Containers for Biorepository Collections

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Hello Specificians,

Thank you for your continued engagement and valuable input regarding the implementation and conceptualization of containers (now named Collection Object Groups or "COGs) in Specify 7. We have received a number of perspectives and use cases related to containers and greatly appreciate your thoughts. We are continuing to discuss requirements and to evaluate community input. If you have any additional insight on using containers or the need to group related collection objects, please plunk it down here in this topic.

At this stage, we specifically request information on how users conceptualize containers in the context of biorepositories (i.e. biological tissue and molecular sample collections). If you are working with biorepository materials and have insight into the unique requirements and workflows involving containers, we would be delighted to hear from you.

We crave your user stories, use cases, and any specific workflows that necessitate the use of containers in Specify 7. Additionally, if you are utilizing containers in Specify 6, we would be interested in learning about your experience and any improvements you would find helpful for Specify.

Your responses will greatly inform our efforts to design and implement containers (COGs) effectively in Specify 7, to meet the diverse needs of biorepository collections.

Containers in Specify 7

30 September 2022

Some Sample Containers Use Cases:

  • Entomology: A piece of amber containing several insects.
  • Ichthyology: A collection might have a large jar of pickled fish of multiple species (not a “lot”). The jar contains many specimens, each of which have their own Collection Object record. The Container record tracks the large jar with links to the contained specimens.
  • Vertebrate Paleontology: A crate containing cataloged bones of a single dinosaur collected at different times are stored together and permanently grouped in the database in a Container record.
  • Botany: Several lichen species and specimens are identified from the same collected twig, and a Container record associates them to that single cataloged substrate.
  • Geology: A rock could include multiple layer types, inclusions, crystals, etc. Embedded constituents would be cataloged as a individual, discrete Collection Objects although physically adjoined in a common substrate.

We invite any feedback on this topic! Thank you in advance!

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One biorepository example I can think of is in fishes where you may have a lot made up of multiple individuals that have had tissue taken from them. Each fish may have had multiple tubes taken from it (and cataloged separately for some reason - different kind of tissue, etc.) but they will all be related to the same voucher lot thus making it difficult to know which individual fish specimen they came from. In this case, if the tissues are cataloged into a separate tissue collection, you may want to place all tissues from a single individual into a container to relate them as coming from the same individual. A stretch I know…

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I have this situation and I don’t know if it applies to Containers:

I have an Excel file containing Collection Object information. Some objects are in fact vials containing many specimens, males and females. Each vial has a unique catalog number, but none of the specimen in the vials has a catalog number.

Should each vial become a container, even if the specimens it contains have no catalog number? I have in mind to assign a catalog number to specimens only if they are taken out of the vial and analyzed, and linked them to the container. Is it a good idea?

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