Project

General

Profile

« Previous | Next » 

Revision 12879

mappings/VegCore.htm: regenerated from wiki: rename specimenHolderInstitutions to specimen_duplicate_institutions, as decided in the 2014-03-13 conference call (wiki.vegpath.org/2014-03-13_conference_call#schema-changes-2). note that most schema changes (such as this one) involve mappings changes, which are handled automatically by `inputs/run postprocess; yes|make inputs/{NVS,SALVIAS,TEAM}/test`.

View differences:

trunk/inputs/SpeciesLink/Specimen/new_terms.csv
37 37
dwc_geospatial_VerbatimLongitude,DUPLICATE#of:verbatimLongitude#dwc_geospatial_VerbatimLongitude,,exact duplicate
38 38
http__purl_org_dc_terms_modified,modified,,
39 39
dwc_terms_collectionID,collectionURL,,
40
dwc_terms_institutionCode,specimenHolderInstitutions,,
40
dwc_terms_institutionCode,specimen_duplicate_institutions,,
41 41
dwc_terms_collectionCode,collection,,
42 42
dwc_terms_basisOfRecord,basisOfRecord,,
43 43
dwc_terms_identifiedBy,identifiedBy,,
trunk/inputs/bien_web/observation/map.csv
1 1
bien_web,VegCore,Filter,Comments
2 2
observationID,occurrenceID,,
3 3
dataSourceID,*dataSourceID,,
4
dataSourceName,specimenHolderInstitutions,,
4
dataSourceName,specimen_duplicate_institutions,,
5 5
dataSourceNamePrimary,*dataSourceNamePrimary,,
6 6
plotID,locationID,,
7 7
observationType,observationGranularity,,
trunk/inputs/NY/Ecatalog_all/test.xml.ref
9 9
                    <location>
10 10
                        <authorlocationcode>
11 11
                            <_join>
12
                                <1>$specimenHolderInstitutions</1>
12
                                <1>$specimen_duplicate_institutions</1>
13 13
                                <2>$collection</2>
14 14
                                <3>$accessionNumber</3>
15 15
                            </_join>
......
78 78
                                                <collectionnumber>$collectorNumber</collectionnumber>
79 79
                                                <institution_id>
80 80
                                                    <sourcelist>
81
                                                        <name>$specimenHolderInstitutions</name>
81
                                                        <name>$specimen_duplicate_institutions</name>
82 82
                                                        <sourcename>
83 83
                                                            <name>
84 84
                                                                <_split>
85 85
                                                                    <separator>[,;] *</separator>
86
                                                                    <value>$specimenHolderInstitutions</value>
86
                                                                    <value>$specimen_duplicate_institutions</value>
87 87
                                                                </_split>
88 88
                                                            </name>
89 89
                                                        </sourcename>
trunk/inputs/Madidi/IndividualObservation/new_terms.csv
6 6
SeniorCollector,DUPLICATE#of:CollectorString#SeniorCollector,,
7 7
CollectorString,recordedBy,,
8 8
CollectorStringShortened,DUPLICATE#of:CollectorString#CollectorStringShortened,,
9
Institutions,specimenHolderInstitutions,,
9
Institutions,specimen_duplicate_institutions,,
10 10
CollectorAbbrev,DUPLICATE#of:CollectorString#CollectorAbbrev,,
11 11
CurrentDet,scientificName,,
12 12
CurrentDetRank,taxonRank,,
trunk/inputs/QFA/Specimen/map.csv
15 15
identifiedBy,identifiedBy,,
16 16
associatedReferences,associatedReferences,,
17 17
kingdom,kingdom,,
18
institutionCode,specimenHolderInstitutions,,
18
institutionCode,specimen_duplicate_institutions,,
19 19
catalogNumber,accessionNumber,,
20 20
verbatimSRS,verbatimSRS,,
21 21
verbatimLongitude,verbatimLongitude,,
trunk/inputs/JBM/Specimen/map.csv
35 35
type,type,,
36 36
order,order,,
37 37
kingdom,kingdom,,
38
institutionCode,specimenHolderInstitutions,,
38
institutionCode,specimen_duplicate_institutions,,
39 39
datasetID,datasetURL,,
40 40
countryCode,countryCode,,
41 41
catalogNumber,accessionNumber,,
trunk/inputs/UBC/Specimen/map.csv
56 56
previousIdentifications,previousIdentifications,,
57 57
identifiedBy,identifiedBy,,
58 58
associatedSequences,associatedSequences,,
59
institutionCode,specimenHolderInstitutions,,
59
institutionCode,specimen_duplicate_institutions,,
trunk/inputs/SpeciesLink/Specimen/postprocess.sql
1 1
SELECT util.search_path_append('util');
2 2

  
3
SELECT create_if_not_exists($$CREATE INDEX "Specimen.acronym" ON $$||:table_str||$$ ("specimenHolderInstitutions")$$);
3
SELECT create_if_not_exists($$CREATE INDEX "Specimen.acronym" ON $$||:table_str||$$ ("specimen_duplicate_institutions")$$);
4 4

  
5 5
-- Remove institutions that we have direct data for
6 6
DELETE FROM :table
7
WHERE "specimenHolderInstitutions" IN (
7
WHERE "specimen_duplicate_institutions" IN (
8 8
      'MO'
9 9
    , 'NY'
10 10
)
trunk/inputs/SpeciesLink/Specimen/test.xml.ref
12 12
                                <1>$occurrenceID</1>
13 13
                                <2>
14 14
                                    <_join>
15
                                        <1>$specimenHolderInstitutions</1>
15
                                        <1>$specimen_duplicate_institutions</1>
16 16
                                        <2>
17 17
                                            <_join>
18 18
                                                <1>$collection</1>
......
84 84
                                                <collectionnumber>$collectorNumber</collectionnumber>
85 85
                                                <institution_id>
86 86
                                                    <sourcelist>
87
                                                        <name>$specimenHolderInstitutions</name>
87
                                                        <name>$specimen_duplicate_institutions</name>
88 88
                                                        <sourcename>
89 89
                                                            <name>
90 90
                                                                <_split>
91 91
                                                                    <separator>[,;] *</separator>
92
                                                                    <value>$specimenHolderInstitutions</value>
92
                                                                    <value>$specimen_duplicate_institutions</value>
93 93
                                                                </_split>
94 94
                                                            </name>
95 95
                                                        </sourcename>
trunk/inputs/HIBG/Specimen/test.xml.ref
12 12
                                <1>$dataProviderRecordID</1>
13 13
                                <2>
14 14
                                    <_join>
15
                                        <1>$specimenHolderInstitutions</1>
15
                                        <1>$specimen_duplicate_institutions</1>
16 16
                                        <2>
17 17
                                            <_join>
18 18
                                                <1>$collection</1>
......
62 62
                                                <collectionnumber>$collectorNumber</collectionnumber>
63 63
                                                <institution_id>
64 64
                                                    <sourcelist>
65
                                                        <name>$specimenHolderInstitutions</name>
65
                                                        <name>$specimen_duplicate_institutions</name>
66 66
                                                        <sourcename>
67 67
                                                            <name>
68 68
                                                                <_split>
69 69
                                                                    <separator>[,;] *</separator>
70
                                                                    <value>$specimenHolderInstitutions</value>
70
                                                                    <value>$specimen_duplicate_institutions</value>
71 71
                                                                </_split>
72 72
                                                            </name>
73 73
                                                        </sourcename>
trunk/inputs/NY/Ecatalog_all/map.csv
2 2
pkey,OMIT#pkey,,"CatalogNumber, etc. is a better pkey"
3 3
key,OMIT#key,,"CatalogNumber, etc. is a better pkey"
4 4
DateLastModified,modified,,
5
InstitutionCode,specimenHolderInstitutions,,
5
InstitutionCode,specimen_duplicate_institutions,,
6 6
CollectionCode,collection,,
7 7
CatalogNumber,accessionNumber,,
8 8
ScientificName,taxonName,,
trunk/inputs/Madidi/IndividualObservation/test.xml.ref
47 47
                                                <collectionnumber>$collectorNumber</collectionnumber>
48 48
                                                <institution_id>
49 49
                                                    <sourcelist>
50
                                                        <name>$specimenHolderInstitutions</name>
50
                                                        <name>$specimen_duplicate_institutions</name>
51 51
                                                        <sourcename>
52 52
                                                            <name>
53 53
                                                                <_split>
54 54
                                                                    <separator>[,;] *</separator>
55
                                                                    <value>$specimenHolderInstitutions</value>
55
                                                                    <value>$specimen_duplicate_institutions</value>
56 56
                                                                </_split>
57 57
                                                            </name>
58 58
                                                        </sourcename>
trunk/inputs/.herbaria/ih/map.csv
1 1
herbaria,VegCore,Filter,Comments
2 2
eparties_key,*eparties_key,,
3 3
NamOrganisation,*NamOrganisation,,
4
acronym,specimenHolderInstitutions,,
4
acronym,specimen_duplicate_institutions,,
5 5
IhhInstitutionType,*IhhInstitutionType,,
6 6
NamBranch,*NamBranch,,
7 7
NamDepartment,*NamDepartment,,
trunk/inputs/REMIB/Specimen/map.csv
1 1
REMIB,VegCore,Filter,Comments
2 2
row_num,*row_num,,
3
acronym,specimenHolderInstitutions,,
3
acronym,specimen_duplicate_institutions,,
4 4
accession_number,accessionNumber,,"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]
5 5

  
6 6
[1] Using the following query:
trunk/inputs/.herbaria/ih/new_terms.csv
1
acronym,specimenHolderInstitutions,,
1
acronym,specimen_duplicate_institutions,,
trunk/inputs/REMIB/Specimen/new_terms.csv
1
acronym,specimenHolderInstitutions,,
1
acronym,specimen_duplicate_institutions,,
2 2
long_deg,longitude_deg_verbatim,,
3 3
long_min,longitude_min_verbatim,,
4 4
long_sec,longitude_sec_verbatim,,
trunk/inputs/.herbaria/ih/test.xml.ref
7 7
                <next>parent_id</next>
8 8
                <path>
9 9
                    <source>
10
                        <shortname>$specimenHolderInstitutions</shortname>
10
                        <shortname>$specimen_duplicate_institutions</shortname>
11 11
                        <observationtype>specimen</observationtype>
12 12
                        <sourcetype>herbarium</sourcetype>
13 13
                    </source>
trunk/inputs/REMIB/Specimen/test.xml.ref
9 9
                    <location>
10 10
                        <authorlocationcode>
11 11
                            <_join>
12
                                <1>$specimenHolderInstitutions</1>
12
                                <1>$specimen_duplicate_institutions</1>
13 13
                                <3>$accessionNumber</3>
14 14
                            </_join>
15 15
                        </authorlocationcode>
......
57 57
                                                <catalognumber_dwc>$accessionNumber</catalognumber_dwc>
58 58
                                                <institution_id>
59 59
                                                    <sourcelist>
60
                                                        <name>$specimenHolderInstitutions</name>
60
                                                        <name>$specimen_duplicate_institutions</name>
61 61
                                                        <sourcename>
62 62
                                                            <name>
63 63
                                                                <_split>
64 64
                                                                    <separator>[,;] *</separator>
65
                                                                    <value>$specimenHolderInstitutions</value>
65
                                                                    <value>$specimen_duplicate_institutions</value>
66 66
                                                                </_split>
67 67
                                                            </name>
68 68
                                                        </sourcename>
trunk/inputs/HVAA/Specimen/map.csv
1 1
HVAA,VegCore,Filter,Comments
2 2
row_num,*row_num,,
3
institutionCode,specimenHolderInstitutions,,
3
institutionCode,specimen_duplicate_institutions,,
4 4
collectionCode,collection,,
5 5
basisOfRecord,basisOfRecord,,
6 6
catalogNumber,accessionNumber,,
trunk/inputs/HVAA/Specimen/test.xml.ref
12 12
                                <1>$occurrenceID</1>
13 13
                                <2>
14 14
                                    <_join>
15
                                        <1>$specimenHolderInstitutions</1>
15
                                        <1>$specimen_duplicate_institutions</1>
16 16
                                        <2>$collection</2>
17 17
                                        <3>$accessionNumber</3>
18 18
                                    </_join>
......
103 103
                                                <collectionnumber>$collectorNumber</collectionnumber>
104 104
                                                <institution_id>
105 105
                                                    <sourcelist>
106
                                                        <name>$specimenHolderInstitutions</name>
106
                                                        <name>$specimen_duplicate_institutions</name>
107 107
                                                        <sourcename>
108 108
                                                            <name>
109 109
                                                                <_split>
110 110
                                                                    <separator>[,;] *</separator>
111
                                                                    <value>$specimenHolderInstitutions</value>
111
                                                                    <value>$specimen_duplicate_institutions</value>
112 112
                                                                </_split>
113 113
                                                            </name>
114 114
                                                        </sourcename>
trunk/inputs/MT/Specimen/map.csv
7 7
collectionID,collectionURL,,
8 8
occurrenceRemarks,occurrenceRemarks,,
9 9
type,type,,
10
institutionCode,specimenHolderInstitutions,,
10
institutionCode,specimen_duplicate_institutions,,
11 11
rights,rights,,
12 12
family,family,,
13 13
continent,continent,,
trunk/inputs/MT/Specimen/test.xml.ref
26 26
                                                </collectioncode_dwc>
27 27
                                                <institution_id>
28 28
                                                    <sourcelist>
29
                                                        <name>$specimenHolderInstitutions</name>
29
                                                        <name>$specimen_duplicate_institutions</name>
30 30
                                                        <sourcename>
31 31
                                                            <name>
32 32
                                                                <_split>
33 33
                                                                    <separator>[,;] *</separator>
34
                                                                    <value>$specimenHolderInstitutions</value>
34
                                                                    <value>$specimen_duplicate_institutions</value>
35 35
                                                                </_split>
36 36
                                                            </name>
37 37
                                                        </sourcename>
trunk/inputs/XAL/Specimen/map.csv
1 1
XAL:/content/record/,VegCore,Filter,Comments
2 2
row_num,*row_num,,
3 3
darwin:DateLastModified,modified,,
4
darwin:InstitutionCode,specimenHolderInstitutions,,
4
darwin:InstitutionCode,specimen_duplicate_institutions,,
5 5
darwin:CollectionCode,collection,,
6 6
darwin:CatalogNumber,accessionNumber,,
7 7
darwin:ScientificName,taxonName,,
trunk/inputs/XAL/Specimen/test.xml.ref
9 9
                    <location>
10 10
                        <authorlocationcode>
11 11
                            <_join>
12
                                <1>$specimenHolderInstitutions</1>
12
                                <1>$specimen_duplicate_institutions</1>
13 13
                                <2>$collection</2>
14 14
                                <3>$accessionNumber</3>
15 15
                            </_join>
......
69 69
                                                <collectionnumber>$collectorNumber</collectionnumber>
70 70
                                                <institution_id>
71 71
                                                    <sourcelist>
72
                                                        <name>$specimenHolderInstitutions</name>
72
                                                        <name>$specimen_duplicate_institutions</name>
73 73
                                                        <sourcename>
74 74
                                                            <name>
75 75
                                                                <_split>
76 76
                                                                    <separator>[,;] *</separator>
77
                                                                    <value>$specimenHolderInstitutions</value>
77
                                                                    <value>$specimen_duplicate_institutions</value>
78 78
                                                                </_split>
79 79
                                                            </name>
80 80
                                                        </sourcename>
trunk/inputs/XAL/Specimen/new_terms.csv
1 1
darwin:DateLastModified,modified,,
2
darwin:InstitutionCode,specimenHolderInstitutions,,
2
darwin:InstitutionCode,specimen_duplicate_institutions,,
3 3
darwin:CollectionCode,collection,,
4 4
darwin:CatalogNumber,accessionNumber,,
5 5
darwin:ScientificName,taxonName,,
trunk/inputs/NCU/Specimen/map.csv
14 14
CollectionDate,dateCollected,,
15 15
BarCode,OMIT#BarCode,,"Omitted because this isn't specified on all rows, but SpecimenPK is"
16 16
CatalogNumber,accessionNumber,,
17
CatalogSeriesPrefix,specimenHolderInstitutions,,"= specimen.orig_collection.institution.acronym, specimen.specimenholder_institutions(0).acronym"
17
CatalogSeriesPrefix,specimen_duplicate_institutions,,"= specimen.orig_collection.institution.acronym, specimen.specimenholder_institutions(0).acronym"
18 18
Description,occurrenceRemarks,,
19 19
LandOwner,*LandOwner,,
20 20
BlockLocationReason,*BlockLocationReason,,
trunk/inputs/NCU/Specimen/test.xml.ref
12 12
                                <1>$occurrenceID</1>
13 13
                                <2>
14 14
                                    <_join>
15
                                        <1>$specimenHolderInstitutions</1>
15
                                        <1>$specimen_duplicate_institutions</1>
16 16
                                        <2>$collectionURL</2>
17 17
                                        <3>$accessionNumber</3>
18 18
                                    </_join>
......
34 34
                                                <collectionnumber>$collectorNumber</collectionnumber>
35 35
                                                <institution_id>
36 36
                                                    <sourcelist>
37
                                                        <name>$specimenHolderInstitutions</name>
37
                                                        <name>$specimen_duplicate_institutions</name>
38 38
                                                        <sourcename>
39 39
                                                            <name>
40 40
                                                                <_split>
41 41
                                                                    <separator>[,;] *</separator>
42
                                                                    <value>$specimenHolderInstitutions</value>
42
                                                                    <value>$specimen_duplicate_institutions</value>
43 43
                                                                </_split>
44 44
                                                            </name>
45 45
                                                        </sourcename>
trunk/inputs/NCU/Specimen/new_terms.csv
5 5
CurrentScientificName,taxonName,,
6 6
CurrentScientificNameWithAuthor,scientificName,,
7 7
CollectionDate,dateCollected,,
8
CatalogSeriesPrefix,specimenHolderInstitutions,,"= specimen.orig_collection.institution.acronym, specimen.specimenholder_institutions(0).acronym"
8
CatalogSeriesPrefix,specimen_duplicate_institutions,,"= specimen.orig_collection.institution.acronym, specimen.specimenholder_institutions(0).acronym"
9 9
Description,occurrenceRemarks,,
10 10
CityLocality,municipality,,
11 11
Latitude1,decimalLatitude,,
trunk/inputs/ACAD/Specimen/postprocess.sql
1 1
SELECT util.search_path_append('util');
2 2

  
3
SELECT mk_derived_col((:table_str, 'specimenHolderInstitutions'),
4
$$_map('"Acadia University"=>ACAD, *=>*', "specimenHolderInstitutions_verbatim")$$);
3
SELECT mk_derived_col((:table_str, 'specimen_duplicate_institutions'),
4
$$_map('"Acadia University"=>ACAD, *=>*', "specimen_duplicate_institutions_verbatim")$$);
trunk/inputs/ACAD/Specimen/map.csv
8 8
geodeticDatum,geodeticDatum,,
9 9
reproductiveCondition,reproductiveCondition,,
10 10
decimalLongitude,decimalLongitude,,
11
institutionCode,specimenHolderInstitutions_verbatim,,
11
institutionCode,specimen_duplicate_institutions_verbatim,,
12 12
continent,continent,,
13 13
recordedBy,recordedBy,,
14 14
county,county,,
trunk/inputs/ACAD/Specimen/test.xml.ref
12 12
                                <1>$dataProviderRecordID</1>
13 13
                                <2>
14 14
                                    <_join>
15
                                        <1>$specimenHolderInstitutions</1>
15
                                        <1>$specimen_duplicate_institutions</1>
16 16
                                        <2>
17 17
                                            <_join>
18 18
                                                <1>$collection</1>
......
62 62
                                                <collectionnumber>$collectorNumber</collectionnumber>
63 63
                                                <institution_id>
64 64
                                                    <sourcelist>
65
                                                        <name>$specimenHolderInstitutions</name>
65
                                                        <name>$specimen_duplicate_institutions</name>
66 66
                                                        <sourcename>
67 67
                                                            <name>
68 68
                                                                <_split>
69 69
                                                                    <separator>[,;] *</separator>
70
                                                                    <value>$specimenHolderInstitutions</value>
70
                                                                    <value>$specimen_duplicate_institutions</value>
71 71
                                                                </_split>
72 72
                                                            </name>
73 73
                                                        </sourcename>
trunk/inputs/ACAD/Specimen/unmapped_terms.csv
1 1
*row_num
2 2
basisOfRecord
3 3
geodeticDatum
4
specimenHolderInstitutions_verbatim
4
specimen_duplicate_institutions_verbatim
5 5
georeferenceSources
6 6
language
7 7
georeferenceVerificationStatus
trunk/inputs/WIN/Specimen/map.csv
34 34
collectionCode,collection,,
35 35
verbatimCoordinates,verbatimCoordinates,,
36 36
decimalLatitude,decimalLatitude,,
37
institutionCode,specimenHolderInstitutions,,
37
institutionCode,specimen_duplicate_institutions,,
38 38
catalogNumber,accessionNumber,,
39 39
verbatimLatitude,verbatimLatitude,,
40 40
identificationRemarks,identificationRemarks,,
trunk/inputs/WIN/Specimen/test.xml.ref
12 12
                                <1>$dataProviderRecordID</1>
13 13
                                <2>
14 14
                                    <_join>
15
                                        <1>$specimenHolderInstitutions</1>
15
                                        <1>$specimen_duplicate_institutions</1>
16 16
                                        <2>
17 17
                                            <_join>
18 18
                                                <1>$collection</1>
......
66 66
                                                <collectionnumber>$collectorNumber</collectionnumber>
67 67
                                                <institution_id>
68 68
                                                    <sourcelist>
69
                                                        <name>$specimenHolderInstitutions</name>
69
                                                        <name>$specimen_duplicate_institutions</name>
70 70
                                                        <sourcename>
71 71
                                                            <name>
72 72
                                                                <_split>
73 73
                                                                    <separator>[,;] *</separator>
74
                                                                    <value>$specimenHolderInstitutions</value>
74
                                                                    <value>$specimen_duplicate_institutions</value>
75 75
                                                                </_split>
76 76
                                                            </name>
77 77
                                                        </sourcename>
trunk/inputs/BRIT/specimen_flat/map.csv
1 1
BRIT,VegCore,Filter,Comments
2 2
specimen_id,dataProviderRecordID,,
3
Institution_Code,specimenHolderInstitutions,,
3
Institution_Code,specimen_duplicate_institutions,,
4 4
Global_Unique_Identifier,UNUSED#Global_Unique_Identifier,,
5 5
Collector_Abbrev_Name,recordedBy_primary,,the primary collector
6 6
Collection_Team,recordedBy_additional,,additional collectors
trunk/inputs/BRIT/specimen_flat/test.xml.ref
12 12
                                <1>$dataProviderRecordID</1>
13 13
                                <2>
14 14
                                    <_join>
15
                                        <1>$specimenHolderInstitutions</1>
15
                                        <1>$specimen_duplicate_institutions</1>
16 16
                                        <3>$accessionNumber</3>
17 17
                                    </_join>
18 18
                                </2>
......
79 79
                                                <collectionnumber>$collectorNumber</collectionnumber>
80 80
                                                <institution_id>
81 81
                                                    <sourcelist>
82
                                                        <name>$specimenHolderInstitutions</name>
82
                                                        <name>$specimen_duplicate_institutions</name>
83 83
                                                        <sourcename>
84 84
                                                            <name>
85 85
                                                                <_split>
86 86
                                                                    <separator>[,;] *</separator>
87
                                                                    <value>$specimenHolderInstitutions</value>
87
                                                                    <value>$specimen_duplicate_institutions</value>
88 88
                                                                </_split>
89 89
                                                            </name>
90 90
                                                        </sourcename>
trunk/inputs/TEX/Specimen/map.csv
36 36
DATA ENTRY BY,*DATA ENTRY BY,,
37 37
DATA ENTRY DATE,*DATA ENTRY DATE,,
38 38
DATA EDITED DATE,modified,,
39
:TEX,specimenHolderInstitutions,,
39
:TEX,specimen_duplicate_institutions,,
40 40
:United States,country,,
trunk/inputs/TEX/Specimen2/map.csv
44 44
DET DATE,dateIdentified,,
45 45
DETERMINER INSTITUTION,*DETERMINER INSTITUTION,,
46 46
DET NOTES,identificationRemarks,,
47
:TEX,specimenHolderInstitutions,,
47
:TEX,specimen_duplicate_institutions,,
48 48
:United States,country,,
trunk/inputs/U/Specimen/map.csv
31 31
Ecology,habitat,,
32 32
Phenology,reproductiveCondition,,
33 33
Notes,occurrenceRemarks,,
34
:U,specimenHolderInstitutions,,
34
:U,specimen_duplicate_institutions,,
trunk/inputs/GBIF/raw_occurrence_record_plants/postprocess.sql
1 1
SELECT util.search_path_append('util');
2 2

  
3 3
SELECT create_if_not_exists($$CREATE INDEX raw_occurrence_record_plants_institution_code
4
ON raw_occurrence_record_plants ("specimenHolderInstitutions")$$)
4
ON raw_occurrence_record_plants ("specimen_duplicate_institutions")$$)
5 5
; -- runtime: 45 min ("2629095.310 ms") @starscream
6 6

  
7 7
-- Remove institutions that we have direct data for
8 8
-- runtime: 3.5 min ("208377.225 ms") @starscream
9 9
-- rerun time: ~0 ("Time: 2.271 ms") thanks to index (*after* manual vacuuming)
10 10
DELETE FROM :table
11
WHERE "specimenHolderInstitutions" IN (
11
WHERE "specimen_duplicate_institutions" IN (
12 12
      'ACAD'
13 13
    , 'ARIZ'
14 14
    , 'BRIT'
trunk/inputs/GBIF/raw_occurrence_record_plants/map.csv
4 4
data_provider_id,*data_provider_id,,
5 5
data_resource_id,*data_resource_id,,
6 6
resource_access_point_id,*resource_access_point_id,,
7
institution_code,specimenHolderInstitutions,,
7
institution_code,specimen_duplicate_institutions,,
8 8
collection_code,collection,,
9 9
catalogue_number,accessionNumber,,
10 10
scientific_name,scientificName,,
trunk/inputs/GBIF/raw_occurrence_record_plants/test.xml.ref
12 12
                                <1>$dataProviderRecordID</1>
13 13
                                <2>
14 14
                                    <_join>
15
                                        <1>$specimenHolderInstitutions</1>
15
                                        <1>$specimen_duplicate_institutions</1>
16 16
                                        <2>$collection</2>
17 17
                                        <3>$accessionNumber</3>
18 18
                                    </_join>
......
61 61
                                                <collectioncode_dwc>$collection</collectioncode_dwc>
62 62
                                                <institution_id>
63 63
                                                    <sourcelist>
64
                                                        <name>$specimenHolderInstitutions</name>
64
                                                        <name>$specimen_duplicate_institutions</name>
65 65
                                                        <sourcename>
66 66
                                                            <name>
67 67
                                                                <_split>
68 68
                                                                    <separator>[,;] *</separator>
69
                                                                    <value>$specimenHolderInstitutions</value>
69
                                                                    <value>$specimen_duplicate_institutions</value>
70 70
                                                                </_split>
71 71
                                                            </name>
72 72
                                                        </sourcename>
trunk/inputs/GBIF/map.csv
4 4
data_provider_id,*data_provider_id,,
5 5
data_resource_id,*data_resource_id,,
6 6
resource_access_point_id,*resource_access_point_id,,
7
institution_code,specimenHolderInstitutions,,
7
institution_code,specimen_duplicate_institutions,,
8 8
collection_code,collection,,
9 9
catalogue_number,accessionNumber,,
10 10
scientific_name,scientificName,,
trunk/inputs/QFA/Specimen/test.xml.ref
12 12
                                <1>$dataProviderRecordID</1>
13 13
                                <2>
14 14
                                    <_join>
15
                                        <1>$specimenHolderInstitutions</1>
15
                                        <1>$specimen_duplicate_institutions</1>
16 16
                                        <2>
17 17
                                            <_join>
18 18
                                                <1>$collection</1>
......
61 61
                                                <collectionnumber>$collectorNumber</collectionnumber>
62 62
                                                <institution_id>
63 63
                                                    <sourcelist>
64
                                                        <name>$specimenHolderInstitutions</name>
64
                                                        <name>$specimen_duplicate_institutions</name>
65 65
                                                        <sourcename>
66 66
                                                            <name>
67 67
                                                                <_split>
68 68
                                                                    <separator>[,;] *</separator>
69
                                                                    <value>$specimenHolderInstitutions</value>
69
                                                                    <value>$specimen_duplicate_institutions</value>
70 70
                                                                </_split>
71 71
                                                            </name>
72 72
                                                        </sourcename>
trunk/inputs/JBM/Specimen/test.xml.ref
12 12
                                <1>$dataProviderRecordID</1>
13 13
                                <2>
14 14
                                    <_join>
15
                                        <1>$specimenHolderInstitutions</1>
15
                                        <1>$specimen_duplicate_institutions</1>
16 16
                                        <2>
17 17
                                            <_join>
18 18
                                                <1>$collection</1>
......
63 63
                                                <collectionnumber>$collectorNumber</collectionnumber>
64 64
                                                <institution_id>
65 65
                                                    <sourcelist>
66
                                                        <name>$specimenHolderInstitutions</name>
66
                                                        <name>$specimen_duplicate_institutions</name>
67 67
                                                        <sourcename>
68 68
                                                            <name>
69 69
                                                                <_split>
70 70
                                                                    <separator>[,;] *</separator>
71
                                                                    <value>$specimenHolderInstitutions</value>
71
                                                                    <value>$specimen_duplicate_institutions</value>
72 72
                                                                </_split>
73 73
                                                            </name>
74 74
                                                        </sourcename>
trunk/inputs/UBC/Specimen/test.xml.ref
12 12
                                <1>$dataProviderRecordID</1>
13 13
                                <2>
14 14
                                    <_join>
15
                                        <1>$specimenHolderInstitutions</1>
15
                                        <1>$specimen_duplicate_institutions</1>
16 16
                                        <2>
17 17
                                            <_join>
18 18
                                                <1>$collection</1>
......
61 61
                                                <collectionnumber>$collectorNumber</collectionnumber>
62 62
                                                <institution_id>
63 63
                                                    <sourcelist>
64
                                                        <name>$specimenHolderInstitutions</name>
64
                                                        <name>$specimen_duplicate_institutions</name>
65 65
                                                        <sourcename>
66 66
                                                            <name>
67 67
                                                                <_split>
68 68
                                                                    <separator>[,;] *</separator>
69
                                                                    <value>$specimenHolderInstitutions</value>
69
                                                                    <value>$specimen_duplicate_institutions</value>
70 70
                                                                </_split>
71 71
                                                            </name>
72 72
                                                        </sourcename>
trunk/inputs/SpeciesLink/Specimen/map.csv
40 40
dwc_geospatial_VerbatimLongitude,DUPLICATE#of:verbatimLongitude#dwc_geospatial_VerbatimLongitude,,exact duplicate
41 41
http__purl_org_dc_terms_modified,modified,,
42 42
dwc_terms_collectionID,collectionURL,,
43
dwc_terms_institutionCode,specimenHolderInstitutions,,
43
dwc_terms_institutionCode,specimen_duplicate_institutions,,
44 44
dwc_terms_collectionCode,collection,,
45 45
dwc_terms_basisOfRecord,basisOfRecord,,
46 46
dwc_terms_identifiedBy,identifiedBy,,
trunk/inputs/HIBG/Specimen/map.csv
26 26
datasetName,dataset,,
27 27
bibliographicCitation,bibliographicCitation,,
28 28
datasetID,datasetURL,,
29
institutionCode,specimenHolderInstitutions,,
29
institutionCode,specimen_duplicate_institutions,,
30 30
recordNumber,collectorNumber,,
31 31
order,order,,
32 32
kingdom,kingdom,,
trunk/inputs/bien_web/observation/test.xml.ref
24 24
                                                <collectionnumber>$collectorNumber</collectionnumber>
25 25
                                                <institution_id>
26 26
                                                    <sourcelist>
27
                                                        <name>$specimenHolderInstitutions</name>
27
                                                        <name>$specimen_duplicate_institutions</name>
28 28
                                                        <sourcename>
29 29
                                                            <name>
30 30
                                                                <_split>
31 31
                                                                    <separator>[,;] *</separator>
32
                                                                    <value>$specimenHolderInstitutions</value>
32
                                                                    <value>$specimen_duplicate_institutions</value>
33 33
                                                                </_split>
34 34
                                                            </name>
35 35
                                                        </sourcename>
trunk/inputs/Madidi/IndividualObservation/map.csv
17 17
CollectorString,recordedBy,,
18 18
CollectorStringShortened,DUPLICATE#of:CollectorString#CollectorStringShortened,,
19 19
CollectionNumber,collectorNumber,,
20
Institutions,specimenHolderInstitutions,,
20
Institutions,specimen_duplicate_institutions,,
21 21
InstitutionString,*InstitutionString,,
22 22
CollectorAbbrev,DUPLICATE#of:CollectorString#CollectorAbbrev,,
23 23
CurrentDet,scientificName,,
trunk/inputs/UNCC/Specimen/map.csv
45 45
sheetno,associatedMedia,,?
46 46
cultivated,cultivated__main__verbatim,,
47 47
filler,*filler,,"Where used, same as family"
48
:UNCC,specimenHolderInstitutions,,
48
:UNCC,specimen_duplicate_institutions,,
trunk/inputs/REMIB/Specimen/postprocess.sql
1 1
SELECT util.search_path_append('util');
2 2

  
3
SELECT create_if_not_exists($$CREATE INDEX "Specimen.specimenHolderInstitutions" ON $$||:table_str||$$ ("specimenHolderInstitutions")$$);
3
SELECT create_if_not_exists($$CREATE INDEX "Specimen.specimen_duplicate_institutions" ON $$||:table_str||$$ ("specimen_duplicate_institutions")$$);
4 4

  
5 5
-- remove frameshifted rows
6
DELETE FROM :table WHERE "specimenHolderInstitutions" IS NULL;
6
DELETE FROM :table WHERE "specimen_duplicate_institutions" IS NULL;
7 7
DELETE FROM :table WHERE "yearCollected" !~ '^(?:1[7-9]|20)\d{2}$';
8 8
DELETE FROM :table WHERE country_verbatim ~ '\d';
9 9
DELETE FROM :table WHERE longitude_deg_verbatim ~ '[[:alpha:]]' AND longitude_deg_verbatim NOT IN ('RESTRINGIDO');
......
14 14

  
15 15
-- Remove institutions that we have direct data for
16 16
DELETE FROM :table
17
WHERE "specimenHolderInstitutions" IN (
17
WHERE "specimen_duplicate_institutions" IN (
18 18
    -- Comments are from e-mail from Brad Boyle on 2013-1-16
19 19
    'MO' -- "all MO records in REMIB are also available from MO's own website"
20 20
    --, 'ARIZ' -- Some REMIB ARIZ specimens not yet in ARIZ itself
trunk/inputs/MO/Specimen/map.csv
25 25
minimummonth,monthCollected,,
26 26
minimumyear,yearCollected,,
27 27
description,specimenDescription,,
28
acronyms,specimenHolderInstitutions,,
28
acronyms,specimen_duplicate_institutions,,
29 29
notes,locationRemarks,,
30 30
determinationyear,yearIdentified,,
31 31
determinedby,identifiedBy,,
trunk/inputs/TRT/Specimen/test.xml.ref
12 12
                                <1>$dataProviderRecordID</1>
13 13
                                <2>
14 14
                                    <_join>
15
                                        <1>$specimenHolderInstitutions</1>
15
                                        <1>$specimen_duplicate_institutions</1>
16 16
                                        <2>
17 17
                                            <_join>
18 18
                                                <1>$collection</1>
......
81 81
                                                <collectionnumber>$collectorNumber</collectionnumber>
82 82
                                                <institution_id>
83 83
                                                    <sourcelist>
84
                                                        <name>$specimenHolderInstitutions</name>
84
                                                        <name>$specimen_duplicate_institutions</name>
85 85
                                                        <sourcename>
86 86
                                                            <name>
87 87
                                                                <_split>
88 88
                                                                    <separator>[,;] *</separator>
89
                                                                    <value>$specimenHolderInstitutions</value>
89
                                                                    <value>$specimen_duplicate_institutions</value>
90 90
                                                                </_split>
91 91
                                                            </name>
92 92
                                                        </sourcename>
trunk/inputs/TRT/Specimen/map.csv
56 56
verbatimCoordinateSystem,coordinateUnits,,
57 57
locationRemarks,locationRemarks,,
58 58
genus,genus,,
59
institutionCode,specimenHolderInstitutions,,
59
institutionCode,specimen_duplicate_institutions,,
60 60
higherClassification,higherClassification,,
61 61
verbatimSRS,verbatimSRS,,
62 62
municipality,municipality,,
trunk/inputs/TRTE/Specimen/test.xml.ref
12 12
                                <1>$dataProviderRecordID</1>
13 13
                                <2>
14 14
                                    <_join>
15
                                        <1>$specimenHolderInstitutions</1>
15
                                        <1>$specimen_duplicate_institutions</1>
16 16
                                        <2>
17 17
                                            <_join>
18 18
                                                <1>$collection</1>
......
61 61
                                                <collectionnumber>$collectorNumber</collectionnumber>
62 62
                                                <institution_id>
63 63
                                                    <sourcelist>
64
                                                        <name>$specimenHolderInstitutions</name>
64
                                                        <name>$specimen_duplicate_institutions</name>
65 65
                                                        <sourcename>
66 66
                                                            <name>
67 67
                                                                <_split>
68 68
                                                                    <separator>[,;] *</separator>
69
                                                                    <value>$specimenHolderInstitutions</value>
69
                                                                    <value>$specimen_duplicate_institutions</value>
70 70
                                                                </_split>
71 71
                                                            </name>
72 72
                                                        </sourcename>
trunk/mappings/for_review/VegCore-VegBIEN.csv
5 5
taxonID,"/_if[@name=""if specimen""]/cond/_exists",
6 6
source__version,"/_if[@name=""if specimen""]/else/source/edition",
7 7
source__modified_date,"/_if[@name=""if specimen""]/else/source/pubdate",
8
specimenHolderInstitutions,"/_if[@name=""if specimen""]/else/source/shortname",
8
specimen_duplicate_institutions,"/_if[@name=""if specimen""]/else/source/shortname",
9 9
datasetURL,"/_if[@name=""if specimen""]/else/source/url",
10 10
observationGranularity,"/_if[@name=""if specimen""]/else/source/observationtype",
11 11
sourceType,"/_if[@name=""if specimen""]/else/source/sourcetype",
......
21 21
accessionNumber,"/location/authorlocationcode/_if[@name=""if specimen""]/cond/_exists",
22 22
dataProviderRecordID,"/location/authorlocationcode/_if[@name=""if specimen""]/cond/_exists",
23 23
occurrenceID,"/location/authorlocationcode/_if[@name=""if specimen""]/cond/_exists",
24
specimenHolderInstitutions,"/location/authorlocationcode/_if[@name=""if specimen""]/then",
24
specimen_duplicate_institutions,"/location/authorlocationcode/_if[@name=""if specimen""]/then",
25 25
collection,"/location/authorlocationcode/_if[@name=""if catalogNumber""]/then",
26 26
collectionURL,"/location/authorlocationcode/_if[@name=""if catalogNumber""]/then",
27 27
voucherType,"/location/authorlocationcode/_if[@name=""if indirect voucher""]/cond",
......
163 163
accessionNumber,"//institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
164 164
dataProviderRecordID,"//institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
165 165
occurrenceID,"//institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
166
specimenHolderInstitutions,"//institution_id/sourcelist/_if[@name=""if specimen""]/then/name",
167
specimenHolderInstitutions,"//institution_id/sourcelist/sourcename/name/_split:[separator=""[,;] *""]/value",
166
specimen_duplicate_institutions,"//institution_id/sourcelist/_if[@name=""if specimen""]/then/name",
167
specimen_duplicate_institutions,"//institution_id/sourcelist/sourcename/name/_split:[separator=""[,;] *""]/value",
168 168
dataProviderRecordID,//specimenreplicate/sourceaccessioncode,
169 169
occurrenceID,//specimenreplicate/sourceaccessioncode,
170 170
stemCount,//plantobservation/stemcount,
trunk/inputs/TRTE/Specimen/map.csv
27 27
verbatimEventDate,verbatimEventDate,,
28 28
municipality,municipality,,
29 29
geodeticDatum,geodeticDatum,,
30
institutionCode,specimenHolderInstitutions,,
30
institutionCode,specimen_duplicate_institutions,,
31 31
nomenclaturalCode,nomenclaturalCode,,
32 32
modified,modified,,
33 33
previousIdentifications,previousIdentifications,,
trunk/mappings/VegCore.thesaurus.csv
27 27
?globalUniqueIdentifier,"?occurrenceID,dataProviderRecordID"
28 28
?height,"?height_m,height_ft"
29 29
?heightFirstBranch,"?heightFirstBranch_m,heightFirstBranch_ft"
30
?institutionCode,"?specimenHolderInstitutions,specimenDonorInstitution"
30
?institutionCode,"?specimen_duplicate_institutions,specimenDonorInstitution"
31 31
?intercept,"?intercept_m,intercept_cm"
32 32
?latitude,"?decimalLatitude,verbatimLatitude,latitude_DMS"
33 33
?longitude,"?decimalLongitude,verbatimLongitude,longitude_DMS"
......
139 139
individualOrganismObservationID,individualObservationID
140 140
individualOrganismObservationRelativeX,organismX_m
141 141
individualOrganismObservationRelativeY,organismY_m
142
institutionCode_DwC,specimenHolderInstitutions
142
institutionCode_DwC,specimen_duplicate_institutions
143 143
institutionCode_UNCC,specimenDonorInstitution
144 144
institutionID,specimenHolderURL
145 145
interpretationType,identificationType
......
208 208
species_DwC,specificEpithet
209 209
species_VegBank,speciesBinomial
210 210
specificEpithetScore,matchedSpeciesConfidence_fraction
211
specimenHolderInstitution,specimenHolderInstitutions
211
specimenHolderInstitution,specimen_duplicate_institutions
212
specimenHolderInstitutions,specimen_duplicate_institutions
212 213
ssp,subspecies
213 214
startX,subplotX
214 215
startY,subplotY
trunk/inputs/MO/Specimen/new_terms.csv
15 15
minimummonth,monthCollected,,
16 16
minimumyear,yearCollected,,
17 17
description,specimenDescription,,
18
acronyms,specimenHolderInstitutions,,
18
acronyms,specimen_duplicate_institutions,,
19 19
determinationyear,yearIdentified,,
20 20
determinedby,identifiedBy,,
21 21
qualifier,identificationQualifier,,
trunk/mappings/VegCore-VegBIEN.csv
5 5
taxonID,"/_if[@name=""if specimen""]/cond/_exists",
6 6
source__version,"/_if[@name=""if specimen""]/else/source/edition",
7 7
source__modified_date,"/_if[@name=""if specimen""]/else/source/pubdate",
8
specimenHolderInstitutions,"/_if[@name=""if specimen""]/else/source/shortname/_first/1",
8
specimen_duplicate_institutions,"/_if[@name=""if specimen""]/else/source/shortname/_first/1",
9 9
datasetURL,"/_if[@name=""if specimen""]/else/source/url",
10 10
observationGranularity,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/observationtype",
11 11
sourceType,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype",
......
21 21
accessionNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists",
22 22
dataProviderRecordID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists",
23 23
occurrenceID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists",
24
specimenHolderInstitutions,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then/_first/2",
24
specimen_duplicate_institutions,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then/_first/2",
25 25
collection,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1",
26 26
collectionURL,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2",
27 27
voucherType,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left",
......
163 163
accessionNumber,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
164 164
dataProviderRecordID,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
165 165
occurrenceID,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
166
specimenHolderInstitutions,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2",
167
specimenHolderInstitutions,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value",
166
specimen_duplicate_institutions,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2",
167
specimen_duplicate_institutions,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value",
168 168
dataProviderRecordID,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
169 169
occurrenceID,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
170 170
stemCount,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount,
trunk/inputs/MO/Specimen/test.xml.ref
51 51
                                                <collectionnumber>$collectorNumber</collectionnumber>
52 52
                                                <institution_id>
53 53
                                                    <sourcelist>
54
                                                        <name>$specimenHolderInstitutions</name>
54
                                                        <name>$specimen_duplicate_institutions</name>
55 55
                                                        <sourcename>
56 56
                                                            <name>
57 57
                                                                <_split>
58 58
                                                                    <separator>[,;] *</separator>
59
                                                                    <value>$specimenHolderInstitutions</value>
59
                                                                    <value>$specimen_duplicate_institutions</value>
60 60
                                                                </_split>
61 61
                                                            </name>
62 62
                                                        </sourcename>
trunk/mappings/VegCore.htm
2 2
<html lang="en">
3 3
<head>
4 4
<meta charset="utf-8" />
5
<title>VegCore - BIEN - NCEAS Projects</title>
5
<title>VegCore - BIEN 3 - NCEAS Projects</title>
6 6
<meta name="description" content="Redmine" />
7 7
<meta name="keywords" content="issue,bug,tracker" />
8 8
<meta content="authenticity_token" name="csrf-param" />
9
<meta content="Bq+tsN8KDkEbS+2tdR9MAcJDvj6HdR6M+2aWArRxCQI=" name="csrf-token" />
10
<link rel='shortcut icon' href='/nceas/favicon.ico?1347421715' />
9
<meta content="95unO+G65iL9rsG/UFTftr09mD8Pd+iPgcJ2R0mAwfU=" name="csrf-token" />
10
<link rel='shortcut icon' href='/nceas/favicon.ico?1391043242' />
11 11
<link href="/nceas/stylesheets/jquery/jquery-ui-1.9.2.css?1364512407" media="all" rel="stylesheet" type="text/css" />
12
<link href="/nceas/stylesheets/application.css?1364512407" media="all" rel="stylesheet" type="text/css" />
12
<link href="/nceas/stylesheets/application.css?1391043242" media="all" rel="stylesheet" type="text/css" />
13 13

  
14 14
<script src="/nceas/javascripts/jquery-1.8.3-ui-1.9.2-ujs-2.0.3.js?1364512407" type="text/javascript"></script>
15
<script src="/nceas/javascripts/application.js?1364512407" type="text/javascript"></script>
15
<script src="/nceas/javascripts/application.js?1391043242" type="text/javascript"></script>
16 16
<script type="text/javascript">
17 17
//<![CDATA[
18 18
$(window).load(function(){ warnLeavingUnsaved('The current page contains unsaved text that will be lost if you leave this page.'); });
......
22 22

  
23 23
<!-- page specific tags -->
24 24
</head>
25
<body class="controller-wiki action-show">
25
<body class="project-bien controller-wiki action-show">
26 26
<div id="wrapper">
27 27
<div id="wrapper2">
28 28
<div id="wrapper3">
......
45 45
</form>        
46 46
    </div>
47 47

  
48
    <!--<h1><a href="/nceas/projects/working-groups?jump=wiki" class="root">Working Groups</a> » BIEN</h1>-->
48
    <!--<h1><a href="/nceas/projects/working-groups?jump=wiki" class="root">Working Groups</a> » BIEN 3</h1>-->
49 49
    <img src="/nceas/images/nceas_logo.png" style="top-margin: 15px; left-margin: 15px;"/>
50 50

  
51 51
    <div id="main-menu">
......
63 63
    <div id="sidebar">
64 64
          
65 65
<h3>Wiki</h3>
66
<ul>
67
  <li><a href="/nceas/projects/bien/wiki">Start page</a></li>
68
  <li><a href="/nceas/projects/bien/wiki/index">Index by title</a></li>
69
  <li><a href="/nceas/projects/bien/wiki/date_index">Index by date</a></li>
70
</ul>
66 71

  
67
<a href="/nceas/projects/bien/wiki">Start page</a><br />
68
<a href="/nceas/projects/bien/wiki/index">Index by title</a><br />
69
<a href="/nceas/projects/bien/wiki/date_index">Index by date</a><br />
70 72

  
71

  
72 73
        
73 74
    </div>
74 75

  
......
159 160
	<p><a href="http://VegCore.vegpath.org/ERD/"><img src="http://vegpath.org/VegCore/ERD/VegCore.ERD.png" title="VegCore schema: click for hyperlinked version" alt="VegCore schema: click for hyperlinked version" /></a></p>
160 161

  
161 162

  
162
	<p><a href="#Source" class="wiki-page">Source</a><br /><a href="#Dataset" class="wiki-page">Dataset</a><br /><a href="#Record" class="wiki-page">Record</a><br /><a href="#Occurrence" class="wiki-page">Occurrence</a><br /><a href="#Method" class="wiki-page">Method</a><br /><a href="#Stratum" class="wiki-page">Stratum</a><br /><a href="#Project" class="wiki-page">Project</a><br /><a href="#Event" class="wiki-page">Event</a><br /><a href="#EventParticipant" class="wiki-page">EventParticipant</a><br /><a href="#Coordinates" class="wiki-page">Coordinates</a><br /><a href="#Placename" class="wiki-page">Placename</a><br /><a href="#Geovalidation" class="wiki-page">Geovalidation</a><br /><a href="#Location" class="wiki-page">Location</a><br /><a href="#LocationObservation" class="wiki-page">LocationObservation</a><br /><a href="#Subplot" class="wiki-page">Subplot</a><br /><a href="#SubplotObservation" class="wiki-page">SubplotObservation</a><br /><a href="#SoilObservation" class="wiki-page">SoilObservation</a><br /><a href="#GeologicalContext" class="wiki-page">GeologicalContext</a><br /><a href="#Community" class="wiki-page">Community</a><br /><a href="#TaxonName" class="wiki-page">TaxonName</a><br /><a href="#TaxonConcept" class="wiki-page">TaxonConcept</a><br /><a href="#QualifiedTaxonName" class="wiki-page">QualifiedTaxonName</a><br /><a href="#MatchedTaxon" class="wiki-page">MatchedTaxon</a><br /><a href="#AcceptedTaxon" class="wiki-page">AcceptedTaxon</a><br /><a href="#TaxonOccurrence" class="wiki-page">TaxonOccurrence</a><br /><a href="#TaxonDetermination" class="wiki-page">TaxonDetermination</a><br /><a href="#OriginalTaxonDetermination" class="wiki-page">OriginalTaxonDetermination</a><br /><a href="#TaxonObservation" class="wiki-page">TaxonObservation</a><br /><a href="#AggregateObservation" class="wiki-page">AggregateObservation</a><br /><a href="#Individual" class="wiki-page">Individual</a><br /><a href="#IndividualObservation" class="wiki-page">IndividualObservation</a><br /><a href="#Stem" class="wiki-page">Stem</a><br /><a href="#StemObservation" class="wiki-page">StemObservation</a><br /><a href="#Collection" class="wiki-page">Collection</a><br /><a href="#Specimen" class="wiki-page">Specimen</a><br /><a href="#Voucher" class="wiki-page">Voucher</a><br /><a href="#Measurement" class="wiki-page">Measurement</a><br /><a href="#ResourceRelationship" class="wiki-page">ResourceRelationship</a></p>
163
	<p><a href="#Source" class="wiki-page">Source</a><br /><a href="#Dataset" class="wiki-page">Dataset</a><br /><a href="#Record" class="wiki-page">Record</a><br /><a href="#Occurrence" class="wiki-page">Occurrence</a><br /><a href="#Method" class="wiki-page">Method</a><br /><a href="#Stratum" class="wiki-page">Stratum</a><br /><a href="#Project" class="wiki-page">Project</a><br /><a href="#Event" class="wiki-page">Event</a><br /><a href="#EventParticipant" class="wiki-page">EventParticipant</a><br /><a href="#Coordinates" class="wiki-page">Coordinates</a><br /><a href="#Placename" class="wiki-page">Placename</a><br /><a href="#Geovalidation" class="wiki-page">Geovalidation</a><br /><a href="#Location" class="wiki-page">Location</a><br /><a href="#LocationObservation" class="wiki-page">LocationObservation</a><br /><a href="#Subplot" class="wiki-page">Subplot</a><br /><a href="#SubplotObservation" class="wiki-page">SubplotObservation</a><br /><a href="#SoilObservation" class="wiki-page">SoilObservation</a><br /><a href="#GeologicalContext" class="wiki-page">GeologicalContext</a><br /><a href="#Community" class="wiki-page">Community</a><br /><a href="#TaxonName" class="wiki-page">TaxonName</a><br /><a href="#TaxonConcept" class="wiki-page">TaxonConcept</a><br /><a href="#QualifiedTaxonName" class="wiki-page">QualifiedTaxonName</a><br /><a href="#MatchedTaxon" class="wiki-page">MatchedTaxon</a><br /><a href="#AcceptedTaxon" class="wiki-page">AcceptedTaxon</a><br /><a href="#TaxonOccurrence" class="wiki-page">TaxonOccurrence</a><br /><a href="#TaxonDetermination" class="wiki-page">TaxonDetermination</a><br /><a href="#OriginalTaxonDetermination" class="wiki-page">OriginalTaxonDetermination</a><br /><a href="#AggregateObservation" class="wiki-page">AggregateObservation</a><br /><a href="#Individual" class="wiki-page">Individual</a><br /><a href="#IndividualObservation" class="wiki-page">IndividualObservation</a><br /><a href="#Stem" class="wiki-page">Stem</a><br /><a href="#StemObservation" class="wiki-page">StemObservation</a><br /><a href="#Collection" class="wiki-page">Collection</a><br /><a href="#Specimen" class="wiki-page">Specimen</a><br /><a href="#Voucher" class="wiki-page">Voucher</a><br /><a href="#Measurement" class="wiki-page">Measurement</a><br /><a href="#ResourceRelationship" class="wiki-page">ResourceRelationship</a></p>
163 164

  
164 165

  
165 166
<hr />
......
3592 3593
	<p style="padding-left:3em;">Related: <a href="#Occurrence" class="wiki-page">Occurrence</a></p>
3593 3594

  
3594 3595

  
3595
	<a name="specimenHolderInstitutions"></a>
3596
<h2  style="padding-left:2em;"><a href="#specimenHolderInstitutions" class="wiki-page">specimenHolderInstitutions</a> <img src="_" style="padding-left: 1em;font-size: small;font-weight: normal;" title="from" alt="from" /> <a href="https://projects.nceas.ucsb.edu/nceas/attachments/download/621/vegbien_identifier_examples.xlsx#terms/institutionCode/where_specimen_held"><img src="_" style="font-size: small;" title="Brad Boyle" alt="Brad Boyle" /></a><a href="#specimenHolderInstitutions" class="wiki-anchor">&para;</a></h2>
3596
	<a name="specimen_duplicate_institutions"></a>
3597
<h2  style="padding-left:2em;"><a href="#specimen_duplicate_institutions" class="wiki-page">specimen_duplicate_institutions</a> <img src="_" style="padding-left: 1em;font-size: small;font-weight: normal;" title="from" alt="from" /> <a href="https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/2014-03-13_conference_call?duplicate_institutions_id#schema-changes-2"><img src="_" style="font-size: small;" title="Brad Boyle" alt="Brad Boyle" /></a><a href="#specimen_duplicate_institutions" class="wiki-anchor">&para;</a></h2>
3597 3598

  
3598 3599

  
3599 3600
	<p style="padding-left:5em;">The institution(s) holding a copy of the specimen</p>
......
3602 3603
	<p style="padding-left:5em;">"Identifies the institution where a specimen is held. For herbaria, this will be the acronym of the herbarium. In general, use the verbatim value provided by the data provider, unless this is incorrect. For an aggregator such as GBIF, this column will contain many values corresponding to different data providers. For a primary source (e.g., New York Botanical Garden), all values should be the same (e.g., "NY"). Some herbaria incorrectly list the acronym that sent them the specimen if it was an exchange or trade. This is incorrect. Only the acronym of the herbarium providing the data should be listed here, regardless of whether they collected the specimen themselves or received it as a duplicate from another herbarium." (<a href="https://projects.nceas.ucsb.edu/nceas/attachments/download/621/vegbien_identifier_examples.xlsx#terms/institutionCode" class="external">Brad Boyle</a>)</p>
3603 3604

  
3604 3605

  
3606
	<a name="specimenHolderInstitutions"></a>
3607
<h3  style="padding-left:4em;"><img src="_" style="padding: 0 0.3em 3pt 0.65em;font-weight: normal;" title="Synonym:" alt="Synonym:" /> <a href="#specimenHolderInstitutions" class="wiki-page">specimenHolderInstitutions</a> <img src="_" style="padding-left: 1em;font-size: small;font-weight: normal;" title="from" alt="from" /> <a href="https://projects.nceas.ucsb.edu/nceas/attachments/download/621/vegbien_identifier_examples.xlsx#terms/institutionCode/where_specimen_held"><img src="_" style="font-size: small;" title="Brad Boyle" alt="Brad Boyle" /></a><a href="#specimenHolderInstitutions" class="wiki-anchor">&para;</a></h3>
3608

  
3609

  
3605 3610
	<a name="specimenHolderInstitution"></a>
3606 3611
<h3  style="padding-left:4em;"><img src="_" style="padding: 0 0.3em 3pt 0.65em;font-weight: normal;" title="Synonym:" alt="Synonym:" /> <a href="#specimenHolderInstitution" class="wiki-page">specimenHolderInstitution</a> <img src="_" style="padding-left: 1em;font-size: small;font-weight: normal;" title="from" alt="from" /> <a href="https://projects.nceas.ucsb.edu/nceas/attachments/download/621/vegbien_identifier_examples.xlsx#terms/institutionCode/where_specimen_held"><img src="_" style="font-size: small;" title="Brad Boyle" alt="Brad Boyle" /></a><a href="#specimenHolderInstitution" class="wiki-anchor">&para;</a></h3>
3607 3612

  
......
4291 4296
<p><a href="/nceas/attachments/download/493/ACAD.Specimen.csv" class="icon icon-attachment">ACAD.Specimen.csv</a>    <a href="/nceas/attachments/493/ACAD.Specimen.csv"><img alt="Magnifier" src="/nceas/images/magnifier.png?1347421714" /></a>
4292 4297
  
4293 4298
  <span class="size">(12 KB)</span>
4294
    <span class="author">Aaron Marcuse-Kubitza, 12/05/2012 09:21 am</span>
4299
    <span class="author">Aaron Marcuse-Kubitza, 12/05/2012 09:21 AM</span>
4295 4300
  </p>
4296 4301
<p><a href="/nceas/attachments/download/621/vegbien_identifier_examples.xlsx" class="icon icon-attachment">vegbien_identifier_examples.xlsx</a>  
4297 4302
  <span class="size">(28.6 KB)</span>
4298
    <span class="author">Aaron Marcuse-Kubitza, 01/31/2013 04:40 pm</span>
4303
    <span class="author">Aaron Marcuse-Kubitza, 01/31/2013 04:40 PM</span>
4299 4304
  </p>
4300 4305
<p><a href="/nceas/attachments/download/626/vegbien_identifiers.xlsx" class="icon icon-attachment">vegbien_identifiers.xlsx</a>  
4301 4306
  <span class="size">(30.1 KB)</span>
4302
    <span class="author">Aaron Marcuse-Kubitza, 02/12/2013 12:27 am</span>
4307
    <span class="author">Aaron Marcuse-Kubitza, 02/12/2013 12:27 AM</span>
4303 4308
  </p>
4304 4309
<p><a href="/nceas/attachments/download/629/BIEN%20database%20entities%20related%20to%20data%20provenance%20and%20ownership.docx" class="icon icon-attachment">BIEN database entities related to data provenance and ownership.docx</a>  
4305 4310
  <span class="size">(157 KB)</span>
4306
    <span class="author">Aaron Marcuse-Kubitza, 02/14/2013 04:44 pm</span>
4311
    <span class="author">Aaron Marcuse-Kubitza, 02/14/2013 04:44 PM</span>
4307 4312
  </p>
4308 4313
</div>
4309 4314

  
trunk/mappings/VegCore.vocab.csv
581 581
specimenHolderURL
582 582
specimenOwner
583 583
specimenStampingInstitution
584
specimen_duplicate_institutions
584 585
ssp
585 586
startDate
586 587
startDayOfYear

Also available in: Unified diff