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Algal Data Upload File Specification

Algal 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 algae qualitative analyses:

  • This example contains only the required fields for the upload.
  • This example gives data entry examples for all fields of the upload.

Examples for algae quantitative analyses:

  • This example contains only the required fields for the upload.
  • This example gives data entry examples for all fields of the upload.

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

See BioData Taxonomy Downloads for allowable combinations of BenchTaxonName and BenchTaxonNameReferenceCode

See Algal Data Domain Values for allowable values of LabComponent and BioVolumePerCellMethod

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

LabSampleID

NoSample identifier used by the submitting laboratory

LabRecordID

Yes

LabRecordID is generated and provided by the Lab to uniquely identifying each record 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

LabComponent

Yes

Used to communicate whether the record came from a soft algae or a diatom counting process

BenchTaxonName

Yes

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

  • A published TaxonName can include an author; TaxonName may also include descriptor terms or codes that more clearly define it as a conditional or provisional taxa (e.g. table 10 on page 24 of OFR 00-212)
  • The BenchTaxonNameReferenceCode when combined with the BenchTaxonName must be either "Current" or "Deprecated" in the context of the BioData Taxonomy

BenchTaxonNameReferenceCode

Conditional

The term that is communicated between a Lab and the BioData System as a link to a full citation of a reference

VolumeReceivedByLab_mL

Yes

The total volume in the container in milliliters - as measured by the lab upon receipt

  • If more than one container is received and composited by lab, this should be the sum of the measured volumes

ProportionExamined

Conditional

Proportion of the “VolumeReceivedByLab_mL” that was inspected (counted) by the lab

  • > 0 and <=1
  • Required if (1) lab procedure is quantitative AND (2) record is for a soft algae taxon

NumSoftAlgaeNatUnitsCounted

Conditional

Number of soft algae natural units counted by the taxonomist

  • Integer
  • Raw tally not adjusted for any subsample dilution or concentration factors
  • Required if (1) lab procedure is quantitative AND (2) record is for a soft algae taxon
  • Prohibited with diatom taxa

NumSoftAlgaeCells

Conditional

Number of soft algae cells

  • Integer
  • Tally not adjusted for any dilution or concentration factors
  • Required if (1) lab procedure is quantitative AND (2) record is for a soft algae taxon
  • Prohibited with diatom taxa

NumDiaCellsCounted_Live

Conditional

Number of living diatom cells/valves counted by analyst

  • Integer
  • Raw tally not adjusted for any subsample dilution or concentration
  • Either NumDiaCellsCounted_Live, NumDiaCellsCounted_Dead, OR NumDiaCellsCounted_LiveOrDead is required if (1) lab procedure is quantitative AND (2) record is for a diatom taxon
  • If NumDiaCellsCounted_Live, AND NumDiaCellsCounted_LiveOrDead are reported, NumDiaCellsCounted_Live <= NumDiaCellsCounted_LiveOrDead
  • Prohibited with soft algae taxa, but permitted with diatom taxa identified from the "soft algae count" LabComponent

NumDiaCellsCounted_Dead

Conditional

Number of dead diatom cells/valves counted by analyst

  • Integer
  • Raw tally not adjusted for any subsample dilution or concentration factors
  • Either NumDiaCellsCounted_Live, NumDiaCellsCounted_Dead, OR NumDiaCellsCounted_LiveOrDead is required if (1) lab procedure is quantitative AND (2) record is for a diatom taxon
  • If NumDiaCellsCounted_Dead, AND NumDiaCellsCounted_LiveOrDead are reported, NumDiaCellsCounted_Dead <= NumDiaCellsCounted_LiveOrDead
  • Prohibited with soft algae taxa, but permitted with diatom taxa identified from the "soft algae count" LabComponent

NumDiaCellsCounted_LiveOrDead

Conditional

Number of living or dead diatom cells/valves counted by analyst

  • Integer
  • Raw tally not adjusted for any subsample dilution or concentration factors
  • Either NumDiaCellsCounted_Live, NumDiaCellsCounted_Dead, OR NumDiaCellsCounted_LiveOrDead is required if (1) lab procedure is quantitative AND (2) record is for a diatom taxon
  • If NumDiaCellsCounted_Live, NumDiaCellsCounted_Dead, AND NumDiaCellsCounted_LiveOrDead are reported, NumDiaCellsCounted_Live + NumDiaCellsCounted_Dead must equal NumDiaCellsCounted_LiveOrDead
  • Prohibited with soft algae taxa, but permitted with diatom taxa identified from the "soft algae count" LabComponent

BioVolumePerCell_um3

Condtional

Positive number representing the cell volume in cubic micrometers (µm3)

  • Must be null for qualitative procedures
  • Required if BioVolumePerCellMethod is populated with value

BioVolumePerCellMethod

Conditional

The method used to determine the BioVolumePerCell_um3 value

  • Must be null for qualitative procedures
  • Required if BioVolumePerCell_um3 is populated with value

BenchComment

No

This field is 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

Conditional

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 submitting Organization, as in a subcontract situation, the other organization should be reported)
  • Required if IdentificationDate is present

IdentificationDate

No

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

IdentifiedBy

NoName of person making the identification

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 individual in their organization (i.e. IdentificationEntity and VerificationEntity are the same) or by a different organization (i.e IdentificationEntity and VerificationEntity are different)
  • Required if VerificationDate is present

VerificationDate

No

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

CurationEntity

Conditional

An valid abbreviation for an organization in the BioData system

  • This field should be populated with the organization where the specimen(s) are housed, if some relatively long-term effort is being made to preserve voucher material
  • 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 initial organization, not subsequent transfers, so any subsequent details would need to be obtained from the initial curation entity
  • Required if CurationDate is present

CurationDate

No

Date that the curation of the specimen(s) was initiated (mm/dd/yyyy)

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 the actual specimen(s) examined associated with the particular record

LabTaxonID

NoTaxonomic identifier used by the lab in their system
  • No labels