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Laboratory Sample Tracking Software Compatibility

We use OpenClinica Enterprise for entering clinical trial data. We are looking for a sample tracking system that would be compatible with OpenClinica and alow transfer of clinical data to the sample tracking system. Does anyone know of any systems (ideally Open Source)?


  • CaesarOlimaCaesarOlima Posts: 42
    via Email
    A tool that I have heard mention in the OC vines is OpenSpecimen. It's setup might be a bit intimidating from a newbie. I have not managed to completely set it up and integrate it with OpenClinica but do have a look at it or speak to guys from http://www.openspecimen.org/. Has anyone in the OC community managed to get this task completed? Please share your processes.

    Caesar Olima
  • agapowagapow Posts: 6
    I don't know about compatibility but we recently tangled with this issue. There's a lot of systems out there but with lots of different underlying assumptions and few clearly good OSS solutions. OpenSpecimen seems to have a good rep, so that's as good a place to start as any.
  • lindsay.stevenslindsay.stevens Posts: 404 ✭✭✭
    via Email
    LabKey is one, our research program uses it for blood samples. I haven't
    spent much time in the UI but the webservices API is quite good.

    I have set up automated LabKey sample data transfer into OC to link up with
    existing reports running through community datamart. The process is done by
    a Python script that pulls data from one and pushes it to the other.

    For the opposite direction, it is possible to automate too but it was
    decided to control it closely. Only the final, clean analysis data gets
    used to tag samples. It's important that other subsequent projects don't
    get the wrong samples because of uncleaned data.

    In terms of compatibility I'd say they're the same as any other pair if
    systems. Data is data.
  • mvirtosumvirtosu Posts: 276 ✭✭
    Hi All,

    I have a general question for those who wrote scripts that pull data from OC and push into the lab/specimen system. How do you account for the situation where a subject record is later removed from OC?


  • toskriptoskrip Posts: 279 ✭✭✭

    withdrawal from study does not necessary mean that bio specimen data have to be destroyed (depending on the consent of course). Also when you remove patient from study, the bio specimen samples still physically exist in freezers that is why the lab/specimen system still keeps tracks of them. So to say, we do not trigger anything automatic on patient removal. These cases are handled manually (depending on study, and informed consent that declares what can and can't be done with bio specimen data).


  • lindsay.stevenslindsay.stevens Posts: 404 ✭✭✭
    via Email

    In general by being conservative and only handling special cases like that
    in the code when the business rule for it has been specified up front.
    Otherwise, log the special case for the project team to review and decide
    if / when it happens. Probably they'd choose like Tomas described.
  • mvirtosumvirtosu Posts: 276 ✭✭
    Thanks Tomas and Lindsay!

  • sadigasadiga Posts: 17
    via Email

    OpenSpecimen is best suited for specimen collections based on clinical
    studies since you can build study calendar like you can do in OpenClinica.

    This way you can have a 1:1 link between OpenClinica studies and events
    with OpenSpecimen studies and events.

    We recently integrated OpenSpecimen with RedCap for Stanford. Integration
    with OpenClinica would be in similar lines and something that can be easily

    Mail me at [email protected] if you would like to see more details.

  • mvirtosumvirtosu Posts: 276 ✭✭
    Hi All,

    I have heard that only the paid version of OpenSpecimen can be integrated with OpenClinica. Is that because the free version of OpenSpecimen lacks API functionality?

    In other words, if we wanted to write the middleware between OpenClinica and OpenSpecimen ourselves by listening to OpenClinica and using API to create records in OpenSpecimen, does the free version of OpenSpecimen have the API capability?


  • sadigasadiga Posts: 17
    via Email
    Hi Mihai,

    I am not sure where you heard it. However it is wrong.

    There is no functional difference at the API level between the Enterprise
    version and Community edition of OpenSpecimen.

    We are building a ready-to-use integration plugin which is paid. Here are
    the specs for the same:

    However if you want to build something on your own using the APIs, you are
    most welcome to do it by all means.

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