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1
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SALVIAS,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
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2
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Line,"/location/_if[@name=""if subplot""]/cond/_exists",
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3
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PlotCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",
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4
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PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists",
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5
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coll_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
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6
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SourceVoucher,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_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."
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7
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DetType,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_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."
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8
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coll_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string
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9
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SourceVoucher,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_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."
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10
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PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode",
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11
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PlotCode,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode",
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12
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PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode",
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13
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Line,/location/authorlocationcode,
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14
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Line,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists",
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15
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PlotCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/authorlocationcode",
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16
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PlotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode",
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17
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census_date,/location/locationevent/obsenddate/_*/date/_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:
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18
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-----
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19
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SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count
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20
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FROM ""SALVIAS"".organisms
|
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21
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WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL
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22
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GROUP BY ""PlotID"", ""Line""
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23
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HAVING count(DISTINCT census_date) > 1
|
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24
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-----"
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25
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census_date,/location/locationevent/obsstartdate/_*/date/_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:
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26
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-----
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27
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SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count
|
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28
|
FROM ""SALVIAS"".organisms
|
|
29
|
WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL
|
|
30
|
GROUP BY ""PlotID"", ""Line""
|
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31
|
HAVING count(DISTINCT census_date) > 1
|
|
32
|
-----"
|
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33
|
NoInd,/location/locationevent/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."
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34
|
cover_percent,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover_fraction/_percent_to_fraction/value,
|
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35
|
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."
|
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36
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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."
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37
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Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes,
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38
|
Ind,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,"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."
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39
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PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,"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."
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40
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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."
|
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41
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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
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42
|
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."
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43
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canopy_form,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue",
|
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44
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canopy_position,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue",
|
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45
|
liana_infestation,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=lianaInfestation]]:[@fkey=tablerecord_id]/definedvalue",
|
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46
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temp_dbh,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,"Assuming units based on the units for intercept_cm, which measures the same dimension"
|
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47
|
height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m,
|
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48
|
ht_first_branch_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/heightfirstbranch_m,
|
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49
|
tag2,/location/locationevent/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."
|
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50
|
tag1,/location/locationevent/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."
|
|
51
|
x_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,"Brad: These are important, fundamental values of many tree plots"
|
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52
|
y_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,Brad: See comment above for x_position
|
|
53
|
PlotCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
|
|
54
|
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
|
|
55
|
Ind,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_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."
|
|
56
|
tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_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."
|
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57
|
tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_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."
|
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58
|
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.; According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>"
|
|
59
|
PlotObsID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else","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."
|
|
60
|
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1",
|
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61
|
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2",
|
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62
|
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
|
|
63
|
infra_ep_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
|
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64
|
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
|
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65
|
infra_ep_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2",
|
|
66
|
auth,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/2",Brad: This is the author of the scientificName.
|
|
67
|
auth,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/author,Brad: This is the author of the scientificName.
|
|
68
|
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/family,
|
|
69
|
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/genus,
|
|
70
|
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=species]/taxonname",
|
|
71
|
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=genus]/taxonname",
|
|
72
|
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=family]/taxonname",
|
|
73
|
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/rank,
|
|
74
|
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/species,
|
|
75
|
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonname/_alt/1,
|
|
76
|
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/verbatimrank,
|
|
77
|
cfaff,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/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."
|
|
78
|
OrigFamily,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1,Brad: OMIT
|
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79
|
OrigGenus,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2,
|
|
80
|
OrigSpecies,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/3,Brad: OMIT
|
|
81
|
OrigFamily,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/family,Brad: OMIT
|
|
82
|
OrigGenus,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/genus,
|
|
83
|
OrigSpecies,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/species,Brad: OMIT
|
|
84
|
coll_firstname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join_words/1,Brad: See comment above
|
|
85
|
coll_lastname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_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."
|
|
86
|
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."
|
|
87
|
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
|
|
88
|
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."
|
|
89
|
GenAuth,,** No join mapping for *GenAuth **
|
|
90
|
IsMorpho,,** No join mapping for *IsMorpho **
|
|
91
|
OrigAuth,,** No join mapping for *OrigAuth **
|
|
92
|
OrigRecordID,,** No join mapping for *OrigRecordID **
|
|
93
|
PlotID_index,,** No join mapping for *PlotID_index **
|
|
94
|
SpAuthStatus,,** No join mapping for *SpAuthStatus **
|
|
95
|
coll_inits,,** No join mapping for *coll_inits **
|
|
96
|
collector_code,,** No join mapping for *collector_code ** Brad: OMIT
|
|
97
|
common_name,,** No join mapping for *common_name **
|
|
98
|
det_by,,** No join mapping for *det_by **
|
|
99
|
dist,,** No join mapping for *dist **
|
|
100
|
fam_status,,** No join mapping for *fam_status ** Brad: OMIT. This will be determined later by using TNRS.
|
|
101
|
gen_status,,** No join mapping for *gen_status ** Brad: OMIT. This will be determined later by using TNRS.
|
|
102
|
height_class,,** No join mapping for *height_class **
|
|
103
|
height_m_commercial,,** No join mapping for *height_m_commercial **
|
|
104
|
ind_id,,** No join mapping for *ind_id ** Brad: OMIT
|
|
105
|
infra_auth_1,,** No join mapping for *infra_auth_1 **
|
|
106
|
morphocf,,** No join mapping for *morphocf **
|
|
107
|
morphoname,,** No join mapping for *morphoname **
|
|
108
|
name_status,,"** No join mapping for *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."
|
|
109
|
other_annotations,,** No join mapping for *other_annotations **
|
|
110
|
perp_dist,,** No join mapping for *perp_dist **
|
|
111
|
phenology,,** No join mapping for *phenology **
|
|
112
|
species_code,,** No join mapping for *species_code **
|
|
113
|
temp_liandbh,,** No join mapping for *temp_liandbh **
|
|
114
|
tmp_del,,** No join mapping for *tmp_del **
|
