Project

General

Profile

« Previous | Next » 

Revision 5044

mappings/VegCore-VegBIEN.csv: verbatim* taxonomic terms: Added taxonomicnamewithauthor mappings analogous to those for the non-verbatim taxonomic terms

View differences:

inputs/Madidi/Organism/VegBIEN.csv
46 46
Qualifier,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,
47 47
Field family,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/family,
48 48
Field name,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/genus,Often = Genera
49
Field family,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
50
Field name,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,Often = Genera
49 51
Index collector,/location/locationevent/taxonoccurrence/verbatimcollectorname,
50 52
Specimen,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
51 53
Basal area,,"** No join mapping for *Basal area ** Would be basalDiameter, but need formula to translate"
inputs/Madidi/Organism/test.xml.ref
86 86
                                <taxonpath>
87 87
                                    <family>$Field family</family>
88 88
                                    <genus>$Field name</genus>
89
                                    <taxonomicnamewithauthor>
90
                                        <_join_words>
91
                                            <1>$Field family</1>
92
                                            <2>$Field name</2>
93
                                        </_join_words>
94
                                    </taxonomicnamewithauthor>
89 95
                                </taxonpath>
90 96
                            </taxonpath_id>
91 97
                        </taxondetermination>
inputs/SALVIAS-CSV/Organism/VegBIEN.csv
79 79
cf_aff,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
80 80
orig_family,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/family,Brad: OMIT
81 81
orig_species,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/species,Brad: OMIT
82
orig_family,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,Brad: OMIT
83
orig_species,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,Brad: OMIT
82 84
coll_firstname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join_words/1,Brad: See comment above
83 85
coll_lastname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join_words/2,"Brad: This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
84 86
det_type,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider  asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen."
inputs/SALVIAS-CSV/Organism/test.xml.ref
185 185
                                <taxonpath>
186 186
                                    <family>$orig_family</family>
187 187
                                    <species>$orig_species</species>
188
                                    <taxonomicnamewithauthor>
189
                                        <_join_words>
190
                                            <1>$orig_family</1>
191
                                            <3>$orig_species</3>
192
                                        </_join_words>
193
                                    </taxonomicnamewithauthor>
188 194
                                </taxonpath>
189 195
                            </taxonpath_id>
190 196
                        </taxondetermination>
inputs/SALVIAS/plotObservations/VegBIEN.csv
73 73
OrigFamily,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/family,Brad: OMIT
74 74
OrigGenus,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/genus,
75 75
OrigSpecies,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/species,Brad: OMIT
76
OrigFamily,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,Brad: OMIT
77
OrigGenus,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
78
OrigSpecies,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,Brad: OMIT
76 79
coll_firstname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join_words/1,Brad: See comment above
77 80
coll_lastname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join_words/2,"Brad: This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
78 81
DetType,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider  asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen."
inputs/SALVIAS/plotObservations/test.xml.ref
157 157
                                    <family>$OrigFamily</family>
158 158
                                    <genus>$OrigGenus</genus>
159 159
                                    <species>$OrigSpecies</species>
160
                                    <taxonomicnamewithauthor>
161
                                        <_join_words>
162
                                            <1>$OrigFamily</1>
163
                                            <2>$OrigGenus</2>
164
                                            <3>$OrigSpecies</3>
165
                                        </_join_words>
166
                                    </taxonomicnamewithauthor>
160 167
                                </taxonpath>
161 168
                            </taxonpath_id>
162 169
                        </taxondetermination>
inputs/GBIF/Specimen/VegBIEN.csv
31 31
GBIFFamilyOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/family,
32 32
GBIFGenusOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/genus,
33 33
ScientificNameOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicname,
34
ScientificNameOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
35
GBIFFamilyOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
36
GBIFGenusOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
34 37
Collector,/location/locationevent/taxonoccurrence/verbatimcollectorname,
35 38
CatalogNO,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
36 39
Locality,/location/locationnarrative/_merge/1,
inputs/GBIF/Specimen/test.xml.ref
78 78
                                    <family>$GBIFFamilyOriginal</family>
79 79
                                    <genus>$GBIFGenusOriginal</genus>
80 80
                                    <taxonomicname>$ScientificNameOriginal</taxonomicname>
81
                                    <taxonomicnamewithauthor>$ScientificNameOriginal</taxonomicnamewithauthor>
81 82
                                </taxonpath>
82 83
                            </taxonpath_id>
83 84
                        </taxondetermination>
inputs/VegBank/taxonobservation_/VegBIEN.csv
27 27
interpretationdate,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_*/date/_dateRangeStart/value,
28 28
taxonfit,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,
29 29
authorplantname,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicname,
30
authorplantname,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
30 31
museumaccessionnumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
31 32
Division,,** No join mapping for *Division ** 
32 33
Subclass,,** No join mapping for *Subclass ** 
inputs/VegBank/taxonobservation_/test.xml.ref
54 54
                        </taxondetermination>
55 55
                        <taxondetermination>
56 56
                            <isoriginal>true</isoriginal>
57
                            <taxonpath_id><taxonpath><taxonomicname>$authorplantname</taxonomicname></taxonpath></taxonpath_id>
57
                            <taxonpath_id>
58
                                <taxonpath>
59
                                    <taxonomicname>$authorplantname</taxonomicname>
60
                                    <taxonomicnamewithauthor>$authorplantname</taxonomicnamewithauthor>
61
                                </taxonpath>
62
                            </taxonpath_id>
58 63
                        </taxondetermination>
59 64
                    </taxonoccurrence>
60 65
                </locationevent>
mappings/VegCore-VegBIEN.csv
170 170
verbatimSpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/species,
171 171
verbatimInfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/subspecies,
172 172
verbatimScientificName,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicname,
173
verbatimScientificNameWithAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/1,
174
verbatimScientificName,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
175
verbatimFamily,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
176
verbatimGenus,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
177
verbatimSpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
178
verbatimSubspecies,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/4,
179
verbatimTaxonRank,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/1,
180
verbatimInfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/2,
181
verbatimVariety,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/6/_join_words:[1=var.]/2,
182
verbatimForma,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/7/_join_words:[1=fm.]/2,
183
verbatimCultivar,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/8/_join_words:[1=cult.]/2,
184
verbatimScientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2,
173 185
verbatimIdentificationQualifier,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/taxonfit,
174 186
recordedBy,/location/locationevent/taxonoccurrence/verbatimcollectorname,
175 187
recordedBy.givenName,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join_words/1,
mappings/for_review/VegCore-VegBIEN.csv
170 170
verbatimSpecificEpithet,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/species,
171 171
verbatimInfraspecificEpithet,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/subspecies,
172 172
verbatimScientificName,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicname,
173
verbatimScientificNameWithAuthorship,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor,
174
verbatimScientificName,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor,
175
verbatimFamily,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor,
176
verbatimGenus,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor,
177
verbatimSpecificEpithet,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor,
178
verbatimSubspecies,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor,
179
verbatimTaxonRank,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor,
180
verbatimInfraspecificEpithet,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor,
181
verbatimVariety,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor,
182
verbatimForma,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor,
183
verbatimCultivar,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor,
184
verbatimScientificNameAuthorship,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor,
173 185
verbatimIdentificationQualifier,//taxonoccurrence/taxondetermination[isoriginal=true]/taxonfit,
174 186
recordedBy,//taxonoccurrence/verbatimcollectorname,
175 187
recordedBy.givenName,//taxonoccurrence/verbatimcollectorname,

Also available in: Unified diff