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Revision 5733

Added by Aaron Marcuse-Kubitza about 12 years ago

mappings/VegCore-VegBIEN.csv: taxonName->taxonepithet: Use new _taxonomic_name_is_epithet() instead of _is_higher_taxon(), because it's more specific to the filtering task for this field

View differences:

inputs/UNCC/Specimen/VegBIEN.csv
61 61 
infraname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet,
62 62 
usdaRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank/_alt/1,
63 63 
infrarank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank/_alt/2,
64 
usdaRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/cond/_alt:[2=true]/1/_is_higher_taxon/rank/_alt/1",
65 
infrarank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/cond/_alt:[2=true]/1/_is_higher_taxon/rank/_alt/2",
64 
usdaRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank/_alt/1",
65 
infrarank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank/_alt/2",
66 66 
SciName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/1,
67 67 
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1,
68 68 
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2,
inputs/ACAD/Specimen/VegBIEN.csv
41 41 
kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet",
42 42 
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet,
43 43 
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,
44 
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/cond/_alt:[2=true]/1/_is_higher_taxon/rank",
44 
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank",
45 45 
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/1,
46 46 
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1,
47 47 
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2,
inputs/.NCBI/nodes/VegBIEN.csv
7 7 
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/taxonverbatim/verbatimrank",
8 8 
rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,
9 9 
tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode,
10 
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/cond/_alt:[2=true]/1/_is_higher_taxon/rank",
11 
name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/then",
10 
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank",
11 
name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/then",
12 12 
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",
13 13 
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/3/_if[@name=""if has taxonomic name""]/cond/_has_taxonomic_name/rank",
14 14 
name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/3/_if[@name=""if has taxonomic name""]/then",
inputs/.NCBI/nodes/test.xml.ref
26 26 
                                            <rank>$rank</rank>
27 27 
                                            <sourceaccessioncode>$tax_id</sourceaccessioncode>
28 28 
                                            <taxonepithet>
29 
                                                <_if name="if is higher taxon">
29 
                                                <_if name="if taxonomic name is epithet">
30 30 
                                                    <cond>
31 31 
                                                        <_alt>
32 32 
                                                            <2>true</2>
33 
                                                            <1><_is_higher_taxon><rank>$rank</rank></_is_higher_taxon></1>
33 
                                                            <1><_taxonomic_name_is_epithet><rank>$rank</rank></_taxonomic_name_is_epithet></1>
34 34 
                                                        </_alt>
35 35 
                                                    </cond>
36 36 
                                                    <then>$name_txt</then>
inputs/SALVIAS-CSV/Organism/VegBIEN.csv
78 78 
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet",
79 79 
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet,
80 80 
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,
81 
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/cond/_alt:[2=true]/1/_is_higher_taxon/rank",
81 
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank",
82 82 
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1,
83 83 
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2,
84 84 
specific_epithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,
inputs/SALVIAS/plotObservations/VegBIEN.csv
71 71 
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet",
72 72 
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet,
73 73 
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,
74 
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/cond/_alt:[2=true]/1/_is_higher_taxon/rank",
74 
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank",
75 75 
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1,
76 76 
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2,
77 77 
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,
inputs/.TNRS/tnrs/VegBIEN.csv
31 31 
Infraspecific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet,
32 32 
Name_matched_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,
33 33 
Name_matched_url,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode,
34 
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/cond/_alt:[2=true]/1/_is_higher_taxon/rank",
34 
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank",
35 35 
Family_score,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/matched_label_fit_fraction/_max/1,
36 36 
Genus_score,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/matched_label_fit_fraction/_max/2,
37 37 
Specific_epithet_score,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/matched_label_fit_fraction/_max/3,
inputs/QMOR/Specimen/VegBIEN.csv
48 48 
kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet",
49 49 
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet,
50 50 
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,
51 
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/cond/_alt:[2=true]/1/_is_higher_taxon/rank",
51 
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank",
52 52 
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/1,
53 53 
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1,
54 54 
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2,
mappings/VegCore-VegBIEN.csv
211 211 
scientificNameID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode,
212 212 
taxonConceptID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode,
213 213 
taxonID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode,
214 
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/cond/_alt:[2=true]/1/_is_higher_taxon/rank",
215 
taxonName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/then",
214 
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank",
215 
taxonName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/then",
216 216 
matchedFamilyFit_fraction,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/matched_label_fit_fraction/_max/1,
217 217 
matchedGenusFit_fraction,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/matched_label_fit_fraction/_max/2,
218 218 
matchedSpeciesFit_fraction,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/matched_label_fit_fraction/_max/3,
mappings/for_review/VegCore-VegBIEN.csv
211 211 
scientificNameID,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode,
212 212 
taxonConceptID,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode,
213 213 
taxonID,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode,
214 
taxonRank,"//taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/cond",
215 
taxonName,"//taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/then",
214 
taxonRank,"//taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond",
215 
taxonName,"//taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/then",
216 216 
matchedFamilyFit_fraction,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel/matched_label_fit_fraction,
217 217 
matchedGenusFit_fraction,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel/matched_label_fit_fraction,
218 218 
matchedSpeciesFit_fraction,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel/matched_label_fit_fraction,

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