- github Document reduction issue
- github bio-vcf issue


* GeneNetwork Database

All *Data tables are large

** User access

GN1 uses access table and GN2 uses user table.

** AvgMethod 

Probesetfreeze refers to AvgMethod

** BXDSnPosition

Snp table (all snps)

Mapping in GN1 shows snps when  you select a chromosome.

** CaseAttribute(XRef)

Metadata

** CeleralINFO_mm6

?

** Chr_Length

Default mm9, column for mm8

** Dataset_mbat

Menu for BXD (linkouts)

** DatasetMapInvestigator

Arthur?

** DataSets

Information/metadata

** DatasetStatus

Arthur private/public

** DBList and DBType

Hooked in API (URL encoding)

** Docs

GN2 only (see menu bar)

** Ensembl* 

Probe information

(will be deprecated)

** Genbank

Linkout and not important

** GeneCategory

Not important. GeneWiki notes function classification.

Deprecate.

** GeneChip

** GeneIDXRef

Interspecies gene comparison

** GeneList

Track info

** Genlist_rn3(3)

Rat list

** GeneMap_cuiyan

Link outs

** GeneRIF

Wiki info (nightly updated from NCBI)

XRef should be foreign keys

** Geno

SNP or marker info

** GenoCode

Belongs to someone else

** GenoData

Allele info

** GenoFreeze

Big menu (Freeze refers to menu)

** GenoSE

SE standard err, not used

** GenoXREF

Very important. Key links between Geno, GenoData

** GORef

GO terms

** H2

Heritability for probeset(?)

** Homologene

Homology, not used much

** InbredSet

Group in menu

** Indelall, SnpAll, SnpPattern, SnpSource

Indel Snp browser (variant browser Gn1)

** Info*

Infra system PhP 

Data Info button 

Infosystem users has separate entries

Also Investigators, User, Organizations, 

** LCorrRamin3 

Lit. Correlations Prof. Ramin

** Login

GN2 login info

** MachineAccessLog

Old

** MappingMethod

GN1

** News

GN2

** NStrain

pheno           publishfreeze (menu)
                       xref (keys)
                          xref links to publish (pubmed), phenotype, pubishdata
geno            genofreeze
                       xref (keys)
                          xref links to publish (pubmed), genotype, genodata
probeset/expr.  probesetfreeze
                       xref (keys)
                          xref links to publish (pubmed), probeset, probesetdata
probe/expr.  probefreeze
                       xref (keys)
                          xref links to publish (pubmed), probe, probedata

Each dataset has 3 values (real value (1), number of samples (2), stderr (3))

NStrain = number of phenotype samples

ProbesetFreeze contains all data, incl. metabolomic.

** Probe

Probedata - main molecular data. Probesets, metabolome, 

** Publication and publishdata (all pheno)

Phenotype pubs

** QuickSearch

No longer used

** role

empty

** Sample*

No longer used

** Species & Strain (should be sample)

Menu

** InbredSet 

Menu

** TableComments

Metadata on DB

** Temp*

User upload data

** Tissue

Menu - 3rd level

** TissueP*

Correlation tables

** User collection

User selection - retained

** UserPrivilege

** Vlookup