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Revision 495

VegBIEN: Merged specimen.collectionnumber and catalognumber_dwc fields. Removed NOT NULL constraints on several specimen columns because not all specimens have all identifiers. Mapped to new specimen fields.

View differences:

test/accepted_output/SALVIAS.organisms.VegBIEN.xml
23 23
            <count>1</count>
24 24
            <individualplant>
25 25
                <diameter>662</diameter>
26
                <specimen>
27
                    <reference_id>
28
                        <reference/>
29
                    </reference_id>
30
                    <catalognumber_dwc>14598</catalognumber_dwc>
31
                </specimen>
26 32
                <stem>
27 33
                    <authorcode>8</authorcode>
28 34
                </stem>
......
34 40
                    <rolecode>collector</rolecode>
35 41
                </aux_role>
36 42
            </role_id>
37
            <collectionnumber>14598</collectionnumber>
38 43
            <collector_id>
39 44
                <party>
40 45
                    <surname>Vasquez</surname>
......
303 308
            <count>1</count>
304 309
            <individualplant>
305 310
                <diameter>215</diameter>
311
                <specimen>
312
                    <reference_id>
313
                        <reference/>
314
                    </reference_id>
315
                    <catalognumber_dwc>14669</catalognumber_dwc>
316
                </specimen>
306 317
                <stem>
307 318
                    <authorcode>91</authorcode>
308 319
                </stem>
......
314 325
                    <rolecode>collector</rolecode>
315 326
                </aux_role>
316 327
            </role_id>
317
            <collectionnumber>14669</collectionnumber>
318 328
            <collector_id>
319 329
                <party>
320 330
                    <surname>Vasquez</surname>
test/accepted_output/NYBG.organisms.VegBIEN.xml
44 44
        </plotevent_id>
45 45
        <aggregateoccurrence>
46 46
            <individualplant>
47
                <specimen>
48
                    <reference_id>
49
                        <reference/>
50
                    </reference_id>
51
                    <catalognumber_dwc>9877</catalognumber_dwc>
52
                    <collectioncode_dwc>Herbarium</collectioncode_dwc>
53
                </specimen>
47 54
                <stem>
48 55
                    <definedvalue fkey="tableRecord_ID">
49 56
                        <userdefined_id>
......
75 82
                    <rolecode>collector</rolecode>
76 83
                </aux_role>
77 84
            </role_id>
78
            <collectionnumber>9877</collectionnumber>
79 85
            <collector_id>
80 86
                <party>
81 87
                    <givenname>R.</givenname>
......
360 366
                <authorcode>220541</authorcode>
361 367
            </plotevent>
362 368
        </plotevent_id>
369
        <aggregateoccurrence>
370
            <individualplant>
371
                <specimen>
372
                    <reference_id>
373
                        <reference/>
374
                    </reference_id>
375
                    <catalognumber_dwc>545</catalognumber_dwc>
376
                    <collectioncode_dwc>Herbarium</collectioncode_dwc>
377
                </specimen>
378
            </individualplant>
379
            <count>1</count>
380
        </aggregateoccurrence>
363 381
        <taxondetermination>
364 382
            <role_id>
365 383
                <aux_role>
366 384
                    <rolecode>collector</rolecode>
367 385
                </aux_role>
368 386
            </role_id>
369
            <collectionnumber>545</collectionnumber>
370 387
            <collector_id>
371 388
                <party>
372 389
                    <givenname>J.</givenname>
......
529 546
                </plantname>
530 547
            </plantname_id>
531 548
        </taxondetermination>
532
        <aggregateoccurrence>
533
            <count>1</count>
534
        </aggregateoccurrence>
535 549
    </taxonoccurrence>
536 550
</VegBIEN>
inputs/SALVIAS/map.VegBIEN.organisms.csv
6 6
intercept_cm,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@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."
7 7
temp_dbh,/aggregateoccurrence/individualplant/diameter,
8 8
height_m,/aggregateoccurrence/individualplant/height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
9
coll_number,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string
10
census_date,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/collectiondate/_date/date,
9 11
tag2,/aggregateoccurrence/individualplant/stem/authorcode/_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."
10 12
tag1,/aggregateoccurrence/individualplant/stem/authorcode/_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."
11 13
ht_first_branch_m,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
12 14
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."
13 15
y_position,/aggregateoccurrence/individualplant/stem/yposition,Brad: See comment above for x_position
14
census_date,/specimen/collectiondate/_date/date,
15
coll_number,/taxondetermination[role_id/aux_role/rolecode=collector]/collectionnumber,Brad: Incorrect. Map instead as for voucher_string
16 16
coll_firstname,"/taxondetermination[role_id/aux_role/rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}",Brad: See comment above
17 17
coll_lastname,/taxondetermination[role_id/aux_role/rolecode=collector]/collector_id/party/{surname},"Brad: Correct for VegBank. This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
18 18
census_no,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=censusNo]:[userdefinedtype=varchar]]:[@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."
schemas/vegbien.sql
2259 2259
    individualplant_id integer,
2260 2260
    reference_id integer NOT NULL,
2261 2261
    collectioncode_dwc character varying(255) NOT NULL,
2262
    catalognumber_dwc character varying(255) NOT NULL,
2263
    collectionnumber character varying(100),
2262
    catalognumber_dwc character varying(255),
2264 2263
    collectiondate timestamp with time zone
2265 2264
);
2266 2265

  
mappings/SALVIAS_db-VegBIEN.organisms.csv
6 6
intercept_cm,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@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."
7 7
temp_dbh,/aggregateoccurrence/individualplant/diameter,
8 8
height_m,/aggregateoccurrence/individualplant/height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
9
coll_number,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string
10
census_date,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/collectiondate/_date/date,
9 11
tag2,/aggregateoccurrence/individualplant/stem/authorcode/_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."
10 12
tag1,/aggregateoccurrence/individualplant/stem/authorcode/_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."
11 13
ht_first_branch_m,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
12 14
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."
13 15
y_position,/aggregateoccurrence/individualplant/stem/yposition,Brad: See comment above for x_position
14
census_date,/specimen/collectiondate/_date/date,
15
coll_number,/taxondetermination[role_id/aux_role/rolecode=collector]/collectionnumber,Brad: Incorrect. Map instead as for voucher_string
16 16
coll_firstname,"/taxondetermination[role_id/aux_role/rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}",Brad: See comment above
17 17
coll_lastname,/taxondetermination[role_id/aux_role/rolecode=collector]/collector_id/party/{surname},"Brad: Correct for VegBank. This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
18 18
census_no,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=censusNo]:[userdefinedtype=varchar]]:[@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."
mappings/VegX-VegBIEN.organisms.csv
56 56
/diameterBaseDistance[baseDistance=1.37]/diameter,/aggregateoccurrence/individualplant/diameter
57 57
/height,/aggregateoccurrence/individualplant/height
58 58
/simpleUserdefined[name=stemHeightM]/value,/aggregateoccurrence/individualplant/height
59
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/authorCode,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/catalognumber_dwc
60
/simpleUserdefined[name=collectionDate]/value,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/collectiondate
61
/simpleUserdefined[name=collectionDate]/value/_date/date,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/collectiondate/_date/date
59 62
/*ID->/*s/individualOrganism/identificationLabel,/aggregateoccurrence/individualplant/stem/authorcode
60 63
/*ID->/*s/individualOrganism/identificationLabel/_alt/1,/aggregateoccurrence/individualplant/stem/authorcode/_alt/1
61 64
/*ID->/*s/individualOrganism/identificationLabel/_alt/2,/aggregateoccurrence/individualplant/stem/authorcode/_alt/2
......
71 74
/simpleUserdefined[name=vegetation]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=vegetation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
72 75
/simpleUserdefined[name=xPosition]/value,/aggregateoccurrence/individualplant/stem/xposition
73 76
/simpleUserdefined[name=yPosition]/value,/aggregateoccurrence/individualplant/stem/yposition
74
/simpleUserdefined[name=collectionDate]/value,/specimen/collectiondate
75
/simpleUserdefined[name=collectionDate]/value/_date/date,/specimen/collectiondate/_date/date
76
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/authorCode,/taxondetermination[role_id/aux_role/rolecode=collector]/collectionnumber
77 77
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/partyWithRole/*ID->/parties/party/individualName/givenName","/taxondetermination[role_id/aux_role/rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}"
78 78
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/partyWithRole/*ID->/parties/party/individualName/{givenName/_namePart/{first,middle},surName/_namePart/last}","/taxondetermination[role_id/aux_role/rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}"
79 79
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/partyWithRole/*ID->/parties/party/individualName/surName",/taxondetermination[role_id/aux_role/rolecode=collector]/collector_id/party/{surname}
......
83 83
/simpleUserdefined[name=habit]/value,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=habit]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
84 84
/simpleUserdefined[name=individualCode]/value,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=individualCode]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
85 85
/*ID->/*s/individualOrganism/simpleUserdefined[name=sex]/value,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=sex]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
86
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,/taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname
87 86
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/first,/taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname/_name/first
88
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/last,/taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname/_name/last
89 87
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/note/text,/taxondetermination[role_id/aux_role/rolecode=collector]/notes
90 88
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=fam])/Name","/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=""Computer (automated)"",originaldetermination=false,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}"
91 89
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=gen])/Name","/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=""Computer (automated)"",originaldetermination=false,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}"
......
105 103
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=sp])/AccordingTo/Simple","/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]/*_id/plantconcept/*_id/reference/referencecontributor/*_id/referenceparty/{givenname,surname}"
106 104
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=phyl_div])/Name","/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}"
107 105
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=ssp])/Name","/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}"
106
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,"/{taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname,aggregateoccurrence/individualplant/specimen:[*_id/reference]/collectioncode_dwc/_namePart/last}"
107
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/last,"/{taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname/_name/last,aggregateoccurrence/individualplant/specimen:[*_id/reference]/collectioncode_dwc}"
108 108
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonName)/Simple","/{taxondetermination[role_id/aux_role/rolecode=identifier,!*_id/plantconcept]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/*_id/*/plantname,taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/1}"
109 109
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=sp])/Name","/{taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname},taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/2}"
110 110
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/authorcode/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/authorcode/_alt/3}"
mappings/NYBG-VegBIEN.organisms.csv
14 14
YearCollected,/*_id/plotevent/obsstartdate/_date/year,
15 15
MaximumDepth,/*_id/plotevent/waterdepth/max,
16 16
MinimumDepth,/*_id/plotevent/waterdepth/min,
17
FieldNumber,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/catalognumber_dwc,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?"
17 18
Habitat,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=habitat]:[userdefinedtype=varchar]]:[@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 19
PlantFungusDescription,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=plantFungusDescription]:[userdefinedtype=varchar]]:[@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 20
Substrate,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=substrate]:[userdefinedtype=varchar]]:[@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 21
Vegetation,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=vegetation]:[userdefinedtype=varchar]]:[@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
FieldNumber,/taxondetermination[role_id/aux_role/rolecode=collector]/collectionnumber,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?"
22 22
Collector,"/taxondetermination[role_id/aux_role/rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Correct for VB. Nick: is there a way to specifically identify this party as collector of a specimen?
23 23
Sex,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=sex]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections"
24 24
InstitutionCode,/taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname/_name/first,
25
CollectionCode,/taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname/_name/last,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
26 25
Notes,/taxondetermination[role_id/aux_role/rolecode=collector]/notes,"Brad: mapping OK; NY appears to be using this field for almost anything, but mostly internal collections notes"
27 26
DayIdentified,"/taxondetermination[role_id/aux_role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_date/day",
28 27
MonthIdentified,"/taxondetermination[role_id/aux_role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_date/month",
......
36 35
ScientificNameAuthor,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]/*_id/plantconcept/*_id/reference/referencecontributor/*_id/referenceparty/{givenname,surname}","Brad: Mapping probably incorrect. This DwC element refers to scientific name author; does not correspond to the VegBank and VegX elements you have listed (Bob, Nick�where does name author belong in VegBank and VegX?); Aaron: The mapped VegX element is the author linked to the taxon name, so it seems like this is the scientific name author"
37 36
Phylum,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}",
38 37
Subspecies,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}",
38
CollectionCode,"/{taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname/_name/last,aggregateoccurrence/individualplant/specimen:[*_id/reference]/collectioncode_dwc}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
39 39
ScientificName,"/{taxondetermination[role_id/aux_role/rolecode=identifier,!*_id/plantconcept]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/*_id/*/plantname,taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/1}","Brad: Bob, Nick, please is this mapping OK?"
40 40
Species,"/{taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname},taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/2}",
41 41
UniqueNYInternalRecordNumber,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/authorcode/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/authorcode/_alt/3}","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_db-VegBIEN.organisms.csv
6 6
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."
7 7
temp_dbh,//individualplant/diameter,
8 8
height_m,//individualplant/height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
9
coll_number,//specimen/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string
10
census_date,//specimen/collectiondate/_date/date,
9 11
tag2,//stem/authorcode/_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."
10 12
tag1,//stem/authorcode/_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."
11 13
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
12 14
x_position,//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."
13 15
y_position,//stem/yposition,Brad: See comment above for x_position
14
census_date,//specimen/collectiondate/_date/date,
15
coll_number,/taxondetermination[rolecode=collector]/collectionnumber,Brad: Incorrect. Map instead as for voucher_string
16 16
coll_firstname,"/taxondetermination[rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}",Brad: See comment above
17 17
coll_lastname,/taxondetermination[rolecode=collector]/collector_id/party/{surname},"Brad: Correct for VegBank. This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
18 18
census_no,"/taxondetermination[rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=censusNo]]/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."
mappings/for_review/VegX-VegBIEN.organisms.csv
56 56
/diameterBaseDistance[baseDistance=1.37]/diameter,//individualplant/diameter
57 57
/height,//individualplant/height
58 58
/simpleUserdefined[name=stemHeightM]/value,//individualplant/height
59
//taxonNameUsageConcept/authorCode,//specimen/catalognumber_dwc
60
/simpleUserdefined[name=collectionDate]/value,//specimen/collectiondate
61
/simpleUserdefined[name=collectionDate]/value/_date/date,//specimen/collectiondate/_date/date
59 62
//individualOrganism/identificationLabel,//stem/authorcode
60 63
//individualOrganism/identificationLabel/_alt/1,//stem/authorcode/_alt/1
61 64
//individualOrganism/identificationLabel/_alt/2,//stem/authorcode/_alt/2
......
71 74
/simpleUserdefined[name=vegetation]/value,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=vegetation]]/definedvalue"
72 75
/simpleUserdefined[name=xPosition]/value,//stem/xposition
73 76
/simpleUserdefined[name=yPosition]/value,//stem/yposition
74
/simpleUserdefined[name=collectionDate]/value,//specimen/collectiondate
75
/simpleUserdefined[name=collectionDate]/value/_date/date,//specimen/collectiondate/_date/date
76
//taxonNameUsageConcept/authorCode,/taxondetermination[rolecode=collector]/collectionnumber
77 77
//individualName/givenName,"/taxondetermination[rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}"
78 78
"//parties/party/individualName/{givenName/_namePart/{first,middle},surName/_namePart/last}","/taxondetermination[rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}"
79 79
//individualName/surName,/taxondetermination[rolecode=collector]/collector_id/party/{surname}
......
83 83
/simpleUserdefined[name=habit]/value,"/taxondetermination[rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=habit]]/definedvalue"
84 84
/simpleUserdefined[name=individualCode]/value,"/taxondetermination[rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=individualCode]]/definedvalue"
85 85
//individualOrganism/simpleUserdefined[name=sex]/value,"/taxondetermination[rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=sex]]/definedvalue"
86
//party/organizationName,/taxondetermination[rolecode=collector]/museum_id/party/organizationname
87 86
//party/organizationName/_name/first,/taxondetermination[rolecode=collector]/museum_id/party/organizationname/_name/first
88
//party/organizationName/_name/last,/taxondetermination[rolecode=collector]/museum_id/party/organizationname/_name/last
89 87
//note/text,/taxondetermination[rolecode=collector]/notes
90 88
//*s/taxonConcept[@code=fam]/Name,"/taxondetermination[rolecode=computer,plantlevel=Family]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname}"
91 89
//*s/taxonConcept[@code=gen]/Name,"/taxondetermination[rolecode=computer,plantlevel=Genus]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname}"
......
105 103
//*s/taxonConcept[@code=sp]/AccordingTo/Simple,"/taxondetermination[rolecode=identifier,plantlevel=Species]/*_id/plantconcept/*_id/reference/referencecontributor/*_id/referenceparty/{givenname,surname}"
106 104
//*s/taxonConcept[@code=phyl_div]/Name,"/taxondetermination[rolecode=identifier,plantlevel=Subkingdom]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname}"
107 105
//*s/taxonConcept[@code=ssp]/Name,"/taxondetermination[rolecode=identifier,plantlevel=Subspecies]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname}"
106
//party/organizationName,"/{taxondetermination[rolecode=collector]/museum_id/party/organizationname,aggregateoccurrence/individualplant/specimen/collectioncode_dwc/_namePart/last}"
107
//party/organizationName/_name/last,"/{taxondetermination[rolecode=collector]/museum_id/party/organizationname/_name/last,aggregateoccurrence/individualplant/specimen/collectioncode_dwc}"
108 108
//taxonName/Simple,"/{taxondetermination[rolecode=identifier]/*_id/*/plantname,taxondetermination[rolecode=collector]/*_id/*/plantname/_alt/1}"
109 109
//*s/taxonConcept[@code=sp]/Name,"/{taxondetermination[rolecode=identifier,plantlevel=Species]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname},taxondetermination[rolecode=collector]/*_id/*/plantname/_alt/2}"
110 110
//taxonNameUsageConcept/voucher,"/{taxondetermination[rolecode=collector]/museumaccessionnumber,*_id/plotevent/authorcode/_alt/2,*_id/plotevent/*_id/plot/authorcode/_alt/3}"
mappings/for_review/NYBG-VegBIEN.organisms.csv
14 14
YearCollected,//plotevent/obsstartdate/_date/year,
15 15
MaximumDepth,//waterdepth/max,
16 16
MinimumDepth,//waterdepth/min,
17
FieldNumber,//specimen/catalognumber_dwc,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?"
17 18
Habitat,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=habitat]]/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 19
PlantFungusDescription,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=plantFungusDescription]]/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 20
Substrate,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=substrate]]/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 21
Vegetation,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=vegetation]]/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
FieldNumber,/taxondetermination[rolecode=collector]/collectionnumber,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?"
22 22
Collector,"/taxondetermination[rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Correct for VB. Nick: is there a way to specifically identify this party as collector of a specimen?
23 23
Sex,"/taxondetermination[rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=sex]]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections"
24 24
InstitutionCode,/taxondetermination[rolecode=collector]/museum_id/party/organizationname/_name/first,
25
CollectionCode,/taxondetermination[rolecode=collector]/museum_id/party/organizationname/_name/last,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
26 25
Notes,/taxondetermination[rolecode=collector]/notes,"Brad: mapping OK; NY appears to be using this field for almost anything, but mostly internal collections notes"
27 26
DayIdentified,/taxondetermination[rolecode=identifier]/determinationdate/_date/day,
28 27
MonthIdentified,/taxondetermination[rolecode=identifier]/determinationdate/_date/month,
......
36 35
ScientificNameAuthor,"/taxondetermination[rolecode=identifier,plantlevel=Species]/*_id/plantconcept/*_id/reference/referencecontributor/*_id/referenceparty/{givenname,surname}","Brad: Mapping probably incorrect. This DwC element refers to scientific name author; does not correspond to the VegBank and VegX elements you have listed (Bob, Nick�where does name author belong in VegBank and VegX?); Aaron: The mapped VegX element is the author linked to the taxon name, so it seems like this is the scientific name author"
37 36
Phylum,"/taxondetermination[rolecode=identifier,plantlevel=Subkingdom]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname}",
38 37
Subspecies,"/taxondetermination[rolecode=identifier,plantlevel=Subspecies]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname}",
38
CollectionCode,"/{taxondetermination[rolecode=collector]/museum_id/party/organizationname/_name/last,aggregateoccurrence/individualplant/specimen/collectioncode_dwc}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
39 39
ScientificName,"/{taxondetermination[rolecode=identifier]/*_id/*/plantname,taxondetermination[rolecode=collector]/*_id/*/plantname/_alt/1}","Brad: Bob, Nick, please is this mapping OK?"
40 40
Species,"/{taxondetermination[rolecode=identifier,plantlevel=Species]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname},taxondetermination[rolecode=collector]/*_id/*/plantname/_alt/2}",
41 41
UniqueNYInternalRecordNumber,"/{taxondetermination[rolecode=collector]/museumaccessionnumber,*_id/plotevent/authorcode/_alt/2,*_id/plotevent/*_id/plot/authorcode/_alt/3}","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
8 8
stem_dbh,//individualplant/diameter,
9 9
height_m,//individualplant/height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
10 10
stem_height_m,//individualplant/height,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
11
coll_number,//specimen/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string
11 12
stem_tag1,//stem/authorcode,"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."
12 13
stem_tag2,//stem/authorcode,Brad: see above
13 14
tag2,//stem/authorcode/_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."
......
20 21
stem_liana_infestation,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=lianaInfestation]]/definedvalue",Brad: Should also be userDefined for VegBank. 
21 22
x_position,//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 23
y_position,//stem/yposition,Brad: See comment above for x_position
23
coll_number,/taxondetermination[rolecode=collector]/collectionnumber,Brad: Incorrect. Map instead as for voucher_string
24 24
coll_firstname,"/taxondetermination[rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}",Brad: See comment above
25 25
coll_lastname,/taxondetermination[rolecode=collector]/collector_id/party/{surname},"Brad: Correct for VegBank. This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
26 26
census_no,"/taxondetermination[rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=censusNo]]/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."
mappings/SALVIAS-VegBIEN.organisms.csv
8 8
stem_dbh,/aggregateoccurrence/individualplant/diameter,
9 9
height_m,/aggregateoccurrence/individualplant/height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
10 10
stem_height_m,/aggregateoccurrence/individualplant/height,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
11
coll_number,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string
11 12
stem_tag1,/aggregateoccurrence/individualplant/stem/authorcode,"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."
12 13
stem_tag2,/aggregateoccurrence/individualplant/stem/authorcode,Brad: see above
13 14
tag2,/aggregateoccurrence/individualplant/stem/authorcode/_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."
......
20 21
stem_liana_infestation,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=lianaInfestation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. 
21 22
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 23
y_position,/aggregateoccurrence/individualplant/stem/yposition,Brad: See comment above for x_position
23
coll_number,/taxondetermination[role_id/aux_role/rolecode=collector]/collectionnumber,Brad: Incorrect. Map instead as for voucher_string
24 24
coll_firstname,"/taxondetermination[role_id/aux_role/rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}",Brad: See comment above
25 25
coll_lastname,/taxondetermination[role_id/aux_role/rolecode=collector]/collector_id/party/{surname},"Brad: Correct for VegBank. This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
26 26
census_no,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=censusNo]:[userdefinedtype=varchar]]:[@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."

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