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1 6406 aaronmk
SALVIAS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
2 4987 aaronmk
Line,"/location/_if[@name=""if subplot""]/cond/_exists",
3 4336 aaronmk
PlotCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",
4
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists",
5 6756 aaronmk
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."
6 7464 aaronmk
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode",
7 4324 aaronmk
PlotCode,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode",
8
PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode",
9 4333 aaronmk
Line,/location/authorlocationcode,
10 6432 aaronmk
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 7199 aaronmk
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."
13 4987 aaronmk
Line,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists",
14 5977 aaronmk
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:
15
-----
16
SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count
17
FROM ""SALVIAS"".organisms
18
WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL
19
GROUP BY ""PlotID"", ""Line""
20
HAVING count(DISTINCT census_date) > 1
21
-----"
22 6002 aaronmk
Line,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/cond/_first/2",
23
PlotCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then",
24
Line,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/cond/_first/2",
25
PlotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then",
26 6217 aaronmk
census_date,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value","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:
27 5977 aaronmk
-----
28
SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count
29
FROM ""SALVIAS"".organisms
30
WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL
31
GROUP BY ""PlotID"", ""Line""
32
HAVING count(DISTINCT census_date) > 1
33
-----"
34 6217 aaronmk
census_date,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value","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:
35 5977 aaronmk
-----
36
SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count
37
FROM ""SALVIAS"".organisms
38
WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL
39
GROUP BY ""PlotID"", ""Line""
40
HAVING count(DISTINCT census_date) > 1
41
-----"
42 11107 aaronmk
cfaff,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/taxonfit","Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
43
NoInd,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/count,"Brad: This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
44
cover_percent,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/cover_fraction/_percent_to_fraction/value,
45
census_no,"/location/locationevent/locationevent:[@fkey=parent_id]/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."
46
intercept_cm,/location/locationevent/locationevent:[@fkey=parent_id]/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."
47
Notes,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/notes/_join/1,
48
Ind,/location/locationevent/locationevent:[@fkey=parent_id]/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."
49
coll_number,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2/_alt/1,Brad: Map instead as for voucher_string
50
SourceVoucher,/location/locationevent/locationevent:[@fkey=parent_id]/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."
51
phenology,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/reproductivecondition,
52
PlotObsID,/location/locationevent/locationevent:[@fkey=parent_id]/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."
53
DetType,"/location/locationevent/locationevent:[@fkey=parent_id]/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."
54
DetType,"/location/locationevent/locationevent:[@fkey=parent_id]/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."
55
coll_number,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string
56
SourceVoucher,"/location/locationevent/locationevent:[@fkey=parent_id]/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."
57
canopy_form,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue",
58
canopy_position,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue",
59
liana_infestation,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=lianaInfestation]]:[@fkey=tablerecord_id]/definedvalue",
60
temp_dbh,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,"Assuming units based on the units for intercept_cm, which measures the same dimension"
61
height_m,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m,"""Total height of individual, in meters"" (height_m definition at <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data>)"
62
ht_first_branch_m,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/heightfirstbranch_m,
63
tag2,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/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."
64
tag1,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag/_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."
65
x_position,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_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"
66
y_position,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_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"
67
PlotCode,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
68
PlotID,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
69
PlotObsID,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_if[@name=""if individual""]/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."
70
Ind,"/location/locationevent/locationevent:[@fkey=parent_id]/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."
71
tag2,"/location/locationevent/locationevent:[@fkey=parent_id]/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."
72
tag1,"/location/locationevent/locationevent:[@fkey=parent_id]/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."
73
coll_number,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3/_alt/1",Brad: Map instead as for voucher_string
74
SourceVoucher,"/location/locationevent/locationevent:[@fkey=parent_id]/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."
75
coll_firstname,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/collector_id/party/fullname/_join_words/1,Brad: See comment above
76
coll_lastname,/location/locationevent/locationevent:[@fkey=parent_id]/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."
77
Habit,"/location/locationevent/locationevent:[@fkey=parent_id]/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."
78
PlotObsID,"/location/locationevent/locationevent:[@fkey=parent_id]/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."
79
coll_number,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
80
SourceVoucher,"/location/locationevent/locationevent:[@fkey=parent_id]/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."
81
PlotObsID,"/location/locationevent/locationevent:[@fkey=parent_id]/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."
82 11512 aaronmk
det_by,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/party/fullname,
83
infra_rank_1,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
84
Species,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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",
85
Genus,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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",
86
Family,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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",
87
infra_ep_1,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet,
88
infra_rank_1,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/rank,
89
infra_rank_1,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank",
90
Family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,
91
Genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value,
92
Species,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,
93
infra_ep_1,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
94
infra_rank_1,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
95
infra_ep_1,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2,
96
auth,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2,Brad: This is the author of the scientificName.
97
auth,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/author,Brad: This is the author of the scientificName.
98
Family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/family,
99
Genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/genus,
100
Species,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/specific_epithet,
101
infra_rank_1,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/verbatimrank,
102
cfaff,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/taxonfit,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
103 11107 aaronmk
OrigFamily,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/family,Brad: OMIT
104
OrigGenus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/genus,
105
morphoname,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/morphoname,"Not the morphospecies, which is stored in Species"
106
OrigSpecies,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/specific_epithet,Brad: OMIT
107
DetType,"/location/locationevent/locationevent:[@fkey=parent_id]/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."
108
DetType,"/location/locationevent/locationevent:[@fkey=parent_id]/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."
109
coll_number,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then/_alt/1",Brad: Map instead as for voucher_string
110
SourceVoucher,"/location/locationevent/locationevent:[@fkey=parent_id]/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."
111 6217 aaronmk
census_date,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value,"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:
112 4176 aaronmk
-----
113
SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count
114
FROM ""SALVIAS"".organisms
115
WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL
116
GROUP BY ""PlotID"", ""Line""
117
HAVING count(DISTINCT census_date) > 1
118 4020 aaronmk
-----"
119 6217 aaronmk
census_date,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value,"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:
120 4176 aaronmk
-----
121
SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count
122
FROM ""SALVIAS"".organisms
123
WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL
124
GROUP BY ""PlotID"", ""Line""
125
HAVING count(DISTINCT census_date) > 1
126 4020 aaronmk
-----"
127 8206 aaronmk
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists",
128
Line,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/cond/_exists",
129
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1",
130
Line,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/2",
131 4979 aaronmk
GenAuth,,** No join mapping for *GenAuth **
132
IsMorpho,,** No join mapping for *IsMorpho **
133
OrigAuth,,** No join mapping for *OrigAuth **
134
OrigRecordID,,** No join mapping for *OrigRecordID **
135
SpAuthStatus,,** No join mapping for *SpAuthStatus **
136
coll_inits,,** No join mapping for *coll_inits **
137
collector_code,,** No join mapping for *collector_code ** Brad: OMIT
138 8234 aaronmk
common_name,,** No join mapping for vernacularName **
139 4979 aaronmk
dist,,** No join mapping for *dist **
140 10257 aaronmk
fam_status,,** No non-empty join mapping for OMIT#fam_status ** Brad: OMIT. This will be determined later by using TNRS.
141
gen_status,,** No non-empty join mapping for OMIT#gen_status ** Brad: OMIT. This will be determined later by using TNRS.
142 4979 aaronmk
height_class,,** No join mapping for *height_class **
143
height_m_commercial,,** No join mapping for *height_m_commercial **
144
ind_id,,** No join mapping for *ind_id ** Brad: OMIT
145
infra_auth_1,,** No join mapping for *infra_auth_1 **
146
morphocf,,** No join mapping for *morphocf **
147 10257 aaronmk
name_status,,"** No non-empty join mapping for OMIT#name_status ** Brad: OMIT. Except, note that if species_status=3, this indicate that name is a morphospecies and not a standard latin name. Not exactly sure how to use this in BIEN, but could be useful during the name-scrubbing process with TNRS."
148 4979 aaronmk
other_annotations,,** No join mapping for *other_annotations **
149
perp_dist,,** No join mapping for *perp_dist **
150
species_code,,** No join mapping for *species_code **
151
temp_liandbh,,** No join mapping for *temp_liandbh **
152 6167 aaronmk
tmp_PlotObsID,,** No join mapping for *tmp_PlotObsID **
153 4979 aaronmk
tmp_del,,** No join mapping for *tmp_del **