data.test

# notes:
# - use 4 spaces for display tab
# - repeated tabs get trimmed to one
# - anything beyond ' #' is trimmed (including marker), so are empty lines (post line-trim)
# - \N stand for no value (eg NULL in SQL)
# - PATID, ENCOUTERID and other IDs are inferred from the _id field, including redundant fields

===========================================================================
DEMOGRAPHIC

_id			BIRTH_DATE		SEXUAL_ORIENTATION	GENDER_IDENTITY		SEX		HISPANIC	RACE	BIOBANK_FLAT
------------------------------------------------------------------------------------------------------------
01			2010-01-01		AS					M					A		Y			01		N
02			2010-01-02		AS					F					F		N			02		Y
03			2010-01-03		BI					TM					M		R			03		Y
04			2010-01-04		BI					TF					NI		NI			04		Y
05			2010-01-05		GA					CQ					UN		UN			05		N
06			2010-01-06		GA					SE					OT		OT			06		Y
07			2010-01-07		LE					MU					A		UN			07		Y
08			2010-01-08		LE					DC					F		NI			NI		N


===========================================================================
ENCOUNTER

_id				#	ADMIT_DATE		DISCHARGE_DATE	PROVIDERID	FACILITY_LOCATION	ENC_TYPE	FACILITYID
----------------------------------------------------------------------------------------------------------
01-01			#	2010-02-01		2010-12-01		999999		333					AV			33
01-02			#	2010-03-01		2010-12-01		999999		333					ED			33
02-01			#	2010-02-02		2010-12-02		999998		333					EI			33
03-01			#	2010-02-03		2010-12-03		999998		334					IP			33
04-01			#	2010-02-04		2010-12-04		999997		334					IS			33
05-01			#	2010-02-05		2010-12-05		999997		334					OS			33
06-01			#	2010-02-06		2010-12-06		999996		335					IC			33
07-01			#	2010-02-07		2010-12-07		999996		335					OA			33
08-01			#	2010-02-08		2010-12-08		999995		335					NI			33


===========================================================================
DIAGNOSIS

_id				DX				DX_SOURCE	DX_TYPE
---------------------------------------------------
01-01-01		G25.3			AD			09
01-01-02		Z00.129			AD			10
01-02-01		799.82			DI			10
02-01-01		71677004		FI			11
03-01-01		B34.9			IN			SM
04-01-01		Z00.129			NI			NI
05-01-01		G40.409			UN			UN
06-01-01		G25.3			OT			OT
06-02-01		R56.9			AD			09


===========================================================================
LAB_RESULT_CM

_id				SPECIMEN_SOURCE
-------------------------------
01-01-01		BLOOD
01-02-01		CSF
01-02-02		PLASMA
02-01-01		SERUM
03-01-01		SR_PLS


===========================================================================
PRESCRIBING

_id				RAW_RX_MED_NAME
---------------------------------
01-01-01		paracetamol 1000G
01-01-02		ibuprofen 1000G
01-02-01		paracetamol 500G
07-01-01		ibuprofen 500G
08-01-01		paracetamol 1000G


===========================================================================
PROCEDURES

_id				PX			PX_DATE			PX_TYPE
---------------------------------------------------
01-01-01		82948		2012-01-01		C4
01-01-02		90680		2012-01-01		OT
01-02-01		82948		2012-01-01		C4
07-01-01		90670		2012-01-01		OT
08-01-01		90680		2012-01-01		C4


===========================================================================
VITAL

_id				HT
---------------------
01-01-01		40.01
02-01-01		40.02
04-01-01		40.04
06-01-01		40.06


===========================================================================
DEATH

_id			DEATH_DATE		DEATH_SOURCE
----------------------------------------
01			2011-01-01		L
07			2011-01-08		N


===========================================================================
genomic_metadata

_id		wgs		ubam_file_exists	.xml_file_exists	snp_array	genomic_panel	fastq_file_exists		wes			bam_file_exists 	gvcf_file_exists	.idat_file_exists	vcf_file_exists		platform	
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
01		true	true				false				true		true			false					true		true				false				false				true				Affymetrix 6208
02		true	true				true				false		true			false					true		true				false				true				true				Affymetrix 6208
03		false	true				false				true		false			true					true		false				true				false				false				Affymetrix 6208
04		true	false				true				true		true			true					true		true				false				false				false				Affymetrix 6208
05		false	true				false				true		false			false					true		true				true				true				true				Affymetrix 6208
06		false	true				false				true		false			false					true		true				true				true				true				Affymetrix 6208
07		false	true				false				true		false			false					true		true				true				true				true				Affymetrix 6208
08		false	true				false				true		false			false					true		true				true				true				true				Affymetrix 6208


===========================================================================
sample_metadata

_id		sample_exists		tissue_type			sample_type
-----------------------------------------------------------
01		true				Bone/Vertebrae		Whole Blood
02		true				Bone/Vertebrae		Whole Blood
03		false				\N					\N
04		false				\N					\N
05		false				\N					\N
06		false				\N					\N
07		false				\N					\N
08		false				\N					\N

===========================================================================
misc

_id		grin_consent	irb_share_forprofit		irb_ror			subject_primary_language	institution_name	irb_recontact	irb_share_identified_data
---------------------------------------------------------------------------------------------------------------------------------------------------------
01		true			true					true			English						CHOP				false			false
02		true			false					true			French						CHOP				false			false
03		true			false					true			Spanish						CHOP				true			false
04		true			false					true			Simlish						CHOP				false			false
05		true			false					false			Klingon						CHOP				false			true
06		true			false					false			Esperanto					CHOP				false			true
07		true			false					false			Javanais					CHOP				false			true
08		false			false					false			Pig Latin					CHOP				false			true