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Revision 1118

Generate DwC-VegBIEN mapping as union of DwC1 and DwC2 mappings

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mappings/DwC-VegBIEN.specimens.csv
1
"DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionCode=$/_ignore/inLabel]/",VegBIEN:/specimenreplicate,Comments,Order
2
country,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=""area|country|territory""])/placename",Brad: Required; reject record if this field NULL,63
3
stateProvince,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=""region|state|province""])/placename",,65
4
county,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=county])/placename,,66
5
coordinatePrecision,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/coordsaccuracy,,89
6
coordinatePrecision/_noCV/value,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/coordsaccuracy/_noCV/value,,89
7
footprintWKT,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/footprintgeometry_dwc,,91
8
locality,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationnarrative/_alt/1,,68
9
verbatimLocality,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationnarrative/_alt/2,"Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one.",69
10
maximumElevationInMeters,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/max,elevationrange/_range/to}",,72
11
minimumElevationInMeters,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/min,elevationrange/_range/from}",,71
12
decimalLatitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[!namedplace_id]/latitude,centerlatitude}/_alt/1/_nullIf:[null=0,type=float]/value",,85
13
verbatimLatitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[!namedplace_id]/latitude,centerlatitude}/_alt/2/_nullIf:[null=0,type=float]/value",,81
14
decimalLongitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[!namedplace_id]/longitude,centerlongitude}/_alt/1/_nullIf:[null=0,type=float]/value",,86
15
verbatimLongitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[!namedplace_id]/longitude,centerlongitude}/_alt/2/_nullIf:[null=0,type=float]/value",,82
16
habitat,/*_id/taxonoccurrence/*_id/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
17
habitat/_merge/1,/*_id/taxonoccurrence/*_id/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname/_merge/1,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
18
habitat/_merge/2,/*_id/taxonoccurrence/*_id/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname/_merge/2,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
19
bien.substrate,/*_id/taxonoccurrence/*_id/locationevent/landscapenarrative,,
20
eventDate,/*_id/taxonoccurrence/*_id/locationevent/obsstartdate,,44
21
eventDate/_alt/2/_date/day,/*_id/taxonoccurrence/*_id/locationevent/obsstartdate/_alt/2/_date/day,,44
22
eventDate/_alt/2/_date/month,/*_id/taxonoccurrence/*_id/locationevent/obsstartdate/_alt/2/_date/month,,44
23
eventDate/_alt/2/_date/year,/*_id/taxonoccurrence/*_id/locationevent/obsstartdate/_alt/2/_date/year,,44
24
maximumDepthInMeters,/*_id/taxonoccurrence/*_id/locationevent/waterdepth/max,,75
25
minimumDepthInMeters,/*_id/taxonoccurrence/*_id/locationevent/waterdepth/min,,74
26
scientificNameAuthorship,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Authority]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname","Brad: Mapping probably incorrect. This DwC element refers to scientific name author; does not correspond to the VegBank and VegX elements you have listed (Bob, Nick�where does name author belong in VegBank and VegX?); Aaron: The mapped VegX element is the author linked to the taxon name, so it seems like this is the scientific name author",153
27
sex,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=sex]]:[@fkey=tableRecord_ID]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
28
dateIdentified,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]/determinationdate",,120
29
dateIdentified/_alt/2/_date/day,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]/determinationdate/_alt/2/_date/day",,120
30
dateIdentified/_alt/2/_date/month,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]/determinationdate/_alt/2/_date/month",,120
31
dateIdentified/_alt/2/_date/year,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]/determinationdate/_alt/2/_date/year",,120
32
identifiedBy,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]:[determinationtype=Author,iscurrent=true]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Bob: does this look correct for VegBank?,119
33
scientificName,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname","Brad: Bob, Nick, please is this mapping OK?",134
34
class,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Class]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,144
35
family,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Family]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,146
36
genus,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Genus]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,147
37
kingdom,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Kingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,142
38
order,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Order]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,145
39
specificEpithet,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Species]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,149
40
phylum,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Subkingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,143
41
infraspecificEpithet,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Subspecies]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,150
42
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
43
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
44
fieldNotes,/description,,
45
fieldNotes/_merge/1,/description/_merge/1,,
46
"fieldNotes/_merge/2/_label[label=""plant fungus""]/value","/description/_merge/2/_label[label=""plant fungus""]/value",,
47
catalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
48
recordNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
49
collectionID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/2,,9
50
fieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
51
institutionCode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1,,
52
occurrenceID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
53
acceptedNameUsage,,,135
54
acceptedNameUsageID,,,128
55
associatedMedia,,,36
56
associatedOccurrences,,,38
57
associatedReferences,,,37
58
associatedSequences,,,39
59
associatedTaxa,,,40
60
basisOfRecord,,Brad: OMIT? See http://rs.tdwg.org/dwc/terms/index.htm#basisOfRecord for definition of this term.,15
61
bed,,,117
62
behavior,,,29
63
continent,,Brad: OMIT,59
64
coordinateUncertaintyInMeters,,,88
65
countryCode,,,64
66
dataGeneralizations,,,17
67
datasetID,,,10
68
datasetName,,,13
69
day,,Brad: OMIT,50
70
dcterms:accessRights,,,5
71
dcterms:bibliographicCitation,,,6
72
dcterms:language,,,2
73
dcterms:modified,,"Brad: Mapping to VegX is incorrect. I think is this merely an internal timestamp indicated when record last modified, not necessarily when determination (taxon name) last modified. Probably we should omit this field, although might be useful for updating changed records from this source.",1
74
dcterms:references,,,7
75
dcterms:rights,,,3
76
dcterms:rightsHolder,,,4
77
dcterms:type,,,0
78
disposition,,,33
79
dynamicProperties,,,18
80
earliestAgeOrLowestStage,,,109
81
earliestEonOrLowestEonothem,,,101
82
earliestEpochOrLowestSeries,,,107
83
earliestEraOrLowestErathem,,,103
84
earliestPeriodOrLowestSystem,,,105
85
endDayOfYear,,,47
86
establishmentMeans,,,30
87
eventID,,,41
88
eventRemarks,,,55
89
eventTime,,Brad: OMIT,45
90
footprintSRS,,,92
91
footprintSpatialFit,,,93
92
formation,,,115
93
geodeticDatum,,,87
94
geologicalContextID,,,100
95
georeferenceProtocol,,,96
96
georeferenceRemarks,,,99
97
georeferenceSources,,,97
98
georeferenceVerificationStatus,,,98
99
georeferencedBy,,Brad: Correct for VB. Nick: is there a way to specifically identify this party as collector of a specimen?,94
100
georeferencedDate,,,95
101
group,,,114
102
higherClassification,,,141
103
higherGeography,,,58
104
higherGeographyID,,,57
105
highestBiostratigraphicZone,,,112
106
identificationID,,,118
107
identificationQualifier,,,124
108
identificationReferences,,,121
109
identificationRemarks,,,123
110
identificationVerificationStatus,,,122
111
individualCount,,Brad: OMIT; not relevant for DwC plant specimen data.,25
112
individualID,,"Brad: OMIT; db-specific element, not relevant to VB/VX",24
113
informationWithheld,,,16
114
institutionID,,,8
115
island,,,62
116
islandGroup,,,61
117
latestAgeOrHighestStage,,,110
118
latestEonOrHighestEonothem,,,102
119
latestEpochOrHighestSeries,,,108
120
latestEraOrHighestErathem,,,104
121
latestPeriodOrHighestSystem,,,106
122
lifeStage,,,27
123
lithostratigraphicTerms,,,113
124
locationAccordingTo,,,78
125
locationID,,,56
126
locationRemarks,,,79
127
lowestBiostratigraphicZone,,,111
128
maximumDistanceAboveSurfaceInMeters,,,77
129
measurementAccuracy,,,169
130
measurementDeterminedBy,,,172
131
measurementDeterminedDate,,,171
132
measurementID,,,166
133
measurementMethod,,,173
134
measurementRemarks,,,174
135
measurementType,,,167
136
measurementUnit,,,170
137
measurementValue,,,168
138
member,,,116
139
minimumDistanceAboveSurfaceInMeters,,,76
140
month,,,49
141
municipality,,,67
142
nameAccordingTo,,,138
143
nameAccordingToID,,,131
144
namePublishedIn,,,139
145
namePublishedInID,,,132
146
namePublishedInYear,,,140
147
nomenclaturalCode,,,155
148
nomenclaturalStatus,,,157
149
occurrenceRemarks,,,21
150
occurrenceStatus,,,31
151
originalNameUsage,,,137
152
originalNameUsageID,,,130
153
otherCatalogNumbers,,,34
154
ownerInstitutionCode,,,14
155
parentNameUsage,,,136
156
parentNameUsageID,,,129
157
pointRadiusSpatialFit,,,90
158
preparations,,Brad: OMIT,32
159
previousIdentifications,,Brad: OMIT,35
160
relatedResourceID,,Brad: OMIT,161
161
relationshipAccordingTo,,,163
162
relationshipEstablishedDate,,,164
163
relationshipOfResource,,Brad: OMIT,162
164
relationshipRemarks,,,165
165
reproductiveCondition,,,28
166
resourceID,,,160
167
resourceRelationshipID,,,159
168
samplingEffort,,,43
169
samplingProtocol,,,42
170
scientificNameID,,,127
171
startDayOfYear,,,46
172
subgenus,,,148
173
taxonConceptID,,,133
174
taxonID,,,126
175
taxonRank,,,151
176
taxonRemarks,,,158
177
taxonomicStatus,,,156
178
typeStatus,,Brad: OMIT (?). Indicates whether this specimen served as type for taxon name. Probably not relevant for BIEN,125
179
verbatimCoordinateSystem,,,83
180
verbatimCoordinates,,,80
181
verbatimDepth,,,73
182
verbatimElevation,,,70
183
verbatimEventDate,,,51
184
verbatimSRS,,,84
185
verbatimTaxonRank,,,152
186
vernacularName,,,154
187
waterBody,,,60
188
year,,,48
mappings/DwC1-DwC.specimens.csv
1
"DwC1::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[InstitutionCode=$/_ignore/inLabel]/","DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionCode=$/_ignore/inLabel]/","Comments"
2
"DateLastModified","dcterms:modified",
3
"InstitutionCode","institutionCode",
4
"CollectionCode","collectionCode",
5
"CatalogNumber","catalogNumber",
6
"ScientificName","scientificName",
7
"BasisOfRecord","basisOfRecord",
8
"Kingdom","kingdom",
9
"Phylum","phylum",
10
"Class","class",
11
"Order","order",
12
"Family","family",
13
"Genus","genus",
14
"Species","specificEpithet",
15
"Subspecies","infraspecificEpithet",
16
"ScientificNameAuthor","scientificNameAuthorship",
17
"IdentifiedBy","identifiedBy",
18
"YearIdentified","dateIdentified/_alt/2/_date/year",
19
"MonthIdentified","dateIdentified/_alt/2/_date/month",
20
"DayIdentified","dateIdentified/_alt/2/_date/day",
21
"TypeStatus","typeStatus",
22
"CollectorNumber","recordNumber",
23
"FieldNumber","fieldNumber",
24
"Collector","recordedBy",
25
"YearCollected","eventDate/_alt/2/_date/year",
26
"MonthCollected","eventDate/_alt/2/_date/month",
27
"DayCollected","eventDate/_alt/2/_date/day",
28
"JulianDay","day",
29
"TimeOfDay","eventTime",
30
"ContinentOcean","continent",
31
"Country","country",
32
"StateProvince","stateProvince",
33
"County","county",
34
"Locality","verbatimLocality",
35
"Longitude","verbatimLongitude",
36
"Latitude","verbatimLatitude",
37
"CoordinatePrecision","coordinatePrecision/_noCV/value",
38
"BoundingBox","footprintWKT",
39
"MinimumElevation","minimumElevationInMeters",
40
"MaximumElevation","maximumElevationInMeters",
41
"MinimumDepth","minimumDepthInMeters",
42
"MaximumDepth","maximumDepthInMeters",
43
"Sex","sex",
44
"PreparationType","preparations",
45
"IndividualCount","individualCount",
46
"PreviousCatalogNumber","previousIdentifications","?"
47
"RelationshipType","relationshipOfResource",
48
"RelatedCatalogItem","relatedResourceID",
49
"Notes","fieldNotes/_merge/1",
mappings/for_review/DwC-VegBIEN.specimens.csv
1 1
"DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionCode=$/_ignore/inLabel]/",VegBIEN:/specimenreplicate,Comments,Order
2
Country,"//*_id/namedplace[placesystem=""area|country|territory""]/placename",Brad: Required; reject record if this field NULL,63
2 3
country,"//*_id/namedplace[placesystem=""area|country|territory""]/placename",Brad: Required; reject record if this field NULL,63
4
StateProvince,"//*_id/namedplace[placesystem=""region|state|province""]/placename",,65
3 5
stateProvince,"//*_id/namedplace[placesystem=""region|state|province""]/placename",,65
6
County,//*_id/namedplace[placesystem=county]/placename,,66
4 7
county,//*_id/namedplace[placesystem=county]/placename,,66
5 8
coordinatePrecision,//location/locationdetermination[]/coordsaccuracy,,89
9
CoordinatePrecision,//location/locationdetermination[]/coordsaccuracy/_noCV/value,,89
6 10
coordinatePrecision/_noCV/value,//location/locationdetermination[]/coordsaccuracy/_noCV/value,,89
11
BoundingBox,//location/locationdetermination[]/footprintgeometry_dwc,,91
7 12
footprintWKT,//location/locationdetermination[]/footprintgeometry_dwc,,91
8 13
locality,//location/locationnarrative/_alt/1,,68
14
Locality,//location/locationnarrative/_alt/2,"Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one.",69
9 15
verbatimLocality,//location/locationnarrative/_alt/2,"Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one.",69
16
MaximumElevation,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/max,elevationrange/_range/to}",,72
10 17
maximumElevationInMeters,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/max,elevationrange/_range/to}",,72
18
MinimumElevation,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/min,elevationrange/_range/from}",,71
11 19
minimumElevationInMeters,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/min,elevationrange/_range/from}",,71
12 20
decimalLatitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[]/latitude,centerlatitude}/_alt/1/_nullIf/value",,85
21
Latitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[]/latitude,centerlatitude}/_alt/2/_nullIf/value",,81
13 22
verbatimLatitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[]/latitude,centerlatitude}/_alt/2/_nullIf/value",,81
14 23
decimalLongitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[]/longitude,centerlongitude}/_alt/1/_nullIf/value",,86
24
Longitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[]/longitude,centerlongitude}/_alt/2/_nullIf/value",,82
15 25
verbatimLongitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[]/longitude,centerlongitude}/_alt/2/_nullIf/value",,82
16 26
habitat,//*/commname,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
17 27
habitat/_merge/1,//*/commname/_merge/1,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
18 28
habitat/_merge/2,//*/commname/_merge/2,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
19 29
bien.substrate,//locationevent/landscapenarrative,,
20 30
eventDate,//locationevent/obsstartdate,,44
31
DayCollected,//locationevent/obsstartdate/_alt/2/_date/day,,44
21 32
eventDate/_alt/2/_date/day,//locationevent/obsstartdate/_alt/2/_date/day,,44
33
MonthCollected,//locationevent/obsstartdate/_alt/2/_date/month,,44
22 34
eventDate/_alt/2/_date/month,//locationevent/obsstartdate/_alt/2/_date/month,,44
35
YearCollected,//locationevent/obsstartdate/_alt/2/_date/year,,44
23 36
eventDate/_alt/2/_date/year,//locationevent/obsstartdate/_alt/2/_date/year,,44
37
MaximumDepth,//waterdepth/max,,75
24 38
maximumDepthInMeters,//waterdepth/max,,75
39
MinimumDepth,//waterdepth/min,,74
25 40
minimumDepthInMeters,//waterdepth/min,,74
41
ScientificNameAuthor,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Authority]/*_id/plantconcept/*_id/*/plantname","Brad: Mapping probably incorrect. This DwC element refers to scientific name author; does not correspond to the VegBank and VegX elements you have listed (Bob, Nick�where does name author belong in VegBank and VegX?); Aaron: The mapped VegX element is the author linked to the taxon name, so it seems like this is the scientific name author",153
26 42
scientificNameAuthorship,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Authority]/*_id/plantconcept/*_id/*/plantname","Brad: Mapping probably incorrect. This DwC element refers to scientific name author; does not correspond to the VegBank and VegX elements you have listed (Bob, Nick�where does name author belong in VegBank and VegX?); Aaron: The mapped VegX element is the author linked to the taxon name, so it seems like this is the scientific name author",153
43
Sex,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Binomial]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=sex]]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
27 44
sex,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Binomial]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=sex]]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
28 45
dateIdentified,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Binomial]/determinationdate",,120
46
DayIdentified,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Binomial]/determinationdate/_alt/2/_date/day",,120
29 47
dateIdentified/_alt/2/_date/day,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Binomial]/determinationdate/_alt/2/_date/day",,120
48
MonthIdentified,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Binomial]/determinationdate/_alt/2/_date/month",,120
30 49
dateIdentified/_alt/2/_date/month,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Binomial]/determinationdate/_alt/2/_date/month",,120
50
YearIdentified,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Binomial]/determinationdate/_alt/2/_date/year",,120
31 51
dateIdentified/_alt/2/_date/year,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Binomial]/determinationdate/_alt/2/_date/year",,120
52
IdentifiedBy,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Binomial]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Bob: does this look correct for VegBank?,119
32 53
identifiedBy,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Binomial]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Bob: does this look correct for VegBank?,119
54
ScientificName,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Binomial]/*_id/plantconcept/*_id/*/plantname","Brad: Bob, Nick, please is this mapping OK?",134
33 55
scientificName,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Binomial]/*_id/plantconcept/*_id/*/plantname","Brad: Bob, Nick, please is this mapping OK?",134
56
Class,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Class]/*_id/plantconcept/*_id/*/plantname",,144
34 57
class,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Class]/*_id/plantconcept/*_id/*/plantname",,144
58
Family,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Family]/*_id/plantconcept/*_id/*/plantname",,146
35 59
family,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Family]/*_id/plantconcept/*_id/*/plantname",,146
60
Genus,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Genus]/*_id/plantconcept/*_id/*/plantname",,147
36 61
genus,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Genus]/*_id/plantconcept/*_id/*/plantname",,147
62
Kingdom,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Kingdom]/*_id/plantconcept/*_id/*/plantname",,142
37 63
kingdom,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Kingdom]/*_id/plantconcept/*_id/*/plantname",,142
64
Order,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Order]/*_id/plantconcept/*_id/*/plantname",,145
38 65
order,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Order]/*_id/plantconcept/*_id/*/plantname",,145
66
Species,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Species]/*_id/plantconcept/*_id/*/plantname",,149
39 67
specificEpithet,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Species]/*_id/plantconcept/*_id/*/plantname",,149
68
Phylum,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Subkingdom]/*_id/plantconcept/*_id/*/plantname",,143
40 69
phylum,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Subkingdom]/*_id/plantconcept/*_id/*/plantname",,143
70
Subspecies,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Subspecies]/*_id/plantconcept/*_id/*/plantname",,150
41 71
infraspecificEpithet,"//taxonoccurrence/taxondetermination[rolecode=identifier,rank=Subspecies]/*_id/plantconcept/*_id/*/plantname",,150
72
Collector,//taxonoccurrence/verbatimcollectorname,,23
42 73
recordedBy,//taxonoccurrence/verbatimcollectorname,,23
74
CollectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
43 75
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
44 76
fieldNotes,/description,,
77
Notes,/description/_merge/1,,
45 78
fieldNotes/_merge/1,/description/_merge/1,,
46 79
"fieldNotes/_merge/2/_label[label=""plant fungus""]/value","/description/_merge/2/_label[label=""plant fungus""]/value",,
80
CatalogNumber,/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
47 81
catalogNumber,/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
82
CollectorNumber,/collectionnumber/_alt/1,,22
48 83
recordNumber,/collectionnumber/_alt/1,,22
49 84
collectionID,/collectionnumber/_alt/2,,9
85
FieldNumber,/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
50 86
fieldNumber,/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
87
InstitutionCode,//party/organizationname/_alt/1,,
51 88
institutionCode,//party/organizationname/_alt/1,,
52 89
occurrenceID,/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
90
BasisOfRecord,,Brad: OMIT? See http://rs.tdwg.org/dwc/terms/index.htm#basisOfRecord for definition of this term.,15
91
ContinentOcean,,Brad: OMIT,59
92
DateLastModified,,"Brad: Mapping to VegX is incorrect. I think is this merely an internal timestamp indicated when record last modified, not necessarily when determination (taxon name) last modified. Probably we should omit this field, although might be useful for updating changed records from this source.",1
93
IndividualCount,,Brad: OMIT; not relevant for DwC plant specimen data.,25
94
JulianDay,,Brad: OMIT,50
95
PreparationType,,Brad: OMIT,32
96
PreviousCatalogNumber,,?; Brad: OMIT,35
97
RelatedCatalogItem,,Brad: OMIT,161
98
RelationshipType,,Brad: OMIT,162
99
TimeOfDay,,Brad: OMIT,45
100
TypeStatus,,Brad: OMIT (?). Indicates whether this specimen served as type for taxon name. Probably not relevant for BIEN,125
53 101
acceptedNameUsage,,,135
54 102
acceptedNameUsageID,,,128
55 103
associatedMedia,,,36
mappings/DwC1-VegBIEN.specimens.csv
1
"DwC1::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[InstitutionCode=$/_ignore/inLabel]/",VegBIEN:/specimenreplicate,Comments,Order
1
"DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionCode=$/_ignore/inLabel]/",VegBIEN:/specimenreplicate,Comments,Order
2 2
Country,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=""area|country|territory""])/placename",Brad: Required; reject record if this field NULL,63
3 3
StateProvince,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=""region|state|province""])/placename",,65
4 4
County,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=county])/placename,,66
mappings/DwC1-DwC2.specimens.csv
1
"DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionCode=$/_ignore/inLabel]/","DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionCode=$/_ignore/inLabel]/","Comments"
2
"DateLastModified","dcterms:modified",
3
"InstitutionCode","institutionCode",
4
"CollectionCode","collectionCode",
5
"CatalogNumber","catalogNumber",
6
"ScientificName","scientificName",
7
"BasisOfRecord","basisOfRecord",
8
"Kingdom","kingdom",
9
"Phylum","phylum",
10
"Class","class",
11
"Order","order",
12
"Family","family",
13
"Genus","genus",
14
"Species","specificEpithet",
15
"Subspecies","infraspecificEpithet",
16
"ScientificNameAuthor","scientificNameAuthorship",
17
"IdentifiedBy","identifiedBy",
18
"YearIdentified","dateIdentified/_alt/2/_date/year",
19
"MonthIdentified","dateIdentified/_alt/2/_date/month",
20
"DayIdentified","dateIdentified/_alt/2/_date/day",
21
"TypeStatus","typeStatus",
22
"CollectorNumber","recordNumber",
23
"FieldNumber","fieldNumber",
24
"Collector","recordedBy",
25
"YearCollected","eventDate/_alt/2/_date/year",
26
"MonthCollected","eventDate/_alt/2/_date/month",
27
"DayCollected","eventDate/_alt/2/_date/day",
28
"JulianDay","day",
29
"TimeOfDay","eventTime",
30
"ContinentOcean","continent",
31
"Country","country",
32
"StateProvince","stateProvince",
33
"County","county",
34
"Locality","verbatimLocality",
35
"Longitude","verbatimLongitude",
36
"Latitude","verbatimLatitude",
37
"CoordinatePrecision","coordinatePrecision/_noCV/value",
38
"BoundingBox","footprintWKT",
39
"MinimumElevation","minimumElevationInMeters",
40
"MaximumElevation","maximumElevationInMeters",
41
"MinimumDepth","minimumDepthInMeters",
42
"MaximumDepth","maximumDepthInMeters",
43
"Sex","sex",
44
"PreparationType","preparations",
45
"IndividualCount","individualCount",
46
"PreviousCatalogNumber","previousIdentifications","?"
47
"RelationshipType","relationshipOfResource",
48
"RelatedCatalogItem","relatedResourceID",
49
"Notes","fieldNotes/_merge/1",
mappings/DwC2-VegBIEN.specimens.csv
1
"DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionCode=$/_ignore/inLabel]/",VegBIEN:/specimenreplicate,Comments,Order
2
country,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=""area|country|territory""])/placename",Brad: Required; reject record if this field NULL,63
3
stateProvince,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=""region|state|province""])/placename",,65
4
county,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=county])/placename,,66
5
coordinatePrecision,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/coordsaccuracy,,89
6
coordinatePrecision/_noCV/value,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/coordsaccuracy/_noCV/value,,89
7
footprintWKT,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/footprintgeometry_dwc,,91
8
locality,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationnarrative/_alt/1,,68
9
verbatimLocality,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationnarrative/_alt/2,"Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one.",69
10
maximumElevationInMeters,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/max,elevationrange/_range/to}",,72
11
minimumElevationInMeters,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/min,elevationrange/_range/from}",,71
12
decimalLatitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[!namedplace_id]/latitude,centerlatitude}/_alt/1/_nullIf:[null=0,type=float]/value",,85
13
verbatimLatitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[!namedplace_id]/latitude,centerlatitude}/_alt/2/_nullIf:[null=0,type=float]/value",,81
14
decimalLongitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[!namedplace_id]/longitude,centerlongitude}/_alt/1/_nullIf:[null=0,type=float]/value",,86
15
verbatimLongitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[!namedplace_id]/longitude,centerlongitude}/_alt/2/_nullIf:[null=0,type=float]/value",,82
16
habitat,/*_id/taxonoccurrence/*_id/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
17
habitat/_merge/1,/*_id/taxonoccurrence/*_id/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname/_merge/1,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
18
habitat/_merge/2,/*_id/taxonoccurrence/*_id/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname/_merge/2,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
19
bien.substrate,/*_id/taxonoccurrence/*_id/locationevent/landscapenarrative,,
20
eventDate,/*_id/taxonoccurrence/*_id/locationevent/obsstartdate,,44
21
eventDate/_alt/2/_date/day,/*_id/taxonoccurrence/*_id/locationevent/obsstartdate/_alt/2/_date/day,,44
22
eventDate/_alt/2/_date/month,/*_id/taxonoccurrence/*_id/locationevent/obsstartdate/_alt/2/_date/month,,44
23
eventDate/_alt/2/_date/year,/*_id/taxonoccurrence/*_id/locationevent/obsstartdate/_alt/2/_date/year,,44
24
maximumDepthInMeters,/*_id/taxonoccurrence/*_id/locationevent/waterdepth/max,,75
25
minimumDepthInMeters,/*_id/taxonoccurrence/*_id/locationevent/waterdepth/min,,74
26
scientificNameAuthorship,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Authority]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname","Brad: Mapping probably incorrect. This DwC element refers to scientific name author; does not correspond to the VegBank and VegX elements you have listed (Bob, Nick�where does name author belong in VegBank and VegX?); Aaron: The mapped VegX element is the author linked to the taxon name, so it seems like this is the scientific name author",153
27
sex,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=sex]]:[@fkey=tableRecord_ID]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
28
dateIdentified,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]/determinationdate",,120
29
dateIdentified/_alt/2/_date/day,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]/determinationdate/_alt/2/_date/day",,120
30
dateIdentified/_alt/2/_date/month,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]/determinationdate/_alt/2/_date/month",,120
31
dateIdentified/_alt/2/_date/year,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]/determinationdate/_alt/2/_date/year",,120
32
identifiedBy,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]:[determinationtype=Author,iscurrent=true]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Bob: does this look correct for VegBank?,119
33
scientificName,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname","Brad: Bob, Nick, please is this mapping OK?",134
34
class,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Class]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,144
35
family,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Family]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,146
36
genus,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Genus]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,147
37
kingdom,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Kingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,142
38
order,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Order]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,145
39
specificEpithet,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Species]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,149
40
phylum,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Subkingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,143
41
infraspecificEpithet,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Subspecies]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,150
42
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
43
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
44
fieldNotes,/description,,
45
fieldNotes/_merge/1,/description/_merge/1,,
46
"fieldNotes/_merge/2/_label[label=""plant fungus""]/value","/description/_merge/2/_label[label=""plant fungus""]/value",,
47
catalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
48
recordNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
49
collectionID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/2,,9
50
fieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
51
institutionCode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1,,
52
occurrenceID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
53
acceptedNameUsage,,,135
54
acceptedNameUsageID,,,128
55
associatedMedia,,,36
56
associatedOccurrences,,,38
57
associatedReferences,,,37
58
associatedSequences,,,39
59
associatedTaxa,,,40
60
basisOfRecord,,Brad: OMIT? See http://rs.tdwg.org/dwc/terms/index.htm#basisOfRecord for definition of this term.,15
61
bed,,,117
62
behavior,,,29
63
continent,,Brad: OMIT,59
64
coordinateUncertaintyInMeters,,,88
65
countryCode,,,64
66
dataGeneralizations,,,17
67
datasetID,,,10
68
datasetName,,,13
69
day,,Brad: OMIT,50
70
dcterms:accessRights,,,5
71
dcterms:bibliographicCitation,,,6
72
dcterms:language,,,2
73
dcterms:modified,,"Brad: Mapping to VegX is incorrect. I think is this merely an internal timestamp indicated when record last modified, not necessarily when determination (taxon name) last modified. Probably we should omit this field, although might be useful for updating changed records from this source.",1
74
dcterms:references,,,7
75
dcterms:rights,,,3
76
dcterms:rightsHolder,,,4
77
dcterms:type,,,0
78
disposition,,,33
79
dynamicProperties,,,18
80
earliestAgeOrLowestStage,,,109
81
earliestEonOrLowestEonothem,,,101
82
earliestEpochOrLowestSeries,,,107
83
earliestEraOrLowestErathem,,,103
84
earliestPeriodOrLowestSystem,,,105
85
endDayOfYear,,,47
86
establishmentMeans,,,30
87
eventID,,,41
88
eventRemarks,,,55
89
eventTime,,Brad: OMIT,45
90
footprintSRS,,,92
91
footprintSpatialFit,,,93
92
formation,,,115
93
geodeticDatum,,,87
94
geologicalContextID,,,100
95
georeferenceProtocol,,,96
96
georeferenceRemarks,,,99
97
georeferenceSources,,,97
98
georeferenceVerificationStatus,,,98
99
georeferencedBy,,Brad: Correct for VB. Nick: is there a way to specifically identify this party as collector of a specimen?,94
100
georeferencedDate,,,95
101
group,,,114
102
higherClassification,,,141
103
higherGeography,,,58
104
higherGeographyID,,,57
105
highestBiostratigraphicZone,,,112
106
identificationID,,,118
107
identificationQualifier,,,124
108
identificationReferences,,,121
109
identificationRemarks,,,123
110
identificationVerificationStatus,,,122
111
individualCount,,Brad: OMIT; not relevant for DwC plant specimen data.,25
112
individualID,,"Brad: OMIT; db-specific element, not relevant to VB/VX",24
113
informationWithheld,,,16
114
institutionID,,,8
115
island,,,62
116
islandGroup,,,61
117
latestAgeOrHighestStage,,,110
118
latestEonOrHighestEonothem,,,102
119
latestEpochOrHighestSeries,,,108
120
latestEraOrHighestErathem,,,104
121
latestPeriodOrHighestSystem,,,106
122
lifeStage,,,27
123
lithostratigraphicTerms,,,113
124
locationAccordingTo,,,78
125
locationID,,,56
126
locationRemarks,,,79
127
lowestBiostratigraphicZone,,,111
128
maximumDistanceAboveSurfaceInMeters,,,77
129
measurementAccuracy,,,169
130
measurementDeterminedBy,,,172
131
measurementDeterminedDate,,,171
132
measurementID,,,166
133
measurementMethod,,,173
134
measurementRemarks,,,174
135
measurementType,,,167
136
measurementUnit,,,170
137
measurementValue,,,168
138
member,,,116
139
minimumDistanceAboveSurfaceInMeters,,,76
140
month,,,49
141
municipality,,,67
142
nameAccordingTo,,,138
143
nameAccordingToID,,,131
144
namePublishedIn,,,139
145
namePublishedInID,,,132
146
namePublishedInYear,,,140
147
nomenclaturalCode,,,155
148
nomenclaturalStatus,,,157
149
occurrenceRemarks,,,21
150
occurrenceStatus,,,31
151
originalNameUsage,,,137
152
originalNameUsageID,,,130
153
otherCatalogNumbers,,,34
154
ownerInstitutionCode,,,14
155
parentNameUsage,,,136
156
parentNameUsageID,,,129
157
pointRadiusSpatialFit,,,90
158
preparations,,Brad: OMIT,32
159
previousIdentifications,,Brad: OMIT,35
160
relatedResourceID,,Brad: OMIT,161
161
relationshipAccordingTo,,,163
162
relationshipEstablishedDate,,,164
163
relationshipOfResource,,Brad: OMIT,162
164
relationshipRemarks,,,165
165
reproductiveCondition,,,28
166
resourceID,,,160
167
resourceRelationshipID,,,159
168
samplingEffort,,,43
169
samplingProtocol,,,42
170
scientificNameID,,,127
171
startDayOfYear,,,46
172
subgenus,,,148
173
taxonConceptID,,,133
174
taxonID,,,126
175
taxonRank,,,151
176
taxonRemarks,,,158
177
taxonomicStatus,,,156
178
typeStatus,,Brad: OMIT (?). Indicates whether this specimen served as type for taxon name. Probably not relevant for BIEN,125
179
verbatimCoordinateSystem,,,83
180
verbatimCoordinates,,,80
181
verbatimDepth,,,73
182
verbatimElevation,,,70
183
verbatimEventDate,,,51
184
verbatimSRS,,,84
185
verbatimTaxonRank,,,152
186
vernacularName,,,154
187
waterBody,,,60
188
year,,,48
mappings/Makefile
5 5
review_ = $(bin)/review <$(1) >for_review/$(1)
6 6
review = $(call review_,$@)
7 7

  
8
coreMaps := DwC-VegBIEN.specimens.csv VegX-VegBIEN.organisms.csv
8
coreMaps := DwC2-VegBIEN.specimens.csv VegX-VegBIEN.organisms.csv
9 9

  
10 10
##### General targets
11 11

  
......
37 37
	$(MAKE) $(@:%=.%.last_cleanup)
38 38
endif
39 39

  
40
##### Maps generated with join
40
##### Maps generated with join/union
41 41

  
42
define join
43
$(bin)/join_sort <$+ >$@
44
$(review)
45
endef
46

  
47 42
joinMaps :=
48 43

  
49
DwC1-VegBIEN.specimens.csv: DwC1-DwC.specimens.csv DwC-VegBIEN.specimens.csv
50
	$(join)
44
DwC1-VegBIEN.specimens.csv: DwC1-DwC2.specimens.csv DwC2-VegBIEN.specimens.csv
45
	$(bin)/join_sort <$+ >$@
51 46
joinMaps += DwC1-VegBIEN.specimens.csv
52 47

  
48
DwC-VegBIEN.specimens.csv: DwC2-VegBIEN.specimens.csv DwC1-VegBIEN.specimens.csv
49
	$(bin)/union <$+|$(bin)/sort 1 0 >$@
50
	$(review)
51
joinMaps += DwC-VegBIEN.specimens.csv
52

  
53 53
join_maps: $(joinMaps) ;
54 54

  
55 55
all += $(joinMaps)

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