Custom Fields in TSV Schemas

When using TSV cancer_matched or germline_variants schemas, you can use custom fields by filling the [Custom Fields] header in the TSV file.

Example

In the following example, we add the fields shimada4Class (an enum with two possible values), patientStatus (an enum with three different value), to the bio entity/patient, the field mycnCn (a floating point number greater than or equal to 0) to the test sample, and one boolean flag for each the test sample and NGS library (testSampleFlag and ngsLibraryFlag).

[Metadata]
schema	cancer_matched
schema_version	v1
title	Example matched cancer tumor/normal study
description	This example shows how to add custom fields

[Custom Fields]
key	annotatedEntity	docs	type	minimum	maximum	unit	choices	pattern
shimada4Class	bioEntity	Shimada 4 classification	enum	.	.	.	favorable,unfavorable	.
patientStatus	bioSample	Status of patient	enum	.	.	.	Deceased_from_disease,No_disease_event,Relapse_progression	.
mycnCn	bioSample	MYCN copy number	number	0.0	.	.	.	.
testSampleNice	testSample	Is test sample nice?	boolean	.	.	.	.	.
ngsLibraryNice	ngsLibrary	Is NGS library nice?	boolean	.	.	.	.	.

[Data]
patientName	sampleName	isTumor	libraryType	folderName	shimada4Class	patientStatus	mycnCn	testSampleFlag	ngsLibraryFlag
P001	N1	N	WES	P001-N1-DNA1-WES1	favorable	Deceased_from_disease	2.0	Y	N
P001	T1	Y	WES	P001-T1-DNA1-WES1	favorable	Deceased_from_disease	2.0	N	Y
P001	T1	Y	mRNA_seq	P001-T1-RNA1-mRNAseq1	favorable	Deceased_from_disease	2.0	Y	Y

Field Types

The valid field types are given together with whether additional restrictions/information is allowed (Y) or even required (R).

Type	Summary	minimum	maximum	unit	choices	pattern
string	a string value
integer	an integer	Y	Y	Y
number	a floating point value	Y	Y	Y
boolean	boolean flag
enum	one of several strings				R
regex	regex-checked string					R