This is a description of the GeneNetwork database extracted from the tables TableFieldAnnotation and TableComments.
Vlookup
It's been used by Arthur for annotation updates.
alias
AlignID
assembly
AvgMethodId
BlatSeq
CASnumber
cdsEnd
cdsStart
ChEBIID
ChEMBLID
ChemSpiderID
Chr
DatasetId
description
ECnumber
exonCount
exonEnds
exonStarts
FullDescription
GeneChipId
GeneId
GNAccesionId
HMDBID
Id
InbredSetId
InfoFileId
InfoPageName
KEGGID
kgID
Mb
MolecularWeight
Name
NMID
NugowikiID
Position
ProbesetBlatMbend
ProbesetBlatMbstart
ProteinID
PubChemID
SnpName
SpeciesId
Strand
Symbol
TissueId
TxEnd
TxStart
UNIIID
VLBlatSeq
VLProbeSetId
useropenids
TO BE IMPLEMENTED (maybe). Table to link to OpenID. Probably not needed.
openidurl
userid
usercollection
GN2 user collection of traits.
changedtimestamp
createdtimestamp
id
members
name
user
UserPrivilege
Used to define if an Assay data set (old "ProbeSetFreeze") can be opened and downloaded.
downloadresultpriv
ProbeSetFreezeId
UserId
USER
GN2 only.
Comment on User type and password.
This table has 47 users in GN2 as of Mar 2016.
active
confirmed
createtime
disable
emailaddress
fullname
grpName
id
lastlogin
name
organization
password
this is a hash value of user's password
privilege
registrationinfo
superuser
userip
TissueProbeSetData
These 'Tissue' tables are used by the Tissue Correlation tool in GN1. Not implemented yet in GN2. Mainly Illumina Mouse version 6.1 data.
Id
TissueID
value
TissueProbeFreeze
These 'Tissue' tables are used by the Tissue Correlation tool in GN1. Not implemented yet in GN2.
ChipId
CreateTime
FullName
Id
InbredSetId
Name
ShortName
StrainId
Tissue
(RWW Nov 2007): A small table that may be used to build pull-down menus in GN1 and GN2. This table contains simple one to three word terms describing the tissue, cell, organ, or other biological material used in the microarray experiment. This table is used in conjunction with the FIND RECORDS "Type" field.
As of Nov 2007 this table contained only 15 rows:
As of Mar 2016 this table contains 158 rows.
Whole Brain
Cerebellum
Hematopoietic Cells
Liver
etc.
How is this table used? Probably to create menu fields. Talk with Chris Mungall and colleagues about controlled vocabulary for APIs.
BIRNlexID
Need to get official IDs for tissues, cells, etc.
BIRNlexName
Need to get official IDs for tissues, cells, etc.
Id
Incremented integer uniquely identifies the record.
Name
Name of the biological material used in the experiment.
ShortName
TissueId
TissueName
temporary
This is probably the content of the user's collection. Lost at end of user's session.
GeneID
HomoloGene
OMIM
OtherGeneID
Symbol
taxid
TempData
Id
NStrain
SE
StrainId
value
Temp
createtime
DataId
description
Id
InbredSetId
IP
Name
StrainXRef
RENAME something like "SubjectXRef". This table links the information in the Strain table with InbredSet and provides order for the strains in the mapping population.
InbredSetId
Foreign key to InbredSet:Id The Id of the mapping population in the InbredSet table.
OrderId
Order of the strains in the Genotype file or mapping population, follows the pattern 10, 20 rather than 1,2.
PedigreeStatus
StrainId
Foreign key to Strain:Id The Id of the mapping population strain in Strain table.
Usedformapping
Strain
RENAME "SubjectDescription" . This table to keep track of case/subject identifiers (cases or F2 or strains). But we have the problem that there may be multiple observation per subject or the time series data for one case, (multiple ages for one strain, etc). Generic sample/case identifiers here.
Contains 14,000 rows as of March 2016. We really need a new table "ObservationOfSubject" (RWW 2016)
Apurva would like to extend this table to include "DateOfBirth" and "BatchNumber".
Alias
Id
GN internal identifier for the strain
Name
official strain name/symbol
Name2
SpeciesId
Foreign key to Species:Id species of strain
Symbol
short strain symbol used in graphs and tables
Species
Contains the internal Ids and names for various species.
Id
internal GeneNetwork species identifier
Name
the common name of the species
Source
This table contains one record for every SNP dataset represented in the Snp table.
[Created by Robert Crowell, August 18, 2005. Annotation of table, Robert Crowell, Aug 22, 2005.]
<b>See also:</b>
<a href="/cgi-bin/beta/schema.py#Snp">Snp</a>
DateAdded
date when the data source was added to our database
DateCreated
date when the data source was produced
Name
name of this source
SourceId
internal GeneNetwork identifier for the source dataset
SNPperlegen
DEPRECATED: use the Snp table instead.
The complete perlegen dataset. This table is deprecated.
Created by Robert Crowell, 2005.
Id
mb
AJ
AKRJ
BALBCBYJ
BTBRTTFJ
C3HHEJ
C57BL6J
DBA2J
FVBNJ
KKH1J
MOLFEIJ
NODLTJ
NZWLACJ
PWDPHJ
WSBEIJ
129S1SVIMJ
chr
B6D2
B6AJ
D2AJ
old
old=1 SNPs belong to the Flint dataset (chr2 only)
source
nes
nc
length
5flanking
5assay
observed
3assay
3flanking
sequence
strand
score
fraction
majorcount
minorcount
ncount
statestring
CASTEIJ
ScoreBlat
chrBlat
MbBlat
SNPmpd
The complete MPD dataset. This table is soon to be deprecated.
id
chr
mb
class
function
129S1SvImJ
129X1SvJ
AHeJ
AJ
AKRJ
ALRLtJ
ALSLtJ
D2Hc0H2dH2T18coSnJ
BALBcByJ
BALBcJ
BPH2J
BPN3J
BTBRTtfJ
BUBBnJ
C3HHeJ
C3HeBFeJ
C57BL10J
C57BL6J
C57BRcdJ
C57LJ
C58J
CASTEiJ
CBACaJ
CBAJ
CEJ
CZECHIIEiJ
DBA1J
DBA2J
FVBNJ
ILnJ
KKHlJ
LGJ
LPJ
MAMyJ
MRLMpJ
NODLtJ
NONLtJ
NZBBlNJ
NZWLacJ
PERAEiJ
PLJ
RFJ
RIIISJ
SBLeJ
SEAGnJ
SJLJ
SMJ
SPRETEiJ
STbJ
SWRJ
WSBEiJ
ZALENDEEiJ
source
ss
ssorientation
rs
nmappings
snpID
insertions
B6D2
B6AJ
D2AJ
SnpPattern
Data used by SNP Browser. Variant browser needs to be redone from scratch using a decent architecture. 80 million SNPs in this table from sequence data of 2011 (Keane et al. Nature) but imputed to many other strains.