Specimens

OpenSpecimen helps capture the entire lifecycle of the specimens starting from the collection, processing, storage, and distribution. This page explains different features of OpenSpecimen to add specimen information in various scenarios.

  • Lineage of specimens: After collection, specimens are often processed into different forms for storage. For example, Blood is collected and processed into Plasma, PBMC, and Buffy Coat. In OpenSpecimen, each level can be indicated as a ‘specimen’ as primary, derivative, or aliquot.

  • Hierarchy of the specimens: To indicate the lineage of specimens, ‘specimen tree’ can be viewed in OpenSpecimen.

  • Different status of the specimen: A color-coding scheme for specimens allows you to quickly identify the status of a specimen as to whether it is collected, stored, distributed, or discarded. For more details, refer to the specimen color coding section on this page.

  • Default specimen annotations: Generic details like specimen type, anatomic location, quantity, etc., are captured in default data entry pages.

  • Custom annotations: Additional annotations like test results and pathology annotations can be captured using custom forms. 

  • Planned collection: For studies where what type of specimens is collected and how it is processed is known in advance, the protocol can be set up with all details to make data entry simpler.

  • Unplanned collection: When specimen collection details are unknown, they can be entered as unplanned specimens.

Planned Specimen Collection

In longitudinal collections, specific time-points for collection, specimen requirements, and processing details are defined at the start of the study. The planned collection workflow of OpenSpecimen allows you to define study calendars and define an SOP of the study.

For more details, refer to Planned specimen collection

Unplanned Specimen Collection

Collections for general biobanking are usually unplanned, i.e., there are no specific time-points, and specimens get collected whenever they are available. For such cases, the unplanned specimen collection workflow of OpenSpecimen is best suited.

For more details, refer to Unplanned specimen collection

Unplanned Derivatives/Aliquots

Depending on the needs or availability, you may often have to create a child or grandchild of a sample without prior planning. OpenSpecimen allows you to collect additional derivatives or aliquots from a specimen’s overview page.

For more details, refer to collecting unplanned derivative/aliquot

Bulk Operation on Specimens

Often there is a need to perform a common operation on multiple specimens like distribution, deletion, transfer, etc. In such cases, OpenSpecimen allows you to select multiple specimens at once and perform a bulk action.

For more details, refer to Bulk operation on specimens

Scanning Specimens using Box Scanners

In high-throughput labs, the use of scanners is quite common. OpenSpecimen allows collecting specimens in bulk using box scanners.

For more details, refer to Scanning specimens from box scanners

Bulk Import Specimen Data

In the case of high-throughput biobanks, the data for thousands of specimens may need to be entered. For this, OpenSpecimen allows importing data in the form of CSV files.

For more details, refer to specimens CSV

Moving Specimens from One Visit to Another

OpenSpecimen allows you to move the specimen from one visit to another to handle the situations like merging multiple sub-studies, accidental collection of specimens under the wrong participant/visit, etc. This can be done across collection protocols, across participants, or the participant visits.

For more details, refer to Moving primary specimens from one visit to another.  

Specimen Color Coding

OpenSpecimen displays the color code for specimens based on its status.

Color

Status

Description

Color

Status

Description

Green

Collected and stored

Specimen is available

Orange

Pending

Specimen yet to be collected

Grey

Missed/Not Collected

Specimen is not collected/missed

Blue

Distributed

Specimen is distributed

Purple

Reserved

Specimens reserved for distribution under specific distribution protocol

Red

Closed

The specimen is not available for any processes

Highlighted with pink color

Pooled 

Specimen is pooled