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Looking for LIMS to connect with OC

I'm new to OpenClinica, and I don't have any idea of how to connect a laboratory information management system to OpenClinica, and I don't even know what is the best LIMS out there that is fully compatible with OC. From where should I start ?
I have heard in LabKey but still I don't know how to connect it to OC.
Shams Waleed, Pharm.D.
Data Analyst | Data Management Unit
ACDIMA Center for Bioequivalence and Pharmaceutical Studies
E-mail: [email protected].com

Comments

  • lindsay.stevenslindsay.stevens Posts: 404 ✭✭✭
    via Email
    Here's my PM reply incase anyone else is interested

    Hi @sunbaghdad,

    The integration moves lab results entered in LabKey over to OpenClinica, so
    we can more easily include that information in reports involving clinical
    data.

    I did it using a Python script, which calls the (very comprehensive) LabKey
    API to retrieve JSON data, maps the data to OpenClinica items, and calls
    the OpenClinica SOAP API to schedule events / insert data, using [0].

    This script is then run every night as a scheduled task on a server. Data
    mapping failures, or other problems, are written to log files for the
    project team to review and resolve.

    If scripting isn't your thing, or you need something user facing, LabKey
    has a rather nice data extraction interface where you can save and export
    datasets in a range of formats, such as CSV. You could then use the
    DataUploader tool [1] to map and import this to OpenClinica (not sure if
    [1] handles repeat visits yet, otherwise there's ODIN [2] or the Access
    Data Uploader [3], or the built in XML import UI).

    I'm not certain about moving data from OpenClinica to LabKey, but it would
    be a similar story - use the OC REST API (or extracts, or datamart) to
    retrieve data from OC, and load into LabKey with a script or via the
    website user interface.

    So I guess like many clinical software system integrations, it's not
    exactly plug and play :) if you have any other questions feel free to ask.

    Best regards,
    Lindsay

    [0] https
    ://github.com/lindsay-stevens/openclinica_scripts
    (see readme on
    "webservices")
    [1] https
    ://github.com/thehyve/Open-
    Clinica
    -Data-
    Uploader

    [2] https
    ://community.openclinica.com/extension/odin

    [3] https
    ://community.openclinica.com/extension/
    ocdataimporter
  • sunbaghdadsunbaghdad Posts: 9
    Thank you so much Lindsay

    But, I'm wondering, LabKey looks like it only works for bio-analytical lab, does it work for medical lab? does it connect to the lab instruments like Cobas ...etc. And get the biochemistry, hematology, urinalysis for each subject and so on?

    If not, what is the alternative to do such a job?
    Shams Waleed, Pharm.D.
    Data Analyst | Data Management Unit
    ACDIMA Center for Bioequivalence and Pharmaceutical Studies
    E-mail: [email protected].com

  • lindsay.stevenslindsay.stevens Posts: 404 ✭✭✭
    I think LabKey can accept any data, so long as it can be provided in a table. From the docs:

    https://www.labkey.org/home/Documentation/wiki-page.view?name=instrumentData

    "Which Assay Instruments Does LabKey Server Support?
    Any instrument that outputs tabular data (that is, any data in a format of columns and rows) can be imported into LabKey Server..."

    Lab results like those you mention are routinely collected in the OpenClinica studies I've worked on. If specimen management isn't a requirement of your project, maybe you don't need LabKey at all. On the other hand, if your project is focused on lab results, specimen management, and so on, maybe LabKey is all you need. And then again, I'm seeing prospective direct-from-EHR projects start to crop up, so maybe soon we won't need any of these systems...

    Anyway, I suggest you read the LabKey docs to evaluate this question. I'm not familiar with LabKey let alone any other LIMS so I can't suggest alternatives.
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