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Revision 10687

Added by Aaron Marcuse-Kubitza over 11 years ago

fix: inputs/VegBank/taxonobservation_/map.csv: Species and below: remapped to _alts of scientificName, because these are actually the full taxonomic name at that rank, not just the epithet. Genus: documented that it includes the genus author.

View differences:

inputs/VegBank/taxonobservation_/map.csv
58 58 
Subclass,*Subclass,,
59 59 
Order,order,,
60 60 
Family,family,,
61 
Genus,genus,,
62 
Species,specificEpithet,,
63 
Subspecies,subspecies,,
64 
Variety,variety,,
65 
Forma,forma,,
61 
Genus,genus,,includes genus author
62 
Species,scientificName,/_alt/3/_alt/4,*full* taxonomic name at that rank
63 
Subspecies,scientificName,/_alt/3/_alt/3,*full* taxonomic name at that rank
64 
Variety,scientificName,/_alt/3/_alt/2,*full* taxonomic name at that rank
65 
Forma,scientificName,/_alt/3/_alt/1,*full* taxonomic name at that rank
66 66 
:plot,observationGranularity,,
inputs/VegBank/taxonobservation_/VegBIEN.csv
23 23 
int_origplantscinamenoauth,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/1",
24 24 
int_currplantscifull,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2/_alt/1",
25 25 
plantname,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2/_alt/2","when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
26 
Forma,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2/_alt/3/_alt/1",*full* taxonomic name at that rank
27 
Variety,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2/_alt/3/_alt/2",*full* taxonomic name at that rank
28 
Subspecies,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2/_alt/3/_alt/3",*full* taxonomic name at that rank
29 
Species,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2/_alt/3/_alt/4",*full* taxonomic name at that rank
26 30 
int_currplantscinamenoauth,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3",
27 31 
collectionnumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
28 32 
taxonobservation_id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
29 33 
taxonobservation_id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1,
30 
Forma,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=forma]/taxonepithet",
31 
Variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=variety]/taxonepithet",
32 
Subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=subspecies]/taxonepithet",
33 
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
34 
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",
34 
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",includes genus author
35 35 
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",
36 36 
Order,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=order]/taxonepithet",
37 37 
Class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=class]/taxonepithet",
......
39 39 
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,
40 40 
int_currplantscifull,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1/_alt/1,
41 41 
plantname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1/_alt/2,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
42 
Forma,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1/_alt/3/_alt/1,*full* taxonomic name at that rank
43 
Variety,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1/_alt/3/_alt/2,*full* taxonomic name at that rank
44 
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1/_alt/3/_alt/3,*full* taxonomic name at that rank
45 
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1/_alt/3/_alt/4,*full* taxonomic name at that rank
42 46 
int_currplantscinamenoauth,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1,
43 
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value,
44 
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,
45 
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4,
46 
Variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/6/_join_words:[1=""var. ""]/2",
47 
Forma,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/7/_join_words:[1=""fm. ""]/2",
47 
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value,includes genus author
48 48 
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,
49 
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,
50 
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,
49 
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,includes genus author
51 50 
int_currplantscinamenoauth,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
52 51 
int_currplantscifull,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname/_alt/1,
53 52 
plantname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname/_alt/2,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
53 
Forma,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname/_alt/3/_alt/1,*full* taxonomic name at that rank
54 
Variety,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname/_alt/3/_alt/2,*full* taxonomic name at that rank
55 
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname/_alt/3/_alt/3,*full* taxonomic name at that rank
56 
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname/_alt/3/_alt/4,*full* taxonomic name at that rank
54 57 
taxonobservation_id,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/_if[@name=""if has taxondetermination""]/cond/_exists",
55 58 
interpretationdate,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value,
56 59 
interpretationtype,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationtype,
inputs/VegBank/taxonobservation_/test.xml.ref
36 36 
                                                                    <parent_id>
37 37 
                                                                        <taxonlabel>
38 38 
                                                                            <rank>forma</rank>
39 
                                                                            <taxonepithet>$Forma</taxonepithet>
40 39 
                                                                            <parent_id>
41 40 
                                                                                <taxonlabel>
42 41 
                                                                                    <rank>variety</rank>
43 
                                                                                    <taxonepithet>$Variety</taxonepithet>
44 42 
                                                                                    <parent_id>
45 43 
                                                                                        <taxonlabel>
46 44 
                                                                                            <rank>subspecies</rank>
47 
                                                                                            <taxonepithet>$Subspecies</taxonepithet>
48 45 
                                                                                            <parent_id>
49 46 
                                                                                                <taxonlabel>
50 47 
                                                                                                    <rank>species</rank>
51 
                                                                                                    <taxonepithet>$Species</taxonepithet>
52 48 
                                                                                                    <parent_id>
53 49 
                                                                                                        <taxonlabel>
54 50 
                                                                                                            <rank>genus</rank>
......
105 101 
                                                                        <_alt>
106 102 
                                                                            <1>$int_currplantscifull</1>
107 103 
                                                                            <2>$plantname</2>
104 
                                                                            <3>
105 
                                                                                <_alt>
106 
                                                                                    <1>$Forma</1>
107 
                                                                                    <2>$Variety</2>
108 
                                                                                    <3>$Subspecies</3>
109 
                                                                                    <4>$Species</4>
110 
                                                                                </_alt>
111 
                                                                            </3>
108 112 
                                                                        </_alt>
109 113 
                                                                    </1>
110 114 
                                                                    <2>
111 115 
                                                                        <_alt>
112 116 
                                                                            <1>$int_currplantscinamenoauth</1>
113 
                                                                            <2>
114 
                                                                                <_join_words>
115 
                                                                                    <2><_filter_genus><value>$Genus</value></_filter_genus></2>
116 
                                                                                    <3>$Species</3>
117 
                                                                                    <4>$Subspecies</4>
118 
                                                                                    <6>
119 
                                                                                        <_join_words>
120 
                                                                                            <1>var. </1>
121 
                                                                                            <2>$Variety</2>
122 
                                                                                        </_join_words>
123 
                                                                                    </6>
124 
                                                                                    <7>
125 
                                                                                        <_join_words>
126 
                                                                                            <1>fm. </1>
127 
                                                                                            <2>$Forma</2>
128 
                                                                                        </_join_words>
129 
                                                                                    </7>
130 
                                                                                </_join_words>
131 
                                                                            </2>
117 
                                                                            <2><_filter_genus><value>$Genus</value></_filter_genus></2>
132 118 
                                                                        </_alt>
133 119 
                                                                    </2>
134 120 
                                                                </_alt>
......
139 125 
                                            </taxonlabel_id>
140 126 
                                            <family>$Family</family>
141 127 
                                            <genus>$Genus</genus>
142 
                                            <specific_epithet>$Species</specific_epithet>
143 128 
                                            <taxonname>$int_currplantscinamenoauth</taxonname>
144 129 
                                            <taxonomicname>
145 130 
                                                <_alt>
146 131 
                                                    <1>$int_currplantscifull</1>
147 132 
                                                    <2>$plantname</2>
133 
                                                    <3>
134 
                                                        <_alt>
135 
                                                            <1>$Forma</1>
136 
                                                            <2>$Variety</2>
137 
                                                            <3>$Subspecies</3>
138 
                                                            <4>$Species</4>
139 
                                                        </_alt>
140 
                                                    </3>
148 141 
                                                </_alt>
149 142 
                                            </taxonomicname>
150 143 
                                        </taxonverbatim>

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