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  • How to best manage drop down values at large institutions

    I am hoping to get some insight about how best to manage drop down lists such as Specimen Type.

    We are a large institution with many research teams and labs, and teams are requesting that values be added to the Specimen Type drop down list, which is seen by all users system wide. I am wondering how other large institutions handle this? Do you have a standard way of adding new SP types, and a standard classification system? If so, what exactly is your process for this?

    We are trying to make sure all new SP values are coded and classified consistently while also accommodating research teams who have specific requirements.

    Thank you!
    Sam Walkow
    BC Children’s Hospital

    When someone requests a new specimen type, we ask them to explain why the existing types won’t work and then forward this to our faculty adviser for the OpenSpecimen project. He takes a first pass at the request taking into account the requester’s need and any technical advice our team provides. If he feels the answer is clear, he advises us to add or not add the new type along with an explanation for the requester. If he feels the answer is not clear, we then submit the request to our OpenSpecimen steering committee for broader discussion. The latter seldom happens (maybe only once).

    What we have found is that many groups want something that is very granular and useful only to their study. In theses cases, we do not add the new type and instead add a custom field that allows them to use an existing type and then annotate for the specifics about which very few of our groups would care.

    I hope that helps.

    Thanks for your reply. I think we’ll be taking a similar approach, in that we’ll need to review each request to a system wide drop down list. In your case, if a user can clearly justify the addition of a specimen type, do you simply add it to the dropdown list? Or do you have a hierarchy in place?

    Similar, repetitive and granular additions are what we want to avoid, just like you mentioned. Adding a custom field to capture this instead is a good work around, but we have studies that use the specimen type in the auto label configuration. Since there is no token for custom fields, this is somewhat of a limitation.

    Thanks again for you response,
    Sam

    Our team is technical, so we rely on advice from our faculty adviser since he is better suited to make that call on new specimen types from a research perspective. Let me ask him what criteria he uses so that I give you good information.

    Here is what I got back form our faculty adviser. Hopefully the additional detail is valuable for you.

    "The selection of types available in OS is not very robust for a research institution, so the question of adding types comes up frequently. I never support adding types unless there is good justification both scientifically and logistically and there is not a global type that will adequately describe the collection. I prefer using what is available so as to remain compatible with other users of OS. We do not want to create a tower of Babel.

    Examples: There may be instances where investigators sort cells by subtype, eg T Cells may be Natural Killer (NKT) Cells, Effector, Helper, Memory, Regulatory (suppressor), Mucosal Associated Invariant, or Gamma Delta. All are lymphocytes, but are subclasses. Therefore, It may be good to add Lymphocyte as a specimen type, but the subtypes would be a custom field.
    Science is evolving, so there may come a time when “enteroid” or “organoid” will have to be added. These are human stem cell cultures that replicate human tissues. These will be a new type scientifically by nature of their origin from stem cells and subsequent cloning. Whether they are liver, colon, ileum, or lung is found in a custom field. This is an evolving area of research that has clinical implications and thus will require a type designation in the future.

    Scientists will often isolate subtypes of specimens, especially with cells. These are most often described in custom fields and far less often are new types. Eg, cancer tissue is described in an annotation, but is still tissue and from the original organ. Tissues from metastatic cancer are annotated to give detail concerning the tissue of origin and the location where the metastatic tissue was captured. They are not new types."

    Thanks so much for information Bob. I like the idea of using a higher class type in the system wide drop down, and having a custom field for more granular, study specific options.

    Thanks again for your insight,
    Sam

    Hi Bob,
    We are currently having that discussion about the “types” available in OS.
    I do agree that we have to be aware that we don’t “create the tower of Babel”. What the biobanking world needs to aim for is standardisation across data especially required when biobanks need to collaborate outside of our institutions. If Users of OS could guide the standardisation of data that would be a huge start in the right direction.
    We currently have organoids that need to be added to OS. I also agree that we need the hierarchy for cells.
    After spending months cleaning data in preparation for migration to OS the variation in data input has been mind boggling. We will be able to regulate the input into OS
    best wishes
    Pam