Summary

This article is intended to provide details related to mapping of CRF data in XPT, CSV, and Excel transfer style exports - addressing variable setup in ClinSpark and reporting of those variables. In this article, “Base Fields” refer to variables that are fully or partially intrinsic to the ClinSpark application and not fully modifiable by site users.  “Custom Fields” refer to variables that are based on study design and therefore entirely modifiable by site users.

Configuring the Transfer Report

The behaviour of the Transfer Report can be adjusted through both system level and study level configuration options.

System level configuration is managed through the use of a Global Setting (In Administration > General Settings) with a key of “TransferReportSettings”.

The setting value is controlled by superadmin users; changes must be submitted through the service desk so support team members can modify it. However, non-superadmin users who have access to the System Settings component can view the current setting value at any time by accessing the hyperlink next to MD5 checksum.

The setting file provided will have the extension .globalsetting which can be opened by any standard text editor (such as Notepad).

The setting value is in “JSON” format - a simple data-interchange format that uses human-readable text to store information.

System level settings can be overridden at the study level through the use of study aliases assigned to an item group. Any item group can be used for storing the settings, but we suggest creating a group named ‘Transfer Report Settings’ to aid easily identifying settings within studies.

The use of configuration is perhaps best illustrated through examples. Firstly, consider a Global Setting value that configures the Transfer Report to include unique row identifiers and use ‘-’ as a separator between elements of the Unique Subject Id (USUBJID):

{
  "includeUniqueRowId": true,
  "USUBJIDSeparator": "-"
}

Next, here’s an Item Group containing aliases to configure USUBJID to use a ‘.’ for separator and the Lead-in number for the subject number:

As a general rule, the ‘context’ used for an alias will be ‘TransferReport.’ followed by the setting name used in the Global Setting.

The available settings for both aliases and the global setting are:

A note on date and time formats

When extracting data from ClinSpark in the transfer style exports, users see different datetime formats. The ultimate ClinSpark goal is to report all sorts of date and time information according to the ISO 8601 format (YYY-MM-DDThh:mm:ss+00:00).

For example:

2017-06-01T15:32:43-05:00

…shows a date of 01-June-2017 and time of 15:32:43 in the -05:00 UTC time zone.

While working on these aspects in the background, we would like our users to be aware and manage the following differences currently still present:

System driven datetime information (–DTX columns)

Any datetime information that is system driven, is presented in ISO8601 format. The column containing the system driven entry datetime is called –DTX.

Datetime obtained through data collection (–DTC, –DAT, … )

The majority of the date & time type fields that the customer defines when creating forms, end up in ISO 8601 format in the Transfer Data report.

However, there are some types that do not yet follow this path:

• Incomplete Datetime

• Incomplete Date

• Incomplete Time

• Partial Datetime

• Partial Date

• Partial Time

Incomplete type date time fields end up in the Transfer Data report in the followin format: YYYY-MM_DDTHH:MM:SS.

Datetime obtained through Volunteer Integration form

During screening, Clinspark allows for data available in the volunteer file to be transferred into the study:

• Medical History

• Substance Use

• Concomitant Medication

Due to the fact that the majority of the information is historical - the volunteer might not remember the actual day or month when a condition/intake started - we opted to work with dedicated fields for Day, Month and Year. This allows users to leave the parts that are unknown blank.

The downside of this approach is that the information is transferred from the volunteer file to the study in a string format. As a consequence the following fields are reported in the Transfer Data report in a DDmmmYYYY format, only taking into account the date times entered:

• MHSTDTC

• MHENDTC

• CMSTDTC

• CMENDTC

• SUSTDTC

• SUENDTC

The goal is to ensure that also these date and time fields end up being ISO 8601. A corresponding ClinSpark Development ticket has been added to our backlog.

To end with, to obtain more information on UTC and local time from Wikipedia:

“UTC does not change with a change of seasons, but local time or civil time may change if a time zone jurisdiction observes daylight saving time (summer time). For example, local time on the east coast of the United States is five hours behind UTC during winter, but four hours behind while daylight saving is observed there.”

Further information on working with dates and times using the ISO 8601 basic and extended notations can be found at the SAS® support knowledge base.

It is possible to change the format of dates and times in transfer reports, but this needs to be done by Foundry Health engineering staff via request on the service desk and may incur a fee.

Transfer Data Mapping (Base Fields)

STUDYID

ClinSpark

Study ID, or Protocol Name, is established as part of Study Configuration and is used to uniquely identify a study.

Clinical Data XPT

Protocol Name maps within every dataset under a “STUDYID” variable when reported via a Clinical Data XPT Transfer report.

Clinical Data CSV and Excel

Protocol Name maps within every dataset under a “STUDYID” column header when reported via a Clinical Data CSV or Clinical Data Excel Transfer report.

Variable Attributes

SITEID

ClinSpark

The ‘Location OID’ associated with the Study Site.

Clinical Data XPT

If the Transfer Report settings request inclusion of the SITEID variable, Site ID maps within every dataset under a “SITEID” variable when reported via a Clinical Data XPT Transfer report.

Clinical Data CSV and Excel

If the Transfer Report settings request inclusion of the SITEID variable, Site ID maps within every dataset under a “SITEID” column header when reported via a Clinical Data CSV or Clinical Data Excel Transfer report.

Variable Attributes

DOMAIN

ClinSpark

Domains are established at the Item Group level and are used to define datasets.  CRF Items contained within an Item Group will report within that Item Group’s Domain.

Clinical Data XPT

Each unique dataset manifests as a SAS Xport Transport File when reported via a Clinical Data XPT Transfer report.

Clinical Data CSV

Each unique dataset manifests as a Comma Separated File (CSV) when reported via a Clinical Data CSV Transfer report.

Clinical Data Excel

Each unique dataset manifests as an Excel Tab when reported via a Clinical Data Excel Transfer report

Variable Attributes

USUBJID

ClinSpark

Subject IDs are a Concatenation of Study ID (established as part of Study Configuration), Site ID (the study site Location OID) and Subject Number (established as part of a Cohort Assignment), separated by a suitable separator.  This should uniquely identify a subject across all studies. 

The specific separator used is configured through transfer report settings (with a default of ‘-').

The specific subject number used is configured through transfer report settings, the available options are:

Clinical Data XPT

Subject IDs map within every dataset under a “USUBJID” variable when reported via a Clinical Data XPT Transfer report.

Clinical Data CSV and Excel

Subject IDs map within every dataset under a “USUBJID” column header when reported via a Clinical Data CSV or Clinical Data Excel Transfer report.

Variable Attributes

[domain]GRPID

ClinSpark

Group IDs are used to ‘bind’ together data collected within a unique Form, even when that data spans multiple records or multiple domains.  For example, an “Adverse Event / Concomitant Medication” Form may contain AE Domain data as well as CM Domain data, with that data associated across datasets by way of shared AEGRPID and CMGRPID variables.

Clinical Data XPT

Group IDs map within every dataset under a “[domain]GRPID” variable when reported via a Clinical Data XPT Transfer report.

Clinical Data CSV and Excel

Subject ID’s map within every dataset under a “[domain]GRPID” column header when reported via a Clinical Data CSV or Clinical Data Excel Transfer report.

Variable Attributes

None

[domain]COM

ClinSpark

Domain Comments are established at the Item Group level and are used to further describe the contents of that Item Group.  If a Comment is not specified, Item Group Name will map under this variable.

Clinical Data XPT

Domain Comments map within every dataset under a “[domain]COM” variable when reported via a Clinical Data XPT Transfer report.

Clinical Data CSV and Excel

Domain Comments map within every dataset under a “[domain]COM” column header when reported via a Clinical Data CSV or Clinical Data Excel Transfer report.

Variable Attributes

None

EPOCH

ClinSpark

Epochs are established as part of Study Configuration and define distinct ‘stages’ of the study (i.e. Screening, Lead-In, Treatment, Follow-Up) through which Cohorts will progress.  Epochs only report alongside Scheduled activities (i.e. activities that are part of a schedule of assessments) and are left blank for Unscheduled (i.e. ad-hoc) or Common (i.e. Adverse Event) activities.

Clinical Data XPT

Epochs map within every dataset under an “EPOCH” variable when reported via a Clinical Data XPT Transfer report.

Clinical Data CSV and Excel

Epochs map within every dataset under an “EPOCH” column header when reported via a Clinical Data CSV or Clinical Data Excel Transfer report.

Variable Attributes

None

COHORT

ClinSpark

Cohorts are established as part of Study Configuration and define ‘groups’ of subjects who progress through Epochs (‘stages’) of the study together.  Cohorts only report alongside Scheduled activities (i.e. activities that are part of a schedule of assessments) and are left blank for Unscheduled (i.e. ad-hoc) or Common (i.e. Adverse Event) activities.

Clinical Data XPT

Cohorts map within every dataset under a “COHORT” variable when reported via a Clinical Data XPT Transfer report.

Clinical Data CSV and Excel

Cohorts map within every dataset under a “COHORT” column header when reported via a Clinical Data CSV or Clinical Data Excel Transfer report.

Variable Attributes

None

VISITNUM

ClinSpark

Visit Numbers are established during CRF Design and numerically describe a Visit (‘Study Event’).

Clinical Data XPT

Visit Numbers map within every dataset under a “VISITNUM” variable when reported via a Clinical Data XPT Transfer report.

Clinical Data CSV and Excel

Visit Numbers map within every dataset under a “VISITNUM” column header when reported via a Clinical Data CSV or Clinical Data Excel Transfer report.

Variable Attributes

VISIT

ClinSpark

Visits (or ‘Study Events’) describe study days (i.e. Day 1, Day 2, Day 3) or categories of activities (i.e. AE / CM Details).  Scheduled Study Events are used to organize activities that are scheduled to be collected on a particular day.  Unscheduled Study Events provide a container for ad-hoc activities that were not initially scheduled to be collected during a particular visit or at a particular time point.  Common Study Events provide a container for a sub-set of unscheduled activities (like AEs and Con Meds) so as to quickly differentiate these important activities from other unscheduled activities.

Clinical Data XPT

Visits map within every dataset under a “VISIT” variable when reported via a Clinical Data XPT Transfer report.

Clinical Data CSV and Excel

Visits map within every dataset under a “VISIT” column header when reported via a Clinical Data CSV or Clinical Data Excel Transfer report.

Variable Attributes

[domain]DTC

ClinSpark

DTC variables capture the Collection Time for data fields contained within the same Form.  This is intended to represent the date/time at which a data collector performs an activity.  For more information on how Collection Time is captured, refer to the Collection Time Knowledge Base Article.

Clinical Data XPT

Collection Time maps within every dataset under a “[domain]DTC” variable when reported via a Clinical Data XPT Transfer report.

Clinical Data CSV and Excel

Collection Time maps within every dataset under a “[domain]DTC” column header when reported via a Clinical Data CSV or Clinical Data Excel Transfer report.

Variable Attributes*

None

[domain]TPT

ClinSpark

Timepoints are established during Activity Plan (or schedule of assessments) design and represent the timing of activities relative to a reference activity (typically Dosing).  Timepoints are either positive (if the associated activity is scheduled to be collected post-dose) or negative (if the associated activity is scheduled to be collected pre-dose).  Reference activities, or activities off of which other activity are timed, are denoted by an asterisk (*).  The parenthetical number after a timepoint represents the instance of reference activity within an Activity Plan.  For example, an activity plan might contain multiple days of dosing with the requirement that activities on a particular day reference that day’s dosing.  In order to avoid confusion about which dose an activity is referenced off of, all activities referenced off of the first dose will be marked with a parenthetical one (1), all activities reference off of the second dose will be marked with a parenthetical two (2), and so on.

Clinical Data XPT

Timepoints map within every dataset under a “[domain]TPT” variable when reported via a Clinical Data XPT Transfer report.

Clinical Data CSV and Excel

Timepoints map within every dataset under a “[domain]TPT” column header when reported via a Clinical Data CSV or Clinical Data Excel Transfer report.

Variable Attributes

None

ROWID

ClinSpark

A unique identifier for each row in the dataset. The Transfer Report uses internal identifiers from within ClinSpark to guarantee uniqueness for each ROWID and to guarantee that the value will be unchanged each time the report is created.

Clinical Data XPT

The unique row identifiers maps within every dataset under a “ROWID” variable when reported via a Clinical Data XPT Transfer report.

Clinical Data CSV and Excel

The unique row identifiers maps within every dataset under a “ROWID” variable when reported via a Clinical Data CSV or Clinical Data Excel Transfer report.

Variable Attributes

None

[domain]REPEAT

ClinSpark

An Item Group may be marked as Repeating, allowing the contents of that Item Group to be documented multiple times within a Form.  This is particularly useful for Concomitant Medication documentation, where there may be multiple concomitant medications administered in response to an Adverse Event while the exact number of concomitant medications administered is variable across subjects or unpredictable during study design.  The instance of a Repeating Item Group is reported as #1, #2, #3, etc.

For more information regarding Repeating Item Groups, please refer to the the following Knowledge Base Articles:

Repeating Item Groups Knowledge Base Article

Default Item Groupings Knowledge Base Article

Clinical Data XPT

Item Group repeat numbers map within every dataset under a “[domain]REPEAT” variable when reported via a Clinical Data XPT Transfer report.

Clinical Data CSV and Excel

Item Group repeat numbers map within every dataset under a “[domain]REPEAT” column header when reported via a Clinical Data CSV or Clinical Data Excel Transfer report.

Variable Attributes

None

[sas field name]U

ClinSpark

Units are established at the Item level and report to the right of the associated data field under a header that shares the same SAS Field Name as the corresponding variable with a “U” appended to the end. Please keep in mind that SAS Field Names should never be longer than 8 characters. Since the U will be added to the SAS Field Name of the corresponding variable, the user should be make sure that the SAS Field Name of the variable itself is NOT longer than 7 characters.

E.g. If you would like to collect the length of the subject’s arm. The corresponding SAS Field Name cannot be ARMLNGTH as the corresponding unit column will be called ARMLNGTHU, being 9 characters long and therefore not accepted. ALNGTH and ALNGTHU would work just fine.

Clinical Data XPT

Units map within the containing Item Group’s dataset next to the corresponding variable (with a header of ‘Variable SAS Field Name’ + ‘U’) when reported via a Clinical Data XPT Transfer report.

Clinical Data CSV and Excel

Units map within the containing Item Group’s dataset next to the corresponding variable (with a header of ‘Variable SAS Field Name’ + ‘U’) when reported via a Clinical Data CSV or Clinical Data Excel Transfer report.

Transfer Data Mapping (Custom Fields)

Reporting Custom Data Fields

ClinSpark

Because ClinSpark is an eSource, EDC, and Data Management system, it must support capture of data with both Source or CRF ‘Origin’.  Origin is established at the Item level during CRF Design, where Items marked as CRF Origin are eligible for transfer reporting and Items marked as Protocol Origin are not.

SAS Field Names (or variable names) are established at the Item level during CRF Design and are reported within the containing Items Group’s domain.

Clinical Data XPT

Custom fields map within the containing Item Group’s dataset under the established SAS Field Name variable when reported via a Clinical Data XPT Transfer report.

Clinical Data CSV and Excel

Custom fields map within the containing Item Group’s dataset under the established SAS Field Name column header when reported via a Clinical Data CSV or Clinical Data Excel Transfer report.

Available Data Types

ClinSpark

ClinSpark offers the following data types (established at the Item level) for use with custom data fields, as defined by CDISC ODM:  text, integer, float, date, time, datetime, string, boolean, partial date, partial time, partial datetime, duration datetime, interval datetime, incomplete datetime, incomplete date, incomplete time.

Clinical Data XPT

An example XPT file including all available data types can be found here:

Variable naming is as follows:

Clinical Data CSV and Excel

An example CSV file including all available data types can be found here:

An example Excel file including all available data types can be found here:

Variable naming is as follows:

General Notes about Data Mapping

Horizontal Reporting of Data

ClinSpark

If only a SAS Field Name is specified as part of CRF Item Metadata, those variables will report horizontally as column headers with values listed beneath.

Clinical Data XPT

Clinical Data CSV and Excel

Vertical Reporting of Data

ClinSpark

If a SAS Field Name and a SDS Var Name are specified as part of CRF Item Metadata the SAS Field Name will become a column header and variable SDS Var Names will report vertically beneath the SAS Field Name with corresponding values listed to the right under a [domain]ORRES header.

Clinical Data XPT

Clinical Data CSV and Excel

Omitted Data

Unscheduled Data

The following variables are omitted from transfer reporting for data that is added as unscheduled (i.e. ad-hoc data): EPOCH, COHORT, [domain]TPT.

Canceled Data

Canceled data is suppressed from exporting and provides a means by which unnecessary data my be omitted from transfer reporting.

Nonconformant Data

Nonconformant data is suppressed from transfer reporting, as this data likely requires attention before incorporating into datasets.  Nonconformant markings can always be removed within the application by entering an Annotation against the nonconformant Item field.

Unsaved Data

Unsaved data is suppressed from transfer reporting, as no values have been entered against the corresponding data fields.

Transfer LAB_DATA Mapping

LAB_DATA Exports

ClinSpark

Laboratory results are displayed in ClinSpark and reported in transfer exports according to values and ranges established by the laboratory.  This is to say that laboratory test values, ranges, and alerts are exported exactly as they are reported by the reference lab unless a qualified site user chooses to override reported results within ClinSpark’s Lab Orders module.  In the scenario of overriding results, full audit history is maintained.

Clinical Data XPT

An example XPT file including example laboratory results can be found here:

Clinical Data CSV and Excel

An example CSV file including example laboratory results can be found here:

An example Excel file including example laboratory results can be found here:

LAB_DATA Variables

The following table describes variables found in the LAB_DATA dataset: