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Revision 3818

mappings/Makefile: for_review/VegBIEN-DwC2.specimens.csv: Include all comments column(s), not just the first

View differences:

mappings/for_review/VegBIEN-DwC2.specimens.csv
1
VegBIEN:,DwC,Comments
2
//location/elevation,maximumElevationInMeters,
3
//location/elevation,minimumElevationInMeters,
4
//location/elevationrange,minimumElevationInMeters,
5
//location/elevationrange,maximumElevationInMeters,
6
//location/elevationrange,minimumElevationInMeters,
7
//locationdetermination/coordsaccuracy,coordinateUncertaintyInMeters,
8
//locationdetermination/coordsaccuracy,coordinatePrecision,
9
//locationdetermination/footprintgeometry_dwc,footprintWKT,
10
//locationdetermination/latitude,decimalLatitude,
11
//locationdetermination/latitude,verbatimLatitude,
12
//locationdetermination/longitude,decimalLongitude,
13
//locationdetermination/longitude,verbatimLongitude,
14
//locationdetermination/namedplace_id[rank=county]/placename,county,
15
//locationdetermination/namedplace_id[rank=stateProvince]/placename,stateProvince,
16
//locationdetermination/namedplace_id[rank=country]/placename,country,Brad: Required; reject record if this field NULL
17
//locationdetermination/namedplace_id[rank=continent]/placename,continent,Brad: OMIT
18
//locationevent/obsenddate/_*/date,eventDate,
19
//locationevent/obsstartdate/_*/date,eventDate,
20
//specimenreplicate/catalognumber_dwc,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"
21
//specimenreplicate/collectioncode_dwc,collectionCode,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
22
//specimenreplicate/collectionnumber,recordNumber,
23
//specimenreplicate/collectionnumber,collectionID,
24
//specimenreplicate/collectionnumber,fieldNumber,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?"
25
"//specimenreplicate/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]/definedvalue",sex,"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
//specimenreplicate/description,fieldNotes,
27
//specimenreplicate/description,taxonRemarks,
28
//specimenreplicate/growthform,establishmentMeans,
29
//party/organizationname,institutionCode,
30
//specimenreplicate/iscultivated,establishmentMeans,
31
//specimenreplicate/isnative,establishmentMeans,
32
//specimenreplicate/sourceaccessioncode,occurrenceID,"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"
33
//specimenreplicate/taxondetermination[role=identifier]/determinationdate/_*/date,dateIdentified,
34
//specimenreplicate/taxondetermination[role=identifier]/*_id/party/givenname,identifiedBy,Brad: Bob: does this look correct for VegBank?
35
//specimenreplicate/taxondetermination[role=identifier]/*_id/party/middlename,identifiedBy,Brad: Bob: does this look correct for VegBank?
36
//specimenreplicate/taxondetermination[role=identifier]/*_id/party/surname,identifiedBy,Brad: Bob: does this look correct for VegBank?
37
//plantconcept/plantname_id[rank=binomial]/plantname,scientificName,"Brad: Bob, Nick, please is this mapping OK?"
38
//plantconcept/plantname_id[rank=authority]/plantname,scientificNameAuthorship,"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"
39
//plantconcept/plantname_id[rank=subspecies]/plantname,infraspecificEpithet,
40
//plantconcept/plantname_id[rank=species]/plantname,specificEpithet,
41
//plantconcept/plantname_id[rank=genus]/plantname,genus,
42
//plantconcept/plantname_id[rank=family]/plantname,family,
43
//plantconcept/plantname_id[rank=order]/plantname,order,
44
//plantconcept/plantname_id[rank=class]/plantname,class,
45
//plantconcept/plantname_id[rank=subkingdom]/plantname,phylum,
46
//plantconcept/plantname_id[rank=kingdom]/plantname,kingdom,
47
//specimenreplicate/verbatimcollectorname,recordedBy,
48
//locationevent/waterdepth,maximumDepthInMeters,
49
//locationevent/waterdepth,minimumDepthInMeters,
50
//location/locationnarrative,locality,
51
//location/locationnarrative,verbatimLocality,"Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one."
52
"//location/locationnarrative/_label[label=""habitat""]/value",habitat,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?"
53
//location/sourceaccessioncode,occurrenceID,"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"
54
//location/sourceaccessioncode,institutionCode,
55
//location/sourceaccessioncode,collectionCode,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
56
//location/sourceaccessioncode,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"
57
,acceptedNameUsage,
58
,acceptedNameUsageID,
59
,associatedMedia,
60
,associatedOccurrences,
61
,associatedReferences,
62
,associatedSequences,
63
,associatedTaxa,
64
,basisOfRecord,Brad: OMIT? See http://rs.tdwg.org/dwc/terms/index.htm#basisOfRecord for definition of this term.
65
,bed,
66
,behavior,
67
,countryCode,
68
,dataGeneralizations,
69
,datasetID,
70
,datasetName,
71
,day,Brad: OMIT
72
,dcterms:accessRights,
73
,dcterms:bibliographicCitation,
74
,dcterms:language,
75
,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."
76
,dcterms:references,
77
,dcterms:rights,
78
,dcterms:rightsHolder,
79
,dcterms:type,
80
,disposition,
81
,dynamicProperties,
82
,earliestAgeOrLowestStage,
83
,earliestEonOrLowestEonothem,
84
,earliestEpochOrLowestSeries,
85
,earliestEraOrLowestErathem,
86
,earliestPeriodOrLowestSystem,
87
,endDayOfYear,
88
,eventID,
89
,eventRemarks,
90
,eventTime,Brad: OMIT
91
,footprintSRS,
92
,footprintSpatialFit,
93
,formation,
94
,geodeticDatum,
95
,geologicalContextID,
96
,georeferenceProtocol,
97
,georeferenceRemarks,
98
,georeferenceSources,
99
,georeferenceVerificationStatus,
100
,georeferencedBy,Brad: Correct for VB. Nick: is there a way to specifically identify this party as collector of a specimen?
101
,georeferencedDate,
102
,group,
103
,higherClassification,
104
,higherGeography,
105
,higherGeographyID,
106
,highestBiostratigraphicZone,
107
,identificationID,
108
,identificationQualifier,
109
,identificationReferences,
110
,identificationRemarks,
111
,identificationVerificationStatus,
112
,individualCount,Brad: OMIT; not relevant for DwC plant specimen data.
113
,individualID,"Brad: OMIT; db-specific element, not relevant to VB/VX"
114
,informationWithheld,
115
,institutionID,
116
,island,
117
,islandGroup,
118
,latestAgeOrHighestStage,
119
,latestEonOrHighestEonothem,
120
,latestEpochOrHighestSeries,
121
,latestEraOrHighestErathem,
122
,latestPeriodOrHighestSystem,
123
,lifeStage,
124
,lithostratigraphicTerms,
125
,locationAccordingTo,
126
,locationID,
127
,locationRemarks,
128
,lowestBiostratigraphicZone,
129
,maximumDistanceAboveSurfaceInMeters,
130
,measurementAccuracy,
131
,measurementDeterminedBy,
132
,measurementDeterminedDate,
133
,measurementID,
134
,measurementMethod,
135
,measurementRemarks,
136
,measurementType,
137
,measurementUnit,
138
,measurementValue,
139
,member,
140
,minimumDistanceAboveSurfaceInMeters,
141
,month,
142
,municipality,
143
,nameAccordingTo,
144
,nameAccordingToID,
145
,namePublishedIn,
146
,namePublishedInID,
147
,namePublishedInYear,
148
,nomenclaturalCode,
149
,nomenclaturalStatus,
150
,occurrenceRemarks,
151
,occurrenceStatus,
152
,originalNameUsage,
153
,originalNameUsageID,
154
,otherCatalogNumbers,
155
,ownerInstitutionCode,
156
,parentNameUsage,
157
,parentNameUsageID,
158
,pointRadiusSpatialFit,
159
,preparations,Brad: OMIT
160
,previousIdentifications,Brad: OMIT
161
,relatedResourceID,Brad: OMIT
162
,relationshipAccordingTo,
163
,relationshipEstablishedDate,
164
,relationshipOfResource,Brad: OMIT
165
,relationshipRemarks,
166
,reproductiveCondition,
167
,resourceID,
168
,resourceRelationshipID,
169
,samplingEffort,
170
,samplingProtocol,
171
,scientificNameID,
172
,startDayOfYear,
173
,subgenus,
174
,taxonConceptID,
175
,taxonID,
176
,taxonRank,
177
,taxonomicStatus,
178
,typeStatus,Brad: OMIT (?). Indicates whether this specimen served as type for taxon name. Probably not relevant for BIEN
179
,verbatimCoordinateSystem,
180
,verbatimCoordinates,
181
,verbatimDepth,
182
,verbatimElevation,
183
,verbatimEventDate,
184
,verbatimSRS,
185
,verbatimTaxonRank,
186
,vernacularName,
187
,waterBody,
188
,year,
1
VegBIEN:,DwC,Comments,Order
2
//location/elevation,maximumElevationInMeters,,72
3
//location/elevation,minimumElevationInMeters,,71
4
//location/elevationrange,minimumElevationInMeters,,71
5
//location/elevationrange,maximumElevationInMeters,,72
6
//location/elevationrange,minimumElevationInMeters,,71
7
//locationdetermination/coordsaccuracy,coordinateUncertaintyInMeters,,88
8
//locationdetermination/coordsaccuracy,coordinatePrecision,,89
9
//locationdetermination/footprintgeometry_dwc,footprintWKT,,91
10
//locationdetermination/latitude,decimalLatitude,,85
11
//locationdetermination/latitude,verbatimLatitude,,81
12
//locationdetermination/longitude,decimalLongitude,,86
13
//locationdetermination/longitude,verbatimLongitude,,82
14
//locationdetermination/namedplace_id[rank=county]/placename,county,,66
15
//locationdetermination/namedplace_id[rank=stateProvince]/placename,stateProvince,,65
16
//locationdetermination/namedplace_id[rank=country]/placename,country,Brad: Required; reject record if this field NULL,63
17
//locationdetermination/namedplace_id[rank=continent]/placename,continent,Brad: OMIT,59
18
//locationevent/obsenddate/_*/date,eventDate,,44
19
//locationevent/obsstartdate/_*/date,eventDate,,44
20
//specimenreplicate/catalognumber_dwc,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
21
//specimenreplicate/collectioncode_dwc,collectionCode,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
22
//specimenreplicate/collectionnumber,recordNumber,,22
23
//specimenreplicate/collectionnumber,collectionID,,9
24
//specimenreplicate/collectionnumber,fieldNumber,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
25
"//specimenreplicate/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]/definedvalue",sex,"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
26
//specimenreplicate/description,fieldNotes,,
27
//specimenreplicate/description,taxonRemarks,,158
28
//specimenreplicate/growthform,establishmentMeans,,30
29
//party/organizationname,institutionCode,,
30
//specimenreplicate/iscultivated,establishmentMeans,,30
31
//specimenreplicate/isnative,establishmentMeans,,30
32
//specimenreplicate/sourceaccessioncode,occurrenceID,"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
33
//specimenreplicate/taxondetermination[role=identifier]/determinationdate/_*/date,dateIdentified,,120
34
//specimenreplicate/taxondetermination[role=identifier]/*_id/party/givenname,identifiedBy,Brad: Bob: does this look correct for VegBank?,119
35
//specimenreplicate/taxondetermination[role=identifier]/*_id/party/middlename,identifiedBy,Brad: Bob: does this look correct for VegBank?,119
36
//specimenreplicate/taxondetermination[role=identifier]/*_id/party/surname,identifiedBy,Brad: Bob: does this look correct for VegBank?,119
37
//plantconcept/plantname_id[rank=binomial]/plantname,scientificName,"Brad: Bob, Nick, please is this mapping OK?",134
38
//plantconcept/plantname_id[rank=authority]/plantname,scientificNameAuthorship,"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
39
//plantconcept/plantname_id[rank=subspecies]/plantname,infraspecificEpithet,,150
40
//plantconcept/plantname_id[rank=species]/plantname,specificEpithet,,149
41
//plantconcept/plantname_id[rank=genus]/plantname,genus,,147
42
//plantconcept/plantname_id[rank=family]/plantname,family,,146
43
//plantconcept/plantname_id[rank=order]/plantname,order,,145
44
//plantconcept/plantname_id[rank=class]/plantname,class,,144
45
//plantconcept/plantname_id[rank=subkingdom]/plantname,phylum,,143
46
//plantconcept/plantname_id[rank=kingdom]/plantname,kingdom,,142
47
//specimenreplicate/verbatimcollectorname,recordedBy,,23
48
//locationevent/waterdepth,maximumDepthInMeters,,75
49
//locationevent/waterdepth,minimumDepthInMeters,,74
50
//location/locationnarrative,locality,,68
51
//location/locationnarrative,verbatimLocality,"Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one.",69
52
"//location/locationnarrative/_label[label=""habitat""]/value",habitat,"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
//location/sourceaccessioncode,occurrenceID,"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
54
//location/sourceaccessioncode,institutionCode,,
55
//location/sourceaccessioncode,collectionCode,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
56
//location/sourceaccessioncode,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
57
,acceptedNameUsage,,135
58
,acceptedNameUsageID,,128
59
,associatedMedia,,36
60
,associatedOccurrences,,38
61
,associatedReferences,,37
62
,associatedSequences,,39
63
,associatedTaxa,,40
64
,basisOfRecord,Brad: OMIT? See http://rs.tdwg.org/dwc/terms/index.htm#basisOfRecord for definition of this term.,15
65
,bed,,117
66
,behavior,,29
67
,countryCode,,64
68
,dataGeneralizations,,17
69
,datasetID,,10
70
,datasetName,,13
71
,day,Brad: OMIT,50
72
,dcterms:accessRights,,5
73
,dcterms:bibliographicCitation,,6
74
,dcterms:language,,2
75
,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
76
,dcterms:references,,7
77
,dcterms:rights,,3
78
,dcterms:rightsHolder,,4
79
,dcterms:type,,0
80
,disposition,,33
81
,dynamicProperties,,18
82
,earliestAgeOrLowestStage,,109
83
,earliestEonOrLowestEonothem,,101
84
,earliestEpochOrLowestSeries,,107
85
,earliestEraOrLowestErathem,,103
86
,earliestPeriodOrLowestSystem,,105
87
,endDayOfYear,,47
88
,eventID,,41
89
,eventRemarks,,55
90
,eventTime,Brad: OMIT,45
91
,footprintSRS,,92
92
,footprintSpatialFit,,93
93
,formation,,115
94
,geodeticDatum,,87
95
,geologicalContextID,,100
96
,georeferenceProtocol,,96
97
,georeferenceRemarks,,99
98
,georeferenceSources,,97
99
,georeferenceVerificationStatus,,98
100
,georeferencedBy,Brad: Correct for VB. Nick: is there a way to specifically identify this party as collector of a specimen?,94
101
,georeferencedDate,,95
102
,group,,114
103
,higherClassification,,141
104
,higherGeography,,58
105
,higherGeographyID,,57
106
,highestBiostratigraphicZone,,112
107
,identificationID,,118
108
,identificationQualifier,,124
109
,identificationReferences,,121
110
,identificationRemarks,,123
111
,identificationVerificationStatus,,122
112
,individualCount,Brad: OMIT; not relevant for DwC plant specimen data.,25
113
,individualID,"Brad: OMIT; db-specific element, not relevant to VB/VX",24
114
,informationWithheld,,16
115
,institutionID,,8
116
,island,,62
117
,islandGroup,,61
118
,latestAgeOrHighestStage,,110
119
,latestEonOrHighestEonothem,,102
120
,latestEpochOrHighestSeries,,108
121
,latestEraOrHighestErathem,,104
122
,latestPeriodOrHighestSystem,,106
123
,lifeStage,,27
124
,lithostratigraphicTerms,,113
125
,locationAccordingTo,,78
126
,locationID,,56
127
,locationRemarks,,79
128
,lowestBiostratigraphicZone,,111
129
,maximumDistanceAboveSurfaceInMeters,,77
130
,measurementAccuracy,,169
131
,measurementDeterminedBy,,172
132
,measurementDeterminedDate,,171
133
,measurementID,,166
134
,measurementMethod,,173
135
,measurementRemarks,,174
136
,measurementType,,167
137
,measurementUnit,,170
138
,measurementValue,,168
139
,member,,116
140
,minimumDistanceAboveSurfaceInMeters,,76
141
,month,,49
142
,municipality,,67
143
,nameAccordingTo,,138
144
,nameAccordingToID,,131
145
,namePublishedIn,,139
146
,namePublishedInID,,132
147
,namePublishedInYear,,140
148
,nomenclaturalCode,,155
149
,nomenclaturalStatus,,157
150
,occurrenceRemarks,,21
151
,occurrenceStatus,,31
152
,originalNameUsage,,137
153
,originalNameUsageID,,130
154
,otherCatalogNumbers,,34
155
,ownerInstitutionCode,,14
156
,parentNameUsage,,136
157
,parentNameUsageID,,129
158
,pointRadiusSpatialFit,,90
159
,preparations,Brad: OMIT,32
160
,previousIdentifications,Brad: OMIT,35
161
,relatedResourceID,Brad: OMIT,161
162
,relationshipAccordingTo,,163
163
,relationshipEstablishedDate,,164
164
,relationshipOfResource,Brad: OMIT,162
165
,relationshipRemarks,,165
166
,reproductiveCondition,,28
167
,resourceID,,160
168
,resourceRelationshipID,,159
169
,samplingEffort,,43
170
,samplingProtocol,,42
171
,scientificNameID,,127
172
,startDayOfYear,,46
173
,subgenus,,148
174
,taxonConceptID,,133
175
,taxonID,,126
176
,taxonRank,,151
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
85 85
dwcMaps += DwC-VegBIEN.specimens.csv
86 86

  
87 87
for_review/VegBIEN-DwC2.specimens.csv: for_review/DwC2-VegBIEN.specimens.csv
88
	$(bin)/cols 1 0 2 <$< >$@
88
	$(bin)/cols 1 0 + <$< >$@
89 89
dwcMaps += for_review/VegBIEN-DwC2.specimens.csv
90
# keep Comments column
90
# keep comments column(s)
91 91

  
92 92
dwc_maps: _always $(dwcMaps) ;
93 93

  

Also available in: Unified diff