CDISC / Transcelerate DDF USDM Package

This package provides an implementation of the Digital Data Flow (DDF) CDISC / TransCelerate Unified Study Definitions Model (USDM). Two main parts are provided:

• Within the usdm_model directory are a set of classes reflecting the USDM model as transported using the DDF USDM API
• Within the usdm_excel directory is a class, USDMExcel, that can be used to import an entire study definition from an excel file and build the equivalent json as defined by the API

Warning

This package was, originally, not intended for public use and, consequently, only informal testing has been performed on the package to date. Formal testing has just begun. Use this at your own risk.

Setup

Setup is via pip

pip install usdm

The package requires a single environment variable CDISC_API_KEY that should be set to your CDISC library API key. This is used to access CDISC CT and BC definitions in the CDISC library.

See below for a simple example program.

USDM Model

Not further information as yet.

Excel Import

Example Program

The following code imports an Excel file (in the appropriate structure) and processes it. The data are then exported to a file in JSON API format. Note: The logging is not needed.

import logging
log = logging.basicConfig(level=logging.INFO)

import json
from usdm_excel import USDMExcel

excel = USDMExcel("source_data/simple_1.xlsx")
with open('source_data/simple_1.json', 'w', encoding='utf-8') as f:
  f.write(json.dumps(json.loads(excel.to_json()), indent=2))

Format of Workbook

Example

An example spreadsheet in maintained within the document directory.

Sheets

The workbook consists of several sheets each with a dedicated purpose. All sheets must be present except for those marked optional.

• Study sheet
• Study Identifiers sheet
• Study Amendments sheet
• Study Amendments Changes sheet
• Study Amenedment Impact sheet
• Study Design sheet
• Study Design Arms sheet
• Study Design Epochs sheet
• One or more Timeline sheets
• Study Design Timing sheet
• Study Design Activities sheet (optional)
• Study Design Indications sheet
• Study Design Interventions sheet
• Study Design Populations sheet
• Study Design Characteristcis sheet
• Study Design Objectives and Endpoints sheet
• Study Design Eligibility Criteria sheet
• Study Design Estimands sheet
• Study Design Procedures sheet
• Study Design Encounters sheet
• Study Design Elements sheet
• One or more Document Template sheets
• Document Content sheet
• Study Design Sites sheet (optional)
• Notes Sheet (optional)
• Abbreviations Sheet (optional)
• People Sheet (optional)
• Roles Sheet (optional)
• Dictionaries Sheet
• Configuration sheet

The content of each sheet is described below.

CDISC Terminology

For those cells where CDISC codes are used the user can enter either the CDISC C Code, for example C15602, the CDISC submission value, for example PHASE III TRIAL, or the preferred term, for example Phase III Trial

Multiple Values

Some cells allow for multiple values. These are all comma separated. If users wish to include a comma within such strings then the string can be enclosed in quotes. For example 123, "123,456", 789.

External Terminology

For those cells where external CT is referenced the user can enter code in the form <code>: <code> = . For example SPONSOR: A = decode 1, SPONSOR: B = decode 2. Where multiple codes are needed then the values are separated by commas.

Boolean Values

For boolean fields the following can be used to indicate a true value 'Y', 'YES', 'T', 'TRUE', '1' or the lower case equivalents.

Address Values

An address is of the form: ,district,city,state,postal_code,. All fields are text strings but note that:

• ``: one or more comma separated strings. As many as needed can be included.
• : is either a two or three character ISO-3166 country code.

Examples

• line 1, line 2, A District, A City, A State, 12345, USA, two lines before the district
• line 1, A District, A City, A State, 12345, USA, single line before the district
• "14, X Street", A District, A City, A State, 12345, USA, note the commas to allow a comma to be included
• 14, X Street| A District| A City| A State| 12345| USA, using pipe separators, no need for quotes around the first line

Note that | can be used in place of the commas for backward compatibility.

Identifiers and Cross References

Some content defined within the sheets contain unique identifiers such that the content can be cross referenced in other sheets. This is done so as to link content or expand definitions. Identifiers are simple strings that need to be unique within the workbook. There is a single definition and one or more cross references.

See the infographic for further information.

Timing Values

A number of fields specify timing values, either single relative values or ranges. These can be entered as a Timing Value of or a Timing Range of .. . The unit can be entered as follows:

• Years: 'Y', 'YRS', 'YR', 'YEARS', 'YEAR'
• Months: 'MTHS', 'MTH', 'MONTHS', 'MONTH'
• Weeks: 'W', 'WKS', 'WK', 'WEEKS', 'WEEK'
• Days: 'D', 'DYS', 'DY', 'DAYS', 'DAY'
• Hours: 'H', 'HRS', 'HR', 'HOURS', 'HOUR'
• Minutes: 'M', 'MINS', 'MIN', 'MINUTES', 'MINUTE'
• Seconds: 'S', 'SECS', 'SEC', 'SECONDS', 'SECOND'

So 3 Y, 3 YRS, 3 YR, 3 YEARS, 3 YEAR are all equivalent. Only a single value and unit should be entered, i.e. combination values are not supported.

Templated Text

Some entries can include "tags" that allow the text to reference structured content from elsewhere in the model. An example is an eligibility criterion referring to population definitions or an activity name. These sections of text are formatted as `` within the text. The ...tag_name... refers to an entry within a dictionary (see the dictionaries sheet)

An example of Templated Text is Subjects shall be between and where the min and max ages will be inserted using the dictionary entries that refer to particular attribute values from within the structured parts of the model.

Geographic Scopes & Enrollment

Geographic Scopes appear in a few of the sheets. These take the form Global, Region: or , Country: . Regions and Countries are taken from the ISO3166 value set. Examples are Global or Region: Europe, Country: USA. Where multiple codes are needed then the values are separated by commas. Note, if a global entry is specified then no other values are required and will be ignored.

In some cases (subject recruitment) values are associated with the scopes. The enrollment data is of the form: Global: , Region: = or , Country: =. The enrollment is either a percentage or an absolute value. Regions and Countries are taken from the ISO3166 value set. Examples are Global: 65% or Region: Europe=15, Country: USA=20%. Where multiple codes are needed then the values are separated by commas. Note, if a global entry is specified then no other values are required and will be ignored.

Sheet Descriptions

The sheet descriptions detail the fields found within each sheet and the details of the data required. Note:

• Some fields have multiple names due to model changes and a desire to preserve backwards compatibility. Any of the choices documented can be used.
• Some columns are optional and thus can be included or omitted. Again this is to preserve backwards compatibility. A default value is specified if the column is not included.

Study Sheet

Sheet Name

study

Sheet Contents

The study sheet consists of two parts, the upper section for those single values and then a section for the potentially repeating protocol version informaion

For the single values, the keyword is in column A while the value is in column B.

Row	Row Name	Purpose	Format and Values
1	studyTitle	The study title	Text string
2	studyVersion	String version	Text string
3	studyType or type	The study type	CDISC code reference
4	studyPhase	The study phase	CDISC code reference
5	studyAcronym	The study acronym	Text string
6	studyRationale	the study rationale	Text string
7	businessTherapeuticAreas	The set of business therapuetic area codes	External CT code format. Likely filled with sponsor terms
8	briefTitle	The brief title	Text string
9	officialTitle	The officiall title	Text string
10	publicTitle	The public title	Text string
11	scientificTitle	The scientific title	Text string
12	protocolVersion	The version of the protocol	Text string
13	protocolStatus	The status	CDISC code reference

A header row in row 16 followed by repeating rows from row 17, containing a series of dates:

Column	Column Name	Purpose	Format and Values
A	category	The date category	Either study_version or protocol_document for a date that applies to the study version or the document
B	name	A name for the date	text string
C	description	A date description	Text string, can be blank
D	label	A date label	Text string
E	type	the type of date	CDISC code reference
F	date	The date	Date field, dd/mm/yyyy
H	scopes	The geographic scopes for the date	Geographic scope

Study Identifiers Sheet

Sheet Name

studyIdentifiers

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, each containing a study identifier:

Column	Column Name	Purpose	Format and Values
A	organisationIdentifierScheme, organizationIdentifierScheme or IdentifierScheme	The scheme for the organisation identifier.	Example would be 'DUNS'
B	organisationIdentifier or identifier	Organisation identifier	Text string
C	organisationName or name	Organisation name	Text string
D (optional)	label	Display label	Text string, can be empty. Default value is ''
E	organisationType, organizationType or type	Organisation type	CDISC code reference
F	studyIdentifier	The identifier for the study	Text string
G	organisationAddress, organizationAddress or address	The organisation address	Address

Study Amendments Sheet

Sheet Name

studyAmendments

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing a study amendment:

Column	Column Name	Purpose	Format and Values
A	number	The amendment number	Integer
B	summary	The amendment summary	Text string
C	substantialImpact	True or false value indicating if the amendment is substantial	Boolean
D	primaryReason	Primary reason for the amendment	CDISC code reference
E	secondaryReasons	Secondary reasons for amendment. Multiple values can be supplied separated by a comma	CDISC code reference
F	enrollment	The current state of subject enrollment, either global, regional or country	Geographic scope with enrollment
F (optional)	template	The name of the template for the document to which the amendment applies. Defaults to 'SPONSOR'. See configuration sheet for template names	Text string.

Study Amendments Changes Sheet

Sheet Name

amendmentChanges

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing a study amendment changes:

Column	Column Name	Purpose	Format and Values
A	amendment	The amendment to which the change belongs, references the main amendment sheet	Integer
B	name	Name of the change	Text string
C	description	Description for the change	Text string
D	label	Change label. Default value is ''	Text string
E	rationale	The rationale for the change	Text string
F	summary	Summary of the change	Text string
G	sections	Section references	Comma separated text string consisting of <section>:

Study Amendments Impact Sheet

Sheet Name

amendmentImpact

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing a study amendment impacts:

Column	Column Name	Purpose	Format and Values
A	amendment	The amendment to which the change belongs, references the main amendment sheet	Integer
B	text	Text describing the impact of the amendment	Test string
C	substantial	Indicates the change is substantial	Boolean
D	type	The type of impact	CDISC code referernce

Study Design sheet

Sheet Name

studyDesign

Sheet Contents

The study design sheet consists of two parts, the upper section for those single values and then a section for the arms and epochs.

For the single values, the keyword is in column A while the value is in column B. Some rows can repeat

Row Name	Purpose	Format and Values	Repeat
studyDesignName or name	Study design name	Text string	No
studyDesignDescription or description	Study design description	Text string	No
label	Study design label. Default value is ''	Text string	No
therapeuticAreas	Set of therapeutic area codes	Set of external CT references, comma separated	No
studyDesignRationale	Study design rationale	Text string	No
studyDesignBlindingScheme	Code for the blinding scheme	CDISC code reference	No
trialIntentTypes	Codes for the trial intent types	Comma separated CDISC code references	No
trialTypes	Code for the trial type	CDISC code reference	No
interventionModel		CDISC code reference	No
masking	A masking role	Takes form of Role=description where the role is a CDISC Code Reference	Yes
characteristics	Set of characteristics	Set of CDISC code references	No
mainTimeline	Name of main timeline sheet	This must be present	No
otherTimelines	Names of other timeline sheeText string	Commma separated list of sheet names. Can be empty	No

For the arms and epochs, a simple table is required. The table starts in row 12 and can consists of a header row and 1 or more arm rows.

The header row consists of a cell in column A that is ignored followed by 1 or more cells (columns) containing the epoch names. Each epoch name should have a corresponding entry in the Study Design Epochs sheet, see below.

The arm rows consist of the arm name in the first column followed by a cells for each epoch containing one or more references to study design elements defined in the studyDesignElements sheet. Each arm name should have a corresponding entry in the Study Design Arms sheet, see bwlow.

Study Design Arms sheet

Sheet Name

studyDesignArms

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing the details of a study arm:

Column	Column Name	Purpose	Format and Values
A	studyArmName or name	Identifier	Text string. Should match an arm name in the Study Design sheet
B	studyArmDescription or description	Description	Text string, can be empty
C (optional)	label	Display label	Text string, can be empty. Default value is ''
D	studyArmType or type	The arm type	CDISC code reference
E	studyArmDataOriginDescription or dataOriginDescription	The description of the data origin for the arm	Text string
F	studyArmDataOriginType or dataOriginType	The type of arm data origin	CDISC code reference
G (optional)	notes	Any relevant notes	List of note references, comma separated

Study Design Epochs sheet

Sheet Name

studyDesignEpochs

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing the details of a study epoch:

Column	Column Name	Purpose	Format and Values
A	studyEpochName or name	The epoch name	Text string. Should match an epoch name in the Study Design sheet
B	studyEpochDescription or description	Description	Text string, can be empty
C (optional)	label	Display label	Text string, can be empty. Default value is ''
D	studyEpochType or type	The epoch type	CDISC code reference
E (optional)	notes	Any relevant notes	List of note references, comma separated

V1 Timeline sheets

No longer supported

V2 Timeline sheets

Sheet Name

As defined within the study design sheet, see above.

Sheet Contents

General

This is a complicated sheet. It is, in essence, an enhanced SoA. There are several sections within the sheet:

• The name, description and condition located top right
• The remainder of the sheet is the SoA with:
  • The timing set in the top rows, the "timepoints"
  • The activities down the left hand side
  • The link between activities and "timepoints", the classic 'X'

Name, Description, Condition

The name description and condition are located in columns A and B, rows 1 and 2. It is a vertical name value pair configuration

Row	Row Name	Purpose	Format and Values
1	Name	The timeline name	Text string
2	Description	Timeline description	Text string
3	Condition	Timeline entry condition	Text string

Timing

The timing seciton consists of multiple columns starting in column D. As many columns as needed can be created. A title block is held in Column C. The section consists of eight rows in rows 1 to 8 as follows:

Row	Row Name	Purpose	Format and Values
1	name	Identifier	Text string
2	description	Description	Text string, can be empty
3	label	Display label	Text string, can be empty
4	type	Timepoint type	Activity or Decision
5	default	Timepoint Link	The name (as per row 1) of the next activity in the sequence, the default connection
6	condition	Timepoint Links	The names (as per row 1) of the activities to link to for one or more conditions (command separated list)
7	epoch	Name of the epoch within which the timepoint falls	Text string
8	encounter	Name of the encounter in which the timepoint belongs	Text string. Can be empty

Activity

The activity section consists of three columns, A to C, starting in row 10, row 9 being a title row. As many rows as needed can be added. Note that only one of parent or child activity should be entered on any given row.

Column	Column Name	Purpose	Format and Values
A	Parent Activity	Parent Activity.	Text string
B	Child Activity	Child activity name	Text string
C	BC/Procedure/Timeline	A set of BCs, procedures or timelines. Comma separated or the form detailed below	:---

The BC, procedure, timeline format is defined as follows (using pseudo BNF):

 ::=  |  
 ::=  :  | empty
 ::= PR | BC | TL
 ::= 

BC: Age, BC: Sec, PR:Informed Consent Form, TL:Exercise indicates the activity consists of the bcs Age and Sex, a procedure for the informed consent and a timeline specified in the Exercise sheet.

Link

The link section consists of a set of cells into which an upper case 'X' can be placed to link a timepoint with an activity. Otherwise the cell will be ignored.

Study Design Timing sheet

Sheet Name

studyDesignTiming

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing encounter definitions.

Column	Column Name	Purpose	Format and Values
A	name	Name	Text string
B	description	Description	Text string, can be empty
C	label	Display label	Text string, can be empty
D	type	The type of timing	Either Before, After or Fixed
E	from	Timeing point ref	The name of a timing point from a timeline sheet
E	to	Timeing point ref	The name of a timing point from a timeline sheet
E	timingValue	Timing	The relative value for a Before, After timing value or an absolute time for Fixed
E	toFrom	Timing precision	Either S2S, S2E, E2S, E2E to set the precise timing for a Before, After timing value
E	window	Timing window	A timing range

Study Design Activities sheet

Sheet Name

studyDesignActivities

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing encounter definitions.

Column	Column Name	Purpose	Format and Values
A	activityName or name	Name	Text string
B	activityDescription or description	Description	Text string, can be empty
C (optional)	label	Display label	Text string, can be empty. Default value is ''
D (optional)	notes	Any relevant notes	List of note references, comma separated

Note that this sheet is optional. If the sheet is not provided the activities will be created from those defined in the timeline sheets. These activities will have the name and description set to the name used in the timeline sheet and no condition will be set.

If the sheet is provided but there is no definition in the sheet for an activity referenced in a timeline sheet then the name and description will be set to the name used in the timeline sheet and no condition will be set.

Study Design Indications Sheet

Sheet Name

studyDesignIndications

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing an indication or intervention:

Column	Column Name	Purpose	Format and Values
A	name	The name	Text string
B	description	Description	Text string, can be empty
C	label	Display label	Text string, can be empty
D	isRareDisease	Rare disease flag	Boolean
E	codes	The set of indication or intervention codes	A set of external CT codes, comma separated

Study Design Interventions Sheet

Sheet Name

studyDesignInterventions

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing an intervention. Note that columns J through S can repeat for the same content in columns A to I. For additional administrations rows leave columns A to I blank.

Column	Column Name	Purpose	Format and Values
A	name	Name	Text string
B	description	Description	Text string, can be empty
C	label	Display label	Text string, can be empty
D	codes	The set of intervention codes	A set of external CT codes, comma separated
E	role	The role th eintervanetion plays	A single M11 code
F	type	The intervention type
G	pharmacologicalClass	The pharmalogical class	A single external CT code
H	productDesignation	The product designation	A single M11 code
I	minimumResponseDuration	The minimum response duration
J	administrationName	Name	Text string
K	administrationDescription	Description	Text string, can be empty
L	administrationLabel	Display label	Text string, can be empty
M	administrationRoute	Route of administration	CDISC code reference
N	administrationDose	Dose quantity	Quantity
O	administrationFrequency	Administration freqeunce	CDISC code reference
P	administrationDurationDescription	Description	Text string, can be empty
Q	administrationDurationWillVary	Duration will vary flag	Boolean
R	administrationDurationWillVaryReason	Duration will vary reason	Text string
S	administrationDurationQuantity	administration quantity	Quantity

Study Design Populations sheet

Sheet Name

studyDesignPopulations

Sheet Contents

A header row in row 1 followed by repeating rows from row 2 containing population or sub-population definitions. Note that not every entry in columns E through I need to be filled in, just enough to define either the whole population of the sub-populations. Sub-populations need not be specificed.

Column	Column Name	Purpose	Format and Values
A	level	Level of entry	Set to either MAIN for the main population entry. All other values equate to a cohort (sub population) entry
B	name	Identifier	Text string
C	description	Description	Text string, can be empty
D	label	Display label	Text string, can be empty
E	plannedCompletionNumber	Number of participants to complete the study	Integer
F	plannedEnrollmentNumber	Number of participants to be enrolled	Integer
G	plannedAge	Age range of participants	Range
H	plannedSexOfParticipants	Sex of participants	CDISC code reference
I	includesHealthSubjects	Healthy subjects flag	Boolean
I	characterisitcs	List of characteristics for the cohort (ignored for main population)	Comma separated list of charcateristics name references

Study Design Characteristics sheet

Sheet Name

studyDesignCharacteristics

Sheet Contents

A header row in row 1 followed by repeating rows from row 2 containing characteristics for cohorts.

Column	Column Name	Purpose	Format and Values
A	name	Identifier	Text string
B	description	Description	Text string, can be empty
C	label	Display label	Text string, can be empty
D	text	Criteria text	Templated text
E	dictionary	Dictionary cross reference	The dictionary from which the templated text tags are taken. If no tags are used can be empty

Study Design Objectives and Endpoints sheet

Sheet Name

studyDesignOE

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing objective and endpoint definitions. Note that columns D through G can repeat for the same content in columns A to C. For additional endpoint rows leave columns A to C blank.

Column	Column Name	Purpose	Format and Values
A	objectiveXref or objectiveName	Identifier	Text string
B	objectiveDescription	Description	Text string, can be empty
C (optional)	objectiveLabel	Display label	Text string, can be empty. Default value is ''
D	objectiveText	The objective	Templated text
E	objectiveLevel	Objective level	CDISC code reference
F	objectiveDictionary	Dictionary cross reference	The dictionary from which the templated text tags are taken. If no tags are used can be empty
G	endpointXref or endpointName	Identifier	Text string. Note columns G to M can repeat for each endpoiint for an objective
H	endpointDescription	Description	Text string, can be empty
I (optional)	endpointLabel	Display label	Text string, can be empty. Default value is ''
J	endpointText	The objective	Templated text
K	endpointPurpose
L	endpointLevel	Level	CDISC code reference
M	endpointDictionary	Dictionary cross reference	The dictionary from which the templated text tags are taken. If no tags are used can be empty

Study Design Eligibility Criteria sheet

Sheet Name

studyDesignEligibilityCriteria

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing eligibility definitions.

Column	Column Name	Purpose	Format and Values
A	category	Category	Either Inclusion or Exclusion
B	identifier	Identifier	Text string, the identifier for the criteria
C	name	The name identifier for the criteria	Text string
D	description	Description	Text string, can be empty
E	label	Display label	Text string, can be empty
F	text	Criteria text	Templated text
G	dictionary	Dictionary cross reference	The dictionary from which the templated text tags are taken. If no tags are used can be empty

Study Design Estimands sheet

Sheet Name

studyDesignEstimands

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing estimand definitions. Note that column I and J can repeat for the same content in columns A through H.

Column	Column Name	Purpose	Format and Values
A	xref or name	Identifier	Text string
B	summaryMeasure	The summary measure	Text string
C	populationDescription	Description	Text string, can be empty
D	populationSubset	Name of the related population	Text string
E	intercurrentEventName or name	Name	Text string
F	intercurrentEventDescription or description	Description	Text string, can be empty
G	treatmentXref	Treatment cross reference	Cross reference to a treatment
H	endpointXref	Endpoint cross reference	Cross reference to an endpont
I	intercurrentEventStrategy	The strategy for the event	Text string.
J	intercurrentEventText	The text for the event	Text string.

Study Design Procedures sheet

Sheet Name

studyDesignProcedures

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing procedure definitions.

Column	Column Name	Purpose	Format and Values
A	xref, procedureName or name	Identifier	Text string
B	procedureDescription or description	Type	Text string, can be empty
C (optional)	label	Display label	Text string, can be empty. Default value is ''
D	procedureType	Type	Text string
E	procedureCode or code	Code reference	External CT reference

Study Design Encounters sheet

Sheet Name

studyDesignEncounters

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing encounter definitions.

Column	Column Name	Purpose	Format and Values
A	xref	Identifier	Text string
B	encounterName or name	Name	Text string
C	encounterDescription or description	Description	Text string, can be empty
D (optional)	label	Display label	Text string, can be empty. Default value is ''
E	encounterType or type	The type	CDISC code reference
F	encounterEnvironmentalSetting	Encounter environment	One or more CDISC code references
G	encounterContactModes	Contact modes	One or more CDISC code references
H	transitionStartRule	Start rule	Text string
I	transitionEndRule	End Rule	Text string
J	window	Timing reference that defines the window	Text string

Study Design Elements sheet

Sheet Name

studyDesignElements

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing element definitions.

Column	Column Name	Purpose	Format and Values
A	xref	Identifier	Text string
B	studyElementName or name	Name	Text string
C	studyElementDescription or description	Description	Text string, can be empty
D (optional)	label	Display label	Text string, can be empty. Default value is ''
E	transitionStartRule	Start rule	Text string
F	transitionEndRule	End rule	Text string

Document Template Sheets

Sheet Name

default name: document

Several content sheets can be included within the workbook and named as desired. Typical use might be the inclusion of a sponsor protocol format and the new M11 format

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing the narrative content:

Column	Column Name	Purpose	Format and Values
A	name	Name of the section.	Text string. Can be left blank in which case a default value will be used based on the section number
B	sectionNumber	The section number	Text string with section numbers separated by '.' characters. Section numbers from row to row can only increase by a single level down, e.g. '1.2' to '1.2.1' and not '1.2.1.1'. The section numbers will be used to create parent child relationships in the data created.
C	displaySectionNumber	Display Section Number	Boolean value indicating if the section number should be displayed within the document
D	sectionTitle	Section Title	Text String
E	displaySectionTitle	Display Section Title	Boolean value indicating if the section title should be displayed within the document
F	content	The content reference	The name of item include

Document Content sheet

Sheet Name

default name: documentContent

Several content sheets can be included within the workbook and named as desired. Typical use might be the inclusion of a sponsor protocol format and the new M11 format

Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing the narrative content:

Column	Column Name	Purpose	Format and Values
A	name	Name of the content	Text string. Can be left blank in which case a default value will be used based on the section number
B	text	The content text	HTML formatted text String

There are some prefined macros that can be used to generate content. These are pre processed when the content sheet is read and transated into the appropriate USDM references usdm:ref or usdm:tag. These macros use a similar syntax to the USDM references:

| Macro Name | Purpose | Attributes |
| :--- | :--- | :--- |
| xref | Refer to a data element by name reference | 'klass', 'name' and 'attribute'. The name is the name used within the workbook to define the content. |
| image | Insert an mage into the document | 'file' and 'type'. The file attribute specifies the name of a file in the same directory as the Excel workbook. |
| element | Refer to a predefined element | 'name' of the element. Supported element names are 'study_phase', 'study_short_title', 'study_full_title', 'study_acronym', 'study_rationale', 'study_version_identifier', 'study_identifier', 'study_regulatory_identifiers', 'study_date', 'approval_date', 'organization_name_and_address', 'amendment' and 'amendment_scope' |
| section | Add a pre defined section into the document | 'name' and 'template'. Supported section are 'title_page', 'inclusion', 'exclusion' and 'objective_endpoints'. Supported templates are 'm11' and 'plain' |
| bc | Add in a reference to a BC | 'name' and 'activity' where the name is the name of the BC as used in the SoA and activity is the name of the activity it is referenced from (in case several activities reference the same BC). This macro is needed as the BCs are not explicitly defined and thus named, they are read from the CDISC library and can appear multiple times. |
| note | Insert a note into the document | 'text' |
| abbreviation | Insert one or more abbreviations into the document | 'items', 'separator'. The items is a list of abbreviations to be inserted, comma separated. The separator is the character used to separate the items when displayed, default is a comma. |

Examples of macros are:

### Study Design Sites sheet

#### Sheet Name

`studyDesignSites`

#### Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing organizations and associated sites. Note that columns G through I can repeat for the same content in columns A to F. For additional site rows leave columns A to F blank.

| Column | Column Name | Purpose | Format and Values |
| :--- | :--- | :--- | :--- |
| A | name | Organization name | Text string |
| B | label | Organization display label | Text string, can be empty |
| C | type | Organisation type | CDISC code reference |
| D | identifierScheme | The scheme for the organisation identifier | Example would be 'DUNS' |
| E | identifier | Organisation identifier | Text string |
| F | address | Organisation address | Address |
| G | siteName | Site name | Formated using a pipe delimited form, see below |
| H | siteDescription | Site description | Text string, can be empty|
| I | siteLabel | Site display Label | Text string, can be empty |

### Study Design Conditions sheet

#### Sheet Name

`studyDesignConditions`

#### Sheet Contents

A header row in row 1 followed by repeating rows from row 2, containing the conditions: 

| Column | Column Name | Purpose | Format and Values |
| :--- | :--- | :--- | :--- |
| A | name | Condition name | Text string |
| B | label | Condition display label | Text string, can be empty |
| C | description | Condition description | CDISC code reference |
| D | text | The condition text | Text string |
| E | appliesTo | List of cross references for items to which the condition applies | Comms separated list |
| F | context | List of cross references for the context in which the condition applies | Comma separated list |

### Dictionary Sheet

#### Sheet Name

`dictionaries`

#### Sheet Contents

A header row in row 1 followed by repeating rows from row 2. Each row contains a dictionary and dictionary entry definitions. The sheet defines one or more dictionaries and the entries within each dictionary. Note that columns D through F can repeat for the same content in columns A to C. For additional dictionary entry rows leave columns A to C blank.

| Column | Column Name | Purpose | Format and Values |
| :--- | :--- | :--- | :--- |
| A | name | The dictionary name | Text string | 
| B | description | Description | Text string. Can be empty |	
| C | label | Label | Text string. Can be empty |	
| D | key | The entry key | Text String. Must be unique within the dictionary |
| E | class | The class name | The name of the class within the model from which the data for the dictionary entry is to be taken |
| F | xref | Cross reference name | The name of the instance from which the data is to be taken. Use the entries in the name columns from other sheets |
| G | atrribute | The attribute path or name | The name or path of the attribute from which the data is to be taken |
| H (optonal) | value | The value | A fixed value. If this column is used then the 'class', 'xref' and 'attribute' fields should be empty |

The attribute path follows a simplified 'Xpath' syntax of ```@attribute-name[/class/@attribute-name]``` form. The class attribute pairs can be repeated to arrive as the desired attribute. This has been provided since not all instances of all classes are named which prevents thenm being addressed directly, for example Range of Quantity instances.

An example for accessing the Population planned age, max value is ```@plannedAge/Range/@maxValue```. In this instance the ```class``` column would be set to ```Population``` and the ```xref``` column set to the name of the Population entry in the population shseet. 

Note that the '@' symbol does not need to be included with attribute names but it guides the eye making it easier to read the path.

### Notes Sheet

#### Sheet Name

`notes`

#### Sheet Contents

A header row in row 1 followed by repeating rows from row 2. Each row contains a note. 

| Column | Column Name | Purpose | Format and Values |
| :--- | :--- | :--- | :--- |
| A | name | The note name | Text string | 
| B | text | The note text | Text string. |	
| C | codes | The set of codes | A set of external CT codes, comma separated |	

### Abbreviations Sheet

#### Sheet Name

`abbreviations`

#### Sheet Contents

A header row in row 1 followed by repeating rows from row 2. Each row contains a note. 

| Column | Column Name | Purpose | Format and Values |
| :--- | :--- | :--- | :--- |
| A | abbreviatedText | The abbreviation | Text string | 
| B | expandedText | The full text | Text string. |	
| C (optional) | notes | Any relevant notes | List of note references, comma separated |

### People Sheet

#### Sheet Name

`people`

#### Sheet Contents

A header row in row 1 followed by repeating rows from row 2. Each row contains an assigned person definition. 

| Column | Column Name | Purpose | Format and Values |
| :--- | :--- | :--- | :--- |
| A | name | The dictionary name | Text string | 
| B | description | Description | Text string. Can be empty |	
| C | label | Label | Text string. Can be empty |	
| D | jobTitle | The job title | Text string | 
| E | organization | Cross reference (name) to an organization to which the person is associated | Text string. |	

### Roles Sheet

#### Sheet Name

`roles`

#### Sheet Contents

A header row in row 1 followed by repeating rows from row 2. Each row contains an assigned person definition. 

| Column | Column Name | Purpose | Format and Values |
| :--- | :--- | :--- | :--- |
| A | name | The dictionary name | Text string | 
| B | description | Description | Text string. Can be empty |	
| C | label | Label | Text string. Can be empty |	
| D | people | Cross reference (name) to one or more persons performing the role | Comma separated list of strings. Can be empty. | 
| E | masking | The masking associated with the role. Can be empty if no masking. | Text string. Can be empty |	
| F | role | The role | CDISC code reference | 
| G | organizations | Cross reference (name) to one or more organizations performing the role | Comma separated list of strings. Can be empty. |	

### Configuration Sheet

#### Sheet Name

`configuration`

#### Sheet Contents

A set of rows consisting of configuration parameters. The first column is the type of configuration parameter while the second is the value. The values for specific parameters may vary in their format

| Parameter | Description | Format and Values |
| :--- | :--- | :--- |
| CT Version | Allows for the version of a specific external CT to be set. Multiple rows can be included to set the versions for several CTs | Of the form ctName = Version, for example `SNOMED = 21st June 2012`|
| Empty None | Allows for string fields to be set to '' rather than null/none values so as to accomodate the SDR validation checks | Set to 'EMPTY' to use ''. Any other value will permit  null values to be used |
| Template | Configures a protocol template and the associated template sheet | Entries take the form of templateName = sheetName, for example `Sponsor = sponsorContent`. The template name and the sheet name are simple strings. Template names are at the user's discretion but the string `m11` or `M11` is reserved as the template name for the M11 Template format. The sheet name must match a sheet within the workbook that must be structured as per the template sheet format. |
| Use Template | Deprecated | Deprecated |
| USDM Version | Deprecated | Deprecated |
| SDR Prev Next | Deprecated | Deprecated |
| SDR Root | Deprecated | Deprecated |
| SDR Description | Deprecated | Deprecated |

An example configuration is

| First Column | Second Column |
| :--- | :--- | 
| CT Version | SNOMED=January 31, 2018 |
| CT Version | SPONSOR =   12 |
| CT Version | ICD-10=1 |
| Template | lilly=lillyFormat |
| Template | m11=m11Format |

This sets up three CT versions and two templates.

# Issues

See the [github issues](https://github.com/data4knowledge/usdm/issues)

# Build Notes

## Checklist

1. Everything on main branch?
1. Readme updated with any necessary changes?
1. Version updated?
1. All tests passing?

Then

1. Build and upload
1. Write release note

## Build steps for deployment to pypi.org

- Build with `python3 -m build --sdist --wheel`
- Upload to pypi.org using `twine upload dist/* `
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