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Uploading an external file

Hi All
I have Lab results excel file that I need to add to the visit 1 of the study.
What is the recomended way of uploading electronic data into a CRF ?
Thanks,
Tzafi Glass
Integristat

Comments

  • jaronjaron Posts: 30
    Hi,

    One possibility is to create a CRF with a field for each data point in the lab result file, and to include this CRF in the event definition for Visit 1. If you are looking for the ability to attach the whole excel file (or potentially any file) to an event definition, this feature is not part of the community OpenClinica product, and you will have to consider a feature enhancement in an OpenClinica Enterprise implementation.

    Thanks,
    Jaron Sampson, Akaza Research
    Sent: Wednesday, May 09, 2007 5:49 AM
    To: [email protected]
    Subject: [Users] Uploading an external file

    Hi All
    I have Lab results excel file that I need to add to the visit 1 of the study.
    What is the recomended way of uploading electronic data into a CRF ?
    Thanks,
    Tzafi Glass
    Integristat
  • TzafigTzafig Posts: 14
    Hi,
    I did what you describe, but I would like to laod the data from the excel
    file to the OpenClinica CRF, so that the extract will pick it into the
    SPSS etc.
    I was thinking of somehow re-using the item-insert Java procedure to be
    able to imitate data entry without actualy entering all the data again.
    Thanks,
    Tzafi
    Hi,
    > >
    > >
    > >
    > > One possibility is to create a CRF with a field for each data point
    > > in the lab result file, and to include this CRF in the event definition
    > > for Visit 1. If you are looking for the ability to attach the whole
    > > excel file (or potentially any file) to an event definition, this
    > > feature is not part of the community OpenClinica product, and you will
    > > have to consider a feature enhancement in an OpenClinica Enterprise
    > > implementation.
    > >
    > >
    > >
    > > Thanks,
    > >
    > > Jaron Sampson, Akaza Research
    > >
    > >
    > >
    > >
    > >
    > >
  • TzafigTzafig Posts: 14
    Hi,
    I did what you describe, but I would like to laod the data from the excel
    file to the OpenClinica CRF, so that the extract will pick it into the
    SPSS etc.
    I was thinking of somehow re-using the item-insert Java procedure to be
    able to imitate data entry without actualy entering all the data again.
    Thanks,
    Tzafi
    Hi,
    > >
    > >
    > >
    > > One possibility is to create a CRF with a field for each data point
    > > in the lab result file, and to include this CRF in the event definition
    > > for Visit 1. If you are looking for the ability to attach the whole
    > > excel file (or potentially any file) to an event definition, this
    > > feature is not part of the community OpenClinica product, and you will
    > > have to consider a feature enhancement in an OpenClinica Enterprise
    > > implementation.
    > >
    > >
    > >
    > > Thanks,
    > >
    > > Jaron Sampson, Akaza Research
    > >
    > >
    > >
    > >
    > >
    > >
  • jaronjaron Posts: 30
    Hi Tzafi,

    We do have a use case for a feature we will be developing as part of an Enterprise implementation that might suit your needs. The gist of it is that it would allow you to upload CRF data directly from a CDISC XML file, without having to key in the data. This will accommodate any format (Excel, HL7) that could be translated into the CDISC XML file.

    I have put the relevant portions of the use case below.

    Thanks,
    Jaron, Akaza Research

    Importing Data from an External Source
    During the course of a clinical trial, there could be a need to take data from an external application and import into OpenClinica. An example would be some type of lab result needing to be captured for dataset creation in OpenClinica.

    The information could be contained in an XML file, Excel, or a table in another database. It will need to be parsed into the CDSIC ODM XML format before it is imported in OpenClinica. The parsing will take place with the assistance of a Wizard to walk the user on how to complete the import.
    The key point to keep in mind is the data being imported must be readily mapped to existing CDISC ODM XML standards. If the existing data does not map, there will be an error during the import.

    Primary Actors: All users
    Rationale: Users want to import data from an external source into OpenClinica
    Precondition: The data elements from the external source can be appropriately mapped to the current CDISC ODM XML format. The user is currently in a CRF they want the data to be imported into.
    Base Case:


    Step

    User Intention

    System Responsibility







    Basic Course of Events

    1

    The user clicks on the link to called “Import Data




    Pop up wizard is displayed with the following list of external formats that can be imported.
    Access Database
    Microsoft Excel File
    Tab Delimited Text File
    Comma Delimited Text File
    XML
    Next and Cancel buttons at the bottom of the wizard.
    2

    Choose the appropriate format of the external data and click “Next”




    The next screen of the wizard is displayed. It contains a place to browse for the file with the external data and two options on how to import the data.
    Replace duplicates with items imported
    Do not import duplicate items
    Back, Next, and Cancel buttons are displayed at the bottom.
    3a

    Click Back




    User is returned to the previous screen.
    3b

    Browse for the appropriate file and attach it. Choose the way to handle duplicate items and click Next.




    The data will be mapped to the CDSIC ODM XML format and then imported into the CRF on OpenClinica where item_names match.
    If a value is found for an item_name not in the CRF, the system will ignore it.
    If the user chose to replace the duplicate items with the imported values, the system will overwrite any instances of values appearing for an item_name already.
    If the user chose to not import duplicate values, the system will ignore any values that match for the same item_name.
    Extensions

    3a



    If the format of the external application can not be mapped to the CDISC ODM XML format, the transaction will fail and a message will be displayed to a user announcing the failure.
    2b



    None of the item_names in the import match the item_names in the CRF. A message is displayed on the page stating “No item_names matched. Data was not imported.”
    Post condition: User has imported data into a CRF from an external application.




    -----Original Message-----
    Sent: Thursday, May 10, 2007 3:05 AM
    To: [email protected]
    Cc: [email protected]
    Subject: RE: [Users] Uploading an external file

    Hi,

    I did what you describe, but I would like to laod the data from the excel
    file to the OpenClinica CRF, so that the extract will pick it into the
    SPSS etc.

    I was thinking of somehow re-using the item-insert Java procedure to be
    able to imitate data entry without actualy entering all the data again.

    Thanks,
    Tzafi


    Hi,
    >
    >
    >
    > One possibility is to create a CRF with a field for each data point
    > in the lab result file, and to include this CRF in the event definition
    > for Visit 1. If you are looking for the ability to attach the whole
    > excel file (or potentially any file) to an event definition, this
    > feature is not part of the community OpenClinica product, and you will
    > have to consider a feature enhancement in an OpenClinica Enterprise
    > implementation.
    >
    >
    >
    > Thanks,
    >
    > Jaron Sampson, Akaza Research
    >
    >
    >
    >
    >
    >
  • TzafigTzafig Posts: 14
    Hi Jaron,

    The use case sounds very much like my needs. But I have some questions yet,
    How is the file structured? Does it have a row for each item_name or for each patient with columns for items? Can it contain multiple subjects (patients) in one file? Can it have multiple visits on same file?
    Can you share the structure for the loading code and we will customize it for our file structure?
    Sent: ה 10 מאי 2007 19:38
    To: [email protected]
    Subject: RE: [Users] Uploading an external file

    Hi Tzafi,

    We do have a use case for a feature we will be developing as part of an Enterprise implementation that might suit your needs. The gist of it is that it would allow you to upload CRF data directly from a CDISC XML file, without having to key in the data. This will accommodate any format (Excel, HL7) that could be translated into the CDISC XML file.

    I have put the relevant portions of the use case below.

    Thanks,
    Jaron, Akaza Research

    Importing Data from an External Source
    During the course of a clinical trial, there could be a need to take data from an external application and import into OpenClinica. An example would be some type of lab result needing to be captured for dataset creation in OpenClinica.

    The information could be contained in an XML file, Excel, or a table in another database. It will need to be parsed into the CDSIC ODM XML format before it is imported in OpenClinica. The parsing will take place with the assistance of a Wizard to walk the user on how to complete the import.
    The key point to keep in mind is the data being imported must be readily mapped to existing CDISC ODM XML standards. If the existing data does not map, there will be an error during the import.

    Primary Actors: All users
    Rationale: Users want to import data from an external source into OpenClinica
    Precondition: The data elements from the external source can be appropriately mapped to the current CDISC ODM XML format. The user is currently in a CRF they want the data to be imported into.
    Base Case:


    Step

    User Intention

    System Responsibility







    Basic Course of Events

    1

    The user clicks on the link to called “Import Data




    Pop up wizard is displayed with the following list of external formats that can be imported.
    Access Database
    Microsoft Excel File
    Tab Delimited Text File
    Comma Delimited Text File
    XML
    Next and Cancel buttons at the bottom of the wizard.
    2

    Choose the appropriate format of the external data and click “Next”




    The next screen of the wizard is displayed. It contains a place to browse for the file with the external data and two options on how to import the data.
    Replace duplicates with items imported
    Do not import duplicate items
    Back, Next, and Cancel buttons are displayed at the bottom.
    3a

    Click Back




    User is returned to the previous screen.
    3b

    Browse for the appropriate file and attach it. Choose the way to handle duplicate items and click Next.




    The data will be mapped to the CDSIC ODM XML format and then imported into the CRF on OpenClinica where item_names match.
    If a value is found for an item_name not in the CRF, the system will ignore it.
    If the user chose to replace the duplicate items with the imported values, the system will overwrite any instances of values appearing for an item_name already.
    If the user chose to not import duplicate values, the system will ignore any values that match for the same item_name.
    Extensions

    3a



    If the format of the external application can not be mapped to the CDISC ODM XML format, the transaction will fail and a message will be displayed to a user announcing the failure.
    2b



    None of the item_names in the import match the item_names in the CRF. A message is displayed on the page stating “No item_names matched. Data was not imported.”
    Post condition: User has imported data into a CRF from an external application.




    -----Original Message-----
    Sent: Thursday, May 10, 2007 3:05 AM
    To: [email protected]
    Cc: [email protected]
    Subject: RE: [Users] Uploading an external file

    Hi,

    I did what you describe, but I would like to laod the data from the excel
    file to the OpenClinica CRF, so that the extract will pick it into the
    SPSS etc.

    I was thinking of somehow re-using the item-insert Java procedure to be
    able to imitate data entry without actualy entering all the data again.

    Thanks,
    Tzafi


    Hi,
    >
    >
    >
    > One possibility is to create a CRF with a field for each data point
    > in the lab result file, and to include this CRF in the event definition
    > for Visit 1. If you are looking for the ability to attach the whole
    > excel file (or potentially any file) to an event definition, this
    > feature is not part of the community OpenClinica product, and you will
    > have to consider a feature enhancement in an OpenClinica Enterprise
    > implementation.
    >
    >
    >
    > Thanks,
    >
    > Jaron Sampson, Akaza Research
    >
    >
    >
    >
    >
    >
  • JozefJozef Posts: 71
    For CDISC ODM XML format, see:

    www.CDISC.org/standards/index.html

    For an EDC/CDM system, the open, vendor-neutral CDISC ODM standard allows to:
    - automatically set up the EDC system from an ODM file with study definitions
    - import eCRF data, and store them in the database (see e.g. www.XML4Pharma.com/ODMinEDC/index.html)
    - import clinical data from other providers
    - export clinical data files in the (open, vendor-neutral, FDA-preferred) CDISC ODM format

    With best regards,

    Jozef Aerts
  • bobbysidhubobbysidhu Posts: 5
    Message
    Hello Jaron,

    What's the timeline for this addition. A few months, next release...etc...approx when?

    Bobby Sidhu
    Program Analyst
    Centre for Clinical Evaluation & Epidemiology
    Vancouver Coastal Health

    Hi Tzafi,

    We do have a use case for a feature we will be developing as part of an Enterprise implementation that might suit your needs. The gist of it is that it would allow you to upload CRF data directly from a CDISC XML file, without having to key in the data. This will accommodate any format (Excel, HL7) that could be translated into the CDISC XML file.

    I have put the relevant portions of the use case below.

    Thanks,
    Jaron, Akaza Research

    Importing Data from an External Source
    During the course of a clinical trial, there could be a need to take data from an external application and import into OpenClinica. An example would be some type of lab result needing to be captured for dataset creation in OpenClinica.

    The information could be contained in an XML file, Excel, or a table in another database. It will need to be parsed into the CDSIC ODM XML format before it is imported in OpenClinica. The parsing will take place with the assistance of a Wizard to walk the user on how to complete the import.
    The key point to keep in mind is the data being imported must be readily mapped to existing CDISC ODM XML standards. If the existing data does not map, there will be an error during the import.

    Primary Actors: All users
    Rationale: Users want to import data from an external source into OpenClinica
    Precondition: The data elements from the external source can be appropriately mapped to the current CDISC ODM XML format. The user is currently in a CRF they want the data to be imported into.
    Base Case:


    Step

    User Intention

    System Responsibility







    Basic Course of Events

    1

    The user clicks on the link to called “Import Data




    Pop up wizard is displayed with the following list of external formats that can be imported.
    Access Database
    Microsoft Excel File
    Tab Delimited Text File
    Comma Delimited Text File
    XML
    Next and Cancel buttons at the bottom of the wizard.
    2

    Choose the appropriate format of the external data and click “Next”




    The next screen of the wizard is displayed. It contains a place to browse for the file with the external data and two options on how to import the data.
    Replace duplicates with items imported
    Do not import duplicate items
    Back, Next, and Cancel buttons are displayed at the bottom.
    3a

    Click Back




    User is returned to the previous screen.
    3b

    Browse for the appropriate file and attach it. Choose the way to handle duplicate items and click Next.




    The data will be mapped to the CDSIC ODM XML format and then imported into the CRF on OpenClinica where item_names match.
    If a value is found for an item_name not in the CRF, the system will ignore it.
    If the user chose to replace the duplicate items with the imported values, the system will overwrite any instances of values appearing for an item_name already.
    If the user chose to not import duplicate values, the system will ignore any values that match for the same item_name.
    Extensions

    3a



    If the format of the external application can not be mapped to the CDISC ODM XML format, the transaction will fail and a message will be displayed to a user announcing the failure.
    2b



    None of the item_names in the import match the item_names in the CRF. A message is displayed on the page stating “No item_names matched. Data was not imported.”
    Post condition: User has imported data into a CRF from an external application.
  • jaronjaron Posts: 30
    Hi Tzafi,

    The file is an XML file structure, so it does not really have rows and columns. The file is based on the CDISC Operational Data Model, the specifications for that can be found here. The ODM schema can be used to represent any kind of clinical data, and is flexible to be used for lab data submission. The exact contents of a file would vary based on the requirements for the type of submission. Since this use case specifically discusses the attachment of data to a single Event CRF, the file to import would contain information on one Subject. There can be multiple Event CRFs for a single Event (visit), so each file to import might contain only part of the data from a single Event.

    Of course, this is just one feature under analysis (and not yet implemented). If your needs are for a less granular data import feature, for instance where data for multiple Subjects or Visits would be imported in one pass, we would be interested in getting more information about your requirements. The best way to do this is to start a user story describing what you would like to be able to do. In addition, a sample of the format your data comes in now would be very helpful.

    Thanks,
    Jaron
    Sent: Tuesday, May 15, 2007 6:03 AM
    To: [email protected]
    Subject: RE: [Users] Uploading an external file

    Hi Jaron,

    The use case sounds very much like my needs. But I have some questions yet,
    How is the file structured? Does it have a row for each item_name or for each patient with columns for items? Can it contain multiple subjects (patients) in one file? Can it have multiple visits on same file?
    Can you share the structure for the loading code and we will customize it for our file structure?
    Sent: ה 10 מאי 2007 19:38
    To: [email protected]
    Subject: RE: [Users] Uploading an external file

    Hi Tzafi,

    We do have a use case for a feature we will be developing as part of an Enterprise implementation that might suit your needs. The gist of it is that it would allow you to upload CRF data directly from a CDISC XML file, without having to key in the data. This will accommodate any format (Excel, HL7) that could be translated into the CDISC XML file.

    I have put the relevant portions of the use case below.

    Thanks,
    Jaron, Akaza Research

    Importing Data from an External Source
    During the course of a clinical trial, there could be a need to take data from an external application and import into OpenClinica. An example would be some type of lab result needing to be captured for dataset creation in OpenClinica.

    The information could be contained in an XML file, Excel, or a table in another database. It will need to be parsed into the CDSIC ODM XML format before it is imported in OpenClinica. The parsing will take place with the assistance of a Wizard to walk the user on how to complete the import.
    The key point to keep in mind is the data being imported must be readily mapped to existing CDISC ODM XML standards. If the existing data does not map, there will be an error during the import.

    Primary Actors: All users
    Rationale: Users want to import data from an external source into OpenClinica
    Precondition: The data elements from the external source can be appropriately mapped to the current CDISC ODM XML format. The user is currently in a CRF they want the data to be imported into.
    Base Case:


    Step

    User Intention

    System Responsibility







    Basic Course of Events

    1

    The user clicks on the link to called “Import Data




    Pop up wizard is displayed with the following list of external formats that can be imported.
    Access Database
    Microsoft Excel File
    Tab Delimited Text File
    Comma Delimited Text File
    XML
    Next and Cancel buttons at the bottom of the wizard.
    2

    Choose the appropriate format of the external data and click “Next”




    The next screen of the wizard is displayed. It contains a place to browse for the file with the external data and two options on how to import the data.
    Replace duplicates with items imported
    Do not import duplicate items
    Back, Next, and Cancel buttons are displayed at the bottom.
    3a

    Click Back




    User is returned to the previous screen.
    3b

    Browse for the appropriate file and attach it. Choose the way to handle duplicate items and click Next.




    The data will be mapped to the CDSIC ODM XML format and then imported into the CRF on OpenClinica where item_names match.
    If a value is found for an item_name not in the CRF, the system will ignore it.
    If the user chose to replace the duplicate items with the imported values, the system will overwrite any instances of values appearing for an item_name already.
    If the user chose to not import duplicate values, the system will ignore any values that match for the same item_name.
    Extensions

    3a



    If the format of the external application can not be mapped to the CDISC ODM XML format, the transaction will fail and a message will be displayed to a user announcing the failure.
    2b



    None of the item_names in the import match the item_names in the CRF. A message is displayed on the page stating “No item_names matched. Data was not imported.”
    Post condition: User has imported data into a CRF from an external application.




    -----Original Message-----
    Sent: Thursday, May 10, 2007 3:05 AM
    To: [email protected]
    Cc: [email protected]
    Subject: RE: [Users] Uploading an external file

    Hi,

    I did what you describe, but I would like to laod the data from the excel
    file to the OpenClinica CRF, so that the extract will pick it into the
    SPSS etc.

    I was thinking of somehow re-using the item-insert Java procedure to be
    able to imitate data entry without actualy entering all the data again.

    Thanks,
    Tzafi


    Hi,
    >
    >
    >
    > One possibility is to create a CRF with a field for each data point
    > in the lab result file, and to include this CRF in the event definition
    > for Visit 1. If you are looking for the ability to attach the whole
    > excel file (or potentially any file) to an event definition, this
    > feature is not part of the community OpenClinica product, and you will
    > have to consider a feature enhancement in an OpenClinica Enterprise
    > implementation.
    >
    >
    >
    > Thanks,
    >
    > Jaron Sampson, Akaza Research
    >
    >
    >
    >
    >
    >
This discussion has been closed.