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  BOLD Handbook - Batch Specimen Data Submission Protocol

Specimen Data Submission Protocol

SubHeading-Datamanagement

Data submissions are the first step in the process of creating records on BOLD, the Barcode of Life Data Systems. New records are automatically assigned a BOLD Process ID when they enter the system. Process IDs can be used to upload sequences, traces, and images since they are unique to each individual record. There are two ways to enter records into BOLD; through an online form for a small number of records or in batch format.

Batch Specimen Submission Protocol

Individual Specimen Submission Protocol

Overview of Specimen Data Fields

Updating Specimen Data Protocol

Batch Specimen Submission Section

This protocol assists in the submission of bulk data to BOLD through the BOLD Data Managers. This is the most efficient way to populate your project with sets of records, and is recommended for more than 10 records that need to be uploaded at one time. If you have less than 10 new records to submit to your project, please consider using the Individual Specimen Data Submission Protocol, which describes how to utilize the manual interface for adding individual records to BOLD.

Step 1. Create Excel file submission

 

New submissions are project specific, so that their data can be associated with a project on BOLD. If records need to be entered into different projects on BOLD, a separate excel file for each project needs to be created.

To create a batch specimen data submission for a project, please click here to download a Batch Specimen Data Submission template.

The data spreadsheet consists of 4 worksheets; a main specimen identifier worksheet (voucher info) that is linked to three other worksheets: taxonomy, specimen details, and collection data. Table 8-1 through Table 8-4 below describes the information accepted in the batch specimen data submission.
(* denotes the required fields for a record) Figure 8-1 through Figure 8-4 illustrates example data filled into the accepted fields.

The minimal requirements for a new submission on BOLD are:

  • Voucher Info Page - Sample ID
  • Voucher Info Page - Field ID and/or Museum voucher ID
  • Voucher Info Page - Institution Storing
  • Taxonomy Page - Phylum
  • Collection Page - Country

You can submit minimal information to start and then update your records at a later date following the Update Specimen Data Protocol.

Step 2. Submit file to BOLD Data Managers

 
  1. To submit the batch spreadsheet to BOLD, open the project that you would like to have the records uploaded to.
  2. Click on "Specimen Data" under the Uploads menu and select the "Upload" button for Batch Specimen Data Submissions. This option is available to project managers and project users with edit specimen access.
  3. In the form, select the Excel file that you would like to submit to this project, along with email addresses that should be cc'd on further communications regarding the submission, a priority level and note.

Upon submission of the package, an email confirmation will be sent out with a ticket number for that submission. The uploaded data will be processed by our data submission staff who will be in contact if there are any apparent errors or queries regarding the submitted data. Data is usually incorporated into the database within 1 to 2 business days.

For any questions or concerns about this process, please email the Data Management Team through submissions@boldsystems.org.

Example Batch Submission

Here is an example of a properly filled in data submission.

Please click here to download a Batch Specimen Data Submission template.

Use the tabs at the bottom of the Excel workbook to navigate through the four pages.

Specimen Info

Sample ID Field ID Museum voucher ID Collection Code Institution Storing
Sample-demo01 Sample-demo01     Burke Museum
Sample-demo02 Sample-demo02 BRM:ISC:15466 ISC Burke Museum
Sample-demo03 Sample-demo03     Burke Museum
Figure 8-1: Example data for Voucher (Specimen) Info

 

Taxonomy

Sample ID Phylum Class Order Family Subfamily Genus Species Identifier Identifier Email Identifier Institution
Sample-demo01 Arthropoda Insecta Diptera Asilidae Hydropsychinae Efferia Efferia aestuans Joe Smith jsmith@BIO.org Oxford
Sample-demo02 Arthropoda Insecta Diptera Asilidae   Asilus   Joe Smith jsmith@BIO.org Oxford
Sample-demo03 Arthropoda Insecta Diptera         Joe Smith jsmith@BIO.org Oxford
Figure 8-2: Example data for Taxonomy

 

Specimen Details

Sample ID Sex Reproduction Life Stage Extra Info Notes
Sample-demo01 Female Sexual Adult   Commonly called ‘Robber Fly’
Sample-demo02 Male Sexual Adult feeding on fruit  
Sample-demo03 Male Sexual Adult    
Figure 8-3: Example data for Specimen Details

 

Collection Info

Sample ID Collectors Collection Date Continent / Ocean Country State / Province Region Sector Exact Site Latitude Longitude Elevation
Sample-demo01 J. Smith, M. Jones 27-Jul-07 Asia Japan Hokkaido   Eniwa Izarigawa Lake 42.878 141.572 45
Sample-demo02 Joe Smith 15-Oct-09 North America Canada Ontario Wellington County Puslinch Township 100 m downstream from the dam -41.098 -121.176 100
Sample-demo03 Joe Smith 5-Sep-07 Central America Costa Rica Guanacaste ACG Mundo Neuvo   10.772 -85.434  
Figure 8-4: Example data for Collection Info

Individual Specimen Submission Section

This section describes the manual submission of single records to BOLD through the Specimen Data Upload option available in the Project Console to project managers and project users with edit specimen access. This is the fastest way to add an individual record to your project and is recommended for uploads of 10 records or less. If you have more than ten records, or are planning to add new species to the database, you can instead use the Batch Specimen Data Submission Protocol.

Step 1. Navigate to form

  1. Open the project that you would like to have the record(s) uploaded to.
  2. Click on "Specimen Data" under the Uploads menu to access the form. This option is available to project managers and project users with edit specimen access.

Step 2. Fill in Specimen Data and Submit

Table 8-1 through Table 8-4 below describes the information accepted in the specimen data submission.
(* denotes the required fields for a record) The minimal requirements for a new submission on BOLD are:

  • Voucher Info Page - Sample ID
  • Voucher Info Page - Field ID and/or Museum voucher ID
  • Voucher Info Page - Institution Storing
  • Taxonomy Page - Phylum
  • Collection Page - Country

You can submit minimal information to start and then update your records at a later date following the Update Specimen Data Protocol.

singlerecordsub
Figure 8-1: Illustration of the single record submission form

The orange outlined boxes are look-up fields. The lookup field allows you to type in the beginning of the desired name, and the matching options from the BOLD database will appear below. Select the appropriate name from the drop-down box to lock it in. Where the desired option is not available, select the parent option (if a required field) or leave the field blank. Follow the directions to Update Specimen Data to add new taxa, identifiers, countries or state/provinces to the database.

Specimen Data Fields

Sample ID *

Identifier for 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: Numbers, letters, and ^ . : - _ ( ) # 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. (This field or the Museum ID field 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 in the case of a personal collection, Personal:Name of collector:fieldID. (This field or the Field ID field must be filled in)
Collection Code Code associated with a given collection within an institution and is only applicable when Museum ID is provided.  Often used as scope resolution within museums.  
Institution Storing *

Full name of the institution handling storage of the specimen or tissue sample.  Can be a personal collection.

Table 8-1: Field definitions for Voucher (Specimen) Info page on accompanying spreadsheet.

Full Taxonomy Full scientific name for each rank, consisting of phylum *, class, order, family, subfamily (optional), genus, species binomial. Interim names may be used up to family level.
Identifier Full name of primary individual who assigned the specimen to a taxonomic group.
Identifier E-mail 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
Table 8-2: Field definitions for Taxonomy page on accompanying spreadsheet.

Sex The sex of the specimen(s) represented in the Occurrence. Male/female/hermaphrodite only.
Reproduction The presumed method of reproduction. Sexual/asexual/cyclic parthenogen only.
Life Stage The age class or life stage of the specimen(s) at the time of sampling.  Adult/immature only.
If the sex, reproduction or life stage values for your specimen that do not fit the accepted values, then please move the information to the Extra Info or Notes fields.
Extra Info A brief note or project term associated with the specimen for rapid analysis (free text) - Can be displayed on a tree or used to sort records. Limited to a maximum of 50 characters. Designate FAO region here.
Notes Free text or XML tagged text. All XML text should be surrounded by the XML start (<xml>) and stop (<xml>) tags.
Table 8-3: Field definitions for Specimen Details page on accompanying spreadsheet.

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 Date Date of specimen collection, must be in DD-MMM-YYYY format. (e.g. 01-Jan-2005)
Continent/Ocean Continents and Oceans.
Country * 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. (Controlled by Getty Geographical Thesaurus).
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 township, lake, conservation area or sector of park (i.e., the next smaller political or geographical area than region) in which the organism was collected.

Exact Site

Additional text descriptions regarding the exact location of the collection site.

Latitude

The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are north of the Equator, negative values are south of it. Valid values lie between -90 and 90, inclusive.

Longitude

The geographic longitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are east of the Greenwich Meridian, negative values are west of it. Valid values lie between -180 and 180, inclusive.

Elevation/Depth Elevation of sampling site.  Measured in meters relative to sea level.  Negative values indicate a position below sea level.
Table 8-4: Field definitions for Collection Data page on accompanying spreadsheet.

(* denotes the required fields for a record)

Update Specimen Data

This protocol describes both the manual update of a single record and the batch update of a set of records on BOLD. The most efficient way to update an individual record in your project is using the manual update for a single record. However, if you would like to add new taxa, identifiers, countries or state/provinces to the BOLD database or have a set records to update, then the Batch Update protocol below explains how.

A. Manual Update of a Single Record

To modify or update individual records within a project, project managers and project users with edit specimen access can do so manually by selecting the Edit button found in the top right of each individual Specimen Record page. Descriptions of the fields in the form are found above.

B. Batch Update of Multiple Records

Use this protocol to add new taxa, identifiers, countries or state/provinces to the BOLD database or if you have a set of records to update.

  • Within your project (or merged projects, container, or campaign), navigate to the “View All Records” page, and select which records need to updated.
  • Click on “Data Spreadsheets” using the Downloads menu on the left side of the record list.
  • Select only which pages need to be updated and download the excel workbook: Voucher Info, Taxonomy, Specimen Details, and/or Collection Data.
  • Make any changes onto the downloaded sheets and email these in as an update to submissions@boldsystems.org. In the email, please note the following information:
  Update Scope: Project(s), Container or Campaign title(s), or Taxon group and Region
  Project code: If only one project is being updated
  Submission type: Voucher Info, Taxonomy, Specimen Details, and/or Collection Data
  Priority: High, Medium, Low

 

For example, your email may read:

Update Scope: Moths of Southern Ontario
Submission Type: Taxonomy and Collection Data Update
Priority: Medium

Once sent in, a Data Manager will respond with confirmation of receipt within 1 business day. You will be contacted if there are any questions or concerns, and when your update has been uploaded onto BOLD.

NOTE: Any fields left empty will be considered blank and thus removed from BOLD during an update. Do not remove any data from the update sheet if you’d like it to stay on BOLD. The computer cannot distinguish between “blank: do not update this field’ or “blank: delete the content of this field”.

Updates to Voucher Info are slightly different from updates to Taxonomy, Specimen Details, and Collection Data.

a.) Updates to Voucher Info
Identical to new submissions, updates to the voucher info are project specific. The records need to be split into their corresponding project.

b.) Updates to Taxonomy, Specimen Details, and Collection Data
These updates are project independent. Records from any number of projects can be submitted in one submission spreadsheet, and the number of records are (in theory) infinite for this type of update. To select records from more than one project for a Taxonomy, Specimen Details or Collection Data update, you can use the search function, or merge projects in your project list.

 

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

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