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.

In this section: Batch Specimen Submissions Example Spreadsheet for batch new submission Single Specimen Submissions Definition of Specimen Data Fields Updating Specimen Data

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

• 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.

Single record submission form

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 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.

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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