Project

General

Profile

« Previous | Next » 

Revision 671

Added by Aaron Marcuse-Kubitza almost 13 years ago

VegBIEN: Renamed individualplant to plantobservation

View differences:

test/accepted_output/SALVIAS.organisms.VegBIEN.xml
18 18 
        </locationevent_id>
19 19 
        <aggregateoccurrence>
20 20 
            <count>1</count>
21 
            <individualplant>
21 
            <plantobservation>
22 22 
                <stem>
23 23 
                    <authorstemcode>8</authorstemcode>
24 24 
                    <diameter>662</diameter>
25 25 
                </stem>
26 26 
                <authorplantcode>607771</authorplantcode>
27 
            </individualplant>
27 
            </plantobservation>
28 28 
        </aggregateoccurrence>
29 29 
        <definedvalue fkey="tableRecord_ID">
30 30 
            <userdefined_id>
......
187 187 
        </locationevent_id>
188 188 
        <aggregateoccurrence>
189 189 
            <count>1</count>
190 
            <individualplant>
190 
            <plantobservation>
191 191 
                <stem>
192 192 
                    <authorstemcode>91</authorstemcode>
193 193 
                    <diameter>215</diameter>
194 194 
                </stem>
195 195 
                <authorplantcode>607722</authorplantcode>
196 
            </individualplant>
196 
            </plantobservation>
197 197 
        </aggregateoccurrence>
198 198 
        <definedvalue fkey="tableRecord_ID">
199 199 
            <userdefined_id>
test/accepted_output/SALVIAS_db.organisms.VegBIEN.xml
8 8 
        </locationevent_id>
9 9 
        <aggregateoccurrence>
10 10 
            <count>1</count>
11 
            <individualplant>
11 
            <plantobservation>
12 12 
                <authorplantcode>1</authorplantcode>
13 
            </individualplant>
13 
            </plantobservation>
14 14 
        </aggregateoccurrence>
15 15 
        <definedvalue fkey="tableRecord_ID">
16 16 
            <userdefined_id>
......
191 191 
        </locationevent_id>
192 192 
        <aggregateoccurrence>
193 193 
            <count>1</count>
194 
            <individualplant>
194 
            <plantobservation>
195 195 
                <authorplantcode>2</authorplantcode>
196 
            </individualplant>
196 
            </plantobservation>
197 197 
        </aggregateoccurrence>
198 198 
        <definedvalue fkey="tableRecord_ID">
199 199 
            <userdefined_id>
test/accepted_output/NYBG.organisms.VegBIEN.xml
40 40 
            </locationevent>
41 41 
        </locationevent_id>
42 42 
        <aggregateoccurrence>
43 
            <individualplant>
43 
            <plantobservation>
44 44 
                <stem>
45 45 
                    <definedvalue fkey="tableRecord_ID">
46 46 
                        <userdefined_id>
......
62 62 
                    </definedvalue>
63 63 
                </stem>
64 64 
                <authorplantcode>816590</authorplantcode>
65 
            </individualplant>
65 
            </plantobservation>
66 66 
        </aggregateoccurrence>
67 67 
        <specimenreplicate>
68 68 
            <reference_id>
......
361 361 
            <iscurrent>true</iscurrent>
362 362 
        </taxondetermination>
363 363 
        <aggregateoccurrence>
364 
            <individualplant>
364 
            <plantobservation>
365 365 
                <authorplantcode>220541</authorplantcode>
366 
            </individualplant>
366 
            </plantobservation>
367 367 
        </aggregateoccurrence>
368 368 
    </taxonoccurrence>
369 369 
</VegBIEN>
inputs/NYBG/test/VegBIEN.xml.ref
40 40 
            </locationevent>
41 41 
        </locationevent_id>
42 42 
        <aggregateoccurrence>
43 
            <individualplant>
43 
            <plantobservation>
44 44 
                <stem>
45 45 
                    <definedvalue fkey="tableRecord_ID">
46 46 
                        <userdefined_id>
......
63 63 
                </stem>
64 64 
                <authorplantcode>816590
 </authorplantcode>
65 
            </individualplant>
65 
            </plantobservation>
66 66 
        </aggregateoccurrence>
67 67 
        <specimenreplicate>
68 68 
            <reference_id>
......
364 364 
            <iscurrent>true</iscurrent>
365 365 
        </taxondetermination>
366 366 
        <aggregateoccurrence>
367 
            <individualplant>
367 
            <plantobservation>
368 368 
                <authorplantcode>220541
 </authorplantcode>
369 
            </individualplant>
369 
            </plantobservation>
370 370 
        </aggregateoccurrence>
371 371 
    </taxonoccurrence>
372 372 
</VegBIEN>
inputs/NYBG/maps/VegBIEN.organisms.csv
15 15 
YearCollected,/*_id/locationevent/obsstartdate/_date/year,
16 16 
MaximumDepth,/*_id/locationevent/waterdepth/max,
17 17 
MinimumDepth,/*_id/locationevent/waterdepth/min,
18 
Habitat,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=habitat]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?"
19 
PlantFungusDescription,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=plantFungusDescription]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect mapping to VB, also possibly to VX;  this is the specimenDescription field, as used by this institution (NOT a standard DwC element). Very important! Bob, Nick, where would this go in VB and VX?"
20 
Substrate,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=substrate]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect mapping to VB and VX; refers to geological substrate or soils where specimen collected. Often concatenated with habitat, or included with specimen description. Bob, Nick, is there an element for this in VB/VX, or shall we just use userDefined?"
21 
Vegetation,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=vegetation]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Habitat'. Bob, Nick: keep as user defined or create special element?"
18 
Habitat,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=habitat]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?"
19 
PlantFungusDescription,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=plantFungusDescription]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect mapping to VB, also possibly to VX;  this is the specimenDescription field, as used by this institution (NOT a standard DwC element). Very important! Bob, Nick, where would this go in VB and VX?"
20 
Substrate,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=substrate]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect mapping to VB and VX; refers to geological substrate or soils where specimen collected. Often concatenated with habitat, or included with specimen description. Bob, Nick, is there an element for this in VB/VX, or shall we just use userDefined?"
21 
Vegetation,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=vegetation]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Habitat'. Bob, Nick: keep as user defined or create special element?"
22 22 
FieldNumber,/specimenreplicate:[*_id/reference]/catalognumber_dwc,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?"
23 23 
CollectorNumber,/specimenreplicate:[*_id/reference]/collectornumber_dwc,"Brad: OMIT; db-specific element, not relevant to VB/VX"
24 24 
Collector,/specimenreplicate:[*_id/reference]/verbatimcollectorname,Brad: Correct for VB. Nick: is there a way to specifically identify this party as collector of a specimen?
......
41 41 
Species,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",
42 42 
Phylum,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",
43 43 
Subspecies,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/*_id/plantconcept/*_id/*/plantname",
44 
UniqueNYInternalRecordNumber,"/{aggregateoccurrence/individualplant/authorplantcode,specimenreplicate:[*_id/reference]/sourceaccessioncode}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key"
44 
UniqueNYInternalRecordNumber,"/{aggregateoccurrence/plantobservation/authorplantcode,specimenreplicate:[*_id/reference]/sourceaccessioncode}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key"
inputs/SALVIAS/test/VegBIEN.xml.ref
131 131 
        </locationevent_id>
132 132 
        <aggregateoccurrence>
133 133 
            <count>1</count>
134 
            <individualplant>
134 
            <plantobservation>
135 135 
                <authorplantcode>1</authorplantcode>
136 
            </individualplant>
136 
            </plantobservation>
137 137 
        </aggregateoccurrence>
138 138 
        <definedvalue fkey="tableRecord_ID">
139 139 
            <userdefined_id>
......
314 314 
        </locationevent_id>
315 315 
        <aggregateoccurrence>
316 316 
            <count>1</count>
317 
            <individualplant>
317 
            <plantobservation>
318 318 
                <authorplantcode>2</authorplantcode>
319 
            </individualplant>
319 
            </plantobservation>
320 320 
        </aggregateoccurrence>
321 321 
        <definedvalue fkey="tableRecord_ID">
322 322 
            <userdefined_id>
......
490 490 
        </specimenreplicate>
491 491 
    </taxonoccurrence>
492 492 
    <stem id="0">
493 
        <individualplant_id>
494 
            <individualplant>
493 
        <plantobservation_id>
494 
            <plantobservation>
495 495 
                <authorplantcode>1</authorplantcode>
496 496 
                <stemcount>1</stemcount>
497 
            </individualplant>
498 
        </individualplant_id>
497 
            </plantobservation>
498 
        </plantobservation_id>
499 499 
        <diameter>6.59</diameter>
500 500 
    </stem>
501 501 
    <stem id="1">
502 
        <individualplant_id>
503 
            <individualplant>
502 
        <plantobservation_id>
503 
            <plantobservation>
504 504 
                <authorplantcode>2</authorplantcode>
505 505 
                <stemcount>0</stemcount>
506 
            </individualplant>
507 
        </individualplant_id>
506 
            </plantobservation>
507 
        </plantobservation_id>
508 508 
        <diameter>3.09</diameter>
509 509 
    </stem>
510 510 
</VegBIEN>
inputs/SALVIAS/maps/VegBIEN.stems.csv
1 1 
SALVIAS:stems,VegBIEN:/stem,Comments
2 
PlotObsID,/*_id/individualplant/authorplantcode,
3 
NoInd,/*_id/individualplant/stemcount,
2 
PlotObsID,/*_id/plantobservation/authorplantcode,
3 
NoInd,/*_id/plantobservation/stemcount,
4 4 
stem_tag2,/authorstemcode/_alt/1,
5 5 
stem_tag1,/authorstemcode/_alt/2,
6 6 
basal_diam,"/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=basalDiameter]]:[@fkey=tableRecord_ID]/definedvalue",
inputs/SALVIAS/maps/VegBIEN.organisms.csv
3 3 
NoInd,/aggregateoccurrence/count,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
4 4 
cover_percent,/aggregateoccurrence/cover,
5 5 
intercept_cm,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
6 
height_m,/aggregateoccurrence/individualplant/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
7 
tag2,/aggregateoccurrence/individualplant/stem/authorstemcode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
8 
tag1,/aggregateoccurrence/individualplant/stem/authorstemcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
9 
ht_first_branch_m,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
10 
temp_dbh,/aggregateoccurrence/individualplant/stem/diameter,
11 
x_position,/aggregateoccurrence/individualplant/stem/xposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
12 
y_position,/aggregateoccurrence/individualplant/stem/yposition,Brad: See comment above for x_position
6 
height_m,/aggregateoccurrence/plantobservation/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
7 
tag2,/aggregateoccurrence/plantobservation/stem/authorstemcode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
8 
tag1,/aggregateoccurrence/plantobservation/stem/authorstemcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
9 
ht_first_branch_m,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
10 
temp_dbh,/aggregateoccurrence/plantobservation/stem/diameter,
11 
x_position,/aggregateoccurrence/plantobservation/stem/xposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
12 
y_position,/aggregateoccurrence/plantobservation/stem/yposition,Brad: See comment above for x_position
13 13 
census_no,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=censusNo]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."
14 14 
Habit,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=habit]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
15 15 
Ind,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=individualCode]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
......
28 28 
Notes,"/taxondetermination[*_id/role/rolecode=identifier,!*_id/plantconcept]:[determinationtype=Author,iscurrent=true]/notes",
29 29 
OrigFamily,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",Brad: OMIT
30 30 
OrigSpecies,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",Brad: OMIT
31 
PlotObsID,"/{aggregateoccurrence/individualplant/authorplantcode,specimenreplicate:[*_id/reference]/sourceaccessioncode}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
31 
PlotObsID,"/{aggregateoccurrence/plantobservation/authorplantcode,specimenreplicate:[*_id/reference]/sourceaccessioncode}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
schemas/vegbien.for_ERD.my.sql
224 224 
  count int(11),
225 225 
  accessioncode character varying(255),
226 226 
  sourceaccessioncode character varying(100),
227 
  individualplant_id int(11),
227 
  plantobservation_id int(11),
228 228 
  CONSTRAINT aggregateoccurrence_pkey PRIMARY KEY (aggregateoccurrence_id ),
229 
  CONSTRAINT aggregateoccurrence_individualplant_id FOREIGN KEY (individualplant_id)
230 
      REFERENCES individualplant (individualplant_id) MATCH SIMPLE
229 
  CONSTRAINT aggregateoccurrence_plantobservation_id FOREIGN KEY (plantobservation_id)
230 
      REFERENCES plantobservation (plantobservation_id) MATCH SIMPLE
231 231 
      ON UPDATE CASCADE ON DELETE CASCADE,
232 232 
  CONSTRAINT aggregateoccurrence_taxonbinmethod_id FOREIGN KEY (taxonbinmethod_id)
233 233 
      REFERENCES taxonbinmethod (taxonbinmethod_id) MATCH SIMPLE
......
239 239 
  CONSTRAINT aggregateoccurrence_keys_method UNIQUE (taxonoccurrence_id , taxonbinmethod_id )
240 240 
);
241 241 

  		




  242
  
  
    
CREATE TABLE individualplant -- VegBank's stemcount table.


  		




  
  242
  
    
CREATE TABLE plantobservation -- VegBank's stemcount table.


  		




  243
  243
  
    
(


  		




  244
  
  
    
  individualplant_id int(11) NOT NULL AUTO_INCREMENT,


  		




  
  244
  
    
  plantobservation_id int(11) NOT NULL AUTO_INCREMENT,


  		




  245
  245
  
    
  aggregateoccurrence_id int(11) NOT NULL,


  		




  246
  246
  
    
  overallheight double precision,


  		




  247
  247
  
    
  overallheightaccuracy double precision,


  		




  248
  
  
    
  emb_individualplant int(11),


  		




  
  248
  
    
  emb_plantobservation int(11),


  		




  249
  249
  
    
  authorplantcode character varying(20),


  		




  250
  250
  
    
  accessioncode character varying(255),


  		




  251
  251
  
    
  stemcount int(11),


  		




  252
  252
  
    
  sourceaccessioncode character varying(100),


  		




  253
  
  
    
  CONSTRAINT individualplant_pkey PRIMARY KEY (individualplant_id ),


  		




  254
  
  
    
  CONSTRAINT individualplant_aggregateoccurrence_id FOREIGN KEY (aggregateoccurrence_id)


  		




  
  253
  
    
  CONSTRAINT plantobservation_pkey PRIMARY KEY (plantobservation_id ),


  		




  
  254
  
    
  CONSTRAINT plantobservation_aggregateoccurrence_id FOREIGN KEY (aggregateoccurrence_id)


  		




  255
  255
  
    
      REFERENCES aggregateoccurrence (aggregateoccurrence_id) MATCH SIMPLE


  		




  256
  256
  
    
      ON UPDATE CASCADE ON DELETE CASCADE,


  		




  257
  
  
    
  CONSTRAINT individualplant_aggregateoccurrence_id_1_to_1 UNIQUE (aggregateoccurrence_id )


  		




  
  257
  
    
  CONSTRAINT plantobservation_aggregateoccurrence_id_1_to_1 UNIQUE (aggregateoccurrence_id )


  		




  258
  258
  
    
);


  		




  259
  259
  
    

  		




  260
  260
  
    
CREATE TABLE stem -- VegBank's stemlocation table.


  		




  261
  261
  
    
(


  		




  262
  262
  
    
  stem_id int(11) NOT NULL AUTO_INCREMENT,


  		




  263
  
  
    
  individualplant_id int(11) NOT NULL,


  		




  
  263
  
    
  plantobservation_id int(11) NOT NULL,


  		




  264
  264
  
    
  authorstemcode character varying(20),


  		




  265
  265
  
    
  xposition double precision,


  		




  266
  266
  
    
  yposition double precision,


  		




  ......




  274
  274
  
    
  diameteraccuracy double precision,


  		




  275
  275
  
    
  sourceaccessioncode character varying(100),


  		




  276
  276
  
    
  CONSTRAINT stem_pkey PRIMARY KEY (stem_id ),


  		




  277
  
  
    
  CONSTRAINT stem_individualplant_id FOREIGN KEY (individualplant_id)


  		




  278
  
  
    
      REFERENCES individualplant (individualplant_id) MATCH SIMPLE


  		




  
  277
  
    
  CONSTRAINT stem_plantobservation_id FOREIGN KEY (plantobservation_id)


  		




  
  278
  
    
      REFERENCES plantobservation (plantobservation_id) MATCH SIMPLE


  		




  279
  279
  
    
      ON UPDATE CASCADE ON DELETE CASCADE,


  		




  280
  
  
    
  CONSTRAINT stem_keys_accessioncode UNIQUE (individualplant_id , sourceaccessioncode ),


  		




  281
  
  
    
  CONSTRAINT stem_keys_code UNIQUE (individualplant_id , authorstemcode )


  		




  
  280
  
    
  CONSTRAINT stem_keys_accessioncode UNIQUE (plantobservation_id , sourceaccessioncode ),


  		




  
  281
  
    
  CONSTRAINT stem_keys_code UNIQUE (plantobservation_id , authorstemcode )


  		




  282
  282
  
    
);


  		




  283
  283
  
    

  		




  284
  284
  
    
CREATE TABLE specimen -- A physical specimen collected from a plant. Used to link replicates of the same specimen together.


  		












  

    
      schemas/vegbien.for_wiki.sql
    
  





  58
  58
  
    
  count integer,


  		




  59
  59
  
    
  accessioncode character varying(255),


  		




  60
  60
  
    
  sourceaccessioncode character varying(100),


  		




  61
  
  
    
  individualplant_id integer,


  		




  
  61
  
    
  plantobservation_id integer,


  		




  62
  62
  
    
);


  		




  63
  63
  
    

  		




  64
  
  
    
CREATE TABLE individualplant -- VegBank's stemcount table.


  		




  
  64
  
    
CREATE TABLE plantobservation -- VegBank's stemcount table.


  		




  65
  65
  
    
(


  		




  66
  
  
    
  individualplant_id serial NOT NULL,


  		




  
  66
  
    
  plantobservation_id serial NOT NULL,


  		




  67
  67
  
    
  aggregateoccurrence_id integer NOT NULL,


  		




  68
  68
  
    
  overallheight double precision,


  		




  69
  69
  
    
  overallheightaccuracy double precision,


  		




  70
  
  
    
  emb_individualplant integer,


  		




  
  70
  
    
  emb_plantobservation integer,


  		




  71
  71
  
    
  authorplantcode character varying(20),


  		




  72
  72
  
    
  accessioncode character varying(255),


  		




  73
  73
  
    
  stemcount integer,


  		




  ......




  77
  77
  
    
CREATE TABLE stem -- VegBank's stemlocation table.


  		




  78
  78
  
    
(


  		




  79
  79
  
    
  stem_id serial NOT NULL,


  		




  80
  
  
    
  individualplant_id integer NOT NULL,


  		




  
  80
  
    
  plantobservation_id integer NOT NULL,


  		




  81
  81
  
    
  authorstemcode character varying(20),


  		




  82
  82
  
    
  xposition double precision,


  		




  83
  83
  
    
  yposition double precision,


  		












  

    
      schemas/vegbien_empty.sql
    
  





  27
  27
  
    
TRUNCATE disturbanceobs CASCADE;


  		




  28
  28
  
    
TRUNCATE embargo CASCADE;


  		




  29
  29
  
    
TRUNCATE graphic CASCADE;


  		




  30
  
  
    
TRUNCATE individualplant CASCADE;


  		




  31
  30
  
    
TRUNCATE keywords CASCADE;


  		




  32
  31
  
    
TRUNCATE keywords_extra CASCADE;


  		




  33
  32
  
    
TRUNCATE location CASCADE;


  		




  ......




  45
  44
  
    
TRUNCATE plantcorrelation CASCADE;


  		




  46
  45
  
    
TRUNCATE plantlineage CASCADE;


  		




  47
  46
  
    
TRUNCATE plantname CASCADE;


  		




  
  47
  
    
TRUNCATE plantobservation CASCADE;


  		




  48
  48
  
    
TRUNCATE plantstatus CASCADE;


  		




  49
  49
  
    
TRUNCATE plantusage CASCADE;


  		




  50
  50
  
    
TRUNCATE project CASCADE;


  		












  

    
      schemas/vegbien.for_ERD.sql
    
  





  224
  224
  
    
  count integer,


  		




  225
  225
  
    
  accessioncode character varying(255),


  		




  226
  226
  
    
  sourceaccessioncode character varying(100),


  		




  227
  
  
    
  individualplant_id integer,


  		




  
  227
  
    
  plantobservation_id integer,


  		




  228
  228
  
    
  CONSTRAINT aggregateoccurrence_pkey PRIMARY KEY (aggregateoccurrence_id ),


  		




  229
  
  
    
  CONSTRAINT aggregateoccurrence_individualplant_id FOREIGN KEY (individualplant_id)


  		




  230
  
  
    
      REFERENCES individualplant (individualplant_id) MATCH SIMPLE


  		




  
  229
  
    
  CONSTRAINT aggregateoccurrence_plantobservation_id FOREIGN KEY (plantobservation_id)


  		




  
  230
  
    
      REFERENCES plantobservation (plantobservation_id) MATCH SIMPLE


  		




  231
  231
  
    
      ON UPDATE CASCADE ON DELETE CASCADE,


  		




  232
  232
  
    
  CONSTRAINT aggregateoccurrence_taxonbinmethod_id FOREIGN KEY (taxonbinmethod_id)


  		




  233
  233
  
    
      REFERENCES taxonbinmethod (taxonbinmethod_id) MATCH SIMPLE


  		




  ......




  239
  239
  
    
  CONSTRAINT aggregateoccurrence_keys_method UNIQUE (taxonoccurrence_id , taxonbinmethod_id )


  		




  240
  240
  
    
);


  		




  241
  241
  
    

  		




  242
  
  
    
CREATE TABLE individualplant -- VegBank's stemcount table.


  		




  
  242
  
    
CREATE TABLE plantobservation -- VegBank's stemcount table.


  		




  243
  243
  
    
(


  		




  244
  
  
    
  individualplant_id serial NOT NULL,


  		




  
  244
  
    
  plantobservation_id serial NOT NULL,


  		




  245
  245
  
    
  aggregateoccurrence_id integer NOT NULL,


  		




  246
  246
  
    
  overallheight double precision,


  		




  247
  247
  
    
  overallheightaccuracy double precision,


  		




  248
  
  
    
  emb_individualplant integer,


  		




  
  248
  
    
  emb_plantobservation integer,


  		




  249
  249
  
    
  authorplantcode character varying(20),


  		




  250
  250
  
    
  accessioncode character varying(255),


  		




  251
  251
  
    
  stemcount integer,


  		




  252
  252
  
    
  sourceaccessioncode character varying(100),


  		




  253
  
  
    
  CONSTRAINT individualplant_pkey PRIMARY KEY (individualplant_id ),


  		




  254
  
  
    
  CONSTRAINT individualplant_aggregateoccurrence_id FOREIGN KEY (aggregateoccurrence_id)


  		




  
  253
  
    
  CONSTRAINT plantobservation_pkey PRIMARY KEY (plantobservation_id ),


  		




  
  254
  
    
  CONSTRAINT plantobservation_aggregateoccurrence_id FOREIGN KEY (aggregateoccurrence_id)


  		




  255
  255
  
    
      REFERENCES aggregateoccurrence (aggregateoccurrence_id) MATCH SIMPLE


  		




  256
  256
  
    
      ON UPDATE CASCADE ON DELETE CASCADE,


  		




  257
  
  
    
  CONSTRAINT individualplant_aggregateoccurrence_id_1_to_1 UNIQUE (aggregateoccurrence_id )


  		




  
  257
  
    
  CONSTRAINT plantobservation_aggregateoccurrence_id_1_to_1 UNIQUE (aggregateoccurrence_id )


  		




  258
  258
  
    
);


  		




  259
  259
  
    

  		




  260
  260
  
    
CREATE TABLE stem -- VegBank's stemlocation table.


  		




  261
  261
  
    
(


  		




  262
  262
  
    
  stem_id serial NOT NULL,


  		




  263
  
  
    
  individualplant_id integer NOT NULL,


  		




  
  263
  
    
  plantobservation_id integer NOT NULL,


  		




  264
  264
  
    
  authorstemcode character varying(20),


  		




  265
  265
  
    
  xposition double precision,


  		




  266
  266
  
    
  yposition double precision,


  		




  ......




  274
  274
  
    
  diameteraccuracy double precision,


  		




  275
  275
  
    
  sourceaccessioncode character varying(100),


  		




  276
  276
  
    
  CONSTRAINT stem_pkey PRIMARY KEY (stem_id ),


  		




  277
  
  
    
  CONSTRAINT stem_individualplant_id FOREIGN KEY (individualplant_id)


  		




  278
  
  
    
      REFERENCES individualplant (individualplant_id) MATCH SIMPLE


  		




  
  277
  
    
  CONSTRAINT stem_plantobservation_id FOREIGN KEY (plantobservation_id)


  		




  
  278
  
    
      REFERENCES plantobservation (plantobservation_id) MATCH SIMPLE


  		




  279
  279
  
    
      ON UPDATE CASCADE ON DELETE CASCADE,


  		




  280
  
  
    
  CONSTRAINT stem_keys_accessioncode UNIQUE (individualplant_id , sourceaccessioncode ),


  		




  281
  
  
    
  CONSTRAINT stem_keys_code UNIQUE (individualplant_id , authorstemcode )


  		




  
  280
  
    
  CONSTRAINT stem_keys_accessioncode UNIQUE (plantobservation_id , sourceaccessioncode ),


  		




  
  281
  
    
  CONSTRAINT stem_keys_code UNIQUE (plantobservation_id , authorstemcode )


  		




  282
  282
  
    
);


  		




  283
  283
  
    

  		




  284
  284
  
    
CREATE TABLE specimen -- A physical specimen collected from a plant. Used to link replicates of the same specimen together.


  		












  

    
      schemas/vegbien.sql
    
  





  90
  90
  
    
    count integer,


  		




  91
  91
  
    
    accessioncode character varying(255),


  		




  92
  92
  
    
    sourceaccessioncode character varying(100),


  		




  93
  
  
    
    individualplant_id integer


  		




  
  93
  
    
    plantobservation_id integer


  		




  94
  94
  
    
);


  		




  95
  95
  
    

  		




  96
  96
  
    

  		




  ......




  1022
  1022
  
    

  		




  1023
  1023
  
    

  		




  1024
  1024
  
    
--


  		




  1025
  
  
    
-- Name: individualplant; Type: TABLE; Schema: public; Owner: -; Tablespace: 


  		




  1026
  
  
    
--


  		




  1027
  
  
    

  		




  1028
  
  
    
CREATE TABLE individualplant (


  		




  1029
  
  
    
    individualplant_id integer NOT NULL,


  		




  1030
  
  
    
    aggregateoccurrence_id integer NOT NULL,


  		




  1031
  
  
    
    overallheight double precision,


  		




  1032
  
  
    
    overallheightaccuracy double precision,


  		




  1033
  
  
    
    emb_individualplant integer,


  		




  1034
  
  
    
    authorplantcode character varying(20),


  		




  1035
  
  
    
    accessioncode character varying(255),


  		




  1036
  
  
    
    stemcount integer,


  		




  1037
  
  
    
    sourceaccessioncode character varying(100)


  		




  1038
  
  
    
);


  		




  1039
  
  
    

  		




  1040
  
  
    

  		




  1041
  
  
    
--


  		




  1042
  
  
    
-- Name: TABLE individualplant; Type: COMMENT; Schema: public; Owner: -


  		




  1043
  
  
    
--


  		




  1044
  
  
    

  		




  1045
  
  
    
COMMENT ON TABLE individualplant IS 'VegBank''s stemcount table.';


  		




  1046
  
  
    

  		




  1047
  
  
    

  		




  1048
  
  
    
--


  		




  1049
  
  
    
-- Name: individualplant_individualplant_id_seq; Type: SEQUENCE; Schema: public; Owner: -


  		




  1050
  
  
    
--


  		




  1051
  
  
    

  		




  1052
  
  
    
CREATE SEQUENCE individualplant_individualplant_id_seq


  		




  1053
  
  
    
    START WITH 1


  		




  1054
  
  
    
    INCREMENT BY 1


  		




  1055
  
  
    
    NO MINVALUE


  		




  1056
  
  
    
    NO MAXVALUE


  		




  1057
  
  
    
    CACHE 1;


  		




  1058
  
  
    

  		




  1059
  
  
    

  		




  1060
  
  
    
--


  		




  1061
  
  
    
-- Name: individualplant_individualplant_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -


  		




  1062
  
  
    
--


  		




  1063
  
  
    

  		




  1064
  
  
    
ALTER SEQUENCE individualplant_individualplant_id_seq OWNED BY individualplant.individualplant_id;


  		




  1065
  
  
    

  		




  1066
  
  
    

  		




  1067
  
  
    
--


  		




  1068
  1025
  
    
-- Name: keywords; Type: TABLE; Schema: public; Owner: -; Tablespace: 


  		




  1069
  1026
  
    
--


  		




  1070
  1027
  
    

  		




  ......




  1734
  1691
  
    

  		




  1735
  1692
  
    

  		




  1736
  1693
  
    
--


  		




  
  1694
  
    
-- Name: plantobservation; Type: TABLE; Schema: public; Owner: -; Tablespace: 


  		




  
  1695
  
    
--


  		




  
  1696
  
    

  		




  
  1697
  
    
CREATE TABLE plantobservation (


  		




  
  1698
  
    
    plantobservation_id integer NOT NULL,


  		




  
  1699
  
    
    aggregateoccurrence_id integer NOT NULL,


  		




  
  1700
  
    
    overallheight double precision,


  		




  
  1701
  
    
    overallheightaccuracy double precision,


  		




  
  1702
  
    
    emb_plantobservation integer,


  		




  
  1703
  
    
    authorplantcode character varying(20),


  		




  
  1704
  
    
    accessioncode character varying(255),


  		




  
  1705
  
    
    stemcount integer,


  		




  
  1706
  
    
    sourceaccessioncode character varying(100)


  		




  
  1707
  
    
);


  		




  
  1708
  
    

  		




  
  1709
  
    

  		




  
  1710
  
    
--


  		




  
  1711
  
    
-- Name: TABLE plantobservation; Type: COMMENT; Schema: public; Owner: -


  		




  
  1712
  
    
--


  		




  
  1713
  
    

  		




  
  1714
  
    
COMMENT ON TABLE plantobservation IS 'VegBank''s stemcount table.';


  		




  
  1715
  
    

  		




  
  1716
  
    

  		




  
  1717
  
    
--


  		




  
  1718
  
    
-- Name: plantobservation_plantobservation_id_seq; Type: SEQUENCE; Schema: public; Owner: -


  		




  
  1719
  
    
--


  		




  
  1720
  
    

  		




  
  1721
  
    
CREATE SEQUENCE plantobservation_plantobservation_id_seq


  		




  
  1722
  
    
    START WITH 1


  		




  
  1723
  
    
    INCREMENT BY 1


  		




  
  1724
  
    
    NO MINVALUE


  		




  
  1725
  
    
    NO MAXVALUE


  		




  
  1726
  
    
    CACHE 1;


  		




  
  1727
  
    

  		




  
  1728
  
    

  		




  
  1729
  
    
--


  		




  
  1730
  
    
-- Name: plantobservation_plantobservation_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -


  		




  
  1731
  
    
--


  		




  
  1732
  
    

  		




  
  1733
  
    
ALTER SEQUENCE plantobservation_plantobservation_id_seq OWNED BY plantobservation.plantobservation_id;


  		




  
  1734
  
    

  		




  
  1735
  
    

  		




  
  1736
  
    
--


  		




  1737
  1737
  
    
-- Name: plantstatus; Type: TABLE; Schema: public; Owner: -; Tablespace: 


  		




  1738
  1738
  
    
--


  		




  1739
  1739
  
    

  		




  ......




  2362
  2362
  
    

  		




  2363
  2363
  
    
CREATE TABLE stem (


  		




  2364
  2364
  
    
    stem_id integer NOT NULL,


  		




  2365
  
  
    
    individualplant_id integer NOT NULL,


  		




  
  2365
  
    
    plantobservation_id integer NOT NULL,


  		




  2366
  2366
  
    
    authorstemcode character varying(20),


  		




  2367
  2367
  
    
    xposition double precision,


  		




  2368
  2368
  
    
    yposition double precision,


  		




  ......




  3437
  3437
  
    

  		




  3438
  3438
  
    

  		




  3439
  3439
  
    
--


  		




  3440
  
  
    
-- Name: individualplant_id; Type: DEFAULT; Schema: public; Owner: -


  		




  3441
  
  
    
--


  		




  3442
  
  
    

  		




  3443
  
  
    
ALTER TABLE individualplant ALTER COLUMN individualplant_id SET DEFAULT nextval('individualplant_individualplant_id_seq'::regclass);


  		




  3444
  
  
    

  		




  3445
  
  
    

  		




  3446
  
  
    
--


  		




  3447
  3440
  
    
-- Name: location_id; Type: DEFAULT; Schema: public; Owner: -


  		




  3448
  3441
  
    
--


  		




  3449
  3442
  
    

  		




  ......




  3549
  3542
  
    

  		




  3550
  3543
  
    

  		




  3551
  3544
  
    
--


  		




  
  3545
  
    
-- Name: plantobservation_id; Type: DEFAULT; Schema: public; Owner: -


  		




  
  3546
  
    
--


  		




  
  3547
  
    

  		




  
  3548
  
    
ALTER TABLE plantobservation ALTER COLUMN plantobservation_id SET DEFAULT nextval('plantobservation_plantobservation_id_seq'::regclass);


  		




  
  3549
  
    

  		




  
  3550
  
    

  		




  
  3551
  
    
--


  		




  3552
  3552
  
    
-- Name: plantstatus_id; Type: DEFAULT; Schema: public; Owner: -


  		




  3553
  3553
  
    
--


  		




  3554
  3554
  
    

  		




  ......




  4094
  4094
  
    

  		




  4095
  4095
  
    

  		




  4096
  4096
  
    
--


  		




  4097
  
  
    
-- Name: individualplant_aggregateoccurrence_id_1_to_1; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: 


  		




  4098
  
  
    
--


  		




  4099
  
  
    

  		




  4100
  
  
    
ALTER TABLE ONLY individualplant


  		




  4101
  
  
    
    ADD CONSTRAINT individualplant_aggregateoccurrence_id_1_to_1 UNIQUE (aggregateoccurrence_id);


  		




  4102
  
  
    

  		




  4103
  
  
    

  		




  4104
  
  
    
--


  		




  4105
  
  
    
-- Name: individualplant_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: 


  		




  4106
  
  
    
--


  		




  4107
  
  
    

  		




  4108
  
  
    
ALTER TABLE ONLY individualplant


  		




  4109
  
  
    
    ADD CONSTRAINT individualplant_pkey PRIMARY KEY (individualplant_id);


  		




  4110
  
  
    

  		




  4111
  
  
    

  		




  4112
  
  
    
--


  		




  4113
  4097
  
    
-- Name: location_keys_code; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: 


  		




  4114
  4098
  
    
--


  		




  4115
  4099
  
    

  		




  ......




  4302
  4286
  
    

  		




  4303
  4287
  
    

  		




  4304
  4288
  
    
--


  		




  
  4289
  
    
-- Name: plantobservation_aggregateoccurrence_id_1_to_1; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: 


  		




  
  4290
  
    
--


  		




  
  4291
  
    

  		




  
  4292
  
    
ALTER TABLE ONLY plantobservation


  		




  
  4293
  
    
    ADD CONSTRAINT plantobservation_aggregateoccurrence_id_1_to_1 UNIQUE (aggregateoccurrence_id);


  		




  
  4294
  
    

  		




  
  4295
  
    

  		




  
  4296
  
    
--


  		




  
  4297
  
    
-- Name: plantobservation_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: 


  		




  
  4298
  
    
--


  		




  
  4299
  
    

  		




  
  4300
  
    
ALTER TABLE ONLY plantobservation


  		




  
  4301
  
    
    ADD CONSTRAINT plantobservation_pkey PRIMARY KEY (plantobservation_id);


  		




  
  4302
  
    

  		




  
  4303
  
    

  		




  
  4304
  
    
--


  		




  4305
  4305
  
    
-- Name: plantstatus_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: 


  		




  4306
  4306
  
    
--


  		




  4307
  4307
  
    

  		




  ......




  4482
  4482
  
    
--


  		




  4483
  4483
  
    

  		




  4484
  4484
  
    
ALTER TABLE ONLY stem


  		




  4485
  
  
    
    ADD CONSTRAINT stem_keys_accessioncode UNIQUE (individualplant_id, sourceaccessioncode);


  		




  
  4485
  
    
    ADD CONSTRAINT stem_keys_accessioncode UNIQUE (plantobservation_id, sourceaccessioncode);


  		




  4486
  4486
  
    

  		




  4487
  4487
  
    

  		




  4488
  4488
  
    
--


  		




  ......




  4490
  4490
  
    
--


  		




  4491
  4491
  
    

  		




  4492
  4492
  
    
ALTER TABLE ONLY stem


  		




  4493
  
  
    
    ADD CONSTRAINT stem_keys_code UNIQUE (individualplant_id, authorstemcode);


  		




  
  4493
  
    
    ADD CONSTRAINT stem_keys_code UNIQUE (plantobservation_id, authorstemcode);


  		




  4494
  4494
  
    

  		




  4495
  4495
  
    

  		




  4496
  4496
  
    
--


  		




  ......




  5017
  5017
  
    

  		




  5018
  5018
  
    

  		




  5019
  5019
  
    
--


  		




  5020
  
  
    
-- Name: emb_individualplant_idx; Type: INDEX; Schema: public; Owner: -; Tablespace: 


  		




  
  5020
  
    
-- Name: emb_location_idx; Type: INDEX; Schema: public; Owner: -; Tablespace: 


  		




  5021
  5021
  
    
--


  		




  5022
  5022
  
    

  		




  5023
  
  
    
CREATE INDEX emb_individualplant_idx ON individualplant USING btree (emb_individualplant);


  		




  
  5023
  
    
CREATE INDEX emb_location_idx ON location USING btree (emb_location);


  		




  5024
  5024
  
    

  		




  5025
  5025
  
    

  		




  5026
  5026
  
    
--


  		




  5027
  
  
    
-- Name: emb_location_idx; Type: INDEX; Schema: public; Owner: -; Tablespace: 


  		




  
  5027
  
    
-- Name: emb_locationevent_idx; Type: INDEX; Schema: public; Owner: -; Tablespace: 


  		




  5028
  5028
  
    
--


  		




  5029
  5029
  
    

  		




  5030
  
  
    
CREATE INDEX emb_location_idx ON location USING btree (emb_location);


  		




  
  5030
  
    
CREATE INDEX emb_locationevent_idx ON locationevent USING btree (emb_locationevent);


  		




  5031
  5031
  
    

  		




  5032
  5032
  
    

  		




  5033
  5033
  
    
--


  		




  5034
  
  
    
-- Name: emb_locationevent_idx; Type: INDEX; Schema: public; Owner: -; Tablespace: 


  		




  
  5034
  
    
-- Name: emb_plantobservation_idx; Type: INDEX; Schema: public; Owner: -; Tablespace: 


  		




  5035
  5035
  
    
--


  		




  5036
  5036
  
    

  		




  5037
  
  
    
CREATE INDEX emb_locationevent_idx ON locationevent USING btree (emb_locationevent);


  		




  
  5037
  
    
CREATE INDEX emb_plantobservation_idx ON plantobservation USING btree (emb_plantobservation);


  		




  5038
  5038
  
    

  		




  5039
  5039
  
    

  		




  5040
  5040
  
    
--


  		




  ......




  5080
  5080
  
    

  		




  5081
  5081
  
    

  		




  5082
  5082
  
    
--


  		




  5083
  
  
    
-- Name: fki_aggregateoccurrence_individualplant_id; Type: INDEX; Schema: public; Owner: -; Tablespace: 


  		




  
  5083
  
    
-- Name: fki_aggregateoccurrence_plantobservation_id; Type: INDEX; Schema: public; Owner: -; Tablespace: 


  		




  5084
  5084
  
    
--


  		




  5085
  5085
  
    

  		




  5086
  
  
    
CREATE INDEX fki_aggregateoccurrence_individualplant_id ON aggregateoccurrence USING btree (individualplant_id);


  		




  
  5086
  
    
CREATE INDEX fki_aggregateoccurrence_plantobservation_id ON aggregateoccurrence USING btree (plantobservation_id);


  		




  5087
  5087
  
    

  		




  5088
  5088
  
    

  		




  5089
  5089
  
    
--


  		




  ......




  5143
  5143
  
    

  		




  5144
  5144
  
    

  		




  5145
  5145
  
    
--


  		




  5146
  
  
    
-- Name: individualplant_aggregateoccurrence_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace: 


  		




  5147
  
  
    
--


  		




  5148
  
  
    

  		




  5149
  
  
    
CREATE INDEX individualplant_aggregateoccurrence_id_x ON individualplant USING btree (aggregateoccurrence_id);


  		




  5150
  
  
    

  		




  5151
  
  
    

  		




  5152
  
  
    
--


  		




  5153
  5146
  
    
-- Name: keywords_table_id_entity_key; Type: INDEX; Schema: public; Owner: -; Tablespace: 


  		




  5154
  5147
  
    
--


  		




  5155
  5148
  
    

  		




  ......




  5451
  5444
  
    

  		




  5452
  5445
  
    

  		




  5453
  5446
  
    
--


  		




  
  5447
  
    
-- Name: plantobservation_aggregateoccurrence_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace: 


  		




  
  5448
  
    
--


  		




  
  5449
  
    

  		




  
  5450
  
    
CREATE INDEX plantobservation_aggregateoccurrence_id_x ON plantobservation USING btree (aggregateoccurrence_id);


  		




  
  5451
  
    

  		




  
  5452
  
    

  		




  
  5453
  
    
--


  		




  5454
  5454
  
    
-- Name: plantstatus_accessioncode_index; Type: INDEX; Schema: public; Owner: -; Tablespace: 


  		




  5455
  5455
  
    
--


  		




  5456
  5456
  
    

  		




  ......




  5654
  5654
  
    

  		




  5655
  5655
  
    

  		




  5656
  5656
  
    
--


  		




  5657
  
  
    
-- Name: stem_individualplant_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace: 


  		




  
  5657
  
    
-- Name: stem_plantobservation_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace: 


  		




  5658
  5658
  
    
--


  		




  5659
  5659
  
    

  		




  5660
  
  
    
CREATE INDEX stem_individualplant_id_x ON stem USING btree (individualplant_id);


  		




  
  5660
  
    
CREATE INDEX stem_plantobservation_id_x ON stem USING btree (plantobservation_id);


  		




  5661
  5661
  
    

  		




  5662
  5662
  
    

  		




  5663
  5663
  
    
--


  		




  ......




  5936
  5936
  
    

  		




  5937
  5937
  
    

  		




  5938
  5938
  
    
--


  		




  5939
  
  
    
-- Name: aggregateoccurrence_individualplant_id; Type: FK CONSTRAINT; Schema: public; Owner: -


  		




  
  5939
  
    
-- Name: aggregateoccurrence_plantobservation_id; Type: FK CONSTRAINT; Schema: public; Owner: -


  		




  5940
  5940
  
    
--


  		




  5941
  5941
  
    

  		




  5942
  5942
  
    
ALTER TABLE ONLY aggregateoccurrence


  		




  5943
  
  
    
    ADD CONSTRAINT aggregateoccurrence_individualplant_id FOREIGN KEY (individualplant_id) REFERENCES individualplant(individualplant_id) ON UPDATE CASCADE ON DELETE CASCADE;


  		




  
  5943
  
    
    ADD CONSTRAINT aggregateoccurrence_plantobservation_id FOREIGN KEY (plantobservation_id) REFERENCES plantobservation(plantobservation_id) ON UPDATE CASCADE ON DELETE CASCADE;


  		




  5944
  5944
  
    

  		




  5945
  5945
  
    

  		




  5946
  5946
  
    
--


  		




  ......




  6192
  6192
  
    

  		




  6193
  6193
  
    

  		




  6194
  6194
  
    
--


  		




  6195
  
  
    
-- Name: individualplant_aggregateoccurrence_id; Type: FK CONSTRAINT; Schema: public; Owner: -


  		




  6196
  
  
    
--


  		




  6197
  
  
    

  		




  6198
  
  
    
ALTER TABLE ONLY individualplant


  		




  6199
  
  
    
    ADD CONSTRAINT individualplant_aggregateoccurrence_id FOREIGN KEY (aggregateoccurrence_id) REFERENCES aggregateoccurrence(aggregateoccurrence_id) ON UPDATE CASCADE ON DELETE CASCADE;


  		




  6200
  
  
    

  		




  6201
  
  
    

  		




  6202
  
  
    
--


  		




  6203
  6195
  
    
-- Name: location_namedplace_id; Type: FK CONSTRAINT; Schema: public; Owner: -


  		




  6204
  6196
  
    
--


  		




  6205
  6197
  
    

  		




  ......




  6480
  6472
  
    

  		




  6481
  6473
  
    

  		




  6482
  6474
  
    
--


  		




  
  6475
  
    
-- Name: plantobservation_aggregateoccurrence_id; Type: FK CONSTRAINT; Schema: public; Owner: -


  		




  
  6476
  
    
--


  		




  
  6477
  
    

  		




  
  6478
  
    
ALTER TABLE ONLY plantobservation


  		




  
  6479
  
    
    ADD CONSTRAINT plantobservation_aggregateoccurrence_id FOREIGN KEY (aggregateoccurrence_id) REFERENCES aggregateoccurrence(aggregateoccurrence_id) ON UPDATE CASCADE ON DELETE CASCADE;


  		




  
  6480
  
    

  		




  
  6481
  
    

  		




  
  6482
  
    
--


  		




  6483
  6483
  
    
-- Name: plantstatus_party_id; Type: FK CONSTRAINT; Schema: public; Owner: -


  		




  6484
  6484
  
    
--


  		




  6485
  6485
  
    

  		




  ......




  6664
  6664
  
    

  		




  6665
  6665
  
    

  		




  6666
  6666
  
    
--


  		




  6667
  
  
    
-- Name: stem_individualplant_id; Type: FK CONSTRAINT; Schema: public; Owner: -


  		




  
  6667
  
    
-- Name: stem_plantobservation_id; Type: FK CONSTRAINT; Schema: public; Owner: -


  		




  6668
  6668
  
    
--


  		




  6669
  6669
  
    

  		




  6670
  6670
  
    
ALTER TABLE ONLY stem


  		




  6671
  
  
    
    ADD CONSTRAINT stem_individualplant_id FOREIGN KEY (individualplant_id) REFERENCES individualplant(individualplant_id) ON UPDATE CASCADE ON DELETE CASCADE;


  		




  
  6671
  
    
    ADD CONSTRAINT stem_plantobservation_id FOREIGN KEY (plantobservation_id) REFERENCES plantobservation(plantobservation_id) ON UPDATE CASCADE ON DELETE CASCADE;


  		




  6672
  6672
  
    

  		




  6673
  6673
  
    

  		




  6674
  6674
  
    
--


  		












  

    
      mappings/SALVIAS_db-VegBIEN.organisms.csv
    
  





  3
  3
  
    
NoInd,/aggregateoccurrence/count,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."


  		




  4
  4
  
    
cover_percent,/aggregateoccurrence/cover,


  		




  5
  5
  
    
intercept_cm,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."


  		




  6
  
  
    
height_m,/aggregateoccurrence/individualplant/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob


  		




  7
  
  
    
tag2,/aggregateoccurrence/individualplant/stem/authorstemcode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."


  		




  8
  
  
    
tag1,/aggregateoccurrence/individualplant/stem/authorstemcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."


  		




  9
  
  
    
ht_first_branch_m,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob


  		




  10
  
  
    
temp_dbh,/aggregateoccurrence/individualplant/stem/diameter,


  		




  11
  
  
    
x_position,/aggregateoccurrence/individualplant/stem/xposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."


  		




  12
  
  
    
y_position,/aggregateoccurrence/individualplant/stem/yposition,Brad: See comment above for x_position


  		




  
  6
  
    
height_m,/aggregateoccurrence/plantobservation/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob


  		




  
  7
  
    
tag2,/aggregateoccurrence/plantobservation/stem/authorstemcode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."


  		




  
  8
  
    
tag1,/aggregateoccurrence/plantobservation/stem/authorstemcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."


  		




  
  9
  
    
ht_first_branch_m,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob


  		




  
  10
  
    
temp_dbh,/aggregateoccurrence/plantobservation/stem/diameter,


  		




  
  11
  
    
x_position,/aggregateoccurrence/plantobservation/stem/xposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."


  		




  
  12
  
    
y_position,/aggregateoccurrence/plantobservation/stem/yposition,Brad: See comment above for x_position


  		




  13
  13
  
    
census_no,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=censusNo]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."


  		




  14
  14
  
    
Habit,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=habit]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."


  		




  15
  15
  
    
Ind,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=individualCode]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."


  		




  ......




  28
  28
  
    
Notes,"/taxondetermination[*_id/role/rolecode=identifier,!*_id/plantconcept]:[determinationtype=Author,iscurrent=true]/notes",


  		




  29
  29
  
    
OrigFamily,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",Brad: OMIT


  		




  30
  30
  
    
OrigSpecies,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",Brad: OMIT


  		




  31
  
  
    
PlotObsID,"/{aggregateoccurrence/individualplant/authorplantcode,specimenreplicate:[*_id/reference]/sourceaccessioncode}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."


  		




  
  31
  
    
PlotObsID,"/{aggregateoccurrence/plantobservation/authorplantcode,specimenreplicate:[*_id/reference]/sourceaccessioncode}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."


  		












  

    
      mappings/VegX-VegBIEN.organisms.csv
    
  





  53
  53
  
    
/simpleUserdefined[name=count]/value,/aggregateoccurrence/count


  		




  54
  54
  
    
/simpleUserdefined[name=coverPercent]/value,/aggregateoccurrence/cover


  		




  55
  55
  
    
/simpleUserdefined[name=interceptCm]/value,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  56
  
  
    
/height,/aggregateoccurrence/individualplant/overallheight


  		




  57
  
  
    
/simpleUserdefined[name=stemHeightM]/value,/aggregateoccurrence/individualplant/overallheight


  		




  58
  
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/relatedItem[relationshipType=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,/aggregateoccurrence/individualplant/stem/*_id/individualplant/authorplantcode


  		




  59
  
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=count]/value,/aggregateoccurrence/individualplant/stem/*_id/individualplant/stemcount


  		




  60
  
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/*ID->/*s/individualOrganism/identificationLabel,/aggregateoccurrence/individualplant/stem/authorstemcode


  		




  61
  
  
    
/*ID->/*s/individualOrganism/identificationLabel,/aggregateoccurrence/individualplant/stem/authorstemcode


  		




  62
  
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/*ID->/*s/individualOrganism/identificationLabel/_alt/1,/aggregateoccurrence/individualplant/stem/authorstemcode/_alt/1


  		




  63
  
  
    
/*ID->/*s/individualOrganism/identificationLabel/_alt/1,/aggregateoccurrence/individualplant/stem/authorstemcode/_alt/1


  		




  64
  
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/*ID->/*s/individualOrganism/identificationLabel/_alt/2,/aggregateoccurrence/individualplant/stem/authorstemcode/_alt/2


  		




  65
  
  
    
/*ID->/*s/individualOrganism/identificationLabel/_alt/2,/aggregateoccurrence/individualplant/stem/authorstemcode/_alt/2


  		




  66
  
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance/value=0]/diameter,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=basalDiameter]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  67
  
  
    
/diameterBaseDistance[baseDistance/value=0]/diameter,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=basalDiameter]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  68
  
  
    
/simpleUserdefined[name=stemCanopyForm]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=canopyForm]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  69
  
  
    
/simpleUserdefined[name=stemCanopyPosition]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=canopyPosition]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  70
  
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance[complexUserDefined/method=Gentry]/value=1.37]/diameter,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=gentryDiameter]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  71
  
  
    
/simpleUserdefined[name=habitat]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=habitat]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  72
  
  
    
/simpleUserdefined[name=htFirstBranchM]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  73
  
  
    
/simpleUserdefined[name=stemHeightFirstBranchM]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  74
  
  
    
/simpleUserdefined[name=stemLianaInfestation]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=lianaInfestation]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  75
  
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/note/text,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=notes]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  76
  
  
    
/simpleUserdefined[name=plantFungusDescription]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=plantFungusDescription]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  77
  
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=stemCanopyForm]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemCanopyForm]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  78
  
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=stemCanopyPosition]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemCanopyPosition]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  79
  
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=stemHeightFirstBranchM]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemHeightFirstBranchM]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  80
  
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=stemLianaInfestation]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemLianaInfestation]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  81
  
  
    
/simpleUserdefined[name=substrate]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=substrate]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  82
  
  
    
/simpleUserdefined[name=vegetation]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=vegetation]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  83
  
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance[!complexUserDefined/method]/value=1.37]/diameter,/aggregateoccurrence/individualplant/stem/diameter


  		




  84
  
  
    
/diameterBaseDistance[baseDistance/value=1.37]/diameter,/aggregateoccurrence/individualplant/stem/diameter


  		




  85
  
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=stemHeightM]/value,/aggregateoccurrence/individualplant/stem/height


  		




  86
  
  
    
/simpleUserdefined[name=xPosition]/value,/aggregateoccurrence/individualplant/stem/xposition


  		




  87
  
  
    
/simpleUserdefined[name=yPosition]/value,/aggregateoccurrence/individualplant/stem/yposition


  		




  
  56
  
    
/height,/aggregateoccurrence/plantobservation/overallheight


  		




  
  57
  
    
/simpleUserdefined[name=stemHeightM]/value,/aggregateoccurrence/plantobservation/overallheight


  		




  
  58
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/relatedItem[relationshipType=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,/aggregateoccurrence/plantobservation/stem/*_id/plantobservation/authorplantcode


  		




  
  59
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=count]/value,/aggregateoccurrence/plantobservation/stem/*_id/plantobservation/stemcount


  		




  
  60
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/*ID->/*s/individualOrganism/identificationLabel,/aggregateoccurrence/plantobservation/stem/authorstemcode


  		




  
  61
  
    
/*ID->/*s/individualOrganism/identificationLabel,/aggregateoccurrence/plantobservation/stem/authorstemcode


  		




  
  62
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/*ID->/*s/individualOrganism/identificationLabel/_alt/1,/aggregateoccurrence/plantobservation/stem/authorstemcode/_alt/1


  		




  
  63
  
    
/*ID->/*s/individualOrganism/identificationLabel/_alt/1,/aggregateoccurrence/plantobservation/stem/authorstemcode/_alt/1


  		




  
  64
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/*ID->/*s/individualOrganism/identificationLabel/_alt/2,/aggregateoccurrence/plantobservation/stem/authorstemcode/_alt/2


  		




  
  65
  
    
/*ID->/*s/individualOrganism/identificationLabel/_alt/2,/aggregateoccurrence/plantobservation/stem/authorstemcode/_alt/2


  		




  
  66
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance/value=0]/diameter,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=basalDiameter]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  67
  
    
/diameterBaseDistance[baseDistance/value=0]/diameter,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=basalDiameter]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  68
  
    
/simpleUserdefined[name=stemCanopyForm]/value,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=canopyForm]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  69
  
    
/simpleUserdefined[name=stemCanopyPosition]/value,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=canopyPosition]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  70
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance[complexUserDefined/method=Gentry]/value=1.37]/diameter,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=gentryDiameter]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  71
  
    
/simpleUserdefined[name=habitat]/value,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=habitat]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  72
  
    
/simpleUserdefined[name=htFirstBranchM]/value,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  73
  
    
/simpleUserdefined[name=stemHeightFirstBranchM]/value,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  74
  
    
/simpleUserdefined[name=stemLianaInfestation]/value,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=lianaInfestation]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  75
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/note/text,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=notes]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  76
  
    
/simpleUserdefined[name=plantFungusDescription]/value,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=plantFungusDescription]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  77
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=stemCanopyForm]/value,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemCanopyForm]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  78
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=stemCanopyPosition]/value,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemCanopyPosition]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  79
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=stemHeightFirstBranchM]/value,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemHeightFirstBranchM]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  80
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=stemLianaInfestation]/value,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemLianaInfestation]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  81
  
    
/simpleUserdefined[name=substrate]/value,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=substrate]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  82
  
    
/simpleUserdefined[name=vegetation]/value,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=vegetation]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  
  83
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance[!complexUserDefined/method]/value=1.37]/diameter,/aggregateoccurrence/plantobservation/stem/diameter


  		




  
  84
  
    
/diameterBaseDistance[baseDistance/value=1.37]/diameter,/aggregateoccurrence/plantobservation/stem/diameter


  		




  
  85
  
    
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=stemHeightM]/value,/aggregateoccurrence/plantobservation/stem/height


  		




  
  86
  
    
/simpleUserdefined[name=xPosition]/value,/aggregateoccurrence/plantobservation/stem/xposition


  		




  
  87
  
    
/simpleUserdefined[name=yPosition]/value,/aggregateoccurrence/plantobservation/stem/yposition


  		




  88
  88
  
    
/simpleUserdefined[name=censusNo]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=censusNo]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  89
  89
  
    
/simpleUserdefined[name=habit]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=habit]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  90
  90
  
    
/simpleUserdefined[name=individualCode]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=individualCode]]:[@fkey=tableRecord_ID]/definedvalue"


  		




  ......




  124
  124
  
    
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=sp])/Name","/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname"


  		




  125
  125
  
    
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=phyl_div])/Name","/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname"


  		




  126
  126
  
    
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=ssp])/Name","/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/*_id/plantconcept/*_id/*/plantname"


  		




  127
  
  
    
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,"/{aggregateoccurrence/individualplant/authorplantcode,specimenreplicate:[*_id/reference]/sourceaccessioncode}"


  		




  
  127
  
    
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,"/{aggregateoccurrence/plantobservation/authorplantcode,specimenreplicate:[*_id/reference]/sourceaccessioncode}"


  		












  

    
      mappings/for_review/SALVIAS_db-VegBIEN.organisms.csv
    
  





  3
  3
  
    
NoInd,//aggregateoccurrence/count,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."


  		




  4
  4
  
    
cover_percent,//aggregateoccurrence/cover,


  		




  5
  5
  
    
intercept_cm,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."


  		




  6
  
  
    
height_m,//individualplant/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob


  		




  
  6
  
    
height_m,//plantobservation/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob


  		




  7
  7
  
    
tag2,//stem/authorstemcode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."


  		




  8
  8
  
    
tag1,//stem/authorstemcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."


  		




  9
  9
  
    
ht_first_branch_m,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob


  		




  ......




  28
  28
  
    
Notes,/taxondetermination[rolecode=identifier]/notes,


  		




  29
  29
  
    
OrigFamily,"/taxondetermination[rolecode=identifier,plantlevel=Family]/*_id/plantconcept/*_id/*/plantname",Brad: OMIT


  		




  30
  30
  
    
OrigSpecies,"/taxondetermination[rolecode=identifier,plantlevel=Species]/*_id/plantconcept/*_id/*/plantname",Brad: OMIT


  		




  31
  
  
    
PlotObsID,"/{aggregateoccurrence/individualplant/authorplantcode,specimenreplicate/sourceaccessioncode}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."


  		




  
  31
  
    
PlotObsID,"/{aggregateoccurrence/plantobservation/authorplantcode,specimenreplicate/sourceaccessioncode}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."


  		












  

    
      mappings/for_review/VegX-VegBIEN.organisms.csv
    
  





  53
  53
  
    
/simpleUserdefined[name=count]/value,//aggregateoccurrence/count


  		




  54
  54
  
    
/simpleUserdefined[name=coverPercent]/value,//aggregateoccurrence/cover


  		




  55
  55
  
    
/simpleUserdefined[name=interceptCm]/value,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]/definedvalue"


  		




  56
  
  
    
/height,//individualplant/overallheight


  		




  57
  
  
    
/simpleUserdefined[name=stemHeightM]/value,//individualplant/overallheight


  		




  58
  
  
    
//taxonNameUsageConcept/voucher,//individualplant/authorplantcode


  		




  59
  
  
    
//*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=count]/value,//individualplant/stemcount


  		




  
  56
  
    
/height,//plantobservation/overallheight


  		




  
  57
  
    
/simpleUserdefined[name=stemHeightM]/value,//plantobservation/overallheight


  		




  
  58
  
    
//taxonNameUsageConcept/voucher,//plantobservation/authorplantcode


  		




  
  59
  
    
//*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=count]/value,//plantobservation/stemcount


  		




  60
  60
  
    
//individualOrganism/identificationLabel,//stem/authorstemcode


  		




  61
  61
  
    
//individualOrganism/identificationLabel,//stem/authorstemcode


  		




  62
  62
  
    
//individualOrganism/identificationLabel/_alt/1,//stem/authorstemcode/_alt/1


  		




  ......




  124
  124
  
    
//*s/taxonConcept[@code=sp]/Name,"/taxondetermination[rolecode=identifier,plantlevel=Species]/*_id/plantconcept/*_id/*/plantname"


  		




  125
  125
  
    
//*s/taxonConcept[@code=phyl_div]/Name,"/taxondetermination[rolecode=identifier,plantlevel=Subkingdom]/*_id/plantconcept/*_id/*/plantname"


  		




  126
  126
  
    
//*s/taxonConcept[@code=ssp]/Name,"/taxondetermination[rolecode=identifier,plantlevel=Subspecies]/*_id/plantconcept/*_id/*/plantname"


  		




  127
  
  
    
//taxonNameUsageConcept/voucher,"/{aggregateoccurrence/individualplant/authorplantcode,specimenreplicate/sourceaccessioncode}"


  		




  
  127
  
    
//taxonNameUsageConcept/voucher,"/{aggregateoccurrence/plantobservation/authorplantcode,specimenreplicate/sourceaccessioncode}"


  		












  

    
      mappings/for_review/NYBG-VegBIEN.organisms.csv
    
  





  39
  39
  
    
Species,"/taxondetermination[rolecode=identifier,plantlevel=Species]/*_id/plantconcept/*_id/*/plantname",


  		




  40
  40
  
    
Phylum,"/taxondetermination[rolecode=identifier,plantlevel=Subkingdom]/*_id/plantconcept/*_id/*/plantname",


  		




  41
  41
  
    
Subspecies,"/taxondetermination[rolecode=identifier,plantlevel=Subspecies]/*_id/plantconcept/*_id/*/plantname",


  		




  42
  
  
    
UniqueNYInternalRecordNumber,"/{aggregateoccurrence/individualplant/authorplantcode,specimenreplicate/sourceaccessioncode}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key"


  		




  
  42
  
    
UniqueNYInternalRecordNumber,"/{aggregateoccurrence/plantobservation/authorplantcode,specimenreplicate/sourceaccessioncode}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key"


  		












  

    
      mappings/for_review/SALVIAS-VegBIEN.organisms.csv
    
  





  5
  5
  
    
no_of_individuals,//aggregateoccurrence/count,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."


  		




  6
  6
  
    
cover_percent,//aggregateoccurrence/cover,


  		




  7
  7
  
    
intercept_cm,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."


  		




  8
  
  
    
height_m,//individualplant/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob


  		




  9
  
  
    
stem_height_m,//individualplant/overallheight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."


  		




  
  8
  
    
height_m,//plantobservation/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob


  		




  
  9
  
    
stem_height_m,//plantobservation/overallheight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."


  		




  10
  10
  
    
stem_tag1,//stem/authorstemcode,"Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."


  		




  11
  11
  
    
stem_tag2,//stem/authorstemcode,Brad: see above


  		




  12
  12
  
    
tag2,//stem/authorstemcode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."


  		




  ......




  37
  37
  
    
notes,/taxondetermination[rolecode=identifier]/notes,


  		




  38
  38
  
    
orig_family,"/taxondetermination[rolecode=identifier,plantlevel=Family]/*_id/plantconcept/*_id/*/plantname",Brad: OMIT


  		




  39
  39
  
    
orig_species,"/taxondetermination[rolecode=identifier,plantlevel=Species]/*_id/plantconcept/*_id/*/plantname",Brad: OMIT


  		




  40
  
  
    
OBSERVATION_ID,"/{aggregateoccurrence/individualplant/authorplantcode,specimenreplicate/sourceaccessioncode}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."


  		




  
  40
  
    
OBSERVATION_ID,"/{aggregateoccurrence/plantobservation/authorplantcode,specimenreplicate/sourceaccessioncode}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."


  		












  

    
      mappings/NYBG-VegBIEN.organisms.csv
    
  





  14
  14
  
    
YearCollected,/*_id/locationevent/obsstartdate/_date/year,


  		




  15
  15
  
    
MaximumDepth,/*_id/locationevent/waterdepth/max,


  		




  16
  16
  
    
MinimumDepth,/*_id/locationevent/waterdepth/min,


  		




  17
  
  
    
Habitat,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=habitat]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?"


  		




  18
  
  
    
PlantFungusDescription,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=plantFungusDescription]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect mapping to VB, also possibly to VX;  this is the specimenDescription field, as used by this institution (NOT a standard DwC element). Very important! Bob, Nick, where would this go in VB and VX?"


  		




  19
  
  
    
Substrate,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=substrate]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect mapping to VB and VX; refers to geological substrate or soils where specimen collected. Often concatenated with habitat, or included with specimen description. Bob, Nick, is there an element for this in VB/VX, or shall we just use userDefined?"


  		




  20
  
  
    
Vegetation,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=vegetation]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Habitat'. Bob, Nick: keep as user defined or create special element?"


  		




  
  17
  
    
Habitat,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=habitat]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?"


  		




  
  18
  
    
PlantFungusDescription,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=plantFungusDescription]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect mapping to VB, also possibly to VX;  this is the specimenDescription field, as used by this institution (NOT a standard DwC element). Very important! Bob, Nick, where would this go in VB and VX?"


  		




  
  19
  
    
Substrate,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=substrate]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect mapping to VB and VX; refers to geological substrate or soils where specimen collected. Often concatenated with habitat, or included with specimen description. Bob, Nick, is there an element for this in VB/VX, or shall we just use userDefined?"


  		




  
  20
  
    
Vegetation,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=vegetation]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Habitat'. Bob, Nick: keep as user defined or create special element?"


  		




  21
  21
  
    
FieldNumber,/specimenreplicate:[*_id/reference]/catalognumber_dwc,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?"


  		




  22
  22
  
    
CollectorNumber,/specimenreplicate:[*_id/reference]/collectornumber_dwc,"Brad: OMIT; db-specific element, not relevant to VB/VX"


  		




  23
  23
  
    
Collector,/specimenreplicate:[*_id/reference]/verbatimcollectorname,Brad: Correct for VB. Nick: is there a way to specifically identify this party as collector of a specimen?


  		




  ......




  39
  39
  
    
Species,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",


  		




  40
  40
  
    
Phylum,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",


  		




  41
  41
  
    
Subspecies,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/*_id/plantconcept/*_id/*/plantname",


  		




  42
  
  
    
UniqueNYInternalRecordNumber,"/{aggregateoccurrence/individualplant/authorplantcode,specimenreplicate:[*_id/reference]/sourceaccessioncode}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key"


  		




  
  42
  
    
UniqueNYInternalRecordNumber,"/{aggregateoccurrence/plantobservation/authorplantcode,specimenreplicate:[*_id/reference]/sourceaccessioncode}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key"


  		












  

    
      mappings/VegX-VegBIEN.stems.csv
    
  





  1
  1
  
    
VegX:/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID],VegBIEN:/stem


  		




  2
  
  
    
/relatedItem[relationshipType=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,/*_id/individualplant/authorplantcode


  		




  3
  
  
    
/simpleUserdefined[name=count]/value,/*_id/individualplant/stemcount


  		




  
  2
  
    
/relatedItem[relationshipType=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,/*_id/plantobservation/authorplantcode


  		




  
  3
  
    
/simpleUserdefined[name=count]/value,/*_id/plantobservation/stemcount


  		




  4
  4
  
    
/*ID->/*s/individualOrganism/identificationLabel,/authorstemcode


  		




  5
  5
  
    
/*ID->/*s/individualOrganism/identificationLabel/_alt/1,/authorstemcode/_alt/1


  		




  6
  6
  
    
/*ID->/*s/individualOrganism/identificationLabel/_alt/2,/authorstemcode/_alt/2


  		












  

    
      mappings/SALVIAS-VegBIEN.organisms.csv
    
  





  5
  5
  
    
no_of_individuals,/aggregateoccurrence/count,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."


  		




  6
  6
  
    
cover_percent,/aggregateoccurrence/cover,


  		




  7
  7
  
    
intercept_cm,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."


  		




  8
  
  
    
height_m,/aggregateoccurrence/individualplant/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob


  		




  9
  
  
    
stem_height_m,/aggregateoccurrence/individualplant/overallheight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."


  		




  10
  
  
    
stem_tag1,/aggregateoccurrence/individualplant/stem/authorstemcode,"Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."


  		




  11
  
  
    
stem_tag2,/aggregateoccurrence/individualplant/stem/authorstemcode,Brad: see above


  		




  12
  
  
    
tag2,/aggregateoccurrence/individualplant/stem/authorstemcode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."


  		




  13
  
  
    
tag1,/aggregateoccurrence/individualplant/stem/authorstemcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."


  		




  14
  
  
    
basal_diam,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=basalDiameter]]:[@fkey=tableRecord_ID]/definedvalue",


  		




  15
  
  
    
stem_canopy_form,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=canopyForm]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. 


  		




  16
  
  
    
stem_canopy_position,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=canopyPosition]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. 


  		




  17
  
  
    
ht_first_branch_m,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob


  		




  18
  
  
    
stem_height_first_branch_m,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."


  		




  19
  
  
    
stem_liana_infestation,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=lianaInfestation]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. 


  		




  20
  
  
    
stem_dbh,/aggregateoccurrence/individualplant/stem/diameter,


  		




  21
  
  
    
x_position,/aggregateoccurrence/individualplant/stem/xposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."


  		




  22
  
  
    
y_position,/aggregateoccurrence/individualplant/stem/yposition,Brad: See comment above for x_position


  		




  
  8
  
    
height_m,/aggregateoccurrence/plantobservation/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob


  		




  
  9
  
    
stem_height_m,/aggregateoccurrence/plantobservation/overallheight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."


  		




  
  10
  
    
stem_tag1,/aggregateoccurrence/plantobservation/stem/authorstemcode,"Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."


  		




  
  11
  
    
stem_tag2,/aggregateoccurrence/plantobservation/stem/authorstemcode,Brad: see above


  		




  
  12
  
    
tag2,/aggregateoccurrence/plantobservation/stem/authorstemcode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."


  		




  
  13
  
    
tag1,/aggregateoccurrence/plantobservation/stem/authorstemcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."


  		




  
  14
  
    
basal_diam,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=basalDiameter]]:[@fkey=tableRecord_ID]/definedvalue",


  		




  
  15
  
    
stem_canopy_form,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=canopyForm]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. 


  		




  
  16
  
    
stem_canopy_position,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=canopyPosition]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. 


  		




  
  17
  
    
ht_first_branch_m,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob


  		




  
  18
  
    
stem_height_first_branch_m,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."


  		




  
  19
  
    
stem_liana_infestation,"/aggregateoccurrence/plantobservation/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=lianaInfestation]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. 


  		




  
  20
  
    
stem_dbh,/aggregateoccurrence/plantobservation/stem/diameter,


  		




  
  21
  
    
x_position,/aggregateoccurrence/plantobservation/stem/xposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."


  		




  
  22
  
    
y_position,/aggregateoccurrence/plantobservation/stem/yposition,Brad: See comment above for x_position


  		




  23
  23
  
    
census_no,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=censusNo]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."


  		




  24
  24
  
    
habit,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=habit]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."


  		




  25
  25
  
    
individual_code,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=individualCode]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."


  		




  ......




  37
  37
  
    
notes,"/taxondetermination[*_id/role/rolecode=identifier,!*_id/plantconcept]:[determinationtype=Author,iscurrent=true]/notes",


  		




  38
  38
  
    
orig_family,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",Brad: OMIT


  		




  39
  39
  
    
orig_species,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",Brad: OMIT


  		




  40
  
  
    
OBSERVATION_ID,"/{aggregateoccurrence/individualplant/authorplantcode,specimenreplicate:[*_id/reference]/sourceaccessioncode}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."


  		




  
  40
  
    
OBSERVATION_ID,"/{aggregateoccurrence/plantobservation/authorplantcode,specimenreplicate:[*_id/reference]/sourceaccessioncode}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."


  		












  

    
      mappings/Makefile
    
  





  44
  44
  
    
	env \


  		




  45
  45
  
    
left_in_root='/*s/individualOrganismObservation->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]' \


  		




  46
  46
  
    
left_out_root='/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]' \


  		




  47
  
  
    
right_in_root='/taxonoccurrence/aggregateoccurrence/individualplant/stem' \


  		




  
  47
  
    
right_in_root='/taxonoccurrence/aggregateoccurrence/plantobservation/stem' \


  		




  48
  48
  
    
right_out_root='/stem' \


  		




  49
  49
  
    
$(chRoot)


  		












Also available in:  Unified diff