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1 537 aaronmk
-- Existing tables
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3 596 aaronmk
CREATE TABLE role
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(
5
  role_id int(11) NOT NULL AUTO_INCREMENT,
6
  rolecode character varying(30) NOT NULL,
7
  roledescription character varying(200),
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  CONSTRAINT role_pkey PRIMARY KEY (role_id )
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);
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11
CREATE TABLE reference
12
(
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  reference_id int(11) NOT NULL AUTO_INCREMENT,
14
  shortname character varying(250),
15
  fulltext__ text,
16
  referencetype character varying(250)
17
);
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19
CREATE TABLE party
20
(
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  party_id int(11) NOT NULL AUTO_INCREMENT,
22
  salutation character varying(20),
23
  givenname character varying(50),
24
  middlename character varying(50),
25
  surname character varying(50),
26
  organizationname character varying(100)
27
);
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CREATE TABLE plantname
30
(
31
  plantname_id int(11) NOT NULL AUTO_INCREMENT,
32
  plantname character varying(255) NOT NULL,
33
  reference_id int(11),
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  dateentered timestamp NULL DEFAULT now(),
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  CONSTRAINT plantname_pkey PRIMARY KEY (plantname_id ),
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  CONSTRAINT plantname_reference_id FOREIGN KEY (reference_id)
37
      REFERENCES reference (reference_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE
39
);
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CREATE TABLE plantconcept
42
(
43
  plantconcept_id int(11) NOT NULL AUTO_INCREMENT,
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  plantname_id int(11) NOT NULL,
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  reference_id int(11),
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  plantcode character varying(23),
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  plantdescription text,
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  d_obscount int(11),
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  d_currentaccepted int(1),
50
  accessioncode character varying(255),
51
  CONSTRAINT plantconcept_pkey PRIMARY KEY (plantconcept_id ),
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  CONSTRAINT plantconcept_plantname_id FOREIGN KEY (plantname_id)
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      REFERENCES plantname (plantname_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
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  CONSTRAINT plantconcept_reference_id FOREIGN KEY (reference_id)
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      REFERENCES reference (reference_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE
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);
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CREATE TABLE stratummethod
61
(
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  stratummethod_id int(11) NOT NULL AUTO_INCREMENT,
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  reference_id int(11),
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  stratummethodname character varying(30) NOT NULL,
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  stratummethoddescription text,
66
  stratumassignment character varying(50),
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  accessioncode character varying(255),
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  CONSTRAINT stratummethod_pkey PRIMARY KEY (stratummethod_id ),
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  CONSTRAINT stratummethod_reference_id FOREIGN KEY (reference_id)
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      REFERENCES reference (reference_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE
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);
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CREATE TABLE stratumtype
75
(
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  stratumtype_id int(11) NOT NULL AUTO_INCREMENT,
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  stratummethod_id int(11) NOT NULL,
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  stratumindex character varying(10),
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  stratumname character varying(30),
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  stratumdescription text,
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  CONSTRAINT stratumtype_pkey PRIMARY KEY (stratumtype_id ),
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  CONSTRAINT stratumtype_stratummethod_id FOREIGN KEY (stratummethod_id)
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      REFERENCES stratummethod (stratummethod_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE
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);
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CREATE TABLE namedplace
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(
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  namedplace_id int(11) NOT NULL AUTO_INCREMENT,
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  placesystem character varying(50),
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  placename character varying(100) NOT NULL,
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  placedescription text,
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  placecode character varying(15),
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  owner character varying(100),
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  reference_id int(11),
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  d_obscount int(11),
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  accessioncode character varying(255),
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  CONSTRAINT namedplace_pkey PRIMARY KEY (namedplace_id ),
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  CONSTRAINT namedplace_reference_id FOREIGN KEY (reference_id)
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      REFERENCES reference (reference_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
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  CONSTRAINT namedplace_keys UNIQUE (placesystem , placename )
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);
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CREATE TABLE locationplace
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(
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  locationplace_id int(11) NOT NULL AUTO_INCREMENT,
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  location_id int(11) NOT NULL,
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  calculated int(1),
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  namedplace_id int(11) NOT NULL,
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  CONSTRAINT locationplace_pkey PRIMARY KEY (locationplace_id ),
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  CONSTRAINT locationplace_location_id FOREIGN KEY (location_id)
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      REFERENCES location (location_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
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  CONSTRAINT locationplace_namedplace_id FOREIGN KEY (namedplace_id)
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      REFERENCES namedplace (namedplace_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
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  CONSTRAINT locationplace_keys UNIQUE (location_id , namedplace_id )
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);
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CREATE TABLE project
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(
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  project_id int(11) NOT NULL AUTO_INCREMENT,
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  projectname character varying(150) NOT NULL,
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  projectdescription text,
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  startdate timestamp NULL,
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  stopdate timestamp NULL,
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  d_obscount int(11),
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  d_lastlocationaddeddate timestamp NULL,
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  accessioncode character varying(255),
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  CONSTRAINT project_pkey PRIMARY KEY (project_id ),
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  CONSTRAINT project_keys UNIQUE (projectname , startdate , stopdate )
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);
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-- New tables
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CREATE TABLE location
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(
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  location_id int(11) NOT NULL AUTO_INCREMENT,
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  authorlocationcode character varying(30),
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  reference_id int(11),
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  parent_id int(11),
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  reallatitude double precision,
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  reallongitude double precision,
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  locationaccuracy double precision,
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  confidentialitystatus int(11) NOT NULL DEFAULT 0,
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  confidentialityreason character varying(200),
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  publiclatitude double precision,
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  publiclongitude double precision,
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  `... (truncated) ...` int(11),
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  accessioncode character varying(255),
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  sublocationxposition double precision,
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  sublocationyposition double precision,
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  namedplace_id int(11),
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  CONSTRAINT location_pkey PRIMARY KEY (location_id ),
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  CONSTRAINT location_namedplace_id FOREIGN KEY (namedplace_id)
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      REFERENCES namedplace (namedplace_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
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  CONSTRAINT location_parent_id FOREIGN KEY (parent_id)
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      REFERENCES location (location_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
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  CONSTRAINT location_reference_id FOREIGN KEY (reference_id)
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      REFERENCES reference (reference_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
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  CONSTRAINT location_keys_code UNIQUE (reference_id , authorlocationcode ),
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  CONSTRAINT location_keys_coords UNIQUE (reference_id , reallatitude , reallongitude ),
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  CONSTRAINT location_keys_subplot_code UNIQUE (parent_id , authorlocationcode ),
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  CONSTRAINT location_keys_subplot_coords UNIQUE (parent_id , sublocationxposition , sublocationyposition )
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);
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CREATE TABLE locationevent -- VegBank's observation table.
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(
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  locationevent_id int(11) NOT NULL AUTO_INCREMENT,
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  previous_id int(11),
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  location_id int(11),
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  project_id int(11),
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  authoreventcode character varying(30),
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  `... (truncated) ...` int(11),
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  accessioncode character varying(255),
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  sourceaccessioncode character varying(100),
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  CONSTRAINT locationevent_pkey PRIMARY KEY (locationevent_id ),
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  CONSTRAINT locationevent_location_id FOREIGN KEY (location_id)
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      REFERENCES location (location_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
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  CONSTRAINT locationevent_project_id FOREIGN KEY (project_id)
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      REFERENCES project (project_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
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  CONSTRAINT locationevent_keys_accessioncode UNIQUE (location_id , project_id , sourceaccessioncode ),
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  CONSTRAINT locationevent_keys_code UNIQUE (location_id , project_id , authoreventcode )
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);
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CREATE TABLE taxonoccurrence -- VegBank's taxonobservation table.
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(
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  taxonoccurrence_id int(11) NOT NULL AUTO_INCREMENT,
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  locationevent_id int(11),
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  authorplantname character varying(255),
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  reference_id int(11),
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  taxoninferencearea double precision,
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  emb_taxonoccurrence int(11),
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  `... (truncated) ...` int(11),
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  accessioncode character varying(255),
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  CONSTRAINT taxonoccurrence_pkey PRIMARY KEY (taxonoccurrence_id ),
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  CONSTRAINT taxonoccurrence_locationevent_id FOREIGN KEY (locationevent_id)
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      REFERENCES locationevent (locationevent_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
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  CONSTRAINT taxonoccurrence_reference_id FOREIGN KEY (reference_id)
207
      REFERENCES reference (reference_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE
209
);
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CREATE TABLE aggregateoccurrence -- VegBank's taxonimportance table.
212
(
213
  aggregateoccurrence_id int(11) NOT NULL AUTO_INCREMENT,
214
  taxonoccurrence_id int(11) NOT NULL,
215 584 aaronmk
  taxonbinmethod_id int(11),
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  cover double precision,
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  basalarea double precision,
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  biomass double precision,
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  inferencearea double precision,
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  stratumbase double precision,
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  stratumheight double precision,
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  emb_aggregateoccurrence int(11),
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  covercode character varying(10),
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  count int(11),
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  accessioncode character varying(255),
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  sourceaccessioncode character varying(100),
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  CONSTRAINT aggregateoccurrence_pkey PRIMARY KEY (aggregateoccurrence_id ),
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  CONSTRAINT aggregateoccurrence_taxonbinmethod_id FOREIGN KEY (taxonbinmethod_id)
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      REFERENCES taxonbinmethod (taxonbinmethod_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
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  CONSTRAINT aggregateoccurrence_taxonoccurrence_id FOREIGN KEY (taxonoccurrence_id)
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      REFERENCES taxonoccurrence (taxonoccurrence_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
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  CONSTRAINT aggregateoccurrence_keys_accessioncode UNIQUE (taxonoccurrence_id , sourceaccessioncode ),
235
  CONSTRAINT aggregateoccurrence_keys_method UNIQUE (taxonoccurrence_id , taxonbinmethod_id )
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);
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CREATE TABLE individualplant -- VegBank's stemcount table.
239
(
240
  individualplant_id int(11) NOT NULL AUTO_INCREMENT,
241
  aggregateoccurrence_id int(11) NOT NULL,
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  overallheight double precision,
243
  overallheightaccuracy double precision,
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  emb_individualplant int(11),
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  authorplantcode character varying(20),
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  accessioncode character varying(255),
247
  stemcount int(11),
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  sourceaccessioncode character varying(100),
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  CONSTRAINT individualplant_pkey PRIMARY KEY (individualplant_id ),
250
  CONSTRAINT individualplant_aggregateoccurrence_id FOREIGN KEY (aggregateoccurrence_id)
251
      REFERENCES aggregateoccurrence (aggregateoccurrence_id) MATCH SIMPLE
252
      ON UPDATE CASCADE ON DELETE CASCADE,
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  CONSTRAINT individualplant_keys_accessioncode UNIQUE (aggregateoccurrence_id , sourceaccessioncode ),
254
  CONSTRAINT individualplant_keys_code UNIQUE (aggregateoccurrence_id , authorplantcode )
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);
256
257
CREATE TABLE stem -- VegBank's stemlocation table.
258
(
259
  stem_id int(11) NOT NULL AUTO_INCREMENT,
260
  individualplant_id int(11) NOT NULL,
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  authorstemcode character varying(20),
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  xposition double precision,
263
  yposition double precision,
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  health character varying(50),
265
  emb_stem int(11),
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  diameter double precision,
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  height double precision,
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  heightaccuracy double precision,
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  age double precision,
270
  accessioncode character varying(255),
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  diameteraccuracy double precision,
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  sourceaccessioncode character varying(100),
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  CONSTRAINT stem_pkey PRIMARY KEY (stem_id ),
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  CONSTRAINT stem_individualplant_id FOREIGN KEY (individualplant_id)
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      REFERENCES individualplant (individualplant_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
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  CONSTRAINT stem_keys_accessioncode UNIQUE (individualplant_id , sourceaccessioncode ),
278
  CONSTRAINT stem_keys_code UNIQUE (individualplant_id , authorstemcode )
279 536 aaronmk
);
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CREATE TABLE specimen -- A herbarium specimen. Contains Darwin Core specimen data.
282
(
283
  specimen_id int(11) NOT NULL AUTO_INCREMENT,
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  reference_id int(11) NOT NULL,
285
  collectioncode_dwc character varying(255),
286
  catalognumber_dwc character varying(255),
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  collectiondate timestamp NULL,
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  museum_id int(11),
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  sourceaccessioncode character varying(100),
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  accessioncode character varying(255),
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  taxonoccurrence_id int(11) NOT NULL,
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  verbatimcollectorname character varying(255),
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  authorspecimencode character varying(20),
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  CONSTRAINT specimen_pkey PRIMARY KEY (specimen_id ),
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  CONSTRAINT specimen_museum_id FOREIGN KEY (museum_id)
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      REFERENCES party (party_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
298
  CONSTRAINT specimen_reference_id_fkey FOREIGN KEY (reference_id)
299
      REFERENCES reference (reference_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
301
  CONSTRAINT specimen_taxonoccurrence_id FOREIGN KEY (taxonoccurrence_id)
302
      REFERENCES taxonoccurrence (taxonoccurrence_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
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  CONSTRAINT specimen_keys_accessioncode UNIQUE (reference_id , collectioncode_dwc , sourceaccessioncode ),
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  CONSTRAINT specimen_keys_catalognumber UNIQUE (reference_id , collectioncode_dwc , catalognumber_dwc ),
306
  CONSTRAINT specimen_keys_code UNIQUE (reference_id , collectioncode_dwc , authorspecimencode )
307 537 aaronmk
);
308
309 544 aaronmk
CREATE TABLE voucher
310
(
311
  voucher_id int(11) NOT NULL AUTO_INCREMENT,
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  taxonoccurrence_id int(11) NOT NULL,
313
  specimen_id int(11) NOT NULL,
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  accessioncode character varying(255),
315
  CONSTRAINT voucher_pkey PRIMARY KEY (voucher_id ),
316
  CONSTRAINT voucher_specimen_id FOREIGN KEY (specimen_id)
317
      REFERENCES specimen (specimen_id) MATCH SIMPLE
318
      ON UPDATE CASCADE ON DELETE CASCADE,
319
  CONSTRAINT voucher_taxonoccurrence_id FOREIGN KEY (taxonoccurrence_id)
320
      REFERENCES taxonoccurrence (taxonoccurrence_id) MATCH SIMPLE
321
      ON UPDATE CASCADE ON DELETE CASCADE,
322
  CONSTRAINT voucher_keys UNIQUE (taxonoccurrence_id , specimen_id )
323
);
324
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CREATE TABLE taxondetermination -- VegBank's taxoninterpretation table.
326
(
327
  taxondetermination_id int(11) NOT NULL AUTO_INCREMENT,
328
  taxonoccurrence_id int(11) NOT NULL,
329
  plantconcept_id int(11) NOT NULL,
330 575 aaronmk
  party_id int(11),
331 536 aaronmk
  role_id int(11) NOT NULL,
332
  determinationtype character varying(30),
333
  reference_id int(11),
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  isoriginal int(1) NOT NULL DEFAULT false,
335
  iscurrent int(1) NOT NULL DEFAULT false,
336 536 aaronmk
  taxonfit character varying(50),
337
  taxonconfidence character varying(50),
338
  grouptype character varying(20),
339
  notes text,
340
  notespublic int(1),
341
  notesmgt int(1),
342
  revisions int(1),
343 591 aaronmk
  determinationdate timestamp NULL,
344 536 aaronmk
  emb_taxondetermination int(11),
345
  accessioncode character varying(255),
346
  CONSTRAINT taxondetermination_pkey PRIMARY KEY (taxondetermination_id ),
347
  CONSTRAINT taxondetermination_party_id FOREIGN KEY (party_id)
348
      REFERENCES party (party_id) MATCH SIMPLE
349
      ON UPDATE CASCADE ON DELETE CASCADE,
350
  CONSTRAINT taxondetermination_plantconcept_id FOREIGN KEY (plantconcept_id)
351
      REFERENCES plantconcept (plantconcept_id) MATCH SIMPLE
352
      ON UPDATE CASCADE ON DELETE CASCADE,
353
  CONSTRAINT taxondetermination_reference_id FOREIGN KEY (reference_id)
354
      REFERENCES reference (reference_id) MATCH SIMPLE
355
      ON UPDATE CASCADE ON DELETE CASCADE,
356
  CONSTRAINT taxondetermination_role_id FOREIGN KEY (role_id)
357 596 aaronmk
      REFERENCES role (role_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
359
  CONSTRAINT taxondetermination_taxonoccurrence_id FOREIGN KEY (taxonoccurrence_id)
360
      REFERENCES taxonoccurrence (taxonoccurrence_id) MATCH SIMPLE
361
      ON UPDATE CASCADE ON DELETE CASCADE
362
);
363
364 552 aaronmk
CREATE TABLE stratum
365
(
366
  stratum_id int(11) NOT NULL AUTO_INCREMENT,
367
  locationevent_id int(11) NOT NULL,
368
  stratumtype_id int(11) NOT NULL,
369
  stratummethod_id int(11),
370
  stratumname character varying(30),
371
  stratumheight double precision,
372
  stratumbase double precision,
373
  stratumcover double precision,
374
  stratumdescription character varying(200),
375
  CONSTRAINT stratum_pkey PRIMARY KEY (stratum_id ),
376
  CONSTRAINT stratum_locationevent_id FOREIGN KEY (locationevent_id)
377
      REFERENCES locationevent (locationevent_id) MATCH SIMPLE
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      ON UPDATE CASCADE ON DELETE CASCADE,
379
  CONSTRAINT stratum_stratumtype_id FOREIGN KEY (stratumtype_id)
380
      REFERENCES stratumtype (stratumtype_id) MATCH SIMPLE
381 559 aaronmk
      ON UPDATE CASCADE ON DELETE CASCADE
382 552 aaronmk
);
383
384 537 aaronmk
CREATE TABLE sizeclass -- A range of size measurements used to aggregate organisms.
385 536 aaronmk
(
386 537 aaronmk
  sizeclass_id int(11) NOT NULL AUTO_INCREMENT,
387
  mindiameter double precision,
388
  minheight double precision,
389
  maxdiameter double precision,
390
  maxheight double precision,
391 536 aaronmk
  accessioncode character varying(255),
392 537 aaronmk
  CONSTRAINT sizeclass_pkey PRIMARY KEY (sizeclass_id )
393 536 aaronmk
);
394
395 592 aaronmk
CREATE TABLE taxonbinmethod
396 536 aaronmk
(
397 584 aaronmk
  taxonbinmethod_id int(11) NOT NULL,
398 592 aaronmk
  label character varying(255),
399
  stratumtype_id int(11),
400 536 aaronmk
  sizeclass_id int(11),
401
  coverindex_id int(11),
402
  accessioncode character varying(255),
403 584 aaronmk
  CONSTRAINT taxonbinmethod_pkey PRIMARY KEY (taxonbinmethod_id ),
404
  CONSTRAINT taxonbinmethod_sizeclass_id FOREIGN KEY (sizeclass_id)
405 536 aaronmk
      REFERENCES sizeclass (sizeclass_id) MATCH SIMPLE
406 583 aaronmk
      ON UPDATE CASCADE ON DELETE CASCADE,
407 592 aaronmk
  CONSTRAINT taxonbinmethod_stratumtype_id FOREIGN KEY (stratumtype_id)
408
      REFERENCES stratumtype (stratumtype_id) MATCH SIMPLE
409
      ON UPDATE CASCADE ON DELETE CASCADE
410 536 aaronmk
);