Revision 596
Added by Aaron Marcuse-Kubitza almost 13 years ago
| test/accepted_output/SALVIAS.organisms.VegBIEN.xml | ||
|---|---|---|
| 43 | 43 |
</specimen> |
| 44 | 44 |
<taxondetermination> |
| 45 | 45 |
<role_id> |
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<aux_role>
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<role> |
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| 47 | 47 |
<rolecode>collector</rolecode> |
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</aux_role>
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| 48 |
</role> |
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| 49 | 49 |
</role_id> |
| 50 | 50 |
<definedvalue fkey="tableRecord_ID"> |
| 51 | 51 |
<userdefined_id> |
| ... | ... | |
| 95 | 95 |
</taxondetermination> |
| 96 | 96 |
<taxondetermination> |
| 97 | 97 |
<role_id> |
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<aux_role>
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<role> |
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| 99 | 99 |
<rolecode>computer</rolecode> |
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</aux_role>
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</role> |
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| 101 | 101 |
</role_id> |
| 102 | 102 |
<plantconcept_id> |
| 103 | 103 |
<plantconcept> |
| ... | ... | |
| 119 | 119 |
</taxondetermination> |
| 120 | 120 |
<taxondetermination> |
| 121 | 121 |
<role_id> |
| 122 |
<aux_role>
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| 122 |
<role> |
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| 123 | 123 |
<rolecode>computer</rolecode> |
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</aux_role>
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</role> |
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| 125 | 125 |
</role_id> |
| 126 | 126 |
<plantconcept_id> |
| 127 | 127 |
<plantconcept> |
| ... | ... | |
| 143 | 143 |
</taxondetermination> |
| 144 | 144 |
<taxondetermination> |
| 145 | 145 |
<role_id> |
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<aux_role>
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<role> |
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| 147 | 147 |
<rolecode>computer</rolecode> |
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</aux_role>
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| 148 |
</role> |
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| 149 | 149 |
</role_id> |
| 150 | 150 |
<plantconcept_id> |
| 151 | 151 |
<plantconcept> |
| ... | ... | |
| 167 | 167 |
</taxondetermination> |
| 168 | 168 |
<taxondetermination> |
| 169 | 169 |
<role_id> |
| 170 |
<aux_role>
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| 170 |
<role> |
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| 171 | 171 |
<rolecode>identifier</rolecode> |
| 172 |
</aux_role>
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| 172 |
</role> |
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| 173 | 173 |
</role_id> |
| 174 | 174 |
<plantconcept_id> |
| 175 | 175 |
<plantconcept> |
| ... | ... | |
| 192 | 192 |
</taxondetermination> |
| 193 | 193 |
<taxondetermination> |
| 194 | 194 |
<role_id> |
| 195 |
<aux_role>
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<role> |
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| 196 | 196 |
<rolecode>identifier</rolecode> |
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</aux_role>
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</role> |
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| 198 | 198 |
</role_id> |
| 199 | 199 |
<plantconcept_id> |
| 200 | 200 |
<plantconcept> |
| ... | ... | |
| 259 | 259 |
</specimen> |
| 260 | 260 |
<taxondetermination> |
| 261 | 261 |
<role_id> |
| 262 |
<aux_role>
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<role> |
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| 263 | 263 |
<rolecode>collector</rolecode> |
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</aux_role>
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</role> |
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| 265 | 265 |
</role_id> |
| 266 | 266 |
<definedvalue fkey="tableRecord_ID"> |
| 267 | 267 |
<userdefined_id> |
| ... | ... | |
| 311 | 311 |
</taxondetermination> |
| 312 | 312 |
<taxondetermination> |
| 313 | 313 |
<role_id> |
| 314 |
<aux_role>
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<role> |
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| 315 | 315 |
<rolecode>computer</rolecode> |
| 316 |
</aux_role>
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| 316 |
</role> |
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| 317 | 317 |
</role_id> |
| 318 | 318 |
<plantconcept_id> |
| 319 | 319 |
<plantconcept> |
| ... | ... | |
| 335 | 335 |
</taxondetermination> |
| 336 | 336 |
<taxondetermination> |
| 337 | 337 |
<role_id> |
| 338 |
<aux_role>
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<role> |
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| 339 | 339 |
<rolecode>computer</rolecode> |
| 340 |
</aux_role>
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| 340 |
</role> |
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| 341 | 341 |
</role_id> |
| 342 | 342 |
<plantconcept_id> |
| 343 | 343 |
<plantconcept> |
| ... | ... | |
| 359 | 359 |
</taxondetermination> |
| 360 | 360 |
<taxondetermination> |
| 361 | 361 |
<role_id> |
| 362 |
<aux_role>
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<role> |
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| 363 | 363 |
<rolecode>computer</rolecode> |
| 364 |
</aux_role>
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| 364 |
</role> |
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| 365 | 365 |
</role_id> |
| 366 | 366 |
<plantconcept_id> |
| 367 | 367 |
<plantconcept> |
| ... | ... | |
| 383 | 383 |
</taxondetermination> |
| 384 | 384 |
<taxondetermination> |
| 385 | 385 |
<role_id> |
| 386 |
<aux_role>
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| 386 |
<role> |
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| 387 | 387 |
<rolecode>identifier</rolecode> |
| 388 |
</aux_role>
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| 388 |
</role> |
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| 389 | 389 |
</role_id> |
| 390 | 390 |
<plantconcept_id> |
| 391 | 391 |
<plantconcept> |
| ... | ... | |
| 408 | 408 |
</taxondetermination> |
| 409 | 409 |
<taxondetermination> |
| 410 | 410 |
<role_id> |
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<aux_role>
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<role> |
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| 412 | 412 |
<rolecode>identifier</rolecode> |
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</aux_role>
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</role> |
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| 414 | 414 |
</role_id> |
| 415 | 415 |
<plantconcept_id> |
| 416 | 416 |
<plantconcept> |
| test/accepted_output/SALVIAS_db.organisms.VegBIEN.xml | ||
|---|---|---|
| 20 | 20 |
</aggregateoccurrence> |
| 21 | 21 |
<taxondetermination> |
| 22 | 22 |
<role_id> |
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<aux_role>
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<role> |
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<rolecode>collector</rolecode> |
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</aux_role>
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</role> |
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| 26 | 26 |
</role_id> |
| 27 | 27 |
<definedvalue fkey="tableRecord_ID"> |
| 28 | 28 |
<userdefined_id> |
| ... | ... | |
| 82 | 82 |
</taxondetermination> |
| 83 | 83 |
<taxondetermination> |
| 84 | 84 |
<role_id> |
| 85 |
<aux_role>
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<role> |
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| 86 | 86 |
<rolecode>computer</rolecode> |
| 87 |
</aux_role>
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</role> |
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| 88 | 88 |
</role_id> |
| 89 | 89 |
<plantconcept_id> |
| 90 | 90 |
<plantconcept> |
| ... | ... | |
| 106 | 106 |
</taxondetermination> |
| 107 | 107 |
<taxondetermination> |
| 108 | 108 |
<role_id> |
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<aux_role>
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<role> |
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| 110 | 110 |
<rolecode>computer</rolecode> |
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</aux_role>
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</role> |
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| 112 | 112 |
</role_id> |
| 113 | 113 |
<plantconcept_id> |
| 114 | 114 |
<plantconcept> |
| ... | ... | |
| 130 | 130 |
</taxondetermination> |
| 131 | 131 |
<taxondetermination> |
| 132 | 132 |
<role_id> |
| 133 |
<aux_role>
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| 133 |
<role> |
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| 134 | 134 |
<rolecode>computer</rolecode> |
| 135 |
</aux_role>
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</role> |
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| 136 | 136 |
</role_id> |
| 137 | 137 |
<plantconcept_id> |
| 138 | 138 |
<plantconcept> |
| ... | ... | |
| 154 | 154 |
</taxondetermination> |
| 155 | 155 |
<taxondetermination> |
| 156 | 156 |
<role_id> |
| 157 |
<aux_role>
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<role> |
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| 158 | 158 |
<rolecode>computer</rolecode> |
| 159 |
</aux_role>
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</role> |
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| 160 | 160 |
</role_id> |
| 161 | 161 |
<plantconcept_id> |
| 162 | 162 |
<plantconcept> |
| ... | ... | |
| 178 | 178 |
</taxondetermination> |
| 179 | 179 |
<taxondetermination> |
| 180 | 180 |
<role_id> |
| 181 |
<aux_role>
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<role> |
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| 182 | 182 |
<rolecode>identifier</rolecode> |
| 183 |
</aux_role>
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</role> |
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| 184 | 184 |
</role_id> |
| 185 | 185 |
<plantconcept_id> |
| 186 | 186 |
<plantconcept> |
| ... | ... | |
| 203 | 203 |
</taxondetermination> |
| 204 | 204 |
<taxondetermination> |
| 205 | 205 |
<role_id> |
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<aux_role>
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<role> |
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| 207 | 207 |
<rolecode>identifier</rolecode> |
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</aux_role>
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</role> |
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| 209 | 209 |
</role_id> |
| 210 | 210 |
<plantconcept_id> |
| 211 | 211 |
<plantconcept> |
| ... | ... | |
| 253 | 253 |
</aggregateoccurrence> |
| 254 | 254 |
<taxondetermination> |
| 255 | 255 |
<role_id> |
| 256 |
<aux_role>
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<role> |
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| 257 | 257 |
<rolecode>collector</rolecode> |
| 258 |
</aux_role>
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</role> |
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| 259 | 259 |
</role_id> |
| 260 | 260 |
<definedvalue fkey="tableRecord_ID"> |
| 261 | 261 |
<userdefined_id> |
| ... | ... | |
| 315 | 315 |
</taxondetermination> |
| 316 | 316 |
<taxondetermination> |
| 317 | 317 |
<role_id> |
| 318 |
<aux_role>
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<role> |
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| 319 | 319 |
<rolecode>computer</rolecode> |
| 320 |
</aux_role>
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</role> |
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| 321 | 321 |
</role_id> |
| 322 | 322 |
<plantconcept_id> |
| 323 | 323 |
<plantconcept> |
| ... | ... | |
| 339 | 339 |
</taxondetermination> |
| 340 | 340 |
<taxondetermination> |
| 341 | 341 |
<role_id> |
| 342 |
<aux_role>
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| 342 |
<role> |
|
| 343 | 343 |
<rolecode>computer</rolecode> |
| 344 |
</aux_role>
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| 344 |
</role> |
|
| 345 | 345 |
</role_id> |
| 346 | 346 |
<plantconcept_id> |
| 347 | 347 |
<plantconcept> |
| ... | ... | |
| 363 | 363 |
</taxondetermination> |
| 364 | 364 |
<taxondetermination> |
| 365 | 365 |
<role_id> |
| 366 |
<aux_role>
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| 366 |
<role> |
|
| 367 | 367 |
<rolecode>computer</rolecode> |
| 368 |
</aux_role>
|
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| 368 |
</role> |
|
| 369 | 369 |
</role_id> |
| 370 | 370 |
<plantconcept_id> |
| 371 | 371 |
<plantconcept> |
| ... | ... | |
| 387 | 387 |
</taxondetermination> |
| 388 | 388 |
<taxondetermination> |
| 389 | 389 |
<role_id> |
| 390 |
<aux_role>
|
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| 390 |
<role> |
|
| 391 | 391 |
<rolecode>computer</rolecode> |
| 392 |
</aux_role>
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</role> |
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| 393 | 393 |
</role_id> |
| 394 | 394 |
<plantconcept_id> |
| 395 | 395 |
<plantconcept> |
| ... | ... | |
| 411 | 411 |
</taxondetermination> |
| 412 | 412 |
<taxondetermination> |
| 413 | 413 |
<role_id> |
| 414 |
<aux_role>
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<role> |
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| 415 | 415 |
<rolecode>identifier</rolecode> |
| 416 |
</aux_role>
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</role> |
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| 417 | 417 |
</role_id> |
| 418 | 418 |
<plantconcept_id> |
| 419 | 419 |
<plantconcept> |
| ... | ... | |
| 436 | 436 |
</taxondetermination> |
| 437 | 437 |
<taxondetermination> |
| 438 | 438 |
<role_id> |
| 439 |
<aux_role>
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<role> |
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| 440 | 440 |
<rolecode>identifier</rolecode> |
| 441 |
</aux_role>
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| 441 |
</role> |
|
| 442 | 442 |
</role_id> |
| 443 | 443 |
<plantconcept_id> |
| 444 | 444 |
<plantconcept> |
| test/accepted_output/NYBG.organisms.VegBIEN.xml | ||
|---|---|---|
| 92 | 92 |
</specimen> |
| 93 | 93 |
<taxondetermination> |
| 94 | 94 |
<role_id> |
| 95 |
<aux_role>
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<role> |
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| 96 | 96 |
<rolecode>collector</rolecode> |
| 97 |
</aux_role>
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</role> |
|
| 98 | 98 |
</role_id> |
| 99 | 99 |
<determinationtype>Author</determinationtype> |
| 100 | 100 |
<originaldetermination>true</originaldetermination> |
| ... | ... | |
| 114 | 114 |
</taxondetermination> |
| 115 | 115 |
<taxondetermination> |
| 116 | 116 |
<role_id> |
| 117 |
<aux_role>
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|
| 117 |
<role> |
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| 118 | 118 |
<rolecode>identifier</rolecode> |
| 119 |
</aux_role>
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| 119 |
</role> |
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| 120 | 120 |
</role_id> |
| 121 | 121 |
<plantconcept_id> |
| 122 | 122 |
<plantconcept> |
| ... | ... | |
| 139 | 139 |
</taxondetermination> |
| 140 | 140 |
<taxondetermination> |
| 141 | 141 |
<role_id> |
| 142 |
<aux_role>
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<role> |
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| 143 | 143 |
<rolecode>identifier</rolecode> |
| 144 |
</aux_role>
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</role> |
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| 145 | 145 |
</role_id> |
| 146 | 146 |
<plantconcept_id> |
| 147 | 147 |
<plantconcept> |
| ... | ... | |
| 164 | 164 |
</taxondetermination> |
| 165 | 165 |
<taxondetermination> |
| 166 | 166 |
<role_id> |
| 167 |
<aux_role>
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|
| 167 |
<role> |
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| 168 | 168 |
<rolecode>identifier</rolecode> |
| 169 |
</aux_role>
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| 169 |
</role> |
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| 170 | 170 |
</role_id> |
| 171 | 171 |
<plantconcept_id> |
| 172 | 172 |
<plantconcept> |
| ... | ... | |
| 189 | 189 |
</taxondetermination> |
| 190 | 190 |
<taxondetermination> |
| 191 | 191 |
<role_id> |
| 192 |
<aux_role>
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| 192 |
<role> |
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| 193 | 193 |
<rolecode>identifier</rolecode> |
| 194 |
</aux_role>
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</role> |
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| 195 | 195 |
</role_id> |
| 196 | 196 |
<plantconcept_id> |
| 197 | 197 |
<plantconcept> |
| ... | ... | |
| 214 | 214 |
</taxondetermination> |
| 215 | 215 |
<taxondetermination> |
| 216 | 216 |
<role_id> |
| 217 |
<aux_role>
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<role> |
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| 218 | 218 |
<rolecode>identifier</rolecode> |
| 219 |
</aux_role>
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| 219 |
</role> |
|
| 220 | 220 |
</role_id> |
| 221 | 221 |
<plantconcept_id> |
| 222 | 222 |
<plantconcept> |
| ... | ... | |
| 239 | 239 |
</taxondetermination> |
| 240 | 240 |
<taxondetermination> |
| 241 | 241 |
<role_id> |
| 242 |
<aux_role>
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<role> |
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| 243 | 243 |
<rolecode>identifier</rolecode> |
| 244 |
</aux_role>
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</role> |
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| 245 | 245 |
</role_id> |
| 246 | 246 |
<plantconcept_id> |
| 247 | 247 |
<plantconcept> |
| ... | ... | |
| 319 | 319 |
</specimen> |
| 320 | 320 |
<taxondetermination> |
| 321 | 321 |
<role_id> |
| 322 |
<aux_role>
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<role> |
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| 323 | 323 |
<rolecode>collector</rolecode> |
| 324 |
</aux_role>
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|
| 324 |
</role> |
|
| 325 | 325 |
</role_id> |
| 326 | 326 |
<determinationtype>Author</determinationtype> |
| 327 | 327 |
<originaldetermination>true</originaldetermination> |
| ... | ... | |
| 341 | 341 |
</taxondetermination> |
| 342 | 342 |
<taxondetermination> |
| 343 | 343 |
<role_id> |
| 344 |
<aux_role>
|
|
| 344 |
<role> |
|
| 345 | 345 |
<rolecode>identifier</rolecode> |
| 346 |
</aux_role>
|
|
| 346 |
</role> |
|
| 347 | 347 |
</role_id> |
| 348 | 348 |
<plantconcept_id> |
| 349 | 349 |
<plantconcept> |
| ... | ... | |
| 366 | 366 |
</taxondetermination> |
| 367 | 367 |
<taxondetermination> |
| 368 | 368 |
<role_id> |
| 369 |
<aux_role>
|
|
| 369 |
<role> |
|
| 370 | 370 |
<rolecode>identifier</rolecode> |
| 371 |
</aux_role>
|
|
| 371 |
</role> |
|
| 372 | 372 |
</role_id> |
| 373 | 373 |
<plantconcept_id> |
| 374 | 374 |
<plantconcept> |
| ... | ... | |
| 391 | 391 |
</taxondetermination> |
| 392 | 392 |
<taxondetermination> |
| 393 | 393 |
<role_id> |
| 394 |
<aux_role>
|
|
| 394 |
<role> |
|
| 395 | 395 |
<rolecode>identifier</rolecode> |
| 396 |
</aux_role>
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|
| 396 |
</role> |
|
| 397 | 397 |
</role_id> |
| 398 | 398 |
<plantconcept_id> |
| 399 | 399 |
<plantconcept> |
| inputs/SALVIAS/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 14 | 14 |
census_date,/specimen:[*_id/reference]/collectiondate/_date/date, |
| 15 | 15 |
coll_firstname,"/specimen:[*_id/reference]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}",Brad: See comment above
|
| 16 | 16 |
coll_lastname,/specimen:[*_id/reference]/collector_id/party/{surname},"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."
|
| 17 |
census_no,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=censusNo]:[userdefinedtype=varchar]]:[@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."
|
|
| 18 |
cfaff,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=cfAff]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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."
|
|
| 19 |
DetType,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=determinationType]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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."
|
|
| 20 |
Habit,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=habit]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
|
|
| 21 |
Ind,"/taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=individualCode]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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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| 22 |
Notes,"/taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/notes",
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| 23 |
auth,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/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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| 24 |
Family,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",
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|
| 25 |
Genus,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",
|
|
| 26 |
Species,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",
|
|
| 27 |
infra_rank_1,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/{*_id/*/plantname/_name/first,*_id/plantconcept:[*_id/reference]/_name/first}",
|
|
| 28 |
infra_ep_1,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/_name/last",
|
|
| 29 |
OrigFamily,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",Brad: OMIT
|
|
| 30 |
OrigSpecies,"/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname/_alt/2,taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname}",Brad: OMIT
|
|
| 17 |
census_no,"/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=censusNo]:[userdefinedtype=varchar]]:[@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." |
|
| 18 |
cfaff,"/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=cfAff]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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." |
|
| 19 |
DetType,"/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=determinationType]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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." |
|
| 20 |
Habit,"/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=habit]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait." |
|
| 21 |
Ind,"/taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=individualCode]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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." |
|
| 22 |
Notes,"/taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/notes", |
|
| 23 |
auth,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/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. |
|
| 24 |
Family,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname", |
|
| 25 |
Genus,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname", |
|
| 26 |
Species,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname", |
|
| 27 |
infra_rank_1,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/{*_id/*/plantname/_name/first,*_id/plantconcept:[*_id/reference]/_name/first}",
|
|
| 28 |
infra_ep_1,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/_name/last", |
|
| 29 |
OrigFamily,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",Brad: OMIT |
|
| 30 |
OrigSpecies,"/{taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname/_alt/2,taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname}",Brad: OMIT
|
|
| 31 | 31 |
PlotObsID,":[aggregateoccurrence/count/_alt/2=1]/{aggregateoccurrence/individualplant/authorplantcode,specimen:[*_id/reference]/sourceaccessioncode,*_id/locationevent/authoreventcode/_alt/2,*_id/locationevent/*_id/location:[confidentialitystatus=0]/authorlocationcode/_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.for_ERD.my.sql | ||
|---|---|---|
| 1 | 1 |
-- Existing tables |
| 2 | 2 |
|
| 3 |
CREATE TABLE aux_role
|
|
| 3 |
CREATE TABLE role |
|
| 4 | 4 |
( |
| 5 | 5 |
role_id int(11) NOT NULL AUTO_INCREMENT, |
| 6 | 6 |
rolecode character varying(30) NOT NULL, |
| 7 | 7 |
roledescription character varying(200), |
| 8 |
CONSTRAINT aux_role_pkey PRIMARY KEY (role_id )
|
|
| 8 |
CONSTRAINT role_pkey PRIMARY KEY (role_id ) |
|
| 9 | 9 |
); |
| 10 | 10 |
|
| 11 | 11 |
CREATE TABLE reference |
| ... | ... | |
| 359 | 359 |
REFERENCES reference (reference_id) MATCH SIMPLE |
| 360 | 360 |
ON UPDATE CASCADE ON DELETE CASCADE, |
| 361 | 361 |
CONSTRAINT taxondetermination_role_id FOREIGN KEY (role_id) |
| 362 |
REFERENCES aux_role (role_id) MATCH SIMPLE
|
|
| 362 |
REFERENCES role (role_id) MATCH SIMPLE |
|
| 363 | 363 |
ON UPDATE CASCADE ON DELETE CASCADE, |
| 364 | 364 |
CONSTRAINT taxondetermination_taxonoccurrence_id FOREIGN KEY (taxonoccurrence_id) |
| 365 | 365 |
REFERENCES taxonoccurrence (taxonoccurrence_id) MATCH SIMPLE |
| schemas/vegbien_empty.sql | ||
|---|---|---|
| 1 | 1 |
TRUNCATE address CASCADE; |
| 2 | 2 |
TRUNCATE aggregateoccurrence CASCADE; |
| 3 |
TRUNCATE aux_role CASCADE; |
|
| 4 | 3 |
TRUNCATE classcontributor CASCADE; |
| 5 | 4 |
TRUNCATE commclass CASCADE; |
| 6 | 5 |
TRUNCATE commconcept CASCADE; |
| ... | ... | |
| 56 | 55 |
TRUNCATE referencejournal CASCADE; |
| 57 | 56 |
TRUNCATE referenceparty CASCADE; |
| 58 | 57 |
TRUNCATE revision CASCADE; |
| 58 |
TRUNCATE role CASCADE; |
|
| 59 | 59 |
TRUNCATE sizeclass CASCADE; |
| 60 | 60 |
TRUNCATE soilobs CASCADE; |
| 61 | 61 |
TRUNCATE soiltaxon CASCADE; |
| schemas/vegbien.for_ERD.sql | ||
|---|---|---|
| 1 | 1 |
-- Existing tables |
| 2 | 2 |
|
| 3 |
CREATE TABLE aux_role
|
|
| 3 |
CREATE TABLE role |
|
| 4 | 4 |
( |
| 5 | 5 |
role_id serial NOT NULL, |
| 6 | 6 |
rolecode character varying(30) NOT NULL, |
| 7 | 7 |
roledescription character varying(200), |
| 8 |
CONSTRAINT aux_role_pkey PRIMARY KEY (role_id )
|
|
| 8 |
CONSTRAINT role_pkey PRIMARY KEY (role_id ) |
|
| 9 | 9 |
); |
| 10 | 10 |
|
| 11 | 11 |
CREATE TABLE reference |
| ... | ... | |
| 359 | 359 |
REFERENCES reference (reference_id) MATCH SIMPLE |
| 360 | 360 |
ON UPDATE CASCADE ON DELETE CASCADE, |
| 361 | 361 |
CONSTRAINT taxondetermination_role_id FOREIGN KEY (role_id) |
| 362 |
REFERENCES aux_role (role_id) MATCH SIMPLE
|
|
| 362 |
REFERENCES role (role_id) MATCH SIMPLE |
|
| 363 | 363 |
ON UPDATE CASCADE ON DELETE CASCADE, |
| 364 | 364 |
CONSTRAINT taxondetermination_taxonoccurrence_id FOREIGN KEY (taxonoccurrence_id) |
| 365 | 365 |
REFERENCES taxonoccurrence (taxonoccurrence_id) MATCH SIMPLE |
| schemas/vegbien.sql | ||
|---|---|---|
| 120 | 120 |
|
| 121 | 121 |
|
| 122 | 122 |
-- |
| 123 |
-- Name: aux_role; Type: TABLE; Schema: public; Owner: -; Tablespace: |
|
| 124 |
-- |
|
| 125 |
|
|
| 126 |
CREATE TABLE aux_role ( |
|
| 127 |
role_id integer NOT NULL, |
|
| 128 |
rolecode character varying(30) NOT NULL, |
|
| 129 |
roledescription character varying(200), |
|
| 130 |
roleproject integer, |
|
| 131 |
roleobservation integer, |
|
| 132 |
roletaxonint integer, |
|
| 133 |
roleclassint integer, |
|
| 134 |
accessioncode character varying(255) |
|
| 135 |
); |
|
| 136 |
|
|
| 137 |
|
|
| 138 |
-- |
|
| 139 |
-- Name: aux_role_role_id_seq; Type: SEQUENCE; Schema: public; Owner: - |
|
| 140 |
-- |
|
| 141 |
|
|
| 142 |
CREATE SEQUENCE aux_role_role_id_seq |
|
| 143 |
START WITH 1 |
|
| 144 |
INCREMENT BY 1 |
|
| 145 |
NO MINVALUE |
|
| 146 |
NO MAXVALUE |
|
| 147 |
CACHE 1; |
|
| 148 |
|
|
| 149 |
|
|
| 150 |
-- |
|
| 151 |
-- Name: aux_role_role_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: - |
|
| 152 |
-- |
|
| 153 |
|
|
| 154 |
ALTER SEQUENCE aux_role_role_id_seq OWNED BY aux_role.role_id; |
|
| 155 |
|
|
| 156 |
|
|
| 157 |
-- |
|
| 158 | 123 |
-- Name: classcontributor; Type: TABLE; Schema: public; Owner: -; Tablespace: |
| 159 | 124 |
-- |
| 160 | 125 |
|
| ... | ... | |
| 2135 | 2100 |
ALTER SEQUENCE revision_revision_id_seq OWNED BY revision.revision_id; |
| 2136 | 2101 |
|
| 2137 | 2102 |
|
| 2103 |
-- |
|
| 2104 |
-- Name: role; Type: TABLE; Schema: public; Owner: -; Tablespace: |
|
| 2105 |
-- |
|
| 2106 |
|
|
| 2107 |
CREATE TABLE role ( |
|
| 2108 |
role_id integer NOT NULL, |
|
| 2109 |
rolecode character varying(30) NOT NULL, |
|
| 2110 |
roledescription character varying(200), |
|
| 2111 |
roleproject integer, |
|
| 2112 |
roleobservation integer, |
|
| 2113 |
roletaxonint integer, |
|
| 2114 |
roleclassint integer, |
|
| 2115 |
accessioncode character varying(255) |
|
| 2116 |
); |
|
| 2117 |
|
|
| 2118 |
|
|
| 2119 |
-- |
|
| 2120 |
-- Name: role_role_id_seq; Type: SEQUENCE; Schema: public; Owner: - |
|
| 2121 |
-- |
|
| 2122 |
|
|
| 2123 |
CREATE SEQUENCE role_role_id_seq |
|
| 2124 |
START WITH 1 |
|
| 2125 |
INCREMENT BY 1 |
|
| 2126 |
NO MINVALUE |
|
| 2127 |
NO MAXVALUE |
|
| 2128 |
CACHE 1; |
|
| 2129 |
|
|
| 2130 |
|
|
| 2131 |
-- |
|
| 2132 |
-- Name: role_role_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: - |
|
| 2133 |
-- |
|
| 2134 |
|
|
| 2135 |
ALTER SEQUENCE role_role_id_seq OWNED BY role.role_id; |
|
| 2136 |
|
|
| 2137 |
|
|
| 2138 | 2138 |
SET default_with_oids = false; |
| 2139 | 2139 |
|
| 2140 | 2140 |
-- |
| ... | ... | |
| 3213 | 3213 |
|
| 3214 | 3214 |
|
| 3215 | 3215 |
-- |
| 3216 |
-- Name: role_id; Type: DEFAULT; Schema: public; Owner: - |
|
| 3217 |
-- |
|
| 3218 |
|
|
| 3219 |
ALTER TABLE aux_role ALTER COLUMN role_id SET DEFAULT nextval('aux_role_role_id_seq'::regclass);
|
|
| 3220 |
|
|
| 3221 |
|
|
| 3222 |
-- |
|
| 3223 | 3216 |
-- Name: classcontributor_id; Type: DEFAULT; Schema: public; Owner: - |
| 3224 | 3217 |
-- |
| 3225 | 3218 |
|
| ... | ... | |
| 3577 | 3570 |
|
| 3578 | 3571 |
|
| 3579 | 3572 |
-- |
| 3573 |
-- Name: role_id; Type: DEFAULT; Schema: public; Owner: - |
|
| 3574 |
-- |
|
| 3575 |
|
|
| 3576 |
ALTER TABLE role ALTER COLUMN role_id SET DEFAULT nextval('role_role_id_seq'::regclass);
|
|
| 3577 |
|
|
| 3578 |
|
|
| 3579 |
-- |
|
| 3580 | 3580 |
-- Name: sizeclass_id; Type: DEFAULT; Schema: public; Owner: - |
| 3581 | 3581 |
-- |
| 3582 | 3582 |
|
| ... | ... | |
| 3798 | 3798 |
|
| 3799 | 3799 |
|
| 3800 | 3800 |
-- |
| 3801 |
-- Name: aux_role_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: |
|
| 3802 |
-- |
|
| 3803 |
|
|
| 3804 |
ALTER TABLE ONLY aux_role |
|
| 3805 |
ADD CONSTRAINT aux_role_pkey PRIMARY KEY (role_id); |
|
| 3806 |
|
|
| 3807 |
|
|
| 3808 |
-- |
|
| 3809 | 3801 |
-- Name: classcontributor_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: |
| 3810 | 3802 |
-- |
| 3811 | 3803 |
|
| ... | ... | |
| 4350 | 4342 |
|
| 4351 | 4343 |
|
| 4352 | 4344 |
-- |
| 4345 |
-- Name: role_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: |
|
| 4346 |
-- |
|
| 4347 |
|
|
| 4348 |
ALTER TABLE ONLY role |
|
| 4349 |
ADD CONSTRAINT role_pkey PRIMARY KEY (role_id); |
|
| 4350 |
|
|
| 4351 |
|
|
| 4352 |
-- |
|
| 4353 | 4353 |
-- Name: sizeclass_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: |
| 4354 | 4354 |
-- |
| 4355 | 4355 |
|
| ... | ... | |
| 4666 | 4666 |
|
| 4667 | 4667 |
|
| 4668 | 4668 |
-- |
| 4669 |
-- Name: aux_role_accessioncode_index; Type: INDEX; Schema: public; Owner: -; Tablespace: |
|
| 4670 |
-- |
|
| 4671 |
|
|
| 4672 |
CREATE UNIQUE INDEX aux_role_accessioncode_index ON aux_role USING btree (accessioncode); |
|
| 4673 |
|
|
| 4674 |
|
|
| 4675 |
-- |
|
| 4676 | 4669 |
-- Name: classcontributor_commclass_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace: |
| 4677 | 4670 |
-- |
| 4678 | 4671 |
|
| ... | ... | |
| 5555 | 5548 |
|
| 5556 | 5549 |
|
| 5557 | 5550 |
-- |
| 5551 |
-- Name: role_accessioncode_index; Type: INDEX; Schema: public; Owner: -; Tablespace: |
|
| 5552 |
-- |
|
| 5553 |
|
|
| 5554 |
CREATE UNIQUE INDEX role_accessioncode_index ON role USING btree (accessioncode); |
|
| 5555 |
|
|
| 5556 |
|
|
| 5557 |
-- |
|
| 5558 | 5558 |
-- Name: soilobs_locationevent_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace: |
| 5559 | 5559 |
-- |
| 5560 | 5560 |
|
| ... | ... | |
| 5887 | 5887 |
-- |
| 5888 | 5888 |
|
| 5889 | 5889 |
ALTER TABLE ONLY classcontributor |
| 5890 |
ADD CONSTRAINT classcontributor_role_id FOREIGN KEY (role_id) REFERENCES aux_role(role_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
| 5890 |
ADD CONSTRAINT classcontributor_role_id FOREIGN KEY (role_id) REFERENCES role(role_id) ON UPDATE CASCADE ON DELETE CASCADE; |
|
| 5891 | 5891 |
|
| 5892 | 5892 |
|
| 5893 | 5893 |
-- |
| ... | ... | |
| 6199 | 6199 |
-- |
| 6200 | 6200 |
|
| 6201 | 6201 |
ALTER TABLE ONLY locationeventcontributor |
| 6202 |
ADD CONSTRAINT locationeventcontributor_role_id FOREIGN KEY (role_id) REFERENCES aux_role(role_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
| 6202 |
ADD CONSTRAINT locationeventcontributor_role_id FOREIGN KEY (role_id) REFERENCES role(role_id) ON UPDATE CASCADE ON DELETE CASCADE; |
|
| 6203 | 6203 |
|
| 6204 | 6204 |
|
| 6205 | 6205 |
-- |
| ... | ... | |
| 6223 | 6223 |
-- |
| 6224 | 6224 |
|
| 6225 | 6225 |
ALTER TABLE ONLY locationeventsynonym |
| 6226 |
ADD CONSTRAINT locationeventsynonym_role_id FOREIGN KEY (role_id) REFERENCES aux_role(role_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
| 6226 |
ADD CONSTRAINT locationeventsynonym_role_id FOREIGN KEY (role_id) REFERENCES role(role_id) ON UPDATE CASCADE ON DELETE CASCADE; |
|
| 6227 | 6227 |
|
| 6228 | 6228 |
|
| 6229 | 6229 |
-- |
| ... | ... | |
| 6295 | 6295 |
-- |
| 6296 | 6296 |
|
| 6297 | 6297 |
ALTER TABLE ONLY note |
| 6298 |
ADD CONSTRAINT note_role_id FOREIGN KEY (role_id) REFERENCES aux_role(role_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
| 6298 |
ADD CONSTRAINT note_role_id FOREIGN KEY (role_id) REFERENCES role(role_id) ON UPDATE CASCADE ON DELETE CASCADE; |
|
| 6299 | 6299 |
|
| 6300 | 6300 |
|
| 6301 | 6301 |
-- |
| ... | ... | |
| 6327 | 6327 |
-- |
| 6328 | 6328 |
|
| 6329 | 6329 |
ALTER TABLE ONLY partymember |
| 6330 |
ADD CONSTRAINT partymember_role_id FOREIGN KEY (role_id) REFERENCES aux_role(role_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
| 6330 |
ADD CONSTRAINT partymember_role_id FOREIGN KEY (role_id) REFERENCES role(role_id) ON UPDATE CASCADE ON DELETE CASCADE; |
|
| 6331 | 6331 |
|
| 6332 | 6332 |
|
| 6333 | 6333 |
-- |
| ... | ... | |
| 6471 | 6471 |
-- |
| 6472 | 6472 |
|
| 6473 | 6473 |
ALTER TABLE ONLY projectcontributor |
| 6474 |
ADD CONSTRAINT projectcontributor_role_id FOREIGN KEY (role_id) REFERENCES aux_role(role_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
| 6474 |
ADD CONSTRAINT projectcontributor_role_id FOREIGN KEY (role_id) REFERENCES role(role_id) ON UPDATE CASCADE ON DELETE CASCADE; |
|
| 6475 | 6475 |
|
| 6476 | 6476 |
|
| 6477 | 6477 |
-- |
| ... | ... | |
| 6671 | 6671 |
-- |
| 6672 | 6672 |
|
| 6673 | 6673 |
ALTER TABLE ONLY taxondetermination |
| 6674 |
ADD CONSTRAINT taxondetermination_role_id FOREIGN KEY (role_id) REFERENCES aux_role(role_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
| 6674 |
ADD CONSTRAINT taxondetermination_role_id FOREIGN KEY (role_id) REFERENCES role(role_id) ON UPDATE CASCADE ON DELETE CASCADE; |
|
| 6675 | 6675 |
|
| 6676 | 6676 |
|
| 6677 | 6677 |
-- |
| mappings/SALVIAS_db-VegBIEN.organisms.csv | ||
|---|---|---|
| 14 | 14 |
census_date,/specimen:[*_id/reference]/collectiondate/_date/date, |
| 15 | 15 |
coll_firstname,"/specimen:[*_id/reference]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}",Brad: See comment above
|
| 16 | 16 |
coll_lastname,/specimen:[*_id/reference]/collector_id/party/{surname},"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."
|
| 17 |
census_no,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=censusNo]:[userdefinedtype=varchar]]:[@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."
|
|
| 18 |
cfaff,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=cfAff]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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."
|
|
| 19 |
DetType,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=determinationType]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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."
|
|
| 20 |
Habit,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=habit]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
|
|
| 21 |
Ind,"/taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=individualCode]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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."
|
|
| 22 |
Notes,"/taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/notes",
|
|
| 23 |
auth,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/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.
|
|
| 24 |
Family,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",
|
|
| 25 |
Genus,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",
|
|
| 26 |
Species,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",
|
|
| 27 |
infra_rank_1,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/{*_id/*/plantname/_name/first,*_id/plantconcept:[*_id/reference]/_name/first}",
|
|
| 28 |
infra_ep_1,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/_name/last",
|
|
| 29 |
OrigFamily,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",Brad: OMIT
|
|
| 30 |
OrigSpecies,"/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname/_alt/2,taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname}",Brad: OMIT
|
|
| 17 |
census_no,"/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=censusNo]:[userdefinedtype=varchar]]:[@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." |
|
| 18 |
cfaff,"/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=cfAff]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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." |
|
| 19 |
DetType,"/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=determinationType]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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." |
|
| 20 |
Habit,"/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=habit]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait." |
|
| 21 |
Ind,"/taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=individualCode]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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." |
|
| 22 |
Notes,"/taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/notes", |
|
| 23 |
auth,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/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. |
|
| 24 |
Family,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname", |
|
| 25 |
Genus,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname", |
|
| 26 |
Species,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname", |
|
| 27 |
infra_rank_1,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/{*_id/*/plantname/_name/first,*_id/plantconcept:[*_id/reference]/_name/first}",
|
|
| 28 |
infra_ep_1,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/_name/last", |
|
| 29 |
OrigFamily,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",Brad: OMIT |
|
| 30 |
OrigSpecies,"/{taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname/_alt/2,taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname}",Brad: OMIT
|
|
| 31 | 31 |
PlotObsID,":[aggregateoccurrence/count/_alt/2=1]/{aggregateoccurrence/individualplant/authorplantcode,specimen:[*_id/reference]/sourceaccessioncode,*_id/locationevent/authoreventcode/_alt/2,*_id/locationevent/*_id/location:[confidentialitystatus=0]/authorlocationcode/_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 | ||
|---|---|---|
| 95 | 95 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,"/specimen:[*_id/reference]/{museum_id/party/organizationname,collectioncode_dwc/_namePart/last}"
|
| 96 | 96 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/first,/specimen:[*_id/reference]/{museum_id/party/organizationname/_name/first}
|
| 97 | 97 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/last,"/specimen:[*_id/reference]/{museum_id/party/organizationname/_name/last,collectioncode_dwc}"
|
| 98 |
/simpleUserdefined[name=censusNo]/value,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=censusNo]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
| 99 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/note","/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=cfAff]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
| 100 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/groupType","/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=determinationType]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
| 101 |
/simpleUserdefined[name=habit]/value,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=habit]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
| 102 |
/*ID->/*s/individualOrganism/simpleUserdefined[name=sex]/value,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=sex]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
| 103 |
/simpleUserdefined[name=individualCode]/value,"/taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=individualCode]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
| 104 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/note/text,"/taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/notes"
|
|
| 105 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonName)/Simple","/taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname/_alt/1"
|
|
| 106 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=auth])/Name","/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname"
|
|
| 107 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=fam])/Name","/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname"
|
|
| 108 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=gen])/Name","/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname"
|
|
| 109 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=sp])/Name","/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname"
|
|
| 110 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=TaxonomicRankBelowSubspeciesEnum])/Rank","/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/{*_id/*/plantname/_name/first,*_id/plantconcept:[*_id/reference]/_name/first}"
|
|
| 111 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=TaxonomicRankBelowSubspeciesEnum])/Name","/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/_name/last"
|
|
| 112 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/date/_date/day","/taxondetermination[role_id/aux_role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_date/day"
|
|
| 113 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/date/_date/month","/taxondetermination[role_id/aux_role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_date/month"
|
|
| 114 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/date/_date/year","/taxondetermination[role_id/aux_role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_date/year"
|
|
| 115 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/partyWithRole/*ID->/parties/party/individualName/{givenName/_namePart/{first,middle},surName/_namePart/last}","/taxondetermination[role_id/aux_role/rolecode=identifier,!*_id/plantconcept]:[determinationtype=Author,currentdetermination=true]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}"
|
|
| 116 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=auth])/Name","/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname"
|
|
| 117 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=cl])/Name","/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Class]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname"
|
|
| 118 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=fam])/Name","/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname"
|
|
| 119 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=gen])/Name","/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname"
|
|
| 120 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=reg])/Name","/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Kingdom]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname"
|
|
| 121 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=ord])/Name","/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Order]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname"
|
|
| 122 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=phyl_div])/Name","/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname"
|
|
| 123 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=ssp])/Name","/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname"
|
|
| 124 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=sp])/Name","/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname/_alt/2,taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname}"
|
|
| 98 |
/simpleUserdefined[name=censusNo]/value,"/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=censusNo]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
|
| 99 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/note","/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=cfAff]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
|
| 100 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/groupType","/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=determinationType]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
|
| 101 |
/simpleUserdefined[name=habit]/value,"/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=habit]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
|
| 102 |
/*ID->/*s/individualOrganism/simpleUserdefined[name=sex]/value,"/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=sex]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
|
| 103 |
/simpleUserdefined[name=individualCode]/value,"/taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=individualCode]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
|
| 104 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/note/text,"/taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/notes" |
|
| 105 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonName)/Simple","/taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname/_alt/1" |
|
| 106 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=auth])/Name","/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname" |
|
| 107 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=fam])/Name","/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname" |
|
| 108 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=gen])/Name","/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname" |
|
| 109 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=sp])/Name","/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname" |
|
| 110 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=TaxonomicRankBelowSubspeciesEnum])/Rank","/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/{*_id/*/plantname/_name/first,*_id/plantconcept:[*_id/reference]/_name/first}"
|
|
| 111 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=TaxonomicRankBelowSubspeciesEnum])/Name","/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/_name/last" |
|
| 112 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/date/_date/day","/taxondetermination[role_id/role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_date/day" |
|
| 113 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/date/_date/month","/taxondetermination[role_id/role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_date/month" |
|
| 114 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/date/_date/year","/taxondetermination[role_id/role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_date/year" |
|
| 115 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/partyWithRole/*ID->/parties/party/individualName/{givenName/_namePart/{first,middle},surName/_namePart/last}","/taxondetermination[role_id/role/rolecode=identifier,!*_id/plantconcept]:[determinationtype=Author,currentdetermination=true]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}"
|
|
| 116 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=auth])/Name","/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname" |
|
| 117 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=cl])/Name","/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Class]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname" |
|
| 118 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=fam])/Name","/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname" |
|
| 119 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=gen])/Name","/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname" |
|
| 120 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=reg])/Name","/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Kingdom]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname" |
|
| 121 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=ord])/Name","/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Order]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname" |
|
| 122 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=phyl_div])/Name","/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname" |
|
| 123 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=ssp])/Name","/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname" |
|
| 124 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=sp])/Name","/{taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname/_alt/2,taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname}"
|
|
| 125 | 125 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,":[aggregateoccurrence/count/_alt/2=1]/{aggregateoccurrence/individualplant/authorplantcode,specimen:[*_id/reference]/sourceaccessioncode,*_id/locationevent/authoreventcode/_alt/2,*_id/locationevent/*_id/location:[confidentialitystatus=0]/authorlocationcode/_alt/3}"
|
| mappings/NYBG-VegBIEN.organisms.csv | ||
|---|---|---|
| 23 | 23 |
CollectorNumber,/specimen:[*_id/reference]/collectornumber_dwc,"Brad: OMIT; db-specific element, not relevant to VB/VX" |
| 24 | 24 |
InstitutionCode,/specimen:[*_id/reference]/{museum_id/party/organizationname/_name/first},
|
| 25 | 25 |
CollectionCode,"/specimen:[*_id/reference]/{museum_id/party/organizationname/_name/last,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
|
| 26 |
Sex,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=sex]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections"
|
|
| 27 |
Notes,"/taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/notes","Brad: mapping OK; NY appears to be using this field for almost anything, but mostly internal collections notes"
|
|
| 28 |
ScientificName,"/taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname/_alt/1","Brad: Bob, Nick, please is this mapping OK?"
|
|
| 29 |
DayIdentified,"/taxondetermination[role_id/aux_role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_date/day",
|
|
| 30 |
MonthIdentified,"/taxondetermination[role_id/aux_role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_date/month",
|
|
| 31 |
YearIdentified,"/taxondetermination[role_id/aux_role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_date/year",
|
|
| 32 |
IdentifiedBy,"/taxondetermination[role_id/aux_role/rolecode=identifier,!*_id/plantconcept]:[determinationtype=Author,currentdetermination=true]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Bob: does this look correct for VegBank?
|
|
| 33 |
ScientificNameAuthor,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname","Brad: Mapping probably incorrect. This DwC element refers to scientific name author; does not correspond to the VegBank and VegX elements you have listed (Bob, Nick�where does name author belong in VegBank and VegX?); Aaron: The mapped VegX element is the author linked to the taxon name, so it seems like this is the scientific name author"
|
|
| 34 |
Class,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Class]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",
|
|
| 35 |
Family,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",
|
|
| 36 |
Genus,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",
|
|
| 37 |
Kingdom,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Kingdom]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",
|
|
| 38 |
Order,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Order]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",
|
|
| 39 |
Phylum,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",
|
|
| 40 |
Subspecies,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",
|
|
| 41 |
Species,"/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname/_alt/2,taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname}",
|
|
| 26 |
Sex,"/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=sex]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections" |
|
| 27 |
Notes,"/taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/notes","Brad: mapping OK; NY appears to be using this field for almost anything, but mostly internal collections notes" |
|
| 28 |
ScientificName,"/taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname/_alt/1","Brad: Bob, Nick, please is this mapping OK?" |
|
| 29 |
DayIdentified,"/taxondetermination[role_id/role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_date/day", |
|
| 30 |
MonthIdentified,"/taxondetermination[role_id/role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_date/month", |
|
| 31 |
YearIdentified,"/taxondetermination[role_id/role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_date/year", |
|
| 32 |
IdentifiedBy,"/taxondetermination[role_id/role/rolecode=identifier,!*_id/plantconcept]:[determinationtype=Author,currentdetermination=true]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Bob: does this look correct for VegBank?
|
|
| 33 |
ScientificNameAuthor,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname","Brad: Mapping probably incorrect. This DwC element refers to scientific name author; does not correspond to the VegBank and VegX elements you have listed (Bob, Nick�where does name author belong in VegBank and VegX?); Aaron: The mapped VegX element is the author linked to the taxon name, so it seems like this is the scientific name author" |
|
| 34 |
Class,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Class]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname", |
|
| 35 |
Family,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname", |
|
| 36 |
Genus,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname", |
|
| 37 |
Kingdom,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Kingdom]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname", |
|
| 38 |
Order,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Order]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname", |
|
| 39 |
Phylum,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname", |
|
| 40 |
Subspecies,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname", |
|
| 41 |
Species,"/{taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname/_alt/2,taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname}",
|
|
| 42 | 42 |
UniqueNYInternalRecordNumber,":[aggregateoccurrence/count/_alt/2=1]/{aggregateoccurrence/individualplant/authorplantcode,specimen:[*_id/reference]/sourceaccessioncode,*_id/locationevent/authoreventcode/_alt/2,*_id/locationevent/*_id/location:[confidentialitystatus=0]/authorlocationcode/_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/SALVIAS-VegBIEN.organisms.csv | ||
|---|---|---|
| 23 | 23 |
coll_number,/specimen:[*_id/reference]/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string |
| 24 | 24 |
coll_firstname,"/specimen:[*_id/reference]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}",Brad: See comment above
|
| 25 | 25 |
coll_lastname,/specimen:[*_id/reference]/collector_id/party/{surname},"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."
|
| 26 |
census_no,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=censusNo]:[userdefinedtype=varchar]]:[@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."
|
|
| 27 |
cf_aff,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=cfAff]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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."
|
|
| 28 |
det_type,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=determinationType]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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."
|
|
| 29 |
habit,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=habit]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
|
|
| 30 |
individual_code,"/taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=individualCode]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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."
|
|
| 31 |
notes,"/taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/notes",
|
|
| 32 |
specific_authority,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/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.
|
|
| 33 |
family,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",
|
|
| 34 |
genus,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",
|
|
| 35 |
specific_epithet,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",
|
|
| 36 |
infra_rank_1,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/{*_id/*/plantname/_name/first,*_id/plantconcept:[*_id/reference]/_name/first}",
|
|
| 37 |
infra_ep_1,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/_name/last",
|
|
| 38 |
orig_family,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",Brad: OMIT
|
|
| 39 |
orig_species,"/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname/_alt/2,taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname}",Brad: OMIT
|
|
| 26 |
census_no,"/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=censusNo]:[userdefinedtype=varchar]]:[@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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| 27 |
cf_aff,"/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=cfAff]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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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| 28 |
det_type,"/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=determinationType]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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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| 29 |
habit,"/taxondetermination[role_id/role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=habit]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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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| 30 |
individual_code,"/taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=individualCode]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","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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| 31 |
notes,"/taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,currentdetermination=true]/notes", |
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| 32 |
specific_authority,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/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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| 33 |
family,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname", |
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| 34 |
genus,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname", |
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| 35 |
specific_epithet,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname", |
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| 36 |
infra_rank_1,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/{*_id/*/plantname/_name/first,*_id/plantconcept:[*_id/reference]/_name/first}",
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| 37 |
infra_ep_1,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept:[*_id/reference]/_name/last", |
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| 38 |
orig_family,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname",Brad: OMIT |
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| 39 |
orig_species,"/{taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname/_alt/2,taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept:[*_id/reference]/*_id/*/plantname}",Brad: OMIT
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| 40 | 40 |
OBSERVATION_ID,":[aggregateoccurrence/count/_alt/2=1]/{aggregateoccurrence/individualplant/authorplantcode,specimen:[*_id/reference]/sourceaccessioncode,*_id/locationevent/authoreventcode/_alt/2,*_id/locationevent/*_id/location:[confidentialitystatus=0]/authorlocationcode/_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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Also available in: Unified diff
VegBIEN: Renamed aux_role to role