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Revision 5686

Added by Aaron Marcuse-Kubitza about 12 years ago

mappings/VegCore-VegBIEN.csv: Do not include the taxonName in the concatenated taxonomicname because it is NOT globally unique. The same name may be used at different taxonomic ranks and mean different things, and lower taxa may have the name appear in multiple genuses or species, meaning different things.

View differences:

inputs/.NCBI/higher_taxa/VegBIEN.csv
9 9 
tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode,
10 10 
name_txt,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet,
11 11 
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
12 
name_txt,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/6,
13 12 
rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,
14 13 
4,,** No join mapping for *4 **
15 14 
5,,** No join mapping for *5 **
inputs/.NCBI/higher_taxa/test.xml.ref
26 26 
                                            <rank>$rank</rank>
27 27 
                                            <sourceaccessioncode>$tax_id</sourceaccessioncode>
28 28 
                                            <taxonepithet>$name_txt</taxonepithet>
29 
                                            <taxonomicname>$name_txt</taxonomicname>
30 29 
                                        </taxonlabel>
31 30 
                                    </taxonlabel_id>
32 31 
                                    <verbatimrank>$rank</verbatimrank>
mappings/VegCore-VegBIEN.csv
237 237 
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
238 238 
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
239 239 
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2,
240 
taxonName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/6,
241 
variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/7/_join_words:[1=""var. ""]/2",
242 
forma,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/8/_join_words:[1=""fm. ""]/2",
243 
cultivar,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/9/_join_words:[1=""cult. ""]/2",
240 
variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/6/_join_words:[1=""var. ""]/2",
241 
forma,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/7/_join_words:[1=""fm. ""]/2",
242 
cultivar,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/8/_join_words:[1=""cult. ""]/2",
244 243 
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/2,
245 244 
taxonomicStatus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonstatus,
246 245 
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,
mappings/for_review/VegCore-VegBIEN.csv
237 237 
infraspecificEpithet,"//taxonlabel/taxonomicname/_if[@name=""if has infraspecificEpithet""]/cond",
238 238 
taxonRank,"//taxonlabel/taxonomicname/_if[@name=""if has infraspecificEpithet""]/then",
239 239 
infraspecificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname,
240 
taxonName,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname,
241 240 
variety,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname,
242 241 
forma,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname,
243 242 
cultivar,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname,

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