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A Make2D-DB II DATABASE: version 2.50, built 18-Jul-2006 Dumped on 2006-07-18
The Make2D-DB II Tool
analyte Structure
F-Key
Name
Type
Description
analyteid
serial
PRIMARY KEY
sample.sampleid
sampleid
integer
A trigger inserts sampleID from parent if child has parent (analyteParentID),
Should be "Not NULL", but is not for more flexibility
* Applied Trigger: Trigger_Analyte_sampleIDTracker *
analytepreparation.analytepreparationid
analytepreparationid
integer
description
text
analyte.analyteid
analyteparentid
integer
analyzable.analyzableid
fromanalyzablesource
integer
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
analyte Constraints
Name
Constraint
analyte_check
CHECK ((((fromanalyzablesource IS NULL) AND (analyteparentid IS NULL)) OR ((fromanalyzablesource IS NOT NULL) AND (analyteparentid IS NOT NULL))))
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to analyte
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
analytepreparation Structure
F-Key
Name
Type
Description
analytepreparationid
serial
PRIMARY KEY
preparationprotocol
text
uri
character varying(4096)
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to analytepreparation
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
In the future: with Analyte children referencing an "Analyzable" class (super-class?)
that containis all various "subAnalyzable" (e.g. Gel, LC,..) from which the children are obtained.
Otherwise, use just a simple relational correspondance.
analyzable Structure
F-Key
Name
Type
Description
analyzableid
serial
PRIMARY KEY
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to analyzable
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
author Structure
F-Key
Name
Type
Description
author
character varying(1024)
UNIQUE#1
NOT NULL
reference.referenceid
article
integer
UNIQUE#1
NOT NULL
authorpriority
smallint
NOT NULL
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Permissions which apply to author
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
authorgroup Structure
F-Key
Name
Type
Description
author
character varying(1024)
UNIQUE#1
NOT NULL
reference.referenceid
article
integer
UNIQUE#1
NOT NULL
Article reference could be limited only to e.g. ReferenceLocationSubmission and ReferenceLocationJournal
authorpriority
smallint
NOT NULL
DEFAULT 1
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Permissions which apply to authorgroup
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
authorparent Structure
F-Key
Name
Type
Description
author
character varying(1024)
NOT NULL
reference.referenceid
article
integer
NOT NULL
authorpriority
smallint
NOT NULL
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Permissions which apply to authorparent
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
biologicalprocess Structure
F-Key
Name
Type
Description
entry.ac
ac
character varying(32)
UNIQUE#1
NOT NULL
goid
character varying(32)
UNIQUE#1
NOT NULL
goname
character varying(256)
gosynoymsnames
character varying(1024)
godefinition
character varying(1024)
lastupdate
timestamp without time zone
mappedenzymeclassification
character varying(16)
mappedtransportclassification
character varying(16)
goparents
character varying(32)[]
gochildren
character varying(32)[]
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
biologicalprocess Constraints
Name
Constraint
geneontologyparent_mappedenzymeclassification_check
CHECK (((mappedenzymeclassification)::text ~ '^[0-9](.([0-9]+|-)){3}$'::text))
Permissions which apply to biologicalprocess
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to biosource
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
Biological source can be defined at various levels (for more flexibility).
biosourceinformation Structure
F-Key
Name
Type
Description
biosourceinformationid
serial
PRIMARY KEY
organism.organismid
organismid
integer
NOT NULL
organismstrain
character varying(256)
straindetailsdescription
text
individualscount
character varying(256)
genotype
character varying(16)
developmentalstage
character varying(256)
anatomy
character varying(256)
tissue.tissueid
tissueid
integer
cell
character varying(256)
cellline
character varying(256)
measuredproperties
text
environmet
character varying(256)
treatment
text
phenotype
text
behaviour
text
pathology
text
provider
character varying(256)
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to biosourceinformation
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
biosourcepreparation Structure
F-Key
Name
Type
Description
biosourcepreparationid
serial
PRIMARY KEY
preparationprotocol
text
uri
character varying(4096)
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to biosourcepreparation
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
book Structure
F-Key
Name
Type
Description
bookid
serial
PRIMARY KEY
booktitle
character varying(256)
UNIQUE
NOT NULL
editors
character varying(256)
NOT NULL
publisher
character varying(128)
NOT NULL
city
character varying(64)
NOT NULL
year
smallint
NOT NULL
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
book Constraints
Name
Constraint
book_year_check
CHECK (("year" > 0))
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to book
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
cellularcomponent Structure
F-Key
Name
Type
Description
entry.ac
ac
character varying(32)
UNIQUE#1
NOT NULL
goid
character varying(32)
UNIQUE#1
NOT NULL
goname
character varying(256)
gosynoymsnames
character varying(1024)
godefinition
character varying(1024)
lastupdate
timestamp without time zone
mappedenzymeclassification
character varying(16)
mappedtransportclassification
character varying(16)
goparents
character varying(32)[]
gochildren
character varying(32)[]
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
cellularcomponent Constraints
Name
Constraint
geneontologyparent_mappedenzymeclassification_check
CHECK (((mappedenzymeclassification)::text ~ '^[0-9](.([0-9]+|-)){3}$'::text))
Permissions which apply to cellularcomponent
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
FOREIGN KEY (article, unpublished) REFERENCES ReferenceLocationJournal(referenceID, unpublished)
-> but not defined as UNIQUE in ReferenceLocationJournal
citer Structure
F-Key
Name
Type
Description
author
character varying(1024)
UNIQUE#1
NOT NULL
referencelocationjournal.referenceid
article
integer
UNIQUE#1
NOT NULL
authorpriority
smallint
NOT NULL
unpublished
boolean
NOT NULL
DEFAULT true
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
citer Constraints
Name
Constraint
citer_unpublished_check
CHECK ((unpublished = true))
Permissions which apply to citer
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
commententry2d Structure
F-Key
Name
Type
Description
entry.ac
ac
character varying(32)
commenttopic.commenttopicid
commenttopicid
integer
commentfreetext
text
NOT NULL
geldimension
smallint
DEFAULT 2
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
commententry2d Constraints
Name
Constraint
commententry2d_geldimension_check
CHECK (((geldimension = 1) OR (geldimension = 2)))
Permissions which apply to commententry2d
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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Index -
Schema core
commententryfreetext Structure
F-Key
Name
Type
Description
entry.ac
ac
character varying(32)
commenttopic.commenttopicid
commenttopicid
integer
commentfreetext
text
NOT NULL
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Permissions which apply to commententryfreetext
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
commententryparent Structure
F-Key
Name
Type
Description
entry.ac
ac
character varying(32)
commenttopic.commenttopicid
commenttopicid
integer
commentfreetext
text
NOT NULL
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Permissions which apply to commententryparent
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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Index -
Schema core
commenttopic Structure
F-Key
Name
Type
Description
commenttopicid
serial
PRIMARY KEY
commenttopicname
character varying(64)
UNIQUE
NOT NULL
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to commenttopic
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
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Index -
Schema core
Contact person/institution is different and distinct than references.
Currently applied (optional) on projects, samples, gel preparations, gel informatics and spot analysis
contact Structure
F-Key
Name
Type
Description
contactid
serial
PRIMARY KEY
name
character varying(256)
NOT NULL
email
character varying(256)
institution
character varying(256)
address
text
remark
text
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to contact
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
ID (0) is the default local interface.
To do: extend to all available interfaces via ExPASy
dynamicremotemake2ddbinterface Structure
F-Key
Name
Type
Description
interfaceid
serial
PRIMARY KEY
interfaceuri
text
UNIQUE#1
NOT NULL
dbnumber
integer
UNIQUE#1
DEFAULT 1
dbname
character varying(128)
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Permissions which apply to dynamicremotemake2ddbinterface
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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Index -
Schema core
The term "Entry" has been prefered more than the term "Protein".
The Entry entity defines an alternative perspective (the widely used protein based view) to represent data.
* Applied Trigger: Trigger_Entry_AC_upperCase *
* Applied Trigger, DEPRECATED!: Trigger_Entry_synchronizeGeneralAndMapAnnotationFlags *
* Applied Trigger: Trigger_Entry_annotationChanged *
* Applied Trigger: Trigger_Entry_showFlagSwitchTrue *
entry Structure
F-Key
Name
Type
Description
ac
character varying(32)
PRIMARY KEY
id
character varying(32)
UNIQUE
NOT NULL
entryclass
character varying(32)
DEFAULT 'STANDARD'::character varying
identmethod
character varying(16)
DEFAULT '2DG'::character varying
description
text
release.releasenum#1
releasecreation
integer
NOT NULL
DEFAULT 1
release.subrelease#1
subreleasecreation
integer
NOT NULL
genenames
character varying(1024)
keywords
character varying(1024)
organism.organismid
organismid
integer
At the protein level, the annotated organism is not forcibly the same as for the analyzed sample
organismstrain
character varying(256)
entrychecksum
character(16)
showflag
boolean
NOT NULL
DEFAULT true
showflagswitch
boolean
NOT NULL
DEFAULT true
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to entry
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
Corresponds to the SWISS-2DPAGE "IM" (IMage) line.
* Applied Trigger: Trigger_EntryGelImage_showFlagSwitchTrue *
entrygelimage Structure
F-Key
Name
Type
Description
entry.ac
ac
character varying(32)
PRIMARY KEY
gel.gelid
gelid
integer
PRIMARY KEY
showflag
boolean
NOT NULL
DEFAULT true
showflagswitch
boolean
NOT NULL
DEFAULT true
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Permissions which apply to entrygelimage
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
Corresponds to the SWISS-2DPAGE "MT" (MasTer) line [Specific to SWISS-2DPAGE].
* Applied Trigger: Trigger_EntryGelMaster_showFlagSwitchTrue *
entrygelmaster Structure
F-Key
Name
Type
Description
entry.ac
ac
character varying(32)
PRIMARY KEY
gel.gelid
gelid
integer
PRIMARY KEY
showflag
boolean
NOT NULL
DEFAULT true
showflagswitch
boolean
NOT NULL
DEFAULT true
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Permissions which apply to entrygelmaster
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
This table content is not used *for the moment* by the entry views! (to do: Entry.geneNames dynamically constructed from this table)
entrygene Structure
F-Key
Name
Type
Description
entry.ac
ac
character varying(32)
UNIQUE#1
NOT NULL
genename.geneid
geneid
integer
UNIQUE#1
NOT NULL
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Permissions which apply to entrygene
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
entrytheoreticalpimw Structure
F-Key
Name
Type
Description
entry.ac
ac
character varying(32)
NOT NULL
modifiedproteindescription
text
theoreticalpi
numeric(4,2)
NOT NULL
theoreticalmw
integer
NOT NULL
algorithmoriginandversion
text
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Permissions which apply to entrytheoreticalpimw
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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♦
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select2d
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Index -
Schema core
entryversion2d Structure
F-Key
Name
Type
Description
entry.ac
ac
character varying(32)
PRIMARY KEY
version
integer
NOT NULL
DEFAULT 1
versiondate
date
NOT NULL
DEFAULT ('now'::text)::date
annotationchanged
boolean
DEFAULT false
annotationchecksum
character(16)
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Permissions which apply to entryversion2d
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
♦
♦
♦
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select2d
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Index -
Schema core
entryversiongeneral Structure
F-Key
Name
Type
Description
entry.ac
ac
character varying(32)
PRIMARY KEY
version
integer
NOT NULL
DEFAULT 1
versiondate
date
NOT NULL
DEFAULT ('now'::text)::date
annotationchanged
boolean
DEFAULT false
annotationchecksum
character(16)
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Permissions which apply to entryversiongeneral
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
* Applied Trigger: Trigger_EntryVersionParent_annotationChanged_true *
entryversionparent Structure
F-Key
Name
Type
Description
entry.ac
ac
character varying(32)
NOT NULL
version
integer
NOT NULL
DEFAULT 1
versiondate
date
NOT NULL
DEFAULT ('now'::text)::date
annotationchanged
boolean
DEFAULT false
annotationchecksum
character(16)
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Permissions which apply to entryversionparent
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
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select2d
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Index -
Schema core
* Applied Trigger: Trigger_EntryXrefDB_annotationChanged *
* Applied Rules: Rule_EntryXrefDB_annotationChanged_ins and _del *
entryxrefdb Structure
F-Key
Name
Type
Description
entry.ac
ac
character varying(32)
UNIQUE#1
NOT NULL
xrefdb.xrefdbcode
xrefdbcode
integer
UNIQUE#1
NOT NULL
xrefprimaryidentifier
character varying(32)
UNIQUE#1
NOT NULL
xrefsecondaryidentifier
character varying(1024)
xreftertiaryidentifier
character varying(1024)
xrefotheridentifiers
character varying(1024)
activated
boolean
DEFAULT true
userstamp
character varying(128)
DEFAULT "current_user"()
update
timestamp without time zone
DEFAULT now()
Permissions which apply to entryxrefdb
User
Select
Insert
Update
Delete
Reference
Rule
Trigger
mostaguir
♦
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select2d
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Index -
Schema core
* Applied Trigger: Trigger_EntryXrefDB_no_dynamic_redundancy *