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Revision 4385

Added by Aaron Marcuse-Kubitza about 12 years ago

inputs/Madidi/1.organisms/map.csv: Mapped columns

View differences:

inputs/Madidi/1.organisms/map.csv
1 
Madidi,Veg+,Comments
2 
Expedition,,
3 
Inventory name,,
1 
Madidi[Veg+],Veg+,Comments
2 
Expedition,projectName,
3 
Inventory name,plotName,
4 4 
Number of inventory (general),,
5 5 
Number of inventory (expedition),,
6 6 
"Type Inventory (C, PP, TP)",,
7 
Inventory code,,
8 
Tag number,,
9 
Tree number,,
10 
Number of subplot,,
11 
Index collector,,
12 
Specimen,,
7 
Inventory code,locationID,
8 
Tag number,tag,
9 
Tree number,recordNumber,
10 
Number of subplot,subplot,
11 
Index collector,recordedBy,
12 
Specimen,catalogNumber,
13 13 
Similar specimen,,
14 14 
Plot specimen,,
15 15 
Expedition specimen,,
16 16 
Project specimen,,
17 
Field family,,
18 
Field name,,
19 
Family (revised),,
20 
Specie+autor,,
21 
Genera,,
22 
Specific epithet,,
23 
Species and morphotypes,,
24 
Autor (revised),,
25 
Determined by,,
26 
Qualifier,,
17 
Field family,verbatimFamily,
18 
Field name,verbatimGenus,Often = Genera
19 
Family (revised),family,
20 
Specie+autor,scientificName,
21 
Genera,genus,
22 
Specific epithet,specificEpithet,
23 
Species and morphotypes,,"Contains less than ""Specie+autor"""
24 
Autor (revised),scientificNameAuthorship,
25 
Determined by,identifiedBy,
26 
Qualifier,identificationQualifier,
27 27 
Common name,,
28 28 
Circumference,,
29 
Diameter,,
30 
Trunk,,
31 
Total height,,
32 
Bole height,,
33 
Habit,,
29 
Diameter,diameterBreastHeight,
30 
Trunk,authorStemCode,
31 
Total height,height,
32 
Bole height,,trunk height
34 33 
Phenology,,
35 34 
Crown position,,
36 35 
Crown shape,,
37 
Liana presence,,
38 
Basal area,,
39 
Subplot X,,
40 
Subplot Y,,
36 
Liana presence,lianaInfestation,
37 
Basal area,,"Would be basalDiameter, but need formula to translate"
38 
Subplot X,organismX,
39 
Subplot Y,organismY,
41 40 
Plot X,,
42 41 
Plot Y,,
43 
Observations,,
42 
Observations,fieldNotes,
inputs/Madidi/1.organisms/map.full.csv
1 
Madidi,Veg+,Comments
1 
Madidi[Veg+],Veg+,Comments
2 
Habit,Habit
3 
Trunk,authorStemCode,
4 
Specimen,catalogNumber,
5 
Diameter,diameterBreastHeight,
6 
Family (revised),family,
7 
Observations,fieldNotes,
8 
Genera,genus,
9 
Total height,height,
10 
Qualifier,identificationQualifier,
11 
Determined by,identifiedBy,
12 
Liana presence,lianaInfestation,
13 
Inventory code,locationID,
14 
Subplot X,organismX,
15 
Subplot Y,organismY,
16 
Inventory name,plotName,
17 
Expedition,projectName,
18 
Tree number,recordNumber,
19 
Index collector,recordedBy,
20 
Specie+autor,scientificName,
21 
Autor (revised),scientificNameAuthorship,
22 
Specific epithet,specificEpithet,
23 
Number of subplot,subplot,
24 
Tag number,tag,
25 
Field family,verbatimFamily,
26 
Field name,verbatimGenus,Often = Genera
inputs/Madidi/1.organisms/VegBIEN.csv
1 
Madidi,VegBIEN:,Comments
1 
Madidi[Veg+],VegBIEN:,Comments
2 
Number of subplot,"/location/_if[@name=""if subplot""]/cond/_exists/_first/2",
3 
Inventory name,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",
4 
Inventory code,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists",
5 
Specimen,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_join/3/_if[@name=""if indirect voucher""]/else",
6 
Inventory code,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode",
7 
Inventory name,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode",
8 
Inventory code,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode",
9 
Number of subplot,/location/authorlocationcode,
10 
Expedition,/location/locationevent/*_id/project/projectname,
11 
Number of subplot,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists/_first/2",
12 
Observations,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes,
13 
Tree number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber/_alt/2,
14 
Specimen,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
15 
Trunk,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode,
16 
Liana presence,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=lianaInfestation]]:[@fkey=tablerecord_id]/definedvalue",
17 
Diameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight,
18 
Total height,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height,
19 
Tag number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2
20 
Subplot X,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition,
21 
Subplot Y,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition,
22 
Tree number,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,
23 
Specie+autor,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
24 
Habit,"/location/locationevent/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=*]/value","According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>"
25 
Determined by,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first,
26 
Determined by,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle,
27 
Determined by,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/surname/_namePart/last,
28 
Specie+autor,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname",
29 
Autor (revised),"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[binomial,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname/_alt/1",
30 
Specific epithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname",
31 
Genera,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname",
32 
Family (revised),"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",
33 
Qualifier,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,
34 
Field name,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname",Often = Genera
35 
Field family,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",
36 
Index collector,/location/locationevent/taxonoccurrence/verbatimcollectorname,
37 
Specimen,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
inputs/Madidi/1.organisms/test.xml.ref
1 1 
Put template:
2 
<VegBIEN/>Inserted 1 new rows into database
2 
<VegBIEN>
3 
    <location id="-1">
4 
        <parent_id>
5 
            <location>
6 
                <authorlocationcode>$Inventory name</authorlocationcode>
7 
                <sourceaccessioncode>$Inventory code</sourceaccessioncode>
8 
            </location>
9 
        </parent_id>
10 
        <authorlocationcode>$Number of subplot</authorlocationcode>
11 
        <locationevent>
12 
            <project_id><project><projectname>$Expedition</projectname></project></project_id>
13 
            <taxonoccurrence>
14 
                <aggregateoccurrence>
15 
                    <notes>$Observations</notes>
16 
                    <plantobservation>
17 
                        <collectionnumber>$Tree number</collectionnumber>
18 
                        <specimenreplicate><catalognumber_dwc>$Specimen</catalognumber_dwc></specimenreplicate>
19 
                        <stemobservation>
20 
                            <authorstemcode>$Trunk</authorstemcode>
21 
                            <definedvalue fkey="tablerecord_id">
22 
                                <userdefined_id>
23 
                                    <userdefined>
24 
                                        <tablename>stemobservation</tablename>
25 
                                        <userdefinedname>lianaInfestation</userdefinedname>
26 
                                    </userdefined>
27 
                                </userdefined_id>
28 
                                <definedvalue>$Liana presence</definedvalue>
29 
                            </definedvalue>
30 
                            <diameterbreastheight>$Diameter</diameterbreastheight>
31 
                            <height>$Total height</height>
32 
                            <stemtag>
33 
                                <iscurrent>true</iscurrent>
34 
                                <tag>$Tag number</tag>
35 
                            </stemtag>
36 
                            <xposition>$Subplot X</xposition>
37 
                            <yposition>$Subplot Y</yposition>
38 
                        </stemobservation>
39 
                    </plantobservation>
40 
                </aggregateoccurrence>
41 
                <authortaxoncode>
42 
                    <_alt>
43 
                        <1>$Tree number</1>
44 
                        <2>$Specie+autor</2>
45 
                    </_alt>
46 
                </authortaxoncode>
47 
                <growthform>
48 
                    <_map>
49 
                        <T>tree</T>
50 
                        <Arbol>tree</Arbol>
51 
                        <palm>tree</palm>
52 
                        <H>hemiepiphyte</H>
53 
                        <Hemiepífito>hemiepiphyte</Hemiepífito>
54 
                        <L>liana</L>
55 
                        <l>liana</l>
56 
                        <L?>liana</L?>
57 
                        <Liana>liana</Liana>
58 
                        <E>epiphyte</E>
59 
                        <S>shrub</S>
60 
                        <Hb>herb</Hb>
61 
                        <vine-herbaceous>vine</vine-herbaceous>
62 
                        <graminoid>grass</graminoid>
63 
                        <rosette>forb</rosette>
64 
                        <*>*</*>
65 
                        <value>$Habit</value>
66 
                    </_map>
67 
                </growthform>
68 
                <taxondetermination>
69 
                    <party_id>
70 
                        <party>
71 
                            <givenname><_namePart><first>$Determined by</first></_namePart></givenname>
72 
                            <middlename><_namePart><middle>$Determined by</middle></_namePart></middlename>
73 
                            <surname><_namePart><last>$Determined by</last></_namePart></surname>
74 
                        </party>
75 
                    </party_id>
76 
                    <plantconcept_id>
77 
                        <plantconcept>
78 
                            <plantname_id>
79 
                                <_simplifyPath>
80 
                                    <next>parent_id</next>
81 
                                    <path>
82 
                                        <plantname>
83 
                                            <rank>binomial</rank>
84 
                                            <plantname>$Specie+autor</plantname>
85 
                                            <parent_id>
86 
                                                <plantname>
87 
                                                    <rank>authority</rank>
88 
                                                    <plantname>$Autor (revised)</plantname>
89 
                                                    <parent_id>
90 
                                                        <plantname>
91 
                                                            <rank>subspecies</rank>
92 
                                                            <parent_id>
93 
                                                                <plantname>
94 
                                                                    <rank>species</rank>
95 
                                                                    <plantname>$Specific epithet</plantname>
96 
                                                                    <parent_id>
97 
                                                                        <plantname>
98 
                                                                            <rank>genus</rank>
99 
                                                                            <plantname>$Genera</plantname>
100 
                                                                            <parent_id>
101 
                                                                                <plantname>
102 
                                                                                    <rank>family</rank>
103 
                                                                                    <plantname>$Family (revised)</plantname>
104 
                                                                                </plantname>
105 
                                                                            </parent_id>
106 
                                                                        </plantname>
107 
                                                                    </parent_id>
108 
                                                                </plantname>
109 
                                                            </parent_id>
110 
                                                        </plantname>
111 
                                                    </parent_id>
112 
                                                </plantname>
113 
                                            </parent_id>
114 
                                        </plantname>
115 
                                    </path>
116 
                                </_simplifyPath>
117 
                            </plantname_id>
118 
                        </plantconcept>
119 
                    </plantconcept_id>
120 
                    <taxonfit>$Qualifier</taxonfit>
121 
                </taxondetermination>
122 
                <taxondetermination>
123 
                    <isoriginal>true</isoriginal>
124 
                    <plantconcept_id>
125 
                        <plantconcept>
126 
                            <plantname_id>
127 
                                <_simplifyPath>
128 
                                    <next>parent_id</next>
129 
                                    <path>
130 
                                        <plantname>
131 
                                            <rank>binomial</rank>
132 
                                            <parent_id>
133 
                                                <plantname>
134 
                                                    <rank>authority</rank>
135 
                                                    <parent_id>
136 
                                                        <plantname>
137 
                                                            <rank>subspecies</rank>
138 
                                                            <parent_id>
139 
                                                                <plantname>
140 
                                                                    <rank>species</rank>
141 
                                                                    <parent_id>
142 
                                                                        <plantname>
143 
                                                                            <rank>genus</rank>
144 
                                                                            <plantname>$Field name</plantname>
145 
                                                                            <parent_id>
146 
                                                                                <plantname>
147 
                                                                                    <rank>family</rank>
148 
                                                                                    <plantname>$Field family</plantname>
149 
                                                                                </plantname>
150 
                                                                            </parent_id>
151 
                                                                        </plantname>
152 
                                                                    </parent_id>
153 
                                                                </plantname>
154 
                                                            </parent_id>
155 
                                                        </plantname>
156 
                                                    </parent_id>
157 
                                                </plantname>
158 
                                            </parent_id>
159 
                                        </plantname>
160 
                                    </path>
161 
                                </_simplifyPath>
162 
                            </plantname_id>
163 
                        </plantconcept>
164 
                    </plantconcept_id>
165 
                </taxondetermination>
166 
                <verbatimcollectorname>$Index collector</verbatimcollectorname>
167 
            </taxonoccurrence>
168 
        </locationevent>
169 
    </location>
170 
</VegBIEN>
171 
Inserted 40 new rows into database

Also available in: Unified diff