Revision 5044
Added by Aaron Marcuse-Kubitza over 12 years ago
inputs/Madidi/Organism/VegBIEN.csv | ||
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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 | ||
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86 | 86 |
<taxonpath> |
87 | 87 |
<family>$Field family</family> |
88 | 88 |
<genus>$Field name</genus> |
89 |
<taxonomicnamewithauthor> |
|
90 |
<_join_words> |
|
91 |
<1>$Field family</1> |
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92 |
<2>$Field name</2> |
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93 |
</_join_words> |
|
94 |
</taxonomicnamewithauthor> |
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89 | 95 |
</taxonpath> |
90 | 96 |
</taxonpath_id> |
91 | 97 |
</taxondetermination> |
inputs/SALVIAS-CSV/Organism/VegBIEN.csv | ||
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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 | ||
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185 | 185 |
<taxonpath> |
186 | 186 |
<family>$orig_family</family> |
187 | 187 |
<species>$orig_species</species> |
188 |
<taxonomicnamewithauthor> |
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189 |
<_join_words> |
|
190 |
<1>$orig_family</1> |
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191 |
<3>$orig_species</3> |
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192 |
</_join_words> |
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193 |
</taxonomicnamewithauthor> |
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188 | 194 |
</taxonpath> |
189 | 195 |
</taxonpath_id> |
190 | 196 |
</taxondetermination> |
inputs/SALVIAS/plotObservations/VegBIEN.csv | ||
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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 |
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77 |
OrigGenus,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2, |
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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 | ||
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157 | 157 |
<family>$OrigFamily</family> |
158 | 158 |
<genus>$OrigGenus</genus> |
159 | 159 |
<species>$OrigSpecies</species> |
160 |
<taxonomicnamewithauthor> |
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161 |
<_join_words> |
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162 |
<1>$OrigFamily</1> |
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163 |
<2>$OrigGenus</2> |
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164 |
<3>$OrigSpecies</3> |
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165 |
</_join_words> |
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166 |
</taxonomicnamewithauthor> |
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160 | 167 |
</taxonpath> |
161 | 168 |
</taxonpath_id> |
162 | 169 |
</taxondetermination> |
inputs/GBIF/Specimen/VegBIEN.csv | ||
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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, |
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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 | ||
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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 | ||
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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 | ||
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54 | 54 |
</taxondetermination> |
55 | 55 |
<taxondetermination> |
56 | 56 |
<isoriginal>true</isoriginal> |
57 |
<taxonpath_id><taxonpath><taxonomicname>$authorplantname</taxonomicname></taxonpath></taxonpath_id> |
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57 |
<taxonpath_id> |
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58 |
<taxonpath> |
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59 |
<taxonomicname>$authorplantname</taxonomicname> |
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60 |
<taxonomicnamewithauthor>$authorplantname</taxonomicnamewithauthor> |
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61 |
</taxonpath> |
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62 |
</taxonpath_id> |
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58 | 63 |
</taxondetermination> |
59 | 64 |
</taxonoccurrence> |
60 | 65 |
</locationevent> |
mappings/VegCore-VegBIEN.csv | ||
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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 | ||
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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
mappings/VegCore-VegBIEN.csv: verbatim* taxonomic terms: Added taxonomicnamewithauthor mappings analogous to those for the non-verbatim taxonomic terms