Child pages
  • Algal Data Upload Files
Skip to end of metadata
Go to start of metadata

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 lab

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 actually 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 when the record is for a diatom taxon.

NumSoftAlgaeCells

Conditional

Number of soft algal 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 when the record is for a diatom taxon.

NumDiaCellsCounted_Live

Conditional

Number of living diatom cells actually 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 when the record is for a soft algae taxon.

NumDiaCellsCounted_Dead

Conditional

Number of dead diatom cells actually 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 when the record is for a soft algae taxon.

NumDiaCellsCounted_LiveOrDead

Conditional

Number of living or dead diatom cells actually 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 when the record is for a soft algae taxon.

BioVolumePerCell_um3

Condtional

Positive number representing the cell volume.

  • Must be null for qualitative procedures.
  • Must be present if BioVolume Per Cell Method is populated with value.

BioVolumePerCellMethod

Conditional

The method used to determine the BioVolume Per Cell value.

  • Must be null for qualitative procedures.
  • Must be present if BioVolume Per Cell 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)
  • This field is required if IdentificationDate is present.

IdentificationDate

Conditional

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

  • This field is required if IdentificationEntity is present.

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).
  • This field is required if VerificationDate is present.

VerificationDate

Conditinal

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

  • This field is required if VerificationEntity is present.

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
  • This field is required if CurationDate is present.

CurationDate

Conditional

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

  • This field is required if CurationEntity 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

LabTaxonID

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