCount"
  • Must be Null when the ParameterCode equals "Presence"

SubsamplingNumerator

Conditional

An integer that when divided by the SubsamplingDenominator (below) will results in the proportion of the sample that was sorted to obtain the number of individuals in the Value field. For example, if 5 grids are sorted from a 30 grid tray, the integer 5 would be entered as the SubsamplingNumerator with 30 as the SubsamplingDenominator.

  • In some cases, a lab may sort less than an entire grid (e.g. 1/4 of a grid), but an integer is required in the SubsamplingNumerator field. For example, if 5.25 grids are sorted from a 30 grid tray, the integer 21 would be entered as the SubsamplingNumerator and the SubsamplingDenominator would need to be adjusted to 120 to maintain the original ratio of 5.25 to 30
  • Must be greater than or equal to one when ParameterCode is "RawCount"
  • Must be Null when the ParameterCode is "Presence"

SubsamplingDenominator

Conditional

An integer that when divided into the SubsamplingNumerator (above) will result in the proportion of the sample that was sorted to obtain the number of individuals in the Value field. For example, if a 30 grid tray is used and 5 grids are sorted from the tray, the integer 30 would be entered as the SubsamplingDenominator with 5 as the SubsamplingNumerator.

  • In some cases, a lab may sort less than an entire grid (e.g. 1/4 of a grid), but an integer is required in the SubsamplingNumerator field. For example, if 5.25 grids are sorted from a 30 grid tray, the integer 21 would be entered as the SubsamplingNumerator and the SubsamplingDenominator would need to be adjusted to 120 to maintain the original ratio of 5.25 to 30
  • Must be greater than or equal to SubsamplingNumerator
  • Must be greater than or equal to one when ParameterCode is "RawCount"
  • Must be Null when the ParameterCode is "Presence"

Artifact

No

Flag for results that are not supported by a specimen thought to be alive at the time of collection, but that a procedure requires to be reported.

  • For example, an empty mollusc shell may indicate that the taxon may have been present, but is not definitive indication, so the artifact would be set to "Yes".

BenchComment

No

Text field used by the lab to convey additional information about the record, that is not provided for in the other fields.

  • Length is limited to 250 characters.

IdentificationEntity

Yes

An valid abbreviation for an organization in the BioData system

  • This field should be populated with the Organization that actually performed the identification of the specimen(s) (i.e. if the identification was performed by an organization other than the Organization uploading the results, as in a subcontract situation, the subcontract Organization should be reported)

IdentificationDate

Yes

Date that the identification of the specimen(s) was completed (mm/dd/yyyy).

VerificationEntity

Conditional

An valid abbreviation for an organization in the BioData system

  • This field may be used by the lab to indicate that the identity of the specimen(s) associated with the record were verified by a second Organization or another individual in the same Organization
  • required if Verification Date is present

VerificationDate

Conditional

Date that the verification of the specimen(s) was completed (mm/dd/yyyy)

  • required if Verification Entity is present.

CurationEntity

Conditional

An valid abbreviation for an organization in the BioData system

  • If some relatively long-term effort is being made to preserve voucher material, this field should be populated with the Organization where the specimen(s) are housed; it is required if Verification Date is present
  • There is no implication regarding the duration of the curation or condition of the curated specimens - only that an initial effort was made to store the specimens with the indicated organization
  • Tracking is limited to the deposition in the initial Organization; subsequent transfers are not tracked

CurationDate

Conditional

Date that the deposition of the specimen(s) occurred (mm/dd/yyyy)

  • required if Curation Entity is present.

ImageLink

No

Persistent URL for images of the specimen(s) associated with the record

  • NOT to be used for link to representative images of the taxon - it is to be used to link to images of specimen(s) actually examined for this particular record
  • No labels