Revision 12879
Added by Aaron Marcuse-Kubitza almost 11 years ago
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,,
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|
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,,
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|
4 |
dataSourceName,specimen_duplicate_institutions,,
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|
5 | 5 |
dataSourceNamePrimary,*dataSourceNamePrimary,, |
6 | 6 |
plotID,locationID,, |
7 | 7 |
observationType,observationGranularity,, |
trunk/inputs/NY/Ecatalog_all/test.xml.ref | ||
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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>
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|
81 |
<name>$specimen_duplicate_institutions</name>
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|
82 | 82 |
<sourcename> |
83 | 83 |
<name> |
84 | 84 |
<_split> |
85 | 85 |
<separator>[,;] *</separator> |
86 |
<value>$specimenHolderInstitutions</value>
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|
86 |
<value>$specimen_duplicate_institutions</value>
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|
87 | 87 |
</_split> |
88 | 88 |
</name> |
89 | 89 |
</sourcename> |
trunk/inputs/Madidi/IndividualObservation/new_terms.csv | ||
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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,,
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|
18 |
institutionCode,specimen_duplicate_institutions,,
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|
19 | 19 |
catalogNumber,accessionNumber,, |
20 | 20 |
verbatimSRS,verbatimSRS,, |
21 | 21 |
verbatimLongitude,verbatimLongitude,, |
trunk/inputs/JBM/Specimen/map.csv | ||
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35 | 35 |
type,type,, |
36 | 36 |
order,order,, |
37 | 37 |
kingdom,kingdom,, |
38 |
institutionCode,specimenHolderInstitutions,,
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|
38 |
institutionCode,specimen_duplicate_institutions,,
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|
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 | ||
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1 | 1 |
SELECT util.search_path_append('util'); |
2 | 2 |
|
3 |
SELECT create_if_not_exists($$CREATE INDEX "Specimen.acronym" ON $$||:table_str||$$ ("specimenHolderInstitutions")$$);
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|
3 |
SELECT create_if_not_exists($$CREATE INDEX "Specimen.acronym" ON $$||:table_str||$$ ("specimen_duplicate_institutions")$$);
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|
4 | 4 |
|
5 | 5 |
-- Remove institutions that we have direct data for |
6 | 6 |
DELETE FROM :table |
7 |
WHERE "specimenHolderInstitutions" IN (
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|
7 |
WHERE "specimen_duplicate_institutions" IN (
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|
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>
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|
92 |
<value>$specimen_duplicate_institutions</value>
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|
93 | 93 |
</_split> |
94 | 94 |
</name> |
95 | 95 |
</sourcename> |
trunk/inputs/HIBG/Specimen/test.xml.ref | ||
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12 | 12 |
<1>$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>
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|
66 | 66 |
<sourcename> |
67 | 67 |
<name> |
68 | 68 |
<_split> |
69 | 69 |
<separator>[,;] *</separator> |
70 |
<value>$specimenHolderInstitutions</value>
|
|
70 |
<value>$specimen_duplicate_institutions</value>
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|
71 | 71 |
</_split> |
72 | 72 |
</name> |
73 | 73 |
</sourcename> |
trunk/inputs/NY/Ecatalog_all/map.csv | ||
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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 | ||
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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>
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|
55 |
<value>$specimen_duplicate_institutions</value>
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|
56 | 56 |
</_split> |
57 | 57 |
</name> |
58 | 58 |
</sourcename> |
trunk/inputs/.herbaria/ih/map.csv | ||
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1 | 1 |
herbaria,VegCore,Filter,Comments |
2 | 2 |
eparties_key,*eparties_key,, |
3 | 3 |
NamOrganisation,*NamOrganisation,, |
4 |
acronym,specimenHolderInstitutions,,
|
|
4 |
acronym,specimen_duplicate_institutions,,
|
|
5 | 5 |
IhhInstitutionType,*IhhInstitutionType,, |
6 | 6 |
NamBranch,*NamBranch,, |
7 | 7 |
NamDepartment,*NamDepartment,, |
trunk/inputs/REMIB/Specimen/map.csv | ||
---|---|---|
1 | 1 |
REMIB,VegCore,Filter,Comments |
2 | 2 |
row_num,*row_num,, |
3 |
acronym,specimenHolderInstitutions,,
|
|
3 |
acronym,specimen_duplicate_institutions,,
|
|
4 | 4 |
accession_number,accessionNumber,,"Not globally unique, only (usually) unique within the institution providing the data (""acronym""). Note that there are nevertheless 11,869 rows where an accession_number appears multiple times within the same institution. [1] |
5 | 5 |
|
6 | 6 |
[1] Using the following query: |
trunk/inputs/.herbaria/ih/new_terms.csv | ||
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1 |
acronym,specimenHolderInstitutions,, |
|
1 |
acronym,specimen_duplicate_institutions,, |
trunk/inputs/REMIB/Specimen/new_terms.csv | ||
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1 |
acronym,specimenHolderInstitutions,,
|
|
1 |
acronym,specimen_duplicate_institutions,,
|
|
2 | 2 |
long_deg,longitude_deg_verbatim,, |
3 | 3 |
long_min,longitude_min_verbatim,, |
4 | 4 |
long_sec,longitude_sec_verbatim,, |
trunk/inputs/.herbaria/ih/test.xml.ref | ||
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7 | 7 |
<next>parent_id</next> |
8 | 8 |
<path> |
9 | 9 |
<source> |
10 |
<shortname>$specimenHolderInstitutions</shortname>
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|
10 |
<shortname>$specimen_duplicate_institutions</shortname>
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|
11 | 11 |
<observationtype>specimen</observationtype> |
12 | 12 |
<sourcetype>herbarium</sourcetype> |
13 | 13 |
</source> |
trunk/inputs/REMIB/Specimen/test.xml.ref | ||
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9 | 9 |
<location> |
10 | 10 |
<authorlocationcode> |
11 | 11 |
<_join> |
12 |
<1>$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">¶</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">¶</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">¶</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">¶</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>
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|
4299 |
<span class="author">Aaron Marcuse-Kubitza, 12/05/2012 09:21 AM</span>
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|
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>
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|
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
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`.