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Revision 740

Renamed mappings/DwC-VegBIEN.specimens.csv to DwC-VegBIEN.organisms.csv because it (currently) uses /taxonoccurrence as the output root

View differences:

mappings/DwC-VegBIEN.specimens.csv
1
"DwC","VegBIEN:/specimen"
2
"dcterms:type",
3
"dcterms:modified",
4
"dcterms:language",
5
"dcterms:rights",
6
"dcterms:rightsHolder",
7
"dcterms:accessRights",
8
"dcterms:bibliographicCitation",
9
"dcterms:references",
10
"institutionID",
11
"collectionID",
12
"datasetID",
13
"institutionCode",
14
"collectionCode",
15
"datasetName",
16
"ownerInstitutionCode",
17
"basisOfRecord",
18
"informationWithheld",
19
"dataGeneralizations",
20
"dynamicProperties",
21
"occurrenceID",
22
"catalogNumber",
23
"occurrenceRemarks",
24
"recordNumber",
25
"recordedBy",
26
"individualID",
27
"individualCount",
28
"sex",
29
"lifeStage",
30
"reproductiveCondition",
31
"behavior",
32
"establishmentMeans",
33
"occurrenceStatus",
34
"preparations",
35
"disposition",
36
"otherCatalogNumbers",
37
"previousIdentifications",
38
"associatedMedia",
39
"associatedReferences",
40
"associatedOccurrences",
41
"associatedSequences",
42
"associatedTaxa",
43
"eventID",
44
"samplingProtocol",
45
"samplingEffort",
46
"eventDate",
47
"eventTime",
48
"startDayOfYear",
49
"endDayOfYear",
50
"year",
51
"month",
52
"day",
53
"verbatimEventDate",
54
"habitat",
55
"fieldNumber",
56
"fieldNotes",
57
"eventRemarks",
58
"locationID",
59
"higherGeographyID",
60
"higherGeography",
61
"continent",
62
"waterBody",
63
"islandGroup",
64
"island",
65
"country",
66
"countryCode",
67
"stateProvince",
68
"county",
69
"municipality",
70
"locality",
71
"verbatimLocality",
72
"verbatimElevation",
73
"minimumElevationInMeters",
74
"maximumElevationInMeters",
75
"verbatimDepth",
76
"minimumDepthInMeters",
77
"maximumDepthInMeters",
78
"minimumDistanceAboveSurfaceInMeters",
79
"maximumDistanceAboveSurfaceInMeters",
80
"locationAccordingTo",
81
"locationRemarks",
82
"verbatimCoordinates",
83
"verbatimLatitude",
84
"verbatimLongitude",
85
"verbatimCoordinateSystem",
86
"verbatimSRS",
87
"decimalLatitude",
88
"decimalLongitude",
89
"geodeticDatum",
90
"coordinateUncertaintyInMeters",
91
"coordinatePrecision",
92
"pointRadiusSpatialFit",
93
"footprintWKT",
94
"footprintSRS",
95
"footprintSpatialFit",
96
"georeferencedBy",
97
"georeferencedDate",
98
"georeferenceProtocol",
99
"georeferenceSources",
100
"georeferenceVerificationStatus",
101
"georeferenceRemarks",
102
"geologicalContextID",
103
"earliestEonOrLowestEonothem",
104
"latestEonOrHighestEonothem",
105
"earliestEraOrLowestErathem",
106
"latestEraOrHighestErathem",
107
"earliestPeriodOrLowestSystem",
108
"latestPeriodOrHighestSystem",
109
"earliestEpochOrLowestSeries",
110
"latestEpochOrHighestSeries",
111
"earliestAgeOrLowestStage",
112
"latestAgeOrHighestStage",
113
"lowestBiostratigraphicZone",
114
"highestBiostratigraphicZone",
115
"lithostratigraphicTerms",
116
"group",
117
"formation",
118
"member",
119
"bed",
120
"identificationID",
121
"identifiedBy",
122
"dateIdentified",
123
"identificationReferences",
124
"identificationVerificationStatus",
125
"identificationRemarks",
126
"identificationQualifier",
127
"typeStatus",
128
"taxonID",
129
"scientificNameID",
130
"acceptedNameUsageID",
131
"parentNameUsageID",
132
"originalNameUsageID",
133
"nameAccordingToID",
134
"namePublishedInID",
135
"taxonConceptID",
136
"scientificName",
137
"acceptedNameUsage",
138
"parentNameUsage",
139
"originalNameUsage",
140
"nameAccordingTo",
141
"namePublishedIn",
142
"namePublishedInYear",
143
"higherClassification",
144
"kingdom",
145
"phylum",
146
"class",
147
"order",
148
"family",
149
"genus",
150
"subgenus",
151
"specificEpithet",
152
"infraspecificEpithet",
153
"taxonRank",
154
"verbatimTaxonRank",
155
"scientificNameAuthorship",
156
"vernacularName",
157
"nomenclaturalCode",
158
"taxonomicStatus",
159
"nomenclaturalStatus",
160
"taxonRemarks",
161
"resourceRelationshipID",
162
"resourceID",
163
"relatedResourceID",
164
"relationshipOfResource",
165
"relationshipAccordingTo",
166
"relationshipEstablishedDate",
167
"relationshipRemarks",
168
"measurementID",
169
"measurementType",
170
"measurementValue",
171
"measurementAccuracy",
172
"measurementUnit",
173
"measurementDeterminedDate",
174
"measurementDeterminedBy",
175
"measurementMethod",
176
"measurementRemarks",
mappings/DwC-VegBIEN.organisms.csv
1
DwC,VegBIEN:/taxonoccurrence,Comments,Order
2
identificationRemarks,,,123
3
minimumDepthInMeters,/*_id/locationevent/waterdepth/min,,74
4
footprintSRS,,,92
5
verbatimLatitude,/*_id/locationevent/*_id/location/reallatitude,,81
6
month,,,49
7
measurementDeterminedDate,,,171
8
informationWithheld,,,16
9
lithostratigraphicTerms,,,113
10
latestPeriodOrHighestSystem,,,106
11
reproductiveCondition,,,28
12
continent,,Brad: OMIT,59
13
endDayOfYear,,,47
14
identificationID,,,118
15
latestEraOrHighestErathem,,,104
16
occurrenceID,"/{aggregateoccurrence/*_id/plantobservation/authorplantcode,specimenreplicate:[*_id/reference]/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
17
locationAccordingTo,,,78
18
latestEpochOrHighestSeries,,,108
19
coordinateUncertaintyInMeters,,,88
20
coordinatePrecision,/*_id/locationevent/*_id/location/locationaccuracy,,89
21
maximumDepthInMeters,/*_id/locationevent/waterdepth/max,,75
22
waterBody,,,60
23
resourceRelationshipID,,,159
24
kingdom,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Kingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,142
25
decimalLatitude,,,85
26
verbatimTaxonRank,,,152
27
earliestEraOrLowestErathem,,,103
28
verbatimCoordinates,,,80
29
acceptedNameUsageID,,,128
30
infraspecificEpithet,,,150
31
namePublishedIn,,,139
32
originalNameUsage,,,137
33
nameAccordingToID,,,131
34
dataGeneralizations,,,17
35
nomenclaturalStatus,,,157
36
dcterms:bibliographicCitation,,,6
37
recordNumber,,,22
38
day,,Brad: OMIT,50
39
individualCount,,Brad: OMIT; not relevant for DwC plant specimen data.,25
40
dcterms:type,,,0
41
measurementType,,,167
42
institutionID,,,8
43
georeferenceVerificationStatus,,,98
44
lifeStage,,,27
45
measurementUnit,,,170
46
locationRemarks,,,79
47
scientificName,"/taxondetermination[*_id/role/rolecode=identifier,!*_id/plantconcept]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname/_alt/1","Brad: Bob, Nick, please is this mapping OK?",134
48
parentNameUsage,,,136
49
datasetID,,,10
50
eventID,,,41
51
lowestBiostratigraphicZone,,,111
52
habitat,"/aggregateoccurrence/*_id/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=habitat]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
53
higherGeographyID,,,57
54
dcterms:references,,,7
55
sex,"/taxondetermination[*_id/role/rolecode=identifier,!*_id/plantconcept]/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
56
dcterms:accessRights,,,5
57
scientificNameAuthorship,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=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
58
associatedTaxa,,,40
59
year,,,48
60
taxonRemarks,,,158
61
dcterms:rightsHolder,,,4
62
namePublishedInYear,,,140
63
identificationVerificationStatus,,,122
64
eventTime,,Brad: OMIT,45
65
basisOfRecord,,Brad: OMIT? See http://rs.tdwg.org/dwc/terms/index.htm#basisOfRecord for definition of this term.,15
66
latestEonOrHighestEonothem,,,102
67
otherCatalogNumbers,,,34
68
georeferenceRemarks,,,99
69
acceptedNameUsage,,,135
70
georeferenceSources,,,97
71
specificEpithet,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,149
72
verbatimLocality,/*_id/locationevent/*_id/location/locationplace/*_id/namedplace/placedescription,"Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one.",69
73
identificationReferences,,,121
74
measurementRemarks,,,174
75
georeferencedBy,/specimenreplicate:[*_id/reference]/verbatimcollectorname,Brad: Correct for VB. Nick: is there a way to specifically identify this party as collector of a specimen?,94
76
geodeticDatum,,,87
77
occurrenceRemarks,,,21
78
collectionCode,"/specimenreplicate:[*_id/reference]/{museum_id/party/organizationname/_name/last,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
79
higherGeography,,,58
80
nameAccordingTo,,,138
81
latestAgeOrHighestStage,,,110
82
fieldNumber,/specimenreplicate:[*_id/reference]/catalognumber_dwc,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
83
measurementMethod,,,173
84
disposition,,,33
85
earliestEpochOrLowestSeries,,,107
86
group,,,114
87
highestBiostratigraphicZone,,,112
88
ownerInstitutionCode,,,14
89
scientificNameID,,,127
90
relationshipEstablishedDate,,,164
91
earliestAgeOrLowestStage,,,109
92
country,"/*_id/locationevent/*_id/location/locationplace(/*_id/namedplace[placesystem=""area|country|territory""])/placename",Brad: Required; reject record if this field NULL,63
93
measurementDeterminedBy,,,172
94
decimalLongitude,,,86
95
locationID,,,56
96
dcterms:rights,,,3
97
relationshipRemarks,,,165
98
startDayOfYear,,,46
99
formation,,,115
100
genus,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,147
101
family,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,146
102
collectionID,,,9
103
dynamicProperties,,,18
104
eventRemarks,,,55
105
municipality,,,67
106
individualID,/specimenreplicate:[*_id/reference]/collectornumber_dwc,"Brad: OMIT; db-specific element, not relevant to VB/VX",24
107
footprintWKT,,,91
108
county,/*_id/locationevent/*_id/location/locationplace(/*_id/namedplace[placesystem=county])/placename,,66
109
associatedMedia,,,36
110
associatedSequences,,,39
111
subgenus,,,148
112
footprintSpatialFit,,,93
113
measurementValue,,,168
114
higherClassification,,,141
115
islandGroup,,,61
116
resourceID,,,160
117
class,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Class]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,144
118
verbatimSRS,,,84
119
associatedOccurrences,,,38
120
catalogNumber,,"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
121
verbatimLongitude,/*_id/locationevent/*_id/location/reallongitude,,82
122
preparations,,Brad: OMIT,32
123
taxonID,,,126
124
nomenclaturalCode,,,155
125
maximumElevationInMeters,"/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/max,elevationrange/_range/to}",,72
126
verbatimCoordinateSystem,,,83
127
measurementID,,,166
128
relatedResourceID,,Brad: OMIT,161
129
datasetName,,,13
130
earliestEonOrLowestEonothem,,,101
131
measurementAccuracy,,,169
132
verbatimDepth,,,73
133
bed,,,117
134
georeferencedDate,,,95
135
behavior,,,29
136
island,,,62
137
parentNameUsageID,,,129
138
minimumElevationInMeters,"/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/min,elevationrange/_range/from}",,71
139
occurrenceStatus,,,31
140
vernacularName,,,154
141
pointRadiusSpatialFit,,,90
142
countryCode,,,64
143
phylum,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,143
144
institutionCode,/specimenreplicate:[*_id/reference]/{museum_id/party/organizationname/_name/first},,11
145
identificationQualifier,,,124
146
namePublishedInID,,,132
147
identifiedBy,"/taxondetermination[*_id/role/rolecode=identifier,!*_id/plantconcept]:[determinationtype=Author,iscurrent=true]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Bob: does this look correct for VegBank?,119
148
earliestPeriodOrLowestSystem,,,105
149
minimumDistanceAboveSurfaceInMeters,,,76
150
dcterms:language,,,2
151
maximumDistanceAboveSurfaceInMeters,,,77
152
taxonConceptID,,,133
153
georeferenceProtocol,,,96
154
locality,,,68
155
associatedReferences,,,37
156
stateProvince,"/*_id/locationevent/*_id/location/locationplace(/*_id/namedplace[placesystem=""region|state|province""])/placename",,65
157
taxonomicStatus,,,156
158
relationshipAccordingTo,,,163
159
member,,,116
160
relationshipOfResource,,Brad: OMIT,162
161
taxonRank,,,151
162
previousIdentifications,,Brad: OMIT,35
163
samplingEffort,,,43
164
verbatimElevation,,,70
165
establishmentMeans,,,30
166
typeStatus,,Brad: OMIT (?). Indicates whether this specimen served as type for taxon name. Probably not relevant for BIEN,125
167
samplingProtocol,,,42
168
originalNameUsageID,,,130
169
eventDate,/*_id/locationevent/obsstartdate/_*/date,,44
170
geologicalContextID,,,100
171
fieldNotes,"/taxondetermination[*_id/role/rolecode=identifier,!*_id/plantconcept]:[determinationtype=Author,iscurrent=true]/notes","Brad: mapping OK; NY appears to be using this field for almost anything, but mostly internal collections notes",54
172
dateIdentified,"/taxondetermination[*_id/role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_*/date",,120
173
verbatimEventDate,,,51
174
recordedBy,,,23
175
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
176
order,"/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Order]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,145

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