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- 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
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