A Make2D-DB II DATABASE: version 2.50, built 18-Jul-2006

Dumped on 2006-07-18

The Make2D-DB II Tool

Index of database structure for schema: core 

Table: analyte

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
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Index - Schema core

Table: analytepreparation

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
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Index - Schema core

Table: analyzable

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
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mostaguir
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Index - Schema core

Table: author

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
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Update
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Reference
Rule
Trigger
mostaguir
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select2d
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Index - Schema core

Table: authorgroup

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
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Reference
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mostaguir
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Index - Schema core

Table: authorparent

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
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Reference
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mostaguir
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select2d
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Index - Schema core

Table: biologicalprocess

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
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Index - Schema core

Table: biosource

biosource Structure
F-Key Name Type Description
biosourceid serial PRIMARY KEY
studygroup.studygroupid studygroupid integer
biosourceinformation.biosourceinformationid biosourceinformationid integer NOT NULL
biosourcepreparation.biosourcepreparationid biosourcepreparationid integer NOT NULL
description 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 biosource
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Index - Schema core

Table: biosourceinformation

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
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Index - Schema core

Table: biosourcepreparation

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
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mostaguir
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Index - Schema core

Table: book

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
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Index - Schema core

Table: cellularcomponent

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
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mostaguir
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Index - Schema core

Table: citer

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
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Index - Schema core

Table: commententry2d

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
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Index - Schema core

Table: commententryfreetext

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
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Index - Schema core

Table: commententryparent

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
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Index - Schema core

Table: commenttopic

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
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Index - Schema core

Table: contact

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
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Index - Schema core

Table: dynamicremotemake2ddbinterface

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
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Index - Schema core

Table: entry

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
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mostaguir
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Index - Schema core

Table: entrygelimage

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
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mostaguir
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Index - Schema core

Table: entrygelmaster

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
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Index - Schema core

Table: entrygene

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
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Index - Schema core

Table: entrytheoreticalpimw

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
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Index - Schema core

Table: entryversion2d

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
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Index - Schema core

Table: entryversiongeneral

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
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Index - Schema core

Table: entryversionparent

* 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
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Index - Schema core

Table: entryxrefdb

* 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)