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Revision 7199

inputs/SALVIAS*/Organism/map.csv: Remapped voucher_string/coll_number to recordNumber instead of catalogNumber, because this number is actually applied by the collector rather than by a herbarium

View differences:

inputs/SALVIAS/plotObservations/map.csv
21 21
y_position,organismY_m,,"""y coordinate in meters"" (y_position definition at <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data>). Brad: See comment above for x_position"
22 22
dist,*dist,,
23 23
perp_dist,*perp_dist,,
24
SourceVoucher,catalogNumber,/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
25
coll_number,catalogNumber,/_alt/1,Brad: Map instead as for voucher_string
24
SourceVoucher,recordNumber,/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
25
coll_number,recordNumber,/_alt/1,Brad: Map instead as for voucher_string
26 26
collector_code,*collector_code,,Brad: OMIT
27 27
coll_inits,*coll_inits,,
28 28
coll_lastname,recordedBy_surName,,"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."
inputs/SALVIAS/plotObservations/VegBIEN.csv
1 1
SALVIAS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
2
coll_number,"/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
3
SourceVoucher,"/_if[@name=""if specimen""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
4 2
Line,"/location/_if[@name=""if subplot""]/cond/_exists",
5 3
PlotCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",
6 4
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists",
7
coll_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
8
SourceVoucher,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
9
coll_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
10
SourceVoucher,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
11 5
DetType,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_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."
12
coll_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string
13
SourceVoucher,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
14 6
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else",
15 7
PlotCode,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode",
16 8
PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode",
17 9
Line,/location/authorlocationcode,
18 10
PlotObsID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
11
coll_number,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
12
SourceVoucher,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
19 13
Line,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists",
20 14
census_date,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists","This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
21 15
-----
......
67 61
intercept_cm,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover_m/_cm_to_m/value,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
68 62
Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes,
69 63
Ind,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/1,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
64
coll_number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2/_alt/1,Brad: Map instead as for voucher_string
65
SourceVoucher,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
70 66
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/2,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
71 67
DetType,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/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."
72
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string
73
SourceVoucher,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
74 68
DetType,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_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."
75
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
76
SourceVoucher,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
69
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string
70
SourceVoucher,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
77 71
canopy_form,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue",
78 72
canopy_position,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue",
79 73
liana_infestation,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=lianaInfestation]]:[@fkey=tablerecord_id]/definedvalue",
......
90 84
Ind,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/1","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
91 85
tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2/_alt/1","The second tag supercedes the first. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
92 86
tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2/_alt/2","The second tag supercedes the first. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
87
coll_number,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3/_alt/1",Brad: Map instead as for voucher_string
88
SourceVoucher,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
93 89
coll_firstname,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join_words/1,Brad: See comment above
94 90
coll_lastname,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_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."
95 91
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","Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
96 92
PlotObsID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
93
coll_number,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
94
SourceVoucher,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
97 95
PlotObsID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/2","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
98 96
det_by,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
99 97
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
......
123 121
OrigGenus,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/genus,
124 122
OrigSpecies,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/specific_epithet,Brad: OMIT
125 123
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."
126
coll_number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then/_alt/1",Brad: Map instead as for voucher_string
127
SourceVoucher,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
128 124
DetType,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_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."
125
coll_number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then/_alt/1",Brad: Map instead as for voucher_string
126
SourceVoucher,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
129 127
PlotID,"/location/sourceaccessioncode/_if[@name=""if locationID""]/cond/_exists",
130 128
Line,"/location/sourceaccessioncode/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/cond/_exists",
131 129
PlotID,"/location/sourceaccessioncode/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1",
inputs/SALVIAS/plotObservations/test.xml.ref
58 58
                                        <authorplantcode>$Ind</authorplantcode>
59 59
                                        <sourceaccessioncode>$PlotObsID</sourceaccessioncode>
60 60
                                        <specimenreplicate>
61
                                            <catalognumber_dwc>
61
                                            <collectionnumber>
62 62
                                                <_if name="if indirect voucher">
63 63
                                                    <cond>
64 64
                                                        <_eq>
......
73 73
                                                        </_alt>
74 74
                                                    </else>
75 75
                                                </_if>
76
                                            </catalognumber_dwc>
76
                                            </collectionnumber>
77 77
                                        </specimenreplicate>
78 78
                                        <stemobservation>
79 79
                                            <definedvalue fkey="tablerecord_id">
......
253 253
                                <voucher>
254 254
                                    <specimenreplicate_id>
255 255
                                        <specimenreplicate>
256
                                            <catalognumber_dwc>
256
                                            <collectionnumber>
257 257
                                                <_if name="if indirect voucher">
258 258
                                                    <cond>
259 259
                                                        <_eq>
......
268 268
                                                        </_alt>
269 269
                                                    </then>
270 270
                                                </_if>
271
                                            </catalognumber_dwc>
271
                                            </collectionnumber>
272 272
                                        </specimenreplicate>
273 273
                                    </specimenreplicate_id>
274 274
                                </voucher>
inputs/SALVIAS/plotObservations/new_terms.csv
15 15
tag2,tag,/_alt/1,"The second tag supercedes the first. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
16 16
x_position,organismX_m,,"""x coordinate in meters"" (x_position definition at <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data>). Brad: These are important, fundamental values of many tree plots"
17 17
y_position,organismY_m,,"""y coordinate in meters"" (y_position definition at <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data>). Brad: See comment above for x_position"
18
SourceVoucher,catalogNumber,/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
19
coll_number,catalogNumber,/_alt/1,Brad: Map instead as for voucher_string
18
SourceVoucher,recordNumber,/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
19
coll_number,recordNumber,/_alt/1,Brad: Map instead as for voucher_string
20 20
coll_lastname,recordedBy_surName,,"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."
21 21
coll_firstname,recordedBy_givenName,,Brad: See comment above
22 22
DetType,voucherType,,"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/map.csv
18 18
tag2,tag,/_alt/2/_alt/1,"The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
19 19
x_position,organismX_m,,"""x coordinate in meters"" (x_position definition at <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data>). Brad: These are important, fundamental values of many tree plots"
20 20
y_position,organismY_m,,"""y coordinate in meters"" (y_position definition at <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data>). Brad: See comment above for x_position"
21
voucher_string,catalogNumber,/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
22
coll_number,catalogNumber,/_alt/1,Brad: Map instead as for voucher_string
21
voucher_string,recordNumber,/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
22
coll_number,recordNumber,/_alt/1,Brad: Map instead as for voucher_string
23 23
collector_code,*collector_code,,Brad: OMIT
24 24
coll_lastname,recordedBy_surName,,"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."
25 25
coll_firstname,recordedBy_givenName,,Brad: See comment above
inputs/SALVIAS-CSV/Organism/VegBIEN.csv
1 1
SALVIAS-CSV,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
2
coll_number,"/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
3
voucher_string,"/_if[@name=""if specimen""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
4 2
subplot,"/location/_if[@name=""if subplot""]/cond/_exists",
5 3
plot_code,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",
6 4
PLOT_ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists",
7
coll_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
8
voucher_string,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
9
coll_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
10
voucher_string,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
11 5
det_type,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_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."
12
coll_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string
13
voucher_string,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
14 6
PLOT_ID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else",
15 7
plot_code,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode",
16 8
PLOT_ID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode",
17 9
subplot,/location/authorlocationcode,
18 10
OBSERVATION_ID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
11
coll_number,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
12
voucher_string,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
19 13
subplot,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists",
20 14
census_date,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists","This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
21 15
-----
......
66 60
census_no,"/location/locationevent/taxonoccurrence/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]:[@fkey=tablerecord_id]/definedvalue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."
67 61
intercept_cm,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover_m/_cm_to_m/value,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
68 62
individual_code,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/1,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
63
coll_number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2/_alt/1,Brad: Map instead as for voucher_string
64
voucher_string,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
69 65
OBSERVATION_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/2,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
70 66
det_type,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/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."
71
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string
72
voucher_string,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
73 67
det_type,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_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."
74
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
75
voucher_string,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
68
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string
69
voucher_string,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
76 70
basal_diam,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter_m,
77 71
stem_canopy_form,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue",
78 72
stem_canopy_position,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue",
......
97 91
stem_tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2/_alt/1/_alt/2","The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."
98 92
tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2/_alt/2/_alt/1","The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
99 93
tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2/_alt/2/_alt/2","The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
94
coll_number,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3/_alt/1",Brad: Map instead as for voucher_string
95
voucher_string,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
100 96
coll_firstname,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join_words/1,Brad: See comment above
101 97
coll_lastname,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_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."
102 98
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","Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
103 99
OBSERVATION_ID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
100
coll_number,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
101
voucher_string,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
104 102
OBSERVATION_ID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/2","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
105 103
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
106 104
specific_epithet,"/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",
......
127 125
orig_family,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/family,Brad: OMIT
128 126
orig_species,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/specific_epithet,Brad: OMIT
129 127
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."
130
coll_number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then/_alt/1",Brad: Map instead as for voucher_string
131
voucher_string,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
132 128
det_type,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_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."
129
coll_number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then/_alt/1",Brad: Map instead as for voucher_string
130
voucher_string,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
133 131
PLOT_ID,"/location/sourceaccessioncode/_if[@name=""if locationID""]/cond/_exists",
134 132
subplot,"/location/sourceaccessioncode/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/cond/_exists",
135 133
PLOT_ID,"/location/sourceaccessioncode/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1",
inputs/SALVIAS-CSV/Organism/test.xml.ref
57 57
                                        <authorplantcode>$individual_code</authorplantcode>
58 58
                                        <sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode>
59 59
                                        <specimenreplicate>
60
                                            <catalognumber_dwc>
60
                                            <collectionnumber>
61 61
                                                <_if name="if indirect voucher">
62 62
                                                    <cond>
63 63
                                                        <_eq>
......
72 72
                                                        </_alt>
73 73
                                                    </else>
74 74
                                                </_if>
75
                                            </catalognumber_dwc>
75
                                            </collectionnumber>
76 76
                                        </specimenreplicate>
77 77
                                        <stemobservation>
78 78
                                            <basaldiameter_m>$basal_diam</basaldiameter_m>
......
279 279
                                <voucher>
280 280
                                    <specimenreplicate_id>
281 281
                                        <specimenreplicate>
282
                                            <catalognumber_dwc>
282
                                            <collectionnumber>
283 283
                                                <_if name="if indirect voucher">
284 284
                                                    <cond>
285 285
                                                        <_eq>
......
294 294
                                                        </_alt>
295 295
                                                    </then>
296 296
                                                </_if>
297
                                            </catalognumber_dwc>
297
                                            </collectionnumber>
298 298
                                        </specimenreplicate>
299 299
                                    </specimenreplicate_id>
300 300
                                </voucher>
inputs/SALVIAS-CSV/Organism/new_terms.csv
13 13
tag2,tag,/_alt/2/_alt/1,"The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
14 14
x_position,organismX_m,,"""x coordinate in meters"" (x_position definition at <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data>). Brad: These are important, fundamental values of many tree plots"
15 15
y_position,organismY_m,,"""y coordinate in meters"" (y_position definition at <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data>). Brad: See comment above for x_position"
16
voucher_string,catalogNumber,/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
17
coll_number,catalogNumber,/_alt/1,Brad: Map instead as for voucher_string
16
voucher_string,recordNumber,/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
17
coll_number,recordNumber,/_alt/1,Brad: Map instead as for voucher_string
18 18
coll_lastname,recordedBy_surName,,"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."
19 19
coll_firstname,recordedBy_givenName,,Brad: See comment above
20 20
det_type,voucherType,,"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."

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