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1
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REMIB,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
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2
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accession_number,"/_if[@name=""if specimen""]/cond/_exists","Not globally unique, only (usually) unique within the institution providing the data (""acronym""). Note that there are nevertheless 11,869 rows where an accession_number appears multiple times within the same institution. [1]
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3
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4
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[1] Using the following query:
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5
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-----
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6
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SELECT acronym, accession_number, count(*)
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7
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FROM ""REMIB"".""Specimen""
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8
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GROUP BY acronym, accession_number
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9
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HAVING count(*) > 1
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10
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-----"
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11
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acronym,"/_if[@name=""if specimen""]/else/source/shortname/_first/1",
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12
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accession_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists","Not globally unique, only (usually) unique within the institution providing the data (""acronym""). Note that there are nevertheless 11,869 rows where an accession_number appears multiple times within the same institution. [1]
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13
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14
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[1] Using the following query:
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15
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-----
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16
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SELECT acronym, accession_number, count(*)
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17
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FROM ""REMIB"".""Specimen""
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18
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GROUP BY acronym, accession_number
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19
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HAVING count(*) > 1
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20
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-----"
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21
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accession_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists","Not globally unique, only (usually) unique within the institution providing the data (""acronym""). Note that there are nevertheless 11,869 rows where an accession_number appears multiple times within the same institution. [1]
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22
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23
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[1] Using the following query:
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24
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-----
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25
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SELECT acronym, accession_number, count(*)
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26
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FROM ""REMIB"".""Specimen""
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27
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GROUP BY acronym, accession_number
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28
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HAVING count(*) > 1
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29
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-----"
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30
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acronym,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then",
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31
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accession_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else","Not globally unique, only (usually) unique within the institution providing the data (""acronym""). Note that there are nevertheless 11,869 rows where an accession_number appears multiple times within the same institution. [1]
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32
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33
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[1] Using the following query:
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34
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-----
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35
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SELECT acronym, accession_number, count(*)
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36
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FROM ""REMIB"".""Specimen""
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37
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GROUP BY acronym, accession_number
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38
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HAVING count(*) > 1
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39
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-----"
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40
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locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1,
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41
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habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3,
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42
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coll_day,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
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43
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coll_month,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
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44
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coll_year,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
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45
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accession_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else","Not globally unique, only (usually) unique within the institution providing the data (""acronym""). Note that there are nevertheless 11,869 rows where an accession_number appears multiple times within the same institution. [1]
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46
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47
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[1] Using the following query:
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48
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-----
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49
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SELECT acronym, accession_number, count(*)
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50
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FROM ""REMIB"".""Specimen""
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51
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GROUP BY acronym, accession_number
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52
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HAVING count(*) > 1
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53
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-----"
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54
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accession_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists","Not globally unique, only (usually) unique within the institution providing the data (""acronym""). Note that there are nevertheless 11,869 rows where an accession_number appears multiple times within the same institution. [1]
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55
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56
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[1] Using the following query:
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57
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-----
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58
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SELECT acronym, accession_number, count(*)
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59
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FROM ""REMIB"".""Specimen""
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60
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GROUP BY acronym, accession_number
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61
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HAVING count(*) > 1
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62
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-----"
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63
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acronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname",
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64
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acronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name",
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65
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collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname,
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66
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family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/value",
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67
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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:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2",
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68
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specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
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69
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specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
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70
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genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",
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71
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genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",
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72
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family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",
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73
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family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet",
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74
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family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/value,
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75
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genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2,
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76
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specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,
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77
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family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,
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78
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genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,
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79
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specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,
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80
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accession_number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then","Not globally unique, only (usually) unique within the institution providing the data (""acronym""). Note that there are nevertheless 11,869 rows where an accession_number appears multiple times within the same institution. [1]
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81
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82
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[1] Using the following query:
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83
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-----
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84
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SELECT acronym, accession_number, count(*)
|
|
85
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FROM ""REMIB"".""Specimen""
|
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86
|
GROUP BY acronym, accession_number
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87
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HAVING count(*) > 1
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|
88
|
-----"
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89
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locality,/location/locationnarrative/_merge/1,
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90
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habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?"
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91
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lat_deg,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value",
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92
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long_deg,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value",
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93
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country,/location/locationplace/*_id/place/country,
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94
|
county,/location/locationplace/*_id/place/county,
|
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95
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lat_deg,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings"
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96
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long_deg,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings"
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97
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country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2,
|
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98
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county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2,
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99
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state,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2,
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100
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state,/location/locationplace/*_id/place/stateprovince,
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101
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lat_min,,** No join mapping for *lat_min **
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102
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lat_sec,,** No join mapping for *lat_sec **
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103
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long_min,,** No join mapping for *long_min **
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104
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long_sec,,** No join mapping for *long_sec **
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105
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preparation,,** No join mapping for preparations **
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