ADaM specifications

mighty.metadata uses YAML files to specify Analysis Data Model (ADaM) datasets. Each YAML file follows a fixed structure with defines properties and entries.

This structure is defined in a JSON-schema that you can access with:

system.file("schema", "adam.json", package = "mighty.metadata")

Below you can find a detailed description of the structure.

Mighty Metadata ADaM Domain Specification

Common schema for ADaM dataset specification in the mightyverse

Type	Required	Additional Properties
object	id label class structure keys columns	No

Properties

Name	Description	Type	Required
id	Name of the ADaM dataset	cdisc/name	Yes
label	Label of the ADaM dataset	string	Yes
include	Conditional expression to include the domain	mighty/include	No
class	CDISC class of the dataset	cdisc/class	Yes
subclass	CDISC subclass of the dataset	cdisc/subclass	No
structure	Text description of the structure of the dataset	string	Yes
keys	Key variables for the dataset	keys	Yes
comment	Comment to the dataset	string	No
usecore	Flag to populate with core variables from ADSL	boolean	No
population	Population and base domain used to create the dataset	mighty/population	No
columns	Columns in the dataset	columns	Yes
rows	Row derivations for mighty	rows	No
parameters	Parameters in a BDS dataset	parameters	No

Definitions

keys

Keys are always unique and of minimum length 1

Type	Items	Min Items	Unique Items
array	cdisc/name	1	Yes
cdisc/name

columns

List of column specifications

Type	Items	Min Items	Unique Items
array	column	1	Yes

column

Specification of a single column

Type	Required	Additional Properties
object	id	No

Properties

Name	Description	Type	Required
id	Name of the column	cdisc/name	Yes
include	Conditional expression to include the column	mighty/include	No
label	Label of the column	string	No
method	How to derive the column (free text)	string	No
origin	Origin type of the column	cdisc/origin	No
codelist	Codelist of possible values of the column	string	No
is_core	Flag for designating a core variables in subject level datasets	boolean	No
format	Data format of the column	standard/dataformat	No
component	Mighty component to create the column	mighty/component	No
depends	dependencies required to create the column	mighty/depends	No
core	Describes whether a variable is required (Req), conditionally required (Cond) or permissible (Perm)	cdisc/core	No
comment	Comment to the column (free text)	string	No

rows

List of row action specifications. Typically used when adding additional rows to the data.

Type	Items	Min Items	Unique Items
array	row	1	Yes

row

Specification of a single row action

Type	Required	Additional Properties
object	id	No

Properties

Name	Description	Type	Required
id	Unique identifier of the action. Used to reference in other places, e.g. as a dependency.	cdisc/name	Yes
include	Conditional expression to include the row	mighty/include	No
method	How to derive the row action (free text)	string	No
component	Mighty component to do the row action	mighty/component	No
depends	Dependencies needed before the action can be carried out	mighty/depends	No

parameters

Specification of parameters in a BDS dataset

Type	Items	Min Items	Unique Items
array	parameter	1	Yes

parameter

Specification of a single BDS parameter

Type	Required	Additional Properties
object	id	No

Properties

Name	Description	Type	Required
id	Parameter id (PARAMCD)	cdisc/name	Yes
include	Conditional expression to include the parameter	mighty/include	No
label	Parameter label (PARAM)	string	No
columns	Additional columns to derive for the parameter, e.g. AVAL and AVALC	columns	No
component	Mighty component used to derive the parameter and all relevant columns	mighty/component	No
depends	Dependencies required to create the parameter	mighty/depends	No

standard

Additional definitions used for e.g. define.xml

dataformat

Format used to display the data

Type	Required
object	type length

Properties

Name	Description	Type	Enum	Minimum	Pattern	Required
type	Data type	string	text , integer , float , datetime , date , time , partialDate , partialTime , partialDatetime , incompleteDatetime, durationDatetime , intervalDatetime			Yes
length	Maximum length of content	integer	NULL	1		Yes
display	SAS display format	string	NULL		.	No

cdisc

Definitions from CDISC standards

name

Uppercase identifier

Type	Pattern
string	^[A-Z][A-Z0-9_]*$

class

Subset of CDISC controlled terminology C103329

Type	Enum
string	SUBJECT LEVEL ANALYSIS DATASET BASIC DATA STRUCTURE OCCURRENCE DATA STRUCTURE ADAM OTHER

subclass

Union of CDISC controlled terminology C165635 and C176227

Type	Enum
string	TIME-TO-EVENT NON-COMPARTMENTAL ANALYSIS POPULATION PHARMACOKINETIC ANALYSIS ADVERSE EVENT

origin

Controlled terminology C170449

Type	Enum
string	Assigned Collected Derived Not Available Other Predecessor Protocol

core

Indicator of whether a variable is required (Req), conditionally required (Cond), or permissible (Perm) in the dataset

Type	Enum
string	Cond Perm Req

mighty

Definitions only relevant when using mighty to generate code

population

mighty - specification of the base domain(s) and any global filters to apply

Type	Required
object	base

Properties

Name	Description	Required	Type
base	mighty - domains to filter and combine to create initial dataset	Yes	mighty/base_input_list
global	mighty - global filters to apply after combining base datasets	No	mighty/global_input_list

base_input_list

mighty - list of base input datasets

Type	Items	Min Items	Unique Items
array	mighty/base_input	1	Yes

base_input

mighty - single base input dataset with filters

Type	Required	Additional Properties
object	domain depends filter	No

Properties

Name	Description	Required	Type
domain	Name of the dataset to use	Yes	cdisc/name
depends	Which columns in the dataset the filter depends on	Yes	mighty/depends
filter		Yes	mighty/filter

global_input_list

mighty - list of global filters

Type	Items	Min Items	Unique Items
array	mighty/global_input	1	Yes

global_input

mighty - single global filter

Type	Required	Additional Properties
object	filter depends	No

Properties

Name	Description	Required	Type
filter		Yes	mighty/filter
depends	Which columns the filter depends on	Yes	mighty/depends

depends_string

A single dependency: COLUMN, DOMAIN.COLUMN, rows.ID, or parameters.ID

Type	Pattern
string	([A-Z][A-Z0-9_](.[A-Z][A-Z0-9_])?)$|(rows|parameters).[A-Z][A-Z0-9_]*$

depends

List of dependencies needed before the component code can be evaluated

Type	Items	Min Items	Unique Items
array	mighty/depends_string	1	Yes
mighty/depends_string

include

Glue expression that evaluates to TRUE or FALSE

Type	Pattern
string	^{.*}$
boolean

filter

Filter specification. Must be an R expression that can be evaluated.

Type
string

component

mighty component used to carry out the desired derivation

Type	Required	Additional Properties
object	id	No

Properties

Name	Description	Type	Required
id	ID of the component. Either name of standard or file path to local component.	string	Yes
with	named list of input arguments needed to render component	object	No