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Revision 6149

Added by Aaron Marcuse-Kubitza about 12 years ago

specimenreplicate: Made institution_id an fkey to referencename instead of party, to later be matched up with reference entries for each aggregator's subprovider

View differences:

mappings/VegCore-VegBIEN.csv
94 94 
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
95 95 
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
96 96 
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2,
97 
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
97 
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/referencename/name,
98 98 
occurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
99 99 
stemCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount,
100 100 
authorStemCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode,
inputs/MT/Specimen/VegBIEN.csv
6 6 
individualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,
7 7 
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
8 8 
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2,
9 
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
9 
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/referencename/name,
10 10 
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
11 11 
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_alt/2/_map:[cultivated=t,wild=f,*=]/value",
12 12 
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value",
inputs/MT/Specimen/test.xml.ref
17 17 
                                            <2>$collectionID</2>
18 18 
                                        </_join>
19 19 
                                    </collectioncode_dwc>
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                                    <institution_id><party><organizationname>$institutionCode</organizationname></party></institution_id>
20 
                                    <institution_id><referencename><name>$institutionCode</name></referencename></institution_id>
21 21 
                                    <sourceaccessioncode>$id</sourceaccessioncode>
22 22 
                                </specimenreplicate>
23 23 
                            </plantobservation>
inputs/XAL/Specimen/VegBIEN.csv
14 14 
darwin:Sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,userdefinedname=sex]]:[@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"
15 15 
darwin:CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
16 16 
darwin:CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
17 
darwin:InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
17 
darwin:InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/referencename/name,
18 18 
darwin:CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",
19 19 
darwin:ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
20 20 
darwin:IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
inputs/ACAD/Specimen/VegBIEN.csv
15 15 
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
16 16 
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
17 17 
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2,
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institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
18 
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/referencename/name,
19 19 
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
20 20 
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",
21 21 
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2",
inputs/ACAD/Specimen/test.xml.ref
43 43 
                                            <2>$collectionID</2>
44 44 
                                        </_join>
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                                    </collectioncode_dwc>
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                                    <institution_id><party><organizationname>$institutionCode</organizationname></party></institution_id>
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                                    <institution_id><referencename><name>$institutionCode</name></referencename></institution_id>
47 47 
                                    <sourceaccessioncode>$id</sourceaccessioncode>
48 48 
                                </specimenreplicate>
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                            </plantobservation>
inputs/GBIF/Specimen/VegBIEN.csv
8 8 
LatestDateCollected,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1/_*/date,
9 9 
CatalogNO,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
10 10 
CollectionCD,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
11 
InstitutionCD,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
11 
InstitutionCD,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/referencename/name,
12 12 
ScientificNameOriginal,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/1",
13 13 
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
14 14 
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
inputs/GBIF/Specimen/test.xml.ref
25 25 
                                <specimenreplicate>
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                                    <catalognumber_dwc>$CatalogNO</catalognumber_dwc>
27 27 
                                    <collectioncode_dwc>$CollectionCD</collectioncode_dwc>
28 
                                    <institution_id><party><organizationname>$InstitutionCD</organizationname></party></institution_id>
28 
                                    <institution_id><referencename><name>$InstitutionCD</name></referencename></institution_id>
29 29 
                                </specimenreplicate>
30 30 
                            </plantobservation>
31 31 
                        </aggregateoccurrence>
inputs/SpeciesLink/Specimen/VegBIEN.csv
54 54 
dwc_dwcore_CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
55 55 
dwc_terms_collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
56 56 
dwc_terms_collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2,
57 
conceptual_darwin_2003_1_0_InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
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dwc_dwcore_InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
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dwc_terms_institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
57 
conceptual_darwin_2003_1_0_InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/referencename/name,
58 
dwc_dwcore_InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/referencename/name,
59 
dwc_terms_institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/referencename/name,
60 60 
dwc_dwcore_GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
61 61 
dwc_terms_recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1/_alt/1",
62 62 
conceptual_darwin_2003_1_0_FieldNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
inputs/SpeciesLink/Specimen/test.xml.ref
148 148 
                                        </_join>
149 149 
                                    </collectioncode_dwc>
150 150 
                                    <institution_id>
151 
                                        <party>
152 
                                            <organizationname>
151 
                                        <referencename>
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                                            <name>
153 153 
                                                <_alt>
154 154 
                                                    <0>$conceptual_darwin_2003_1_0_InstitutionCode</0>
155 155 
                                                    <1>$dwc_dwcore_InstitutionCode</1>
156 156 
                                                    <2>$dwc_terms_institutionCode</2>
157 157 
                                                </_alt>
158 
                                            </organizationname>
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                                        </party>
158 
                                            </name>
159 
                                        </referencename>
160 160 
                                    </institution_id>
161 161 
                                    <sourceaccessioncode>$dwc_dwcore_GlobalUniqueIdentifier</sourceaccessioncode>
162 162 
                                </specimenreplicate>
inputs/bien_web/observation/VegBIEN.csv
13 13 
observationDate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1/_*/date,
14 14 
pctCover,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover_fraction/_percent_to_fraction/value,
15 15 
collectionNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
16 
dataSourceName,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
16 
dataSourceName,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/referencename/name,
17 17 
plotCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
18 18 
plotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
19 19 
collectionNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",
inputs/bien_web/observation/test.xml.ref
16 16 
                            <cover_fraction><_percent_to_fraction><value>$pctCover</value></_percent_to_fraction></cover_fraction>
17 17 
                            <plantobservation>
18 18 
                                <collectionnumber>$collectionNumber</collectionnumber>
19 
                                <specimenreplicate><institution_id><party><organizationname>$dataSourceName</organizationname></party></institution_id></specimenreplicate>
19 
                                <specimenreplicate><institution_id><referencename><name>$dataSourceName</name></referencename></institution_id></specimenreplicate>
20 20 
                            </plantobservation>
21 21 
                        </aggregateoccurrence>
22 22 
                        <authortaxoncode>$collectionNumber</authortaxoncode>
inputs/NY/Specimen/VegBIEN.csv
16 16 
Sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,userdefinedname=sex]]:[@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"
17 17 
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
18 18 
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
19 
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
19 
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/referencename/name,
20 20 
UniqueNYInternalRecordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
21 21 
FieldNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",Usage inconsistent with DwC definition
22 22 
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
inputs/NY/Specimen/test.xml.ref
81 81 
                                <specimenreplicate>
82 82 
                                    <catalognumber_dwc>$CatalogNumber</catalognumber_dwc>
83 83 
                                    <collectioncode_dwc>$CollectionCode</collectioncode_dwc>
84 
                                    <institution_id><party><organizationname>$InstitutionCode</organizationname></party></institution_id>
84 
                                    <institution_id><referencename><name>$InstitutionCode</name></referencename></institution_id>
85 85 
                                    <sourceaccessioncode>$UniqueNYInternalRecordNumber</sourceaccessioncode>
86 86 
                                </specimenreplicate>
87 87 
                            </plantobservation>
inputs/UNCC/Specimen/VegBIEN.csv
20 20 
loanto,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/6/_label[label=""loaned to""]/value",
21 21 
inorout,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/7/_label[label=""in or out""]/value",
22 22 
collectno,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
23 
herbarium,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
23 
herbarium,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/referencename/name,
24 24 
accession,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,"Globally unique, although occasionally duplicated. [1]
25 25 

  		




  26
  26
  
    
[1] Using the following query:


  		












  

    
      inputs/UNCC/Specimen/test.xml.ref
    
  





  62
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                            <plantobservation>


  		




  63
  63
  
    
                                <collectionnumber>$collectno</collectionnumber>


  		




  64
  64
  
    
                                <specimenreplicate>


  		




  65
  
  
    
                                    <institution_id><party><organizationname>$herbarium</organizationname></party></institution_id>


  		




  
  65
  
    
                                    <institution_id><referencename><name>$herbarium</name></referencename></institution_id>


  		




  66
  66
  
    
                                    <sourceaccessioncode>$accession</sourceaccessioncode>


  		




  67
  67
  
    
                                </specimenreplicate>


  		




  68
  68
  
    
                            </plantobservation>


  		












  

    
      inputs/REMIB/Specimen/VegBIEN.csv
    
  





  30
  30
  
    
GROUP BY acronym, accession_number


  		




  31
  31
  
    
HAVING count(*) > 1


  		




  32
  32
  
    
-----"


  		




  33
  
  
    
acronym,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,


  		




  
  33
  
    
acronym,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/referencename/name,


  		




  34
  34
  
    
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[reference_id/reference/shortname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family",


  		




  35
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genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[reference_id/reference/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2",


  		




  36
  36
  
    
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[reference_id/reference/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",


  		












  

    
      inputs/REMIB/Specimen/test.xml.ref
    
  





  41
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                            <plantobservation>


  		




  42
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                                <specimenreplicate>


  		




  43
  43
  
    
                                    <catalognumber_dwc>$accession_number</catalognumber_dwc>


  		




  44
  
  
    
                                    <institution_id><party><organizationname>$acronym</organizationname></party></institution_id>


  		




  
  44
  
    
                                    <institution_id><referencename><name>$acronym</name></referencename></institution_id>


  		




  45
  45
  
    
                                </specimenreplicate>


  		




  46
  46
  
    
                            </plantobservation>


  		




  47
  47
  
    
                        </aggregateoccurrence>


  		












  

    
      inputs/ARIZ/Specimen/VegBIEN.csv
    
  





  19
  19
  
    
CatalogNumberNumeric,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1",


  		




  20
  20
  
    
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/2",Don't overwrite CatalogNumberNumeric


  		




  21
  21
  
    
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name


  		




  22
  
  
    
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,


  		




  
  22
  
    
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/referencename/name,


  		




  23
  23
  
    
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,


  		




  24
  24
  
    
CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",


  		




  25
  25
  
    
ScientificNameAuthor,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2",Contains the binomial in addition to the authority


  		












  

    
      inputs/ARIZ/Specimen/test.xml.ref
    
  





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                                        </_alt>


  		




  82
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                                    </catalognumber_dwc>


  		




  83
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                                    <collectioncode_dwc>$CollectionCode</collectioncode_dwc>


  		




  84
  
  
    
                                    <institution_id><party><organizationname>$InstitutionCode</organizationname></party></institution_id>


  		




  
  84
  
    
                                    <institution_id><referencename><name>$InstitutionCode</name></referencename></institution_id>


  		




  85
  85
  
    
                                    <sourceaccessioncode>$GlobalUniqueIdentifier</sourceaccessioncode>


  		




  86
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                                </specimenreplicate>


  		




  87
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                            </plantobservation>


  		












  

    
      inputs/MO/Specimen/VegBIEN.csv
    
  





  14
  14
  
    
CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,


  		




  15
  15
  
    
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",


  		




  16
  16
  
    
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name


  		




  17
  
  
    
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,


  		




  
  17
  
    
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/referencename/name,


  		




  18
  18
  
    
CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",


  		




  19
  19
  
    
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",


  		




  20
  20
  
    
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,


  		












  

    
      inputs/MO/Specimen/test.xml.ref
    
  





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                                <specimenreplicate>


  		




  58
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                                    <catalognumber_dwc>$CatalogNumber</catalognumber_dwc>


  		




  59
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                                    <collectioncode_dwc>$CollectionCode</collectioncode_dwc>


  		




  60
  
  
    
                                    <institution_id><party><organizationname>$InstitutionCode</organizationname></party></institution_id>


  		




  
  60
  
    
                                    <institution_id><referencename><name>$InstitutionCode</name></referencename></institution_id>


  		




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                                </specimenreplicate>


  		




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                            </plantobservation>


  		




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                        </aggregateoccurrence>


  		












  

    
      inputs/QMOR/Specimen/VegBIEN.csv
    
  





  19
  19
  
    
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",


  		




  20
  20
  
    
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name


  		




  21
  21
  
    
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2,


  		




  22
  
  
    
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,


  		




  
  22
  
    
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/referencename/name,


  		




  23
  23
  
    
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,


  		




  24
  24
  
    
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",


  		




  25
  25
  
    
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,


  		












  

    
      inputs/QMOR/Specimen/test.xml.ref
    
  





  63
  63
  
    
                                            <2>$collectionID</2>


  		




  64
  64
  
    
                                        </_join>


  		




  65
  65
  
    
                                    </collectioncode_dwc>


  		




  66
  
  
    
                                    <institution_id><party><organizationname>$institutionCode</organizationname></party></institution_id>


  		




  
  66
  
    
                                    <institution_id><referencename><name>$institutionCode</name></referencename></institution_id>


  		




  67
  67
  
    
                                    <sourceaccessioncode>$id</sourceaccessioncode>


  		




  68
  68
  
    
                                </specimenreplicate>


  		




  69
  69
  
    
                            </plantobservation>


  		












  

    
      schemas/filter_ERD.csv
    
  





  9
  9
  
    
"^ALTER TABLE \b[^;]*\bFOREIGN KEY\b[^;]*\(submethod_id\) REFERENCES method\b[^;]*;",,inward


  		




  10
  10
  
    
"^ALTER TABLE (?!party|address|referencecontributor|telephone)\b[^;]*\bFOREIGN KEY\b[^;]*\bREFERENCES party\b[^;]*;",,inward


  		




  11
  11
  
    
"^ALTER TABLE (?!reference)\b[^;]*\bFOREIGN KEY\b[^;]*\bREFERENCES reference\b[^;]*;",,inward


  		




  
  12
  
    
"^ALTER TABLE \b[^;]*\bFOREIGN KEY\b[^;]*\bREFERENCES referencename\b[^;]*;",,inward


  		












  

    
      schemas/vegbien.sql
    
  





  6992
  6992
  
    
--


  		




  6993
  6993
  
    

  		




  6994
  6994
  
    
ALTER TABLE ONLY specimenreplicate


  		




  6995
  
  
    
    ADD CONSTRAINT specimenreplicate_institution_id_fkey FOREIGN KEY (institution_id) REFERENCES party(party_id) ON UPDATE CASCADE ON DELETE CASCADE;


  		




  
  6995
  
    
    ADD CONSTRAINT specimenreplicate_institution_id_fkey FOREIGN KEY (institution_id) REFERENCES referencename(referencename_id) ON UPDATE CASCADE ON DELETE CASCADE;


  		




  6996
  6996
  
    

  		




  6997
  6997
  
    

  		




  6998
  6998
  
    
--


  		












  

    
      mappings/for_review/VegCore-VegBIEN.csv
    
  





  94
  94
  
    
catalogNumber,"//specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",


  		




  95
  95
  
    
collectionCode,//specimenreplicate/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


  		




  96
  96
  
    
collectionID,//specimenreplicate/collectioncode_dwc,


  		




  97
  
  
    
institutionCode,//party/organizationname,


  		




  
  97
  
    
institutionCode,//referencename/name,


  		




  98
  98
  
    
occurrenceID,//specimenreplicate/sourceaccessioncode,


  		




  99
  99
  
    
stemCount,//plantobservation/stemcount,


  		




  100
  100
  
    
authorStemCode,//stemobservation/authorstemcode,


  		












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