| Oracle® Health Sciences Omics Data Bank Programmer's Guide Release 3.0.2.1 E35680-12 |
|
|
PDF · Mobi · ePub |
| Oracle® Health Sciences Omics Data Bank Programmer's Guide Release 3.0.2.1 E35680-12 |
|
|
PDF · Mobi · ePub |
The appendix contains the following topics:
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.
| 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 masterVarFootref 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 loaderFoot 1 |
|
2-CHNL_GENE_EXPRESSION |
Gene expression results from 2-channel gene expression analysis |
Dual channel loader |
Footnote 1 CGI masterVar loader is temporarily removed from ODB 3.0 and will be available in the next release.
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:
| FILE_TYPE_CODE | FILE_TYPE_NAME | FILE_TYPE_DESC | FILE_TYPE_VERSION |
|---|---|---|---|
|
VCF |
Variant Call Format |
File containing variant information including SNPs, insertions, and deletions. |
4.1 |
|
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, insertions, deletions, and no-call information. |
2.0 |
|
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 |
Sequencing alignment file for sequencing runs. |
1.4 |
|
SAM |
Sequence Alignmentor Map Format |
Sequencing alignment file for sequencing runs. |
1.4 |
|
TCGA RNA SEQ EXON |
TCGA RNA SEQ EXON |
TCGA RNA Seq tab delimited file format for exon information. |
3.1.4.0 |
|
CNV_SEG |
CNV .seg file |
Segmented data file format is the output of the Circular Binary Segmentation algorithm (Olshen et al., 2004) |
1.0 |
|
2-ChannelExpression |
Agilent TCGA 2-channelExpression 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 ArrayDescription File |
TCGA's Agilent platform G4502A_07_01 ADF file containing the array probe information and corresponding genomic or gene annotation. |
A |
|
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 |
|
COSMIC Coding Mutations, tab-delimited |
COSMIC Coding Mutations, tab-delimited |
COSMIC export file CosmicCompleteExport_vXX_<<date>>.tsv.gz |
1.0 |
|
COSMIC Non-coding Mutations, comma-separated |
COSMIC Non-coding Mutations, comma-separated |
COSMIC export file CosmicNCV_vXX_<<date>>.csv.gz |
1.0 |
This table is pre-seeded with all the possible chromosome names. The user needs to insert any non-standard chromosome names contained in the results files.
| 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 |
This table is pre-seeded with multiple aliases 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.
This table is pre-seeded with all the somatic status codes currently present in the VCF file. The W_EHA_RSLT_SEQUENCING table has the foreign key to this table through SOMATIC_STATUS_WID.
Table A-4 W_EHA SOMATIC STATUS
| SOMATIC STATUS_CODE | SOMATIC_STATUS |
|---|---|
|
0 |
Wildtype |
|
1 |
Germline |
|
2 |
Somatic |
|
3 |
LOH |
|
4 |
Post-transcriptional modification |
|
5 |
Unknown |
This table is pre-seeded with all the prediction codes for SIFT/PolyPhen annotation loader supports.
Table A-5 W_EHA_PREDICTION_CODE
| CODE | CODE_TYPE |
|---|---|
|
tolerated |
SIFT |
|
deleterious |
SIFT |
|
unknown |
polyphen |
|
benign |
polyphen |
|
possibly damaging |
polyphen |
|
probably damaging |
polyphen |
This table is used to store a version label for all reference datatypes loaded in ODB. Version types are inserted during individual reference loads. The only data pre-seeded here is a version label, 'VERSION 3.9', with version type as 'GENETIC_CODE' used by the codon translation reference.
This table is used to store the name of the NCBI translation table for a set of genetic codon translations to amino acids. For each translation set the table stores the descriptive code name, abbreviation of the name, FK to the curation source version, curation src version type, and the external ID for the translations.
| GEN_CODE_NAME | GEN_CODE_ABBR | CURATION_SOURCE | EXTERNAL_ID |
|---|---|---|---|
|
Standard |
SGC0 |
GENETIC_CODE |
1 |
|
Euplotid Nuclear |
SGC9 |
GENETIC_CODE |
10 |
|
Bacterial, Archaeal and Plant Plastid |
Bacterial, Archaeal and Plant Plastid |
GENETIC_CODE |
11 |
|
Alternative Yeast Nuclear |
Alternative Yeast Nuclear |
GENETIC_CODE |
12 |
|
Ascidian Mitochondrial |
Ascidian Mitochondrial |
GENETIC_CODE |
13 |
|
Alternative Flatworm Mitochondrial |
Alternative Flatworm Mitochondrial |
GENETIC_CODE |
14 |
|
Blepharisma Macronuclear |
Blepharisma Macronuclear |
GENETIC_CODE |
15 |
|
Chlorophycean Mitochondrial |
Chlorophycean Mitochondrial |
GENETIC_CODE |
16 |
|
Vertebrate Mitochondrial |
SGC1 |
GENETIC_CODE |
2 |
|
Trematode Mitochondrial |
Trematode Mitochondrial |
GENETIC_CODE |
21 |
|
Scenedesmus obliquus Mitochondrial |
Scenedesmus obliquus Mitochondrial |
GENETIC_CODE |
22 |
|
Thraustochytrium Mitochondrial |
Thraustochytrium Mitochondrial |
GENETIC_CODE |
23 |
|
Pterobranchia Mitochondrial |
Pterobranchia Mitochondrial |
GENETIC_CODE |
24 |
|
Yeast Mitochondrial |
SGC2 |
GENETIC_CODE |
3 |
|
Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma |
SGC3 |
GENETIC_CODE |
4 |
|
Invertebrate Mitochondrial |
SGC4 |
GENETIC_CODE |
5 |
|
Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear |
SGC5 |
GENETIC_CODE |
6 |
|
Echinoderm Mitochondrial; Flatworm Mitochondrial |
SGC8 |
GENETIC_CODE |
9 |
This table is pre-seeded with linkage of every triplet codon with the corresponding Amino Acid for all listed 18 gene code translations in the W_EHA_GEN_CODE table. Initiation codon indicators are also seeded for initiation codons.
Table A-7 W_EHA_GEN_CODE_TABLE (*Initiation codon is populated where given in a separate column)
| GEN_CODE_WID | List of CODON value | AA1+(IS_INITIATION)* for each CODON value |
|---|---|---|
|
1 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
K,N,K,N,T,T,T,T,R,S,R,S,I,I,M(M),I,Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,L(M),L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V,V,*,Y,*,Y,S,S,S,S,*,C,W,C,L,F,L(M),F |
|
2 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
K,N,K,N,T,T,T,T,*,S,*,S,M(M),I(M),M(M),I(M),Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,L,L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V(M),V,*,Y,*,Y,S,S,S,S,W,C,W,C,L,F,L,F |
|
3 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
K,N,K,N,T,T,T,T,R,S,R,S,M(M),I,M(M),I,Q,H,Q,H,P,P,P,P,R,R,R,R,T,T,T,T,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V,V,*,Y,*,Y,S,S,S,S,W,C,W,C,L,F,L,F |
|
4 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
K,N,K,N,T,T,T,T,R,S,R,S,I(M),I(M),M(M),I(M),Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,L(M),L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V(M),V,*,Y,*,Y,S,S,S,S,W,C,W,C,L(M),F,L(M),F |
|
5 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
K,N,K,N,T,T,T,T,S,S,S,S,M(M),I(M),M(M),I(M),Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,L,L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V(M),V,*,Y,*,Y,S,S,S,S,W,C,W,C,L,F,L(M),F |
|
6 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
K,N,K,N,T,T,T,T,R,S,R,S,I,I,M(M),I,Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,L,L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V,V,Q,Y,Q,Y,S,S,S,S,*,C,W,C,L,F,L,F |
|
9 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
N,N,K,N,T,T,T,T,S,S,S,S,I,I,M(M),I,Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,L,L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V(M),V,*,Y,*,Y,S,S,S,S,W,C,W,C,L,F,L,F |
|
10 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
K,N,K,N,T,T,T,T,R,S,R,S,I,I,M(M),I,Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,L,L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V,V,*,Y,*,Y,S,S,S,S,C,C,W,C,L,F,L,F |
|
11 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
K,N,K,N,T,T,T,T,R,S,R,S,I(M),I(M),M(M),I(M),Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,L(M),L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V(M),V,*,Y,*,Y,S,S,S,S,*,C,W,C,L,F,L(M),F |
|
12 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
K,N,K,N,T,T,T,T,R,S,R,S,I,I,M(M),I,Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,S(M),L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V,V,*,Y,*,Y,S,S,S,S,*,C,W,C,L,F,L,F |
|
13 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
K,N,K,N,T,T,T,T,G,S,G,S,M(M),I,M(M),I,Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,L,L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V(M),V,*,Y,*,Y,S,S,S,S,W,C,W,C,L,F,L(M),F |
|
14 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
N,N,K,N,T,T,T,T,S,S,S,S,I,I,M(M),I,Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,L,L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V,V,Y,Y,*,Y,S,S,S,S,W,C,W,C,L,F,L,F |
|
15 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
K,N,K,N,T,T,T,T,R,S,R,S,I,I,M(M),I,Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,L,L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V,V,*,Y,Q,Y,S,S,S,S,*,C,W,C,L,F,L,F |
|
16 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
K,N,K,N,T,T,T,T,R,S,R,S,I,I,M(M),I,Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,L,L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V,V,*,Y,L,Y,S,S,S,S,*,C,W,C,L,F,L,F |
|
21 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
N,N,K,N,T,T,T,T,S,S,S,S,M,I,M(M),I,Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,L,L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V(M),V,*,Y,*,Y,S,S,S,S,W,C,W,C,L,F,L,F |
|
22 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
K,N,K,N,T,T,T,T,R,S,R,S,I,I,M(M),I,Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,L,L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V,V,*,Y,L,Y,*,S,S,S,*,C,W,C,L,F,L,F |
|
23 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
K,N,K,N,T,T,T,T,R,S,R,S,I,I,M(M),I(M),Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,L,L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V(M),V,*,Y,*,Y,S,S,S,S,*,C,W,C,*,F,L,F |
|
24 |
AAA,AAC,AAG,AAT,ACA,ACC,ACG,ACT,AGA,AGC,AGG,AGT,ATA,ATC,ATG,ATT,CAA,CAC,CAG,CAT,CCA,CCC,CCG,CCT,CGA,CGC,CGG,CGT,CTA,CTC,CTG,CTT,GAA,GAC,GAG,GAT,GCA,GCC,GCG,GCT,GGA,GGC,GGG,GGT,GTA,GTC,GTG,GTT,TAA,TAC,TAG,TAT,TCA,TCC,TCG,TCT,TGA,TGC,TGG,TGT,TTA,TTC,TTG,TTT |
K,N,K,N,T,T,T,T,S,S,K,S,I,I,M(M),I,Q,H,Q,H,P,P,P,P,R,R,R,R,L,L,L(M),L,E,D,E,D,A,A,A,A,G,G,G,G,V,V,V(M),V,*,Y,*,Y,S,S,S,S,W,C,W,C,L,F,L(M),F |
This table is used to map how GEN_CODE tables are used with each species and chromosome in ODB.
This table is used to record each installation or patch upgrade of the ODB schema. The current release_version seeded is '3.0.0.1'.
This table stores information about specimen source and is intended to be used primarily with CDM (four records in W_EHA_DATASOURCE). However, if needed, other databases with specimen information can be linked.
| Table Name | Description | Value Pre-seeded |
|---|---|---|
|
DATASOURCE_CD |
Data source for Specimen |
CDM, CDM_PATIENT, CDM_SUBJECT, CDM_BOTH |
|
DATASOURCE_NM |
Name of datasource for Specimen |
CDM, CDM_PATIENT, CDM_SUBJECT, CDM_BOTH |
|
DATASOURCE_DESC |
Description of datasource for specimen |
Cohort Data Model Patient Specimens (first 2 recs), Cohort Data Model Subject Specimens, Cohort Data Model Patient and Subject Specimens |
|
SCHEMA_NAME |
Name of schema |
<<user input parameter at install time>> (for example, 'CDM') |
|
DB_LINK_NAME |
Link to database if needed |
- |
|
VALIDATION_PROC |
Stored procedure used to validate specimens |
ODB_UTIL.VALIDATE_CDM_PATIENT_SPEC, ODB_UTIL.VALIDATE_CDM_PATIENT_SPEC, ODB_UTIL.VALIDATE_CDM_SUBJECT_SPEC, ODB_UTIL.VALIDATE_CDM_BOTH_SPEC |
| 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 |
|
Cosmic Loader |
COSMIC |
Intended to store Cosmic release upgrade version number |
COSMIC.V67 |
|
Genetic Code (seeded) |
GENETIC_CODE |
NCBI translation tables release version |
VERSION 3.9 |
This table is populated with input file identity specific annotations by loaders while loading result data.
| Column Name | Description | If Used Together With Regular Files |
|---|---|---|
|
FILE_URI |
Globally Unique identification tag used to differentiate files named similarly |
User input; otherwise creates and updates with unique string: 'fille://trc/' + etl_proc_wid + '<<input file name>>' |
|
FILE_TYPE_WID |
FK to W_EHA_ RSLT_FILE_TYPE |
Corresponds to WID in RSLT_ FILE_TYPE |
|
FILE_NAME |
Name of file |
User input |
This table is populated with information on loading of files by loaders while loading result data.
| Column Name | Description | If Used Together With Regular Files | If Used Together With SecureFiles |
|---|---|---|---|
|
FILE_WID |
Foreign key to the FILE record |
Corresponds to ROW_WID of W_EHA_FILE |
- |
|
FILE_LOAD_SEQ_NUM |
Sequence of each file that is loaded consecutive times |
Autonumber |
Autonumber |
|
FILE_PATH |
Path to input file |
For example, C:/inputfile.txt |
- |
|
SPECIMEN_VENDOR_NUMBER |
Vendor identifier in linked specimen datasource database |
User input parameter |
- |
|
VERSION_WID |
Foreign key to Version |
Corresponds to ROW_WID of W_EHA_VERSION |
- |
|
FILE_STORAGE_ FLG |
E for External, S for SecureFiles |
E |
S |
|
FILE_SIZE |
File size in bytes |
- |
- |
|
LOADER_NAME |
Name of loader package that generates the load |
For example, 'ODB_RSLT_CNV_UTIL' for CNV loader |
- |
|
DIRECTORY_NAME |
Oracle Directory used for copies of file |
For example, ODB_RES_DIR |
- |
|
DBFS_STORE |
DBFS store name if file is copied to DBFS |
- |
USER input name of file system |
This table is populated with metadata information for each file load.
Table A-13 W_EHA _FILE_LOAD_QLFR
| Column Name | Description | If Used Together With Regular Files | If Used Together With SecureFiles |
|---|---|---|---|
|
FILE_LOAD_WID |
Foreign key to the FILE_LOAD record |
Corresponds to ROW_WID of W_EHA_FILE_LOAD |
- |
|
QUALIFIER_WID |
Foreign key to qualifier table |
Corresponds to ROW_WID of W_EHA_QUALIFIER |
- |
|
QLFR_CHAR_VALUE |
Qualifier character attribute value |
User input qualifier or file qualifier character values |
- |
This table stores foreign keys to W_EHA_FILE and W_EHA_RSLT_ SPECIMEN and links a specific file which is loaded to ODB via the loaders to the specimen that has results in the file.
You must populate study details in this table before loading the results. All imported results fall under the specified study name in the command line argument.
Additionally, you can merge Study records stored in OHCE's W_EHA_STUDY_D table by running a function call from a package in OHCE; COHORT_PROTOCOL_UTIL.Process_Protocols().
The following table indicates result and reference tables or columns that are currently not being populated.
| Table Name | Column Name | Description |
|---|---|---|
|
W_EHA_RSLT_CNV_X |
- |
Copy Number Variation additional data table. |
|
W_EHA_PROBE_ALT_LINK |
- |
Table to store alternative links between probes and genes, for example, if a single probe is linked to multiple genes. |
|
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_FILE_QLFR |
- |
Additional qualifier table |
|
W_EHA_REF_SAMPLE_XREF |
- |
Additional reference table |
|
W_EHA_SPEC_EXTERNAL |
- |
Additional table to link to non-OHSCE specimens |
|
W_EHA_VARIANT_FILE |
- |
Used to link all reference variants to the file used to load that variant |
|
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_VARIANT_QLFR |
- |
Additional variant qualifier table |
|
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|
