| 1 |
2775
|
aaronmk
|
SALVIAS,VegBIEN:/plantobservation,Comments
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| 2 |
3337
|
aaronmk
|
Line,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{./authorlocationcode,*_id/location:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode/_merge/2/_alt/2}","""{./"" sorts it before the location.datasource_id mapping with ""{.}"""
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| 3 |
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PlotCode,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{./parent_id/locationevent/{./authorlocationcode,*_id/location:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode/_alt/2},*_id/location:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode/_merge/1/_alt/2}","Brad: Same as plotCode, above; ""{./"" sorts it before the location.datasource_id mapping with ""{.}"""
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| 4 |
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PlotID,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{./parent_id/locationevent/{./sourceaccessioncode,*_id/location:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode/_alt/1},*_id/location:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode/_merge/1/_alt/1}","Brad: Not sure why this is repeated? This field and plotCode, as the same as above.; ""{./"" sorts it before the location.datasource_id mapping with ""{.}"""
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| 5 |
1843
|
aaronmk
|
Habit,"/aggregateoccurrence/*_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: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
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| 6 |
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infra_rank_1,"/aggregateoccurrence/*_id/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/first",
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| 7 |
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auth,"/aggregateoccurrence/*_id/taxonoccurrence/taxondetermination[role=computer]:[iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname",Brad: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss.
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| 8 |
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infra_ep_1,"/aggregateoccurrence/*_id/taxonoccurrence/taxondetermination[role=computer]:[iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/last",
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| 9 |
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Species,"/aggregateoccurrence/*_id/taxonoccurrence/taxondetermination[role=computer]:[iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname",
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| 10 |
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Genus,"/aggregateoccurrence/*_id/taxonoccurrence/taxondetermination[role=computer]:[iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname",
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| 11 |
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Family,"/aggregateoccurrence/*_id/taxonoccurrence/taxondetermination[role=computer]:[iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",
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| 12 |
2341
|
aaronmk
|
cfaff,"/aggregateoccurrence/*_id/taxonoccurrence/taxondetermination[role=identifier]/{taxonfit/_alt/2,*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname/_name/last}","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."
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| 13 |
2019
|
aaronmk
|
OrigGenus,"/aggregateoccurrence/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname/_name/first/_name/first",
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| 14 |
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OrigSpecies,"/aggregateoccurrence/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname/_name/first/_name/last",Brad: OMIT
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| 15 |
1843
|
aaronmk
|
OrigFamily,"/aggregateoccurrence/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",Brad: OMIT
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| 16 |
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coll_firstname,/aggregateoccurrence/*_id/taxonoccurrence/verbatimcollectorname/_name/first,Brad: See comment above
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| 17 |
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coll_lastname,/aggregateoccurrence/*_id/taxonoccurrence/verbatimcollectorname/_name/last,"Brad: Correct for VegBank. 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."
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| 18 |
727
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aaronmk
|
NoInd,/aggregateoccurrence/count,"Brad: Incorrect for VegX. 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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| 19 |
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cover_percent,/aggregateoccurrence/cover,
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| 20 |
1223
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aaronmk
|
census_no,"/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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| 21 |
1220
|
aaronmk
|
intercept_cm,/aggregateoccurrence/linecover,"Brad: Incorrect for VegBank 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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| 22 |
1843
|
aaronmk
|
height_m,/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
|
| 23 |
3211
|
aaronmk
|
tag1,"/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/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.; Quotes sort it before tag2"
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| 24 |
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tag2,/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/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."
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| 25 |
1843
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aaronmk
|
x_position,/stemobservation/xposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
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| 26 |
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y_position,/stemobservation/yposition,Brad: See comment above for x_position
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| 27 |
3336
|
aaronmk
|
Ind,"/{./authorplantcode,./{aggregateoccurrence:[@merge=1]/*_id:[@merge=1]/taxonoccurrence,_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence:[@merge=1]/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]}/sourceaccessioncode/_alt/2}","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.; ""{./"" sorts it with other _ifs"
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| 28 |
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PlotObsID,"/{./sourceaccessioncode,./{aggregateoccurrence:[@merge=1]/*_id:[@merge=1]/taxonoccurrence,_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence:[@merge=1]/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]}/sourceaccessioncode/_alt/1}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later.; ""{./"" sorts it with other _ifs"
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| 29 |
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coll_number,"/{.}/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence:[@merge=1]/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/1","Brad: Incorrect. Map instead as for voucher_string; ""{.}"" sorts it with other _ifs"
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| 30 |
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SourceVoucher,"/{.}/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence:[@merge=1]/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below.; ""{.}"" sorts it with other _ifs"
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| 31 |
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census_date,"/{.}/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence:[@merge=1]/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate/_*/date","""{.}"" sorts it with other _ifs"
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| 32 |
3223
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aaronmk
|
DetType,/{.}/_ignore/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.; ""{"" sorts it after what uses it, so the _ignore is executed after the _refs"
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| 33 |
1740
|
aaronmk
|
GenAuth,,** No input mapping for GenAuth **
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| 34 |
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IsMorpho,,** No input mapping for IsMorpho **
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| 35 |
1843
|
aaronmk
|
Notes,,** No join mapping for /*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/note/text **
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| 36 |
1740
|
aaronmk
|
OrigAuth,,** No input mapping for OrigAuth **
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| 37 |
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OrigRecordID,,** No input mapping for OrigRecordID **
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| 38 |
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SpAuthStatus,,** No input mapping for SpAuthStatus **
|
| 39 |
1843
|
aaronmk
|
canopy_form,,** No join mapping for /simpleUserdefined[name=canopyForm]/value ** Brad: Should also be userDefined for VegBank.
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| 40 |
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canopy_position,,** No join mapping for /simpleUserdefined[name=canopyPosition]/value ** Brad: Should also be userDefined for VegBank.
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| 41 |
1740
|
aaronmk
|
coll_inits,,** No input mapping for coll_inits **
|
| 42 |
725
|
aaronmk
|
collector_code,,Brad: OMIT
|
| 43 |
1740
|
aaronmk
|
common_name,,** No input mapping for common_name **
|
| 44 |
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det_by,,** No input mapping for det_by **
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| 45 |
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dist,,** No input mapping for dist **
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| 46 |
725
|
aaronmk
|
fam_status,,Brad: OMIT. This will be determined later by using TNRS.
|
| 47 |
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gen_status,,Brad: OMIT. This will be determined later by using TNRS.
|
| 48 |
1740
|
aaronmk
|
height_class,,** No input mapping for height_class **
|
| 49 |
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height_m_commercial,,** No input mapping for height_m_commercial **
|
| 50 |
1843
|
aaronmk
|
ht_first_branch_m,,** No join mapping for /simpleUserdefined[name=heightFirstBranch]/value ** Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
|
| 51 |
725
|
aaronmk
|
ind_id,,Brad: OMIT
|
| 52 |
1740
|
aaronmk
|
infra_auth_1,,** No input mapping for infra_auth_1 **
|
| 53 |
1843
|
aaronmk
|
liana_infestation,,** No join mapping for /simpleUserdefined[name=lianaInfestation]/value ** Brad: Should also be userDefined for VegBank.
|
| 54 |
1740
|
aaronmk
|
morphocf,,** No input mapping for morphocf **
|
| 55 |
|
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morphoname,,** No input mapping for morphoname **
|
| 56 |
725
|
aaronmk
|
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."
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| 57 |
1740
|
aaronmk
|
other_annotations,,** No input mapping for other_annotations **
|
| 58 |
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perp_dist,,** No input mapping for perp_dist **
|
| 59 |
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phenology,,** No input mapping for phenology **
|
| 60 |
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species_code,,** No input mapping for species_code **
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| 61 |
1843
|
aaronmk
|
temp_dbh,,** No join mapping for /diameterBaseDistance[baseDistance/value=1.37]/diameter **
|
| 62 |
1740
|
aaronmk
|
temp_liandbh,,** No input mapping for temp_liandbh **
|
| 63 |
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tmp_del,,** No input mapping for tmp_del **
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