A Additional Result Tables

The appendix contains the following topics:

Pre-Seeded Tables
Populated by User or Loader
Tables or Columns Not Populated Through Loader Scripts

A.1 Pre-Seeded Tables

W_EHA_RSLT_TYPE

This table stores information regarding type of result stored and is based on what data is being inserted into ODB (one row inserted per loader per file). User may choose to seed more types.

Table A-1 W_EHA_RSLT_TYPE

RESULT_TYPE_NAME	RESULT_TYPE_DESC	Which loader inserts
GENE_EXPRESSION	Gene expression results	Gene expression loader
NOCALL	Nocall result for sequencing given allele	CGI masterVar loader
SEQUENCING	Sequencing results including simple variants such as snp, insertions, deletions	VCF, MAF, CGI masterVar^Footref 1 loaders
COPY_NUMBER_VARIATION	Copy Number Variation results	CNV loader
TCGA_RNA_SEQ_EXON	TCGA RNA Seq results for exon information	TCGA RNA seq loader^Foot 1
2-CHNL_GENE_EXPRESSION	Gene expression results from 2-channel gene expression analysis	Dual channel loader

^Footnote 1CGI masterVar loader is temporarily removed from ODB 2.5 and will be available in the next release.

W_EHA_FILE_TYPE

This table is pre-seeded with file types currently handled by loaders, it should contain six rows and the pre-seeded values are mentioned in the following table:

Table A-2 W_EHA_FILE_TYPE

FILE_TYPE_CODE	FILE_TYPE_NAME	FILE_TYPE_DESC	FILE_TYPE_VERSION
VCF	Variant Call Format	File containing variant information including snps, inserts and deletions.	4.1
MAF	Mutation Annotation Format	Mutation Annotation Format containing snps, inserts, and deletions.	2.0
MAF	Mutation Annotation Format	Mutation Annotation Format containing snps, inserts, and deletions.	2.1
MAF	Mutation Annotation Format	Mutation Annotation Format containing snps, inserts, and deletions.	2.2
Tab-delim Expression	Tab delimited Expression file	Gene Expression tab delimited file format containing probe hybridization results, 3 values per hybridization: Intensity, Call, P-value.	A
CGI masterVar	Complete Genomics MasterVar	Master Variation file from Complete Genomics containing snps, inserts, deletions, and no-call information.	2.0
TCGA RNA SEQ EXON	TCGA RNA SEQ EXON	TCGA RNA Seq tab delimited file format for exon information.	3.1.4.0
Genome_Wide_SNP_6	Affymetrix Genome-Wide Human SNP Array 6.0	This file represents the TCGA data format for Affymetrix Genome-Wide Human SNP Array 6.0'.	6.0
2-Channel Expression	Agilent TCGA 2-channel Expression analysis file	TCGA''s Agilent platform Gene Expression analysis file format containing gene level results; Log2-transformed sample or control intensity ratios.	A
CGI cnv	Complete Genomics cnv	Copy Number Variation file from Complete Genomics containing cvg , ploidy and score information.	2.0
2-Channel ADF	Agilent TCGA Array Description File	TCGA's Agilent platform G4502A_07_01 ADF file containing the array probe information and corresponding genomic or gene annotation.	A
SIFT	Sorting Tolerant From Intolerant	SIFT predicts whether an amino acid substitution affects protein function.	4.0
PolyPhen	Polymorphism Phenotyping	PolyPhen predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations.	5.0
BAM	Binary Alignmentor Map Format	Binary sequencing alignment file for sequencing runs.	1.4
SAM	Sequence Alignmentor Map Format	Binary sequencing alignment file for sequencing runs.	1.4
gVCF	genome variant call format	A VCF file following VCF 4.1 specifications combines information on variant calls (SNVs and small-indels) with genotype and read depth information for all non-variant positions in the reference.	20120906a

W_EHA_CHROMOSOME

This table is pre-seeded with all the possible chromosome names in a result. The user needs to insert any non-standard chromosome names contained in the results file.

Table A-3 W_EHA_CHROMOSOME

Table Name	Column Name	Description	Values Pre-seeded
W_EHA_CHROMOSOME	CHROMOSOME	Name of the chromosome	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT

W_EHA_CHROM_MAPPING

This table is pre-seeded with multiple alias for each of the chromosome record in W_EHA_CHROMOSOME. For example, CHR1 can also be represented as 1, similarly chrM will have alias like CHRMT, MT, and M.

W_EHA_PREDICTION_CODE

This table is pre-seeded with all the prediction codes for SIFT or PolyPhen annotation loader support

Table A-4 EHA_PREDICTION_CODE

CODE	CODE_TYPE	CODE_NAME
tolerated	SIFT	tolerated
deleterious	SIFT	deleterious
unknown	polyphen	unknown
benign	polyphen	benign
possibly damaging	polyphen	possibly damaging
probably damaging	polyphen	probably damaging

A.2 Populated by User or Loader

W_EHA_DATASOURCE

This table stores information about specimen source and is intended to be used primarily with CDM (one record in W_EHA_DATASOURCE). However, if needed, other databases with specimen information can be linked.

Table A-5 W_EHA_DATASOURCE

Table Name	Column Name	Description	If used together with Oracle Health Sciences Cohort Explorer (OHSCE) Cohort Data Model
W_EHA_DATASOURCE	DATASOURCE_CD	Data source for Specimen	CDM
W_EHA_DATASOURCE	DATASOURCE_NM	Name of datasource for Specimen	Cohort Data Model
W_EHA_DATASOURCE	DATASOURCE_DESC	Description of datasource for specimen	Cohort Data Model
W_EHA_DATASOURCE	SCHEMA_NAME	Name of schema	CDM
W_EHA_DATASOURCE	DB_LINK_NAME	Link to database if needed

This table is populated by reference loaders while loading new versions of reference files. Each reference loader can populate a version record for a particular version type associated with it.

Table A-6 W_EHA_VERSION

Reference Loader	Version_Type	Description of the File Version	Example VERSION_LABEL values
EMBL Loader	DNA	Ensemble genome reference version specific to the genome build release.	GRCH37.P8 - for embl release 68 files.
Swiss-Prot loader	PROTEIN	Swissprot releases do not have labels assigned to them. However, they have release timestamps. The time stamp of a Uniprot file release is used.	01012012
Pathway loader	PATHWAY	Pathway release files do not have version labels. File release timestamps are used.	03032013
Prediction Loader	POLYPHEN	Polyphen file version and timestamp.	POLY_VER1_22042012
Prediction Loader	SIFT	SIFT file version and timestamp.	SIFT_VER1_22042012
Hugo Loader	HUGO	Hugo does not have a file archive. Use the data the file has been downloaded.	03032013
HGMD Loader	BIOBASE	The timestamp of the HGMD file release is used.	HGMD_04282013
Probe Loader	PROBE	This is a user-specific label. Use a label that describes the target microarray platform.	Affy_Hs_U133+_2.0_GPL570

W_EHA_RSLT_FILE

This table is populated by loaders while loading results.

Table A-7 W_EHA_RSLT_FILE

Table Name	Column Name	Description	If Used Together With Regular Files	If Used Together With SecureFiles
W_EHA_RSLT_FILE	FILE_STORAGE_FLG	E for External, S for SecureFiles	E	S
W_EHA_RSLT_FILE	FILE_PATH	Path to input file	For example, C:/inputfile.txt
W_EHA_RSLT_FILE	VENDOR_NAME	Name of vendor providing file	For example, Affymetrix	For example, Affymetrix
W_EHA_RSLT_FILE	FILE_CONTENT_ID	File identifier utilized by Secure File system	Not used	Generated by SecureFiles
W_EHA_RSLT_FILE	FILE_TYPE_WID	FK to W_EHA_RSLT_FILE_TYPE	Corresponds to WID in RSLT_FILE_TYPE	Corresponds to WID in RSLT_FILE_TYPE

W_EHA_RSLT_FILE_SPEC

This table stores the foreign key to W_EHA_RSLT_FILE and W_EHA_RSLT_SPECIMEN and links a specific file which is loaded to ODB through the loaders to the specimen it belongs to.

W_EHA_RESULT_STUDY

The user should populate study details in this table before loading the results. All imported results fall under the specified study name in the command line argument.

Table A-8 W_EHA_RESULT_STUDY

Table Name	Column Name	Description	Values Pre-seeded
W_EHA_RESULT_STUDY	RESULT_STUDY_NAME	Name of the study	<user-defined values>
W_EHA_RESULT_STUDY	RESULT_STUDY_DESC	Description of the study	<user-defined values>

A.3 Tables or Columns Not Populated Through Loader Scripts

The following table indicates result and reference tables or columns that are currently not being populated.

Table A-9 Unpopulated Tables or Columns

Table Name	Column Name	Description
W_EHA_PROBE	SEQUENCE
W_EHA_PROBE	START_POSITION
W_EHA_RSLT_CNV_X		No loader for this table
W_EHA_PROBE_ALT_LINK		No loader for this table
W_EHA_ADF_COMPOSITE_XREF		Additional reference table
W_EHA_ADF_REPORTER_XREF		Additional reference table
W_EHA_ANATOMICAL_SITE		No loader for this table
W_EHA_HISTOLOGY		No loader for this table
W_EHA_DISEASE_G_VAR_QLFR		Additional qualifier table
W_EHA_GENE_XREF		Additional reference table
W_EHA_QLFR_CATEGORY		One of QC metadata tables
W_EHA_QUALIFIER		One of QC metadata tables
W_EHA_QLFR_TABLE		One of QC metadata tables
W_EHA_QLFR_TRANSLATION		One of QC metadata tables
W_EHA_RSLT_DXP_ANLYS		No loader for this table
W_EHA_RSLT_DXP_ANLYS_MD		No loader for this table
W_EHA_RSLT_DXP_GRP		No loader for this table
W_EHA_RSLT_DXP_GRP_SPEC		No loader for this table
W_EHA_RSLT_FILE_SPEC_QLFR		Additional qualifier table
W_EHA_RSLT_SPEC_QLFR		Additional qualifier table
W_EHA_SOMATIC_VAR_INFO		No loader for this table
W_EHA_SOMATIC_VAR_QLFR		Additional qualifier table
W_EHA_SOMATIC_VAR_XREF		Additional reference table
W_EHA_SOURCE_LIT_REF		No loader for this table
W_EHA_UNIT_OF_MEASURE		One of QC metadata tables
W_EHA_VARIANT_QLFR		Additional variant qualifier table