Handbook

Search Handbook
 

Specimen Data Submission Protocol

Specimen Data submissions are the first step in the process of creating records on BOLD and have to be submitted before images, traces, and sequences can be uploaded. Once the Specimen Data is uploaded, records are created and BOLD Process IDs are automatically assigned to each sample. Sample IDs can be used to upload images, trace files, and sequences.

There are two methods for creating new specimen records on BOLD; 1) Batch Format - which uses a spreadsheet template for uploading large numbers of records, or 2) Single Specimen Format - using an online form.

Batch Specimen Submissions

A batch submission of new specimen data records to BOLD through the BOLD Data Managers is the most efficient way to upload specimen records for those working with large number of samples , including 96-well plates. There are two major steps involved in this process: creating the excel file and submitting the file for validation and upload to BOLD.

  1. Create Excel file submission
    • New submissions are project specific so that the data can be associated with a project on BOLD. If samples need to be submitted to multiple projects, a separate excel file for each project needs to be created:
    • The template consists of 4 worksheets; a main specimen identifier worksheet (voucher info) as well as worksheets for taxonomy, specimen details, and collection data. Minimal information can be submitted to start, and records can be updated at a later date following the Update Specimen Data Protocol.
    • The minimum required data to complete a new specimen record on BOLD are:
      • Sample ID
      • Field ID and/or Museum voucher ID
      • Institution Storing
      • Phylum
      • Country
  2. Submit file to BOLD for processing
    1. Open the destination project on BOLD
    2. Click on Specimen Data under the Uploads menu and select Initiate Batch Submission . This option is available to Project Managers and project users with Edit Specimen access.
    3. Select New for the submission type.
    4. In the form users will need to attach the Excel template they want to submit to the project. Users can also include email addresses for collaborators that should be cc'd on further communications regarding the submission, add a note about the submission, and check off the high priority box, if the submission should be processed with urgency. Once the form is completed, users then click on Submit to send the spreadsheet for the first pass of validation.
    5. If there are any errors detected during this validation, users will need to resolve these re-submit the spreadsheet.

Upon a successful submission of the package, an email confirmation will be sent out with a trackable ticket number. The uploaded data will be processed by our data submission staff who will be in contact with the submitter if any queries regarding the submitted data arise. Data is usually incorporated into the database within 1 to 2 business days as long as there are no issues.

For any questions or concerns about the process of submitting or creating new specimen records in batch, please email the Data Management Team through submissions@boldsystems.org.

Example Batch Submission for Specimen Data Records

BOLD supports the upload of multiple specimen records in a spreadsheet format:

      • excel Template Version 3.0
        A spreadsheet submission template containing all the original and extended data fields

Below is an example of a properly filled out data submission for Template Version 3.0. Use the tabs at the bottom of the Excel workbook to navigate through the four pages.

Example data for Voucher (Specimen) Info Worksheet
Specimen Info
Sample ID Field ID Museum ID Collection Code Institution Storing
Sample-demo01 Sample-demo01 Burke Museum
Sample-demo02 Sample-demo02 15466 ISC Burke Museum
Sample-demo03 15332-988a Burke Museum
Example data for Taxonomy Worksheet
Taxonomy
Sample ID Phylum Class Order Family Subfamily Genus Species Identifier Identifier
Email
Identifier
Institution
Identification
Method
Taxonomy
Notes
Sample-demo01 Arthropoda Insecta Diptera Asilidae Hydro-
psychinae
Efferia Efferia
aestuans
Jose
Lopez
jgonzales
@bio.org
Biodiversity
Institute
morpho-
logical
High
Confidence
in
identification
Sample-demo02 Arthropoda Insecta Diptera Asilidae Dasypo-
goninae
Leptarthrus Leptarthrus
brevirostris
Jose
Lopez
jgonzales
@bio.org
Biodiversity
Institute
morpho-
logical
High
Confidence
in
identification
Sample-demo03 Arthropoda Insecta Diptera Asilidae Dasypo-
goninae
Wilcoxia Jose
Lopez
jgonzales
@bio.org
Biodiversity
Institute
morpho-
logical
Not sure
on genus,
possible
new genus
Example data for Specimen Details Worksheet
Specimen Details
Sample ID Sex Reproduction Life
Stage
Extra Info Notes Voucher Status Tissue
Descriptor
Associated
Taxa
Associated
Specimens
External URLs
Sample-demo01 Male Sexual Adult Region 1 vouchered:
registered collection
leg  
Sample-demo02 Female Sexual Adult Region 1 vouchered:
registered collection
leg www.burke.edu
/spec/15466
Sample-demo03 Sexual Larvae   collected
with predator
vouchered:
registered collection
predator:
Hornet
predator:
BITK002-12
Example data for Collection Info Worksheet Part 1
Collection Info
Sample ID Collectors Collection
Date
Country/Ocean State/
Province
Region Sector Exact Site Latitude Longitude Elevation ...
Sample-demo01 J. Lopez,
M. Lopez
27-JUL-10 Canada Ontario Wellington
County
Guelph Kortright
Preservation
Park
43.511 -80.223 300 m
Sample-demo02 J. Lopez,
M. Lopez
27-JUL-10 Canada Ontario Wellington
County
Guelph Kortright
Preservation
Park
43.511 -80.223 300 m
Sample-demo03 Erica Langley 15-AUG-11 United States Texas Jeff Davis
County
Davis
Mountains
State Park
South
camping area
30.607 -103.934 1475 m
Example data for Collection Info Part 2
Collection Info
... Depth Elevation
Precision
Depth
Precision
GPS Source Coordinate
Accuracy
Event Time Collection Date
Accuracy
Habitat Sampling
Protocol
Collection
Notes
Site Code Collection
Event ID
  2 m     1 m mid summer 2 dry forest Malaise Trap at park
entrance near
Kortright Rd.
#14 #M872a
  2 m     1 m mid summer 2 dry forest Malaise Trap at park
entrance near
Kortright Rd.
#14 #M872a
10 m   garmin unit   morning   hydric-
mesic
hand
picked
next to
Limpia Creek
15332-988

 

Single Specimen Submission

Users may also choose to add single records manually to the system through the Specimen Data Upload option available in the Project Console. This is the fastest way to add an individual record to a project and is recommended for uploads of 10 records or less. This option is available to project managers and project users with access to edit specimen data. There are two steps involved in this process:

  1. Navigate to record submission form for Specimen Data
    1. Open the destination project on BOLD
    2. Click on Specimen Data under the Uploads menu to access the Specimen Data Submission form.
  2. Fill in Specimen Data and Submit

The minimum required data to complete a new specimen record on BOLD are:

  • Sample ID
  • Field ID and/or Museum voucher ID
  • Institution Storing
  • Phylum
  • Country

Records can be updated at a later date following the Update Specimen Data Protocol.

Specimen Submission Single record submission form

Look-up Fields

The green outlined boxes in the above form are look-up fields. These fields allow users to type in the beginning of the desired name to get matching options from BOLD. Select the appropriate name from the drop-down box to lock it in.

Users will not be able to add new identifiers, taxonomy, countries, or provinces in this form. To add new values for these fields, follow the directions on Update Specimen Data.

Definition of Specimen Data Fields
Field definitions for Voucher (Specimen) info page (* denotes required fields for a record)
Sample ID* Identifier for the sample being sequenced, often identical to the Field ID or Museum ID.  Sample identifiers are extended when tissue is sub-sampled for secondary analysis. It is important to use a unique and original format for the Sample IDs. If the Sample IDs provided are not original to BOLD, they will need to be changed before the data can go online. Only the following characters may be used in the Sample ID, Field ID, and Museum ID: A-Z 0-9 ^ . : - _ ( ) # . All other characters will be removed.
Field ID* Identifier for specimen assigned in the field.  Specimens in personal collections will continue to use this as the primary identifier for the specimen. (Either Field ID or the Museum ID must be filled in)
Museum ID* Identifier for specimen assigned by formal collection upon accessioning, also referred to as the catalog number.  This identifier should be made unique by adding scope of the collection or institution.  This is done by following a triplet format Institution acronym:collection code:catalog number in the case of a museum collection and Personal:Name of collector:FieldID , in the case of a personal collection. (Either Field ID or the Museum ID must be filled in)
Collection Code Code associated with a given collection within an institution. The Collection Code is used in conjunction with Museum ID in order to disambiguate a ID that might be used in different collections within the same institution. This field is only to be used if Museum ID field is used.
Institution Storing* The full name of the institution that has physical possession of the voucher specimen. If the voucher is held in a personal research collection, users should enter the personal name.
Field definitions for Taxonomy Page (* denotes required fields for a record)
Full Taxonomy* Full scientific name for each rank, consisting of phylum *, class, order, family, subfamily (optional), genus, and species. Interim names may be used up to family level. Interim names should contain non-Linnean characters such as numbers, punctuation and/or extra capitalization. Taxonomists are encouraged to append interim names with initials. (example: Bos sp. 1KHR)
Identifier Full name of primary individual who assigned the specimen to a taxonomic group.
Identifier Email E-mail address of the primary identifier. In the case where the identifier is deceased or retired, please make note of that in the email field. It is important to provide this information so we can keep the database up-to-date.
Identifier Institution The full name of the identifier's institutional or organizational affiliation if one exists.
Identification Method The method used to identify the specimen. (e.g.: BOLD ID Engine, morphology, field guide)
Tax Notes Additional notes relating to the identification of the organism.
Field Definitions for the Specimen Details Page
Sex The sex of the specimen. BOLD supports: "female", "hermaphrodite", or "male".
Reproduction The presumed method of reproduction. BOLD supports: "sexual", "asexual", or "cyclic parthenogenesis".
Life Stage The age class or life stage of the specimen at the time of sampling. "Adult", "Immature", "pupa", etc.
Extra Info A brief note or project term associated with the specimen for rapid analysis. (max: 50 characters). This field will appear on the Record List and can be included in the Taxon ID tree
Notes General notes regarding the specimen.
Voucher Status Status of the specimen in an accessioning process. Controlled vocabulary:
  • “museum vouchered:type” for type specimens
  • “museum vouchered:type series” for specimens in a type series
  • “vouchered:registered collection” for specimens that are vouchered in formal collection
  • “to be vouchered:holdup/private” for specimens that are not yet vouchered but will be in the future
  • “e-vouchered:dna/tissue+photo” for cases where the specimen has either been lost or consumed in the analytical process but was photographed prior to loss.
  • “dna/tissue vouchered only” for cases where only only DNA or tissue samples remain
  • “no specimen” for cases where all supporting tissue, DNA, or multimedia is missing or unavailable
Tissue Descriptor A brief description of the type of tissue or material analyzed. Example: "muscle", "leg", "thorax", "liver", "blood", "feces", etc.
Associated Taxa A list of taxa associated with the taxon at the time of its collection. References to taxa should be preceded by the relationship. Examples: "host: Quercus alba", "prey: caterpillar".
Associated Specimens A list of specimens associated with the subject specimen at the time of its collection. References to other specimen identifiers should be preceded by the relationship. Examples: "host: PLANT23452, prey: USNM45677" when both prey and host specimens have been captured.
External URLs Web accessible links that provide additional information about the specimen preceded by a descriptor.  Multiple links should be pipe separated ("|"). Example:  "specimen:http://www.antweb.org/specimen.do?name=casent0179894."
Field Definitions for Collection Data (* denotes required fields for a record)
Collectors The full or abbreviated names of the individuals or team responsible for collecting the sample in the field.  Multiple individuals or teams should be separated by a comma.
Collection Event ID A optional event ID for submission purposes that allows for relational data support when multiple specimens are collected from a single site.
Collection Date The date during which the sample was collected. Format (DD-MMM-YYYY) is recommended to disambiguate where possible.
Date Accuracy A numerical representation of the precision of the Collection Date given in days and is represented as +/- the value.  The default value for this field is 0 days.
Event Time The time or time of day during which the sample was collected. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).  Also supported are general terms for time of day: "morning", "afternoon", "evening", "night".
Country/Ocean* The full, unabbreviated name of the country, major political unit, or ocean in which the organism was collected.
State/Province The full, unabbreviated name of the state, province, territory, or prefecture (i.e., the next smallest political region below Country) in which the organism was collected.
Region The full, unabbreviated name of the county, shire, municipality, or park (i.e., the next smallest political region below province/state) in which the organism was collected.
Sector The full, unabbreviated name of the lake, conservation area or sector of park in which the organism was collected. 
Exact Site Additional text descriptions regarding the exact location of the collection site relative to a geographic or biologically relevant landmark.
Site Code The name of the sampling location.  Appropriate when site based sampling is performed.
Habitat A category or description of the habitat in which the event occurred.  Envo ontology terms are recommended.
Sampling Protocol The name of, reference to, or description of the method or protocol used during an event.
Latitude The geographic latitude (in decimal degrees) of the geographic center of a location.
Longitude The geographic longitude (in decimal degrees) of the geographic center of a location.
Coordinate Accuracy A decimal representation of the precision of the coordinates given in the decimalLatitude and decimalLongitude.  This field also supports precision in kilometers which requires the value to be followed by the "km" unit.
Coordinate Source The source of the latitude and longitude measurements.
Elevation Elevation of sampling site.  Measured in meters relative to sea level.  Negative values indicate a position below sea level.
Elevation Precision A numerical representation of the precision of the elevation given in meters and is represented as +/- the elevation value.  This field is only appropriate when a value is entered for elevation.
Depth For organisms collected beneath the surface of a water body.  Measured in meters below surface of water.
Depth Precision A numerical representation of the precision of the depth given in meters and is represented as +/- the depth value.  This field is only appropriate when a value is entered for depth.
Collection Notes Comments or notes about the collection event.
Updating Specimen Data

The most efficient way to update an individual record in a project is using the Edit button on the Specimen Page . However, to add new taxa, identifiers, countries, or state/provinces to BOLD, users will need to use the Batch Update described below.

A. Manual Update of a Single Record

To modify or update individual records within a project, project managers and project users with editing specimen access can do so, manually by selecting the Edit button found in the Specimen Record page.

B. Batch Update of Multiple Records

Use this protocol when multiple records need to be updated, or to add new taxa, identifiers, countries or state/provinces to records that do not currently exist in the BOLD database.

  1. Download and modify the records that need updates:
    1. Within BOLD, navigate to the Record List or use the Record Search function, and select which records need to updated.
    2. Click on Data Spreadsheets using the Downloads menu on the left side of the Record List.
    3. Select only which pages need to be updated and download the excel workbook: Voucher Info, Taxonomy, Specimen Details, and Collection Data.
    4. Make changes onto the downloaded sheets.
  2. Submit file to BOLD for processing:
    1. Navigate back to the Project Console.
    2. Click on Specimen Data under the Uploads menu and select the Initiate Batch Submission button. This option is available to project managers and project users with editing specimen access.
    3. Select Update for the submission type.
    4. In the form users will need to attach the Excel template they want to submit. Users can also include email addresses for collaborators that should be cc'd on further communications regarding the submission, add a note about the submission, and check off the high priority box for submission which should be processed with urgency. Once the form is completed, users then click on Submit to send the spreadsheet for the first pass of validation.
    5. If there are any errors detected during this validation, users will need to resolve these re-submit the spreadsheet.
  3. Upon a successful submission of the package, an email confirmation will be sent out with a tracktable ticket number. The uploaded data will be processed by our data submission staff who will be in contact with the submitter any queries regarding the submitted data arise. Data is usually incorporated into the database within 1 to 2 business days if there are no issues.
NOTE ON UPDATES:

Any fields left empty will be considered blank and thus removed from BOLD. Do not remove any data from the update sheet that should remain on BOLD. The submission program cannot distinguish between “blank: do not update this field’ or “blank: delete the content of this field”.

For any questions or concerns about adding or updating specimen data, please email the Data Management Team through submissions@boldsystems.org.

  • tag_user
  • tag_submission
  • tag_specimen
  • tag_project
  • tag_taxonomy

Back to Top