Revision 518
Added by Aaron Marcuse-Kubitza almost 13 years ago
test/accepted_output/SALVIAS.organisms.VegBIEN.xml | ||
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87 | 87 |
<party_id> |
88 | 88 |
<party/> |
89 | 89 |
</party_id> |
90 |
<museumaccessionnumber>607771</museumaccessionnumber>
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90 |
<sourceaccessionnumber>607771</sourceaccessionnumber>
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91 | 91 |
</taxondetermination> |
92 | 92 |
<taxondetermination> |
93 | 93 |
<role_id> |
... | ... | |
372 | 372 |
<party_id> |
373 | 373 |
<party/> |
374 | 374 |
</party_id> |
375 |
<museumaccessionnumber>607722</museumaccessionnumber>
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375 |
<sourceaccessionnumber>607722</sourceaccessionnumber>
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376 | 376 |
</taxondetermination> |
377 | 377 |
<taxondetermination> |
378 | 378 |
<role_id> |
test/accepted_output/SALVIAS_db.organisms.VegBIEN.xml | ||
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73 | 73 |
<party_id> |
74 | 74 |
<party/> |
75 | 75 |
</party_id> |
76 |
<museumaccessionnumber>1</museumaccessionnumber>
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76 |
<sourceaccessionnumber>1</sourceaccessionnumber>
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77 | 77 |
</taxondetermination> |
78 | 78 |
<taxondetermination> |
79 | 79 |
<role_id> |
... | ... | |
349 | 349 |
<party_id> |
350 | 350 |
<party/> |
351 | 351 |
</party_id> |
352 |
<museumaccessionnumber>2</museumaccessionnumber>
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352 |
<sourceaccessionnumber>2</sourceaccessionnumber>
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353 | 353 |
</taxondetermination> |
354 | 354 |
<taxondetermination> |
355 | 355 |
<role_id> |
test/accepted_output/NYBG.organisms.VegBIEN.xml | ||
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310 | 310 |
<party_id> |
311 | 311 |
<party/> |
312 | 312 |
</party_id> |
313 |
<museumaccessionnumber>816590</museumaccessionnumber>
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313 |
<sourceaccessionnumber>816590</sourceaccessionnumber>
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314 | 314 |
</taxondetermination> |
315 | 315 |
<taxondetermination> |
316 | 316 |
<role_id> |
... | ... | |
525 | 525 |
<party_id> |
526 | 526 |
<party/> |
527 | 527 |
</party_id> |
528 |
<museumaccessionnumber>220541</museumaccessionnumber>
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528 |
<sourceaccessionnumber>220541</sourceaccessionnumber>
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529 | 529 |
</taxondetermination> |
530 | 530 |
<taxondetermination> |
531 | 531 |
<role_id> |
inputs/SALVIAS/maps/VegBIEN.organisms.csv | ||
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28 | 28 |
infra_ep_1,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",originaldetermination=false,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname/_name/last,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname/_name/last}", |
29 | 29 |
OrigFamily,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}",Brad: OMIT |
30 | 30 |
OrigSpecies,"/{taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/2,taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}}",Brad: OMIT |
31 |
PlotObsID,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}","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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31 |
PlotObsID,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}","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." |
schemas/vegbien.sql | ||
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2513 | 2513 |
taxonfit character varying(50), |
2514 | 2514 |
taxonconfidence character varying(50), |
2515 | 2515 |
museum_id integer, |
2516 |
museumaccessionnumber character varying(100),
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2516 |
sourceaccessionnumber character varying(100),
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2517 | 2517 |
grouptype character varying(20), |
2518 | 2518 |
notes text, |
2519 | 2519 |
notespublic boolean, |
... | ... | |
4359 | 4359 |
-- |
4360 | 4360 |
|
4361 | 4361 |
ALTER TABLE ONLY taxondetermination |
4362 |
ADD CONSTRAINT taxondetermination_keys UNIQUE (taxonoccurrence_id, individualplant_id, role_id, plantname_id, museumaccessionnumber);
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4362 |
ADD CONSTRAINT taxondetermination_keys UNIQUE (taxonoccurrence_id, individualplant_id, role_id, plantname_id, sourceaccessionnumber);
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4363 | 4363 |
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4364 | 4364 |
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4365 | 4365 |
-- |
mappings/SALVIAS_db-VegBIEN.organisms.csv | ||
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28 | 28 |
infra_ep_1,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",originaldetermination=false,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname/_name/last,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname/_name/last}", |
29 | 29 |
OrigFamily,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}",Brad: OMIT |
30 | 30 |
OrigSpecies,"/{taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/2,taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}}",Brad: OMIT |
31 |
PlotObsID,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}","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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31 |
PlotObsID,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}","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." |
mappings/VegX-VegBIEN.organisms.csv | ||
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121 | 121 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,"/{taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname,aggregateoccurrence/individualplant/specimen:[*_id/reference]/collectioncode_dwc/_namePart/last}" |
122 | 122 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/first,/{taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname/_name/first} |
123 | 123 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/last,"/{taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname/_name/last,aggregateoccurrence/individualplant/specimen:[*_id/reference]/collectioncode_dwc}" |
124 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}" |
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124 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}" |
mappings/NYBG-VegBIEN.organisms.csv | ||
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38 | 38 |
Species,"/{taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/2,taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}}", |
39 | 39 |
InstitutionCode,/{taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname/_name/first}, |
40 | 40 |
CollectionCode,"/{taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname/_name/last,aggregateoccurrence/individualplant/specimen:[*_id/reference]/collectioncode_dwc}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
41 |
UniqueNYInternalRecordNumber,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key" |
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41 |
UniqueNYInternalRecordNumber,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key" |
mappings/for_review/SALVIAS_db-VegBIEN.organisms.csv | ||
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28 | 28 |
infra_ep_1,"/taxondetermination[rolecode=computer,plantlevel=Subspecies]/{*_id/*/plantname/_name/last,*_id/plantconcept/*_id/*/plantname/_name/last}", |
29 | 29 |
OrigFamily,"/taxondetermination[rolecode=identifier,plantlevel=Family]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname}",Brad: OMIT |
30 | 30 |
OrigSpecies,"/{taxondetermination[rolecode=collector]/*_id/*/plantname/_alt/2,taxondetermination[rolecode=identifier,plantlevel=Species]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname}}",Brad: OMIT |
31 |
PlotObsID,"/{taxondetermination[rolecode=collector]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot/sourceid/_alt/3}","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." |
|
31 |
PlotObsID,"/{taxondetermination[rolecode=collector]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot/sourceid/_alt/3}","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." |
mappings/for_review/VegX-VegBIEN.organisms.csv | ||
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121 | 121 |
//party/organizationName,"/{taxondetermination[rolecode=collector]/museum_id/party/organizationname,aggregateoccurrence/individualplant/specimen/collectioncode_dwc/_namePart/last}" |
122 | 122 |
//party/organizationName/_name/first,/{taxondetermination[rolecode=collector]/museum_id/party/organizationname/_name/first} |
123 | 123 |
//party/organizationName/_name/last,"/{taxondetermination[rolecode=collector]/museum_id/party/organizationname/_name/last,aggregateoccurrence/individualplant/specimen/collectioncode_dwc}" |
124 |
//taxonNameUsageConcept/voucher,"/{taxondetermination[rolecode=collector]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot/sourceid/_alt/3}" |
|
124 |
//taxonNameUsageConcept/voucher,"/{taxondetermination[rolecode=collector]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot/sourceid/_alt/3}" |
mappings/for_review/NYBG-VegBIEN.organisms.csv | ||
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38 | 38 |
Species,"/{taxondetermination[rolecode=collector]/*_id/*/plantname/_alt/2,taxondetermination[rolecode=identifier,plantlevel=Species]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname}}", |
39 | 39 |
InstitutionCode,/{taxondetermination[rolecode=collector]/museum_id/party/organizationname/_name/first}, |
40 | 40 |
CollectionCode,"/{taxondetermination[rolecode=collector]/museum_id/party/organizationname/_name/last,aggregateoccurrence/individualplant/specimen/collectioncode_dwc}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
41 |
UniqueNYInternalRecordNumber,"/{taxondetermination[rolecode=collector]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot/sourceid/_alt/3}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key" |
|
41 |
UniqueNYInternalRecordNumber,"/{taxondetermination[rolecode=collector]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot/sourceid/_alt/3}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key" |
mappings/for_review/SALVIAS-VegBIEN.organisms.csv | ||
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37 | 37 |
infra_ep_1,"/taxondetermination[rolecode=computer,plantlevel=Subspecies]/{*_id/*/plantname/_name/last,*_id/plantconcept/*_id/*/plantname/_name/last}", |
38 | 38 |
orig_family,"/taxondetermination[rolecode=identifier,plantlevel=Family]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname}",Brad: OMIT |
39 | 39 |
orig_species,"/{taxondetermination[rolecode=collector]/*_id/*/plantname/_alt/2,taxondetermination[rolecode=identifier,plantlevel=Species]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname}}",Brad: OMIT |
40 |
OBSERVATION_ID,"/{taxondetermination[rolecode=collector]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot/sourceid/_alt/3}","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." |
|
40 |
OBSERVATION_ID,"/{taxondetermination[rolecode=collector]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot/sourceid/_alt/3}","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." |
mappings/SALVIAS-VegBIEN.organisms.csv | ||
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37 | 37 |
infra_ep_1,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",originaldetermination=false,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname/_name/last,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname/_name/last}", |
38 | 38 |
orig_family,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}",Brad: OMIT |
39 | 39 |
orig_species,"/{taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/2,taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}}",Brad: OMIT |
40 |
OBSERVATION_ID,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}","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." |
|
40 |
OBSERVATION_ID,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}","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." |
Also available in: Unified diff
VegBIEN: Renamed museumaccessionnumber to sourceaccessionnumber