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Revision 11534

inputs/VegBank/taxonobservation_/map.csv, postprocess.sql: mapped identifiedBy (the join_words() of identifiedBy_first, etc.)

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inputs/VegBank/taxon_observation.**/header.csv
1
sort_col,locationID,eventID,*stratumtype_id,*stratum_id,aggregateOrganismObservationID__taxon_presence,aggregateOrganismObservationID__individual_count,aggregateOrganismObservationID,taxonOccurrenceID__overall_plot,*taxonobservation_--plantname_id,*taxonobservation_--plantconcept_id,identificationID,*taxonobservation_--stemlocation_id,*taxonobservation_--taxoninterpretation_plantname_id,*taxonobservation_--taxoninterpretation_party_id,*taxonobservation_--role_id,identificationType,*taxonobservation_--reference_id,taxon_determination__is_original,taxon_determination__is_current,identificationQualifier,identificationVerificationStatus,UNUSED#collector_id,collectorNumber,*taxonobservation_--museum_id,accessionNumber,*taxonobservation_--grouptype,occurrenceRemarks,*taxonobservation_--notespublic,*taxonobservation_--notesmgt,*taxonobservation_--revisions,dateIdentified,dateCollected,*taxonobservation_--emb_taxoninterpretation,*taxonobservation_--taxoninterpretation_accessioncode,OMIT#authorplantname,*taxonobservation_--taxonobservation_reference_id,*taxonobservation_--taxoninferencearea,*taxonobservation_--emb_taxonobservation,OMIT#int_origplantconcept_id,OMIT#int_origplantscifull,OMIT#int_origplantscinamenoauth,OMIT#int_origplantcommon,OMIT#int_origplantcode,OMIT#int_currplantconcept_id,OMIT#int_currplantscifull,OMIT#int_currplantscinamenoauth,OMIT#int_currplantcommon,OMIT#int_currplantcode,*taxonobservation_--taxonobservation_accessioncode,*plantconcept_--plantconcept_reference_id,scientificName,*plantconcept_--plantcode,*plantconcept_--plantdescription,*plantconcept_--d_obscount,*plantconcept_--d_currentaccepted,*plantconcept_--plantconcept_accessioncode,kingdom,*Subkingdom,*Superdivision,*Division,*Subdivision,class,*Subclass,order,family,genus,EQUIV#to:plantname#Species,EQUIV#to:plantname#Subspecies,EQUIV#to:plantname#Variety,EQUIV#to:plantname#Forma,DUPLICATE#of:plantconcept_plantname#plantname,*taxonobservation_--plantname_reference_id,*taxonobservation_--dateentered,observationGranularity,coverPercent,*stemcount_--basalarea,*stemcount_--biomass,*stemcount_--inferencearea,*stemcount_--stratumbase,*stemcount_--stratumheight,*stemcount_--emb_taxonimportance,*stemcount_--covercode,diameterBreastHeight_cm,*stemcount_--stemdiameteraccuracy,height_m,*stemcount_--stemheightaccuracy,individualCount,*stemcount_--stemtaxonarea,*stemcount_--emb_stemcount,stemID,UNUSED#stemcode,UNUSED#stemxposition,UNUSED#stemyposition,*stemlocation_--stemhealth,*stemlocation_--emb_stemlocation,OMIT#stemdiameter,OMIT#stemdiameteraccuracy,OMIT#stemheight,OMIT#stemheightaccuracy,OMIT#stemcount,OMIT#stemtaxonarea,OMIT#emb_stemcount,individualID,*stratum--observation_id,*stratum--stratummethod_id,*stratum--stratumname,*stratum--stratumheight,*stratum--stratumbase,*stratum--stratumcover,*stratum--stratumdescription,*stratumtype--stratummethod_id,*stratumtype--stratumindex,stratum__name,*stratumtype--stratumdescription,*observation_--previousobs_id,projectID,authorEventCode,*observation_--dateaccuracy,*observation_--covermethod_id,*observation_--coverdispersion,*observation_--autotaxoncover,*observation_--stratummethod_id,samplingProtocol,*observation_--taxonobservationarea,*observation_--stemsizelimit,*observation_--stemobservationarea,*observation_--stemsamplemethod,*observation_--originaldata,*observation_--effortlevel,*observation_--plotvalidationlevel,*observation_--floristicquality,*observation_--bryophytequality,*observation_--lichenquality,*observation_--observationnarrative,*observation_--landscapenarrative,*observation_--homogeneity,*observation_--phenologicaspect,*observation_--representativeness,*observation_--standmaturity,*observation_--successionalstatus,*observation_--basalarea,*observation_--hydrologicregime,*observation_--soilmoistureregime,*observation_--soildrainage,*observation_--watersalinity,*observation_--waterdepth,*observation_--shoredistance,*observation_--soildepth,*observation_--organicdepth,*observation_--soiltaxon_id,*observation_--soiltaxonsrc,*observation_--percentbedrock,*observation_--percentrockgravel,*observation_--percentwood,*observation_--percentlitter,*observation_--percentbaresoil,*observation_--percentwater,*observation_--percentother,*observation_--nameother,*observation_--treeht,*observation_--shrubht,*observation_--fieldht,*observation_--nonvascularht,*observation_--submergedht,*observation_--treecover,*observation_--shrubcover,*observation_--fieldcover,*observation_--nonvascularcover,*observation_--floatingcover,*observation_--submergedcover,*observation_--dominantstratum,*observation_--growthform1type,*observation_--growthform2type,*observation_--growthform3type,*observation_--growthform1cover,*observation_--growthform2cover,*observation_--growthform3cover,*observation_--totalcover,*observation_--notespublic,*observation_--notesmgt,*observation_--revisions,startDate,endDate,*observation_--dateentered,*observation_--emb_observation,*observation_--interp_orig_ci_id,*observation_--interp_orig_cc_id,*observation_--interp_orig_sciname,*observation_--interp_orig_code,*observation_--interp_orig_party_id,*observation_--interp_orig_partyname,*observation_--interp_current_ci_id,*observation_--interp_current_cc_id,*observation_--interp_current_sciname,*observation_--interp_current_code,*observation_--interp_current_party_id,*observation_--interp_current_partyname,*observation_--interp_bestfit_ci_id,*observation_--interp_bestfit_cc_id,*observation_--interp_bestfit_sciname,*observation_--interp_bestfit_code,*observation_--interp_bestfit_party_id,*observation_--interp_bestfit_partyname,*observation_--toptaxon1name,*observation_--toptaxon2name,*observation_--toptaxon3name,*observation_--toptaxon4name,*observation_--toptaxon5name,*observation_--numberoftaxa,*observation_--accessioncode,*observation_--hasobservationsynonym,*observation_--soilobs_id,*observation_--soilhorizon,*observation_--soildepthtop,*observation_--soildepthbottom,*observation_--soilcolor,organic_percent,texture,sand_percent,silt_percent,clay_percent,*observation_--soilcoarse,ph,cationExchangeCapacity_cmol_kg,baseSaturation_percent,*observation_--soildescription,*observation_--emb_soilobs,locationName,*plot_--reference_id,parentLocationID,coordinateUncertaintyInMeters__from_coords,accessRights_verbatim,*plot_--confidentialityreason,decimalLatitude,decimalLongitude,*plot_--authore,*plot_--authorn,*plot_--authorzone,*plot_--authordatum,*plot_--authorlocation,locality,*plot_--azimuth,*plot_--dsgpoly,footprintWKT,plotArea_m2,*plot_--standsize,*plot_--placementmethod,*plot_--permanence,*plot_--layoutnarrative,elevationInMeters,*plot_--elevationaccuracy,UNUSED#elevationrange,slopeAspect,minSlopeAspect,maxSlopeAspect,slopeGradient,minSlopeGradient,maxSlopeGradient,*plot_--topoposition,landform,*plot_--surficialdeposits,*plot_--rocktype,stateProvince,country,*plot_--submitter_surname,*plot_--submitter_givenname,*plot_--submitter_email,*plot_--notespublic,*plot_--notesmgt,*plot_--revisions,*plot_--dateentered,*plot_--emb_plot,*plot_--plotrationalenarrative,*plot_--accessioncode,continent,DUPLICATE#of:country#area|country|territory,DUPLICATE#of:stateprovince#region|state|province,county,*plot_--quadrangle,*plot_--Geographic Name,accessRights,coordinateUncertaintyInMeters__from_fuzzing,coordinateUncertaintyInMeters,taxonOccurrenceID
1
sort_col,locationID,eventID,*stratumtype_id,*stratum_id,aggregateOrganismObservationID__taxon_presence,aggregateOrganismObservationID__individual_count,aggregateOrganismObservationID,taxonOccurrenceID__overall_plot,*taxonobservation_--plantname_id,*taxonobservation_--plantconcept_id,*taxonobservation_--party_id,OMIT#authorplantname,*taxonobservation_--taxonobservation_reference_id,*taxonobservation_--taxoninferencearea,*taxonobservation_--emb_taxonobservation,OMIT#int_origplantconcept_id,OMIT#int_origplantscifull,OMIT#int_origplantscinamenoauth,OMIT#int_origplantcommon,OMIT#int_origplantcode,OMIT#int_currplantconcept_id,OMIT#int_currplantscifull,OMIT#int_currplantscinamenoauth,OMIT#int_currplantcommon,OMIT#int_currplantcode,*taxonobservation_--taxonobservation_accessioncode,identificationID,*taxonobservation_--stemlocation_id,*taxonobservation_--taxoninterpretation_plantname_id,*taxonobservation_--role_id,identificationType,*taxonobservation_--reference_id,taxon_determination__is_original,taxon_determination__is_current,identificationQualifier,identificationVerificationStatus,UNUSED#collector_id,collectorNumber,*taxonobservation_--museum_id,accessionNumber,*taxonobservation_--grouptype,occurrenceRemarks,*taxonobservation_--notespublic,*taxonobservation_--notesmgt,*taxonobservation_--revisions,dateIdentified,dateCollected,*taxonobservation_--emb_taxoninterpretation,*taxonobservation_--taxoninterpretation_accessioncode,*taxonobservation--party--salutation,identifiedBy__first,identifiedBy__middle,identifiedBy__last,*taxonobservation--party--organizationname,*taxonobservation--party--currentname_id,*taxonobservation--party--contactinstructions,*taxonobservation--party--email,*taxonobservation--party--partytype,*taxonobservation--party--partypublic,*taxonobservation--party--party_d_obscount,*taxonobservation--party--accessioncode,*plantconcept_--plantconcept_reference_id,scientificName,*plantconcept_--plantcode,*plantconcept_--plantdescription,*plantconcept_--d_obscount,*plantconcept_--d_currentaccepted,*plantconcept_--plantconcept_accessioncode,kingdom,*Subkingdom,*Superdivision,*Division,*Subdivision,class,*Subclass,order,family,genus,EQUIV#to:plantname#Species,EQUIV#to:plantname#Subspecies,EQUIV#to:plantname#Variety,EQUIV#to:plantname#Forma,DUPLICATE#of:plantconcept_plantname#plantname,*taxonobservation_--plantname_reference_id,*taxonobservation_--dateentered,observationGranularity,identifiedBy,coverPercent,*stemcount_--basalarea,*stemcount_--biomass,*stemcount_--inferencearea,*stemcount_--stratumbase,*stemcount_--stratumheight,*stemcount_--emb_taxonimportance,*stemcount_--covercode,diameterBreastHeight_cm,*stemcount_--stemdiameteraccuracy,height_m,*stemcount_--stemheightaccuracy,individualCount,*stemcount_--stemtaxonarea,*stemcount_--emb_stemcount,stemID,UNUSED#stemcode,UNUSED#stemxposition,UNUSED#stemyposition,*stemlocation_--stemhealth,*stemlocation_--emb_stemlocation,OMIT#stemdiameter,OMIT#stemdiameteraccuracy,OMIT#stemheight,OMIT#stemheightaccuracy,OMIT#stemcount,OMIT#stemtaxonarea,OMIT#emb_stemcount,individualID,*stratum--observation_id,*stratum--stratummethod_id,*stratum--stratumname,*stratum--stratumheight,*stratum--stratumbase,*stratum--stratumcover,*stratum--stratumdescription,*stratumtype--stratummethod_id,*stratumtype--stratumindex,stratum__name,*stratumtype--stratumdescription,*observation_--previousobs_id,projectID,authorEventCode,*observation_--dateaccuracy,*observation_--covermethod_id,*observation_--coverdispersion,*observation_--autotaxoncover,*observation_--stratummethod_id,samplingProtocol,*observation_--taxonobservationarea,*observation_--stemsizelimit,*observation_--stemobservationarea,*observation_--stemsamplemethod,*observation_--originaldata,*observation_--effortlevel,*observation_--plotvalidationlevel,*observation_--floristicquality,*observation_--bryophytequality,*observation_--lichenquality,*observation_--observationnarrative,*observation_--landscapenarrative,*observation_--homogeneity,*observation_--phenologicaspect,*observation_--representativeness,*observation_--standmaturity,*observation_--successionalstatus,*observation_--basalarea,*observation_--hydrologicregime,*observation_--soilmoistureregime,*observation_--soildrainage,*observation_--watersalinity,*observation_--waterdepth,*observation_--shoredistance,*observation_--soildepth,*observation_--organicdepth,*observation_--soiltaxon_id,*observation_--soiltaxonsrc,*observation_--percentbedrock,*observation_--percentrockgravel,*observation_--percentwood,*observation_--percentlitter,*observation_--percentbaresoil,*observation_--percentwater,*observation_--percentother,*observation_--nameother,*observation_--treeht,*observation_--shrubht,*observation_--fieldht,*observation_--nonvascularht,*observation_--submergedht,*observation_--treecover,*observation_--shrubcover,*observation_--fieldcover,*observation_--nonvascularcover,*observation_--floatingcover,*observation_--submergedcover,*observation_--dominantstratum,*observation_--growthform1type,*observation_--growthform2type,*observation_--growthform3type,*observation_--growthform1cover,*observation_--growthform2cover,*observation_--growthform3cover,*observation_--totalcover,*observation_--notespublic,*observation_--notesmgt,*observation_--revisions,startDate,endDate,*observation_--dateentered,*observation_--emb_observation,*observation_--interp_orig_ci_id,*observation_--interp_orig_cc_id,*observation_--interp_orig_sciname,*observation_--interp_orig_code,*observation_--interp_orig_party_id,*observation_--interp_orig_partyname,*observation_--interp_current_ci_id,*observation_--interp_current_cc_id,*observation_--interp_current_sciname,*observation_--interp_current_code,*observation_--interp_current_party_id,*observation_--interp_current_partyname,*observation_--interp_bestfit_ci_id,*observation_--interp_bestfit_cc_id,*observation_--interp_bestfit_sciname,*observation_--interp_bestfit_code,*observation_--interp_bestfit_party_id,*observation_--interp_bestfit_partyname,*observation_--toptaxon1name,*observation_--toptaxon2name,*observation_--toptaxon3name,*observation_--toptaxon4name,*observation_--toptaxon5name,*observation_--numberoftaxa,*observation_--accessioncode,*observation_--hasobservationsynonym,*observation_--soilobs_id,*observation_--soilhorizon,*observation_--soildepthtop,*observation_--soildepthbottom,*observation_--soilcolor,organic_percent,texture,sand_percent,silt_percent,clay_percent,*observation_--soilcoarse,ph,cationExchangeCapacity_cmol_kg,baseSaturation_percent,*observation_--soildescription,*observation_--emb_soilobs,locationName,*plot_--reference_id,parentLocationID,coordinateUncertaintyInMeters__from_coords,accessRights_verbatim,*plot_--confidentialityreason,decimalLatitude,decimalLongitude,*plot_--authore,*plot_--authorn,*plot_--authorzone,*plot_--authordatum,*plot_--authorlocation,locality,*plot_--azimuth,*plot_--dsgpoly,footprintWKT,plotArea_m2,*plot_--standsize,*plot_--placementmethod,*plot_--permanence,*plot_--layoutnarrative,elevationInMeters,*plot_--elevationaccuracy,UNUSED#elevationrange,slopeAspect,minSlopeAspect,maxSlopeAspect,slopeGradient,minSlopeGradient,maxSlopeGradient,*plot_--topoposition,landform,*plot_--surficialdeposits,*plot_--rocktype,stateProvince,country,*plot_--submitter_surname,*plot_--submitter_givenname,*plot_--submitter_email,*plot_--notespublic,*plot_--notesmgt,*plot_--revisions,*plot_--dateentered,*plot_--emb_plot,*plot_--plotrationalenarrative,*plot_--accessioncode,continent,DUPLICATE#of:country#area|country|territory,DUPLICATE#of:stateprovince#region|state|province,county,*plot_--quadrangle,*plot_--Geographic Name,accessRights,coordinateUncertaintyInMeters__from_fuzzing,coordinateUncertaintyInMeters,taxonOccurrenceID
inputs/VegBank/taxon_observation.**/map.csv
10 10
taxonOccurrenceID__overall_plot,taxonOccurrenceID__overall_plot,,
11 11
*taxonobservation_--plantname_id,*taxonobservation_--plantname_id,,
12 12
*taxonobservation_--plantconcept_id,*taxonobservation_--plantconcept_id,,
13
*taxonobservation_--party_id,*taxonobservation_--party_id,,
14
OMIT#authorplantname,OMIT#authorplantname,,
15
*taxonobservation_--taxonobservation_reference_id,*taxonobservation_--taxonobservation_reference_id,,
16
*taxonobservation_--taxoninferencearea,*taxonobservation_--taxoninferencearea,,
17
*taxonobservation_--emb_taxonobservation,*taxonobservation_--emb_taxonobservation,,
18
OMIT#int_origplantconcept_id,OMIT#int_origplantconcept_id,,
19
OMIT#int_origplantscifull,OMIT#int_origplantscifull,,
20
OMIT#int_origplantscinamenoauth,OMIT#int_origplantscinamenoauth,,
21
OMIT#int_origplantcommon,OMIT#int_origplantcommon,,
22
OMIT#int_origplantcode,OMIT#int_origplantcode,,
23
OMIT#int_currplantconcept_id,OMIT#int_currplantconcept_id,,
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OMIT#int_currplantscifull,OMIT#int_currplantscifull,,
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OMIT#int_currplantscinamenoauth,OMIT#int_currplantscinamenoauth,,
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OMIT#int_currplantcommon,OMIT#int_currplantcommon,,
27
OMIT#int_currplantcode,OMIT#int_currplantcode,,
28
*taxonobservation_--taxonobservation_accessioncode,*taxonobservation_--taxonobservation_accessioncode,,
13 29
identificationID,identificationID,,
14 30
*taxonobservation_--stemlocation_id,*taxonobservation_--stemlocation_id,,
15 31
*taxonobservation_--taxoninterpretation_plantname_id,*taxonobservation_--taxoninterpretation_plantname_id,,
16
*taxonobservation_--taxoninterpretation_party_id,*taxonobservation_--taxoninterpretation_party_id,,
17 32
*taxonobservation_--role_id,*taxonobservation_--role_id,,
18 33
identificationType,identificationType,,
19 34
*taxonobservation_--reference_id,*taxonobservation_--reference_id,,
......
34 49
dateCollected,dateCollected,,
35 50
*taxonobservation_--emb_taxoninterpretation,*taxonobservation_--emb_taxoninterpretation,,
36 51
*taxonobservation_--taxoninterpretation_accessioncode,*taxonobservation_--taxoninterpretation_accessioncode,,
37
OMIT#authorplantname,OMIT#authorplantname,,
38
*taxonobservation_--taxonobservation_reference_id,*taxonobservation_--taxonobservation_reference_id,,
39
*taxonobservation_--taxoninferencearea,*taxonobservation_--taxoninferencearea,,
40
*taxonobservation_--emb_taxonobservation,*taxonobservation_--emb_taxonobservation,,
41
OMIT#int_origplantconcept_id,OMIT#int_origplantconcept_id,,
42
OMIT#int_origplantscifull,OMIT#int_origplantscifull,,
43
OMIT#int_origplantscinamenoauth,OMIT#int_origplantscinamenoauth,,
44
OMIT#int_origplantcommon,OMIT#int_origplantcommon,,
45
OMIT#int_origplantcode,OMIT#int_origplantcode,,
46
OMIT#int_currplantconcept_id,OMIT#int_currplantconcept_id,,
47
OMIT#int_currplantscifull,OMIT#int_currplantscifull,,
48
OMIT#int_currplantscinamenoauth,OMIT#int_currplantscinamenoauth,,
49
OMIT#int_currplantcommon,OMIT#int_currplantcommon,,
50
OMIT#int_currplantcode,OMIT#int_currplantcode,,
51
*taxonobservation_--taxonobservation_accessioncode,*taxonobservation_--taxonobservation_accessioncode,,
52
*taxonobservation--party--salutation,*taxonobservation--party--salutation,,
53
identifiedBy__first,identifiedBy__first,,
54
identifiedBy__middle,identifiedBy__middle,,
55
identifiedBy__last,identifiedBy__last,,
56
*taxonobservation--party--organizationname,*taxonobservation--party--organizationname,,
57
*taxonobservation--party--currentname_id,*taxonobservation--party--currentname_id,,
58
*taxonobservation--party--contactinstructions,*taxonobservation--party--contactinstructions,,
59
*taxonobservation--party--email,*taxonobservation--party--email,,
60
*taxonobservation--party--partytype,*taxonobservation--party--partytype,,
61
*taxonobservation--party--partypublic,*taxonobservation--party--partypublic,,
62
*taxonobservation--party--party_d_obscount,*taxonobservation--party--party_d_obscount,,
63
*taxonobservation--party--accessioncode,*taxonobservation--party--accessioncode,,
52 64
*plantconcept_--plantconcept_reference_id,*plantconcept_--plantconcept_reference_id,,
53 65
scientificName,scientificName,,
54 66
*plantconcept_--plantcode,*plantconcept_--plantcode,,
......
74 86
*taxonobservation_--plantname_reference_id,*taxonobservation_--plantname_reference_id,,
75 87
*taxonobservation_--dateentered,*taxonobservation_--dateentered,,
76 88
observationGranularity,observationGranularity,,
89
identifiedBy,identifiedBy,,
77 90
coverPercent,coverPercent,,
78 91
*stemcount_--basalarea,*stemcount_--basalarea,,
79 92
*stemcount_--biomass,*stemcount_--biomass,,
inputs/VegBank/taxon_observation.**/test.xml.ref
46 46
                                    <authortaxoncode>$collectorNumber</authortaxoncode>
47 47
                                    <sourceaccessioncode>$taxonOccurrenceID</sourceaccessioncode>
48 48
                                    <taxondetermination>
49
                                        <party_id><party><fullname>$identifiedBy</fullname></party></party_id>
49 50
                                        <taxonverbatim_id>
50 51
                                            <taxonverbatim>
51 52
                                                <taxonlabel_id>
......
240 241
        </path>
241 242
    </_setDefault>
242 243
</VegBIEN>
243
Inserted 25 new rows into database
244
Inserted 26 new rows into database
inputs/VegBank/taxon_observation.**/unmapped_terms.csv
6 6
taxonOccurrenceID__overall_plot
7 7
*taxonobservation_--plantname_id
8 8
*taxonobservation_--plantconcept_id
9
*taxonobservation_--party_id
10
*taxonobservation_--taxonobservation_reference_id
11
*taxonobservation_--taxoninferencearea
12
*taxonobservation_--emb_taxonobservation
13
*taxonobservation_--taxonobservation_accessioncode
9 14
identificationID
10 15
*taxonobservation_--stemlocation_id
11 16
*taxonobservation_--taxoninterpretation_plantname_id
12
*taxonobservation_--taxoninterpretation_party_id
13 17
*taxonobservation_--role_id
14 18
*taxonobservation_--reference_id
15 19
identificationVerificationStatus
......
20 24
*taxonobservation_--revisions
21 25
*taxonobservation_--emb_taxoninterpretation
22 26
*taxonobservation_--taxoninterpretation_accessioncode
23
*taxonobservation_--taxonobservation_reference_id
24
*taxonobservation_--taxoninferencearea
25
*taxonobservation_--emb_taxonobservation
26
*taxonobservation_--taxonobservation_accessioncode
27
*taxonobservation--party--salutation
28
identifiedBy__first
29
identifiedBy__middle
30
identifiedBy__last
31
*taxonobservation--party--organizationname
32
*taxonobservation--party--currentname_id
33
*taxonobservation--party--contactinstructions
34
*taxonobservation--party--email
35
*taxonobservation--party--partytype
36
*taxonobservation--party--partypublic
37
*taxonobservation--party--party_d_obscount
38
*taxonobservation--party--accessioncode
27 39
*plantconcept_--plantconcept_reference_id
28 40
*plantconcept_--plantcode
29 41
*plantconcept_--plantdescription

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