Revision 3829
Added by Aaron Marcuse-Kubitza over 12 years ago
inputs/SALVIAS-CSV/test/import.organisms.xml.ref | ||
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81 | 81 |
</overallheight> |
82 | 82 |
<sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode> |
83 | 83 |
<stemobservation> |
84 |
<basaldiameter>$basal_diam</basaldiameter> |
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85 |
<definedvalue fkey="tablerecord_id"> |
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86 |
<userdefined_id> |
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87 |
<userdefined> |
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88 |
<tablename>stemobservation</tablename> |
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89 |
<userdefinedname>canopyForm</userdefinedname> |
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90 |
</userdefined> |
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91 |
</userdefined_id> |
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92 |
<definedvalue>$stem_canopy_form</definedvalue> |
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93 |
</definedvalue> |
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94 |
<definedvalue fkey="tablerecord_id"> |
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95 |
<userdefined_id> |
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96 |
<userdefined> |
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97 |
<tablename>stemobservation</tablename> |
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98 |
<userdefinedname>canopyPosition</userdefinedname> |
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99 |
</userdefined> |
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100 |
</userdefined_id> |
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101 |
<definedvalue>$stem_canopy_position</definedvalue> |
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102 |
</definedvalue> |
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103 |
<definedvalue fkey="tablerecord_id"> |
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104 |
<userdefined_id> |
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105 |
<userdefined> |
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106 |
<tablename>stemobservation</tablename> |
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107 |
<userdefinedname>lianaInfestation</userdefinedname> |
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108 |
</userdefined> |
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109 |
</userdefined_id> |
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110 |
<definedvalue>$stem_liana_infestation</definedvalue> |
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111 |
</definedvalue> |
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112 |
<definedvalue fkey="tablerecord_id"> |
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113 |
<userdefined_id> |
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114 |
<userdefined> |
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115 |
<tablename>stemobservation</tablename> |
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116 |
<userdefinedname>notes</userdefinedname> |
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117 |
</userdefined> |
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118 |
</userdefined_id> |
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119 |
<definedvalue>$notes</definedvalue> |
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120 |
</definedvalue> |
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121 |
<diameterbreastheight>$stem_dbh</diameterbreastheight> |
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122 |
<heightfirstbranch> |
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123 |
<_alt> |
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124 |
<0>$ht_first_branch_m</0> |
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125 |
<1>$stem_height_first_branch_m</1> |
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126 |
</_alt> |
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127 |
</heightfirstbranch> |
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84 | 128 |
<stemtag> |
85 | 129 |
<iscurrent> |
86 | 130 |
<_alt> |
... | ... | |
265 | 309 |
</sourceaccessioncode> |
266 | 310 |
</location> |
267 | 311 |
</VegBIEN> |
268 |
Inserted 44 new rows into database |
|
312 |
Inserted 56 new rows into database |
inputs/SALVIAS-CSV/maps/VegX.organisms.csv | ||
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33 | 33 |
cover_percent,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/volumeCanopy/*ID->/*s/attribute/ordinal/coverPercent, |
34 | 34 |
intercept_cm,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/volumeCanopy/value,"Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance." |
35 | 35 |
height_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
36 |
ht_first_branch_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=heightFirstBranch]/value,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
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36 |
ht_first_branch_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=heightFirstBranch]/value,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
|
|
37 | 37 |
stem_tag1,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/identificationLabel[@id=1]/_alt/2,"Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems." |
38 | 38 |
stem_tag2,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/identificationLabel[@id=2]/_alt/2,Brad: see above |
39 |
stem_dbh,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/diameterBaseDistance[baseDistance/value=1.37]/diameter,
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40 |
basal_diam,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/diameterBaseDistance[baseDistance/value=0]/diameter, |
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39 |
stem_dbh,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance[!attributeID]/value=1.37]/diameter,
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40 |
basal_diam,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance/value=0]/diameter,
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41 | 41 |
stem_height_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=height]/value,"Brad: Same as for height, but applies to individuals stems, not trees. Rare." |
42 |
stem_height_first_branch_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=heightFirstBranch]/value,"Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare." |
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43 |
stem_canopy_form,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=canopyForm]/value,Brad: Should also be userDefined for VegBank. |
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44 |
stem_canopy_position,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=canopyPosition]/value,Brad: Should also be userDefined for VegBank. |
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45 |
stem_liana_infestation,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=lianaInfestation]/value,Brad: Should also be userDefined for VegBank. |
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46 |
notes,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/note/text, |
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42 |
stem_height_first_branch_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=heightFirstBranch]/value,"Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
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43 |
stem_canopy_form,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=canopyForm]/value,Brad: Should also be userDefined for VegBank.
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44 |
stem_canopy_position,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=canopyPosition]/value,Brad: Should also be userDefined for VegBank.
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45 |
stem_liana_infestation,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=lianaInfestation]/value,Brad: Should also be userDefined for VegBank.
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46 |
notes,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/note/text,
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47 | 47 |
orig_family,"/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=fam])/tcs:Name",Brad: OMIT |
48 | 48 |
orig_species,"/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=binom])/tcs:Name/_name/last",Brad: OMIT |
inputs/SALVIAS-CSV/maps/VegX.organisms.full.csv | ||
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1 | 1 |
SALVIAS-CSV,VegX:,Comments |
2 |
notes,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/note/text, |
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3 |
basal_diam,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance/value=0]/diameter, |
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4 |
stem_dbh,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance[!attributeID]/value=1.37]/diameter, |
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5 |
stem_canopy_form,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=canopyForm]/value,Brad: Should also be userDefined for VegBank. |
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6 |
stem_canopy_position,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=canopyPosition]/value,Brad: Should also be userDefined for VegBank. |
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7 |
ht_first_branch_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=heightFirstBranch]/value,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
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8 |
stem_height_first_branch_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=heightFirstBranch]/value,"Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare." |
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9 |
stem_liana_infestation,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=lianaInfestation]/value,Brad: Should also be userDefined for VegBank. |
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2 | 10 |
no_of_individuals,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/aggregateOrganismObservation[*ID]/*/aggregateValue/value,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this." |
3 | 11 |
cf_aff,"/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=binom])/fit","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." |
4 | 12 |
orig_species,"/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=binom])/tcs:Name/_name/last",Brad: OMIT |
... | ... | |
12 | 20 |
family,"/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=fam])/tcs:Name", |
13 | 21 |
genus,"/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=gen])/tcs:Name", |
14 | 22 |
specific_epithet,"/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=sp])/tcs:Name", |
15 |
notes,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/note/text, |
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16 | 23 |
coll_number,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/voucher/_alt/1,Brad: Incorrect. Map instead as for voucher_string |
17 | 24 |
voucher_string,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/voucher/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
18 | 25 |
tag1,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/identificationLabel[@id=1]/_alt/1,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once." |
19 | 26 |
stem_tag1,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/identificationLabel[@id=1]/_alt/2,"Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems." |
20 | 27 |
tag2,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/identificationLabel[@id=2]/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other." |
21 | 28 |
stem_tag2,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/identificationLabel[@id=2]/_alt/2,Brad: see above |
22 |
basal_diam,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/diameterBaseDistance[baseDistance/value=0]/diameter, |
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23 |
stem_dbh,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/diameterBaseDistance[baseDistance/value=1.37]/diameter, |
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24 | 29 |
height_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
25 | 30 |
x_position,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/relativePlotPosition/relativeX,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX." |
26 | 31 |
y_position,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/relativePlotPosition/relativeY,Brad: See comment above for x_position |
27 | 32 |
individual_code,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=authorPlantCode]/value,"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." |
28 |
stem_canopy_form,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=canopyForm]/value,Brad: Should also be userDefined for VegBank. |
|
29 |
stem_canopy_position,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=canopyPosition]/value,Brad: Should also be userDefined for VegBank. |
|
30 | 33 |
census_no,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=censusNo]/value,"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." |
31 | 34 |
habit,"/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=growthForm]/value/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait." |
32 |
ht_first_branch_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=heightFirstBranch]/value,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
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33 |
stem_height_first_branch_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=heightFirstBranch]/value,"Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare." |
|
34 | 35 |
stem_height_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=height]/value,"Brad: Same as for height, but applies to individuals stems, not trees. Rare." |
35 |
stem_liana_infestation,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=lianaInfestation]/value,Brad: Should also be userDefined for VegBank. |
|
36 | 36 |
OBSERVATION_ID,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=sourceAccessionCode]/value,"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." |
37 | 37 |
cover_percent,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/volumeCanopy/*ID->/*s/attribute/ordinal/coverPercent, |
38 | 38 |
intercept_cm,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/volumeCanopy/value,"Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance." |
inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv | ||
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18 | 18 |
height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
19 | 19 |
stem_height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/overallheight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare." |
20 | 20 |
OBSERVATION_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later.; ""{"" sorts it with other _if:[name=specimenreplicate_via]s" |
21 |
basal_diam,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter, |
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22 |
stem_canopy_form,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue",Brad: Should also be userDefined for VegBank. |
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23 |
stem_canopy_position,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue",Brad: Should also be userDefined for VegBank. |
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24 |
stem_liana_infestation,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=lianaInfestation]]:[@fkey=tablerecord_id]/definedvalue",Brad: Should also be userDefined for VegBank. |
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25 |
notes,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=notes]]:[@fkey=tablerecord_id]/definedvalue", |
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26 |
stem_dbh,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight, |
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27 |
ht_first_branch_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/heightfirstbranch,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
|
28 |
stem_height_first_branch_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/heightfirstbranch,"Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare." |
|
21 | 29 |
tag1,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag/_alt/1","Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once.; Quotes sort it before tag2" |
22 | 30 |
stem_tag1,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag/_alt/2","Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems.; Quotes sort it before tag2" |
23 | 31 |
tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other." |
... | ... | |
43 | 51 |
PLOT_ID,/location/sourceaccessioncode/_merge/1/_alt/1,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above." |
44 | 52 |
plot_code,/location/sourceaccessioncode/_merge/1/_alt/2,"Brad: Same as plotCode, above" |
45 | 53 |
subplot,/location/sourceaccessioncode/_merge/2/_alt/2, |
46 |
basal_diam,,** No join mapping for /*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/diameterBaseDistance[baseDistance/value=0]/diameter ** |
|
47 | 54 |
collector_code,,Brad: OMIT |
48 | 55 |
comments,,Brad: OMIT |
49 | 56 |
fam_status,,Brad: OMIT. This will be determined later by using TNRS. |
50 | 57 |
gen_status,,Brad: OMIT. This will be determined later by using TNRS. |
51 |
ht_first_branch_m,,** No join mapping for /*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=heightFirstBranch]/value ** Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
|
52 | 58 |
ind_id,,Brad: OMIT |
53 |
notes,,** No join mapping for /*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/note/text ** |
|
54 | 59 |
species_status,,"Brad: OMIT. Except, note that if species_status=3, this indicate that name is a morphospecies and not a standard latin name. Not exactly sure how to use this in BIEN, but could be useful during the name-scrubbing process with TNRS." |
55 |
stem_canopy_form,,** No join mapping for /*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=canopyForm]/value ** Brad: Should also be userDefined for VegBank. |
|
56 |
stem_canopy_position,,** No join mapping for /*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=canopyPosition]/value ** Brad: Should also be userDefined for VegBank. |
|
57 |
stem_dbh,,** No join mapping for /*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/diameterBaseDistance[baseDistance/value=1.37]/diameter ** |
|
58 |
stem_height_first_branch_m,,"** No join mapping for /*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=heightFirstBranch]/value ** Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare." |
|
59 |
stem_liana_infestation,,** No join mapping for /*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=lianaInfestation]/value ** Brad: Should also be userDefined for VegBank. |
inputs/SALVIAS/test/import.organisms.xml.ref | ||
---|---|---|
77 | 77 |
<overallheight>$height_m</overallheight> |
78 | 78 |
<sourceaccessioncode>$PlotObsID</sourceaccessioncode> |
79 | 79 |
<stemobservation> |
80 |
<definedvalue fkey="tablerecord_id"> |
|
81 |
<userdefined_id> |
|
82 |
<userdefined> |
|
83 |
<tablename>stemobservation</tablename> |
|
84 |
<userdefinedname>canopyForm</userdefinedname> |
|
85 |
</userdefined> |
|
86 |
</userdefined_id> |
|
87 |
<definedvalue>$canopy_form</definedvalue> |
|
88 |
</definedvalue> |
|
89 |
<definedvalue fkey="tablerecord_id"> |
|
90 |
<userdefined_id> |
|
91 |
<userdefined> |
|
92 |
<tablename>stemobservation</tablename> |
|
93 |
<userdefinedname>canopyPosition</userdefinedname> |
|
94 |
</userdefined> |
|
95 |
</userdefined_id> |
|
96 |
<definedvalue>$canopy_position</definedvalue> |
|
97 |
</definedvalue> |
|
98 |
<definedvalue fkey="tablerecord_id"> |
|
99 |
<userdefined_id> |
|
100 |
<userdefined> |
|
101 |
<tablename>stemobservation</tablename> |
|
102 |
<userdefinedname>lianaInfestation</userdefinedname> |
|
103 |
</userdefined> |
|
104 |
</userdefined_id> |
|
105 |
<definedvalue>$liana_infestation</definedvalue> |
|
106 |
</definedvalue> |
|
107 |
<definedvalue fkey="tablerecord_id"> |
|
108 |
<userdefined_id> |
|
109 |
<userdefined> |
|
110 |
<tablename>stemobservation</tablename> |
|
111 |
<userdefinedname>notes</userdefinedname> |
|
112 |
</userdefined> |
|
113 |
</userdefined_id> |
|
114 |
<definedvalue>$Notes</definedvalue> |
|
115 |
</definedvalue> |
|
116 |
<diameterbreastheight>$temp_dbh</diameterbreastheight> |
|
117 |
<heightfirstbranch>$ht_first_branch_m</heightfirstbranch> |
|
80 | 118 |
<stemtag> |
81 | 119 |
<iscurrent> |
82 | 120 |
<_alt> |
... | ... | |
261 | 299 |
</sourceaccessioncode> |
262 | 300 |
</location> |
263 | 301 |
</VegBIEN> |
264 |
Inserted 38 new rows into database |
|
302 |
Inserted 50 new rows into database |
inputs/SALVIAS/maps/VegX.organisms.csv | ||
---|---|---|
41 | 41 |
height_class,, |
42 | 42 |
height_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
43 | 43 |
height_m_commercial,, |
44 |
ht_first_branch_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=heightFirstBranch]/value,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
|
44 |
ht_first_branch_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=heightFirstBranch]/value,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
|
|
45 | 45 |
NoInd,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/aggregateOrganismObservation[*ID]/*/aggregateValue/value,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this." |
46 | 46 |
cover_percent,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/volumeCanopy/*ID->/*s/attribute/ordinal/coverPercent, |
47 | 47 |
intercept_cm,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/volumeCanopy/value,"Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance." |
... | ... | |
54 | 54 |
OrigSpecies,"/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=binom])/tcs:Name/_name/last",Brad: OMIT |
55 | 55 |
OrigAuth,, |
56 | 56 |
phenology,, |
57 |
canopy_position,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=canopyPosition]/value,Brad: Should also be userDefined for VegBank. |
|
58 |
canopy_form,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=canopyForm]/value,Brad: Should also be userDefined for VegBank. |
|
59 |
liana_infestation,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=lianaInfestation]/value,Brad: Should also be userDefined for VegBank. |
|
60 |
Notes,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/note/text, |
|
61 |
temp_dbh,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/diameterBaseDistance[baseDistance/value=1.37]/diameter,
|
|
57 |
canopy_position,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=canopyPosition]/value,Brad: Should also be userDefined for VegBank.
|
|
58 |
canopy_form,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=canopyForm]/value,Brad: Should also be userDefined for VegBank.
|
|
59 |
liana_infestation,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=lianaInfestation]/value,Brad: Should also be userDefined for VegBank.
|
|
60 |
Notes,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/note/text,
|
|
61 |
temp_dbh,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance[!attributeID]/value=1.37]/diameter,
|
|
62 | 62 |
temp_liandbh,, |
63 | 63 |
tmp_del,, |
inputs/SALVIAS/maps/VegX.organisms.full.csv | ||
---|---|---|
1 | 1 |
SALVIAS,VegX:,Comments |
2 |
Notes,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/note/text, |
|
3 |
temp_dbh,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance[!attributeID]/value=1.37]/diameter, |
|
4 |
canopy_form,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=canopyForm]/value,Brad: Should also be userDefined for VegBank. |
|
5 |
canopy_position,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=canopyPosition]/value,Brad: Should also be userDefined for VegBank. |
|
6 |
ht_first_branch_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=heightFirstBranch]/value,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
|
7 |
liana_infestation,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/simpleUserdefined[name=lianaInfestation]/value,Brad: Should also be userDefined for VegBank. |
|
2 | 8 |
NoInd,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/aggregateOrganismObservation[*ID]/*/aggregateValue/value,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this." |
3 | 9 |
cfaff,"/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=binom])/fit","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." |
4 | 10 |
OrigGenus,"/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=binom])/tcs:Name/_name/first", |
... | ... | |
13 | 19 |
Family,"/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=fam])/tcs:Name", |
14 | 20 |
Genus,"/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=gen])/tcs:Name", |
15 | 21 |
Species,"/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=sp])/tcs:Name", |
16 |
Notes,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/note/text, |
|
17 | 22 |
coll_number,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/voucher/_alt/1,Brad: Incorrect. Map instead as for voucher_string |
18 | 23 |
SourceVoucher,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/voucher/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
19 | 24 |
tag1,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/identificationLabel[@id=1],"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once." |
20 | 25 |
tag2,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/identificationLabel[@id=2],"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other." |
21 |
temp_dbh,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/diameterBaseDistance[baseDistance/value=1.37]/diameter, |
|
22 | 26 |
height_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
23 | 27 |
x_position,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/relativePlotPosition/relativeX,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX." |
24 | 28 |
y_position,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/relativePlotPosition/relativeY,Brad: See comment above for x_position |
25 | 29 |
Ind,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=authorPlantCode]/value,"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." |
26 |
canopy_form,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=canopyForm]/value,Brad: Should also be userDefined for VegBank. |
|
27 |
canopy_position,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=canopyPosition]/value,Brad: Should also be userDefined for VegBank. |
|
28 | 30 |
census_no,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=censusNo]/value,"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." |
29 | 31 |
census_date,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=collectionDate]/value/_*/date, |
30 | 32 |
Habit,"/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=growthForm]/value/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait." |
31 |
ht_first_branch_m,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=heightFirstBranch]/value,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
|
32 |
liana_infestation,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=lianaInfestation]/value,Brad: Should also be userDefined for VegBank. |
|
33 | 33 |
PlotObsID,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=sourceAccessionCode]/value,"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." |
34 | 34 |
cover_percent,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/volumeCanopy/*ID->/*s/attribute/ordinal/coverPercent, |
35 | 35 |
intercept_cm,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/volumeCanopy/value,"Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance." |
inputs/SALVIAS/maps/VegBIEN.organisms.csv | ||
---|---|---|
18 | 18 |
Ind,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot.; ""{"" sorts it with other _if:[name=specimenreplicate_via]s" |
19 | 19 |
height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
20 | 20 |
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later.; ""{"" sorts it with other _if:[name=specimenreplicate_via]s" |
21 |
canopy_form,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue",Brad: Should also be userDefined for VegBank. |
|
22 |
canopy_position,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue",Brad: Should also be userDefined for VegBank. |
|
23 |
liana_infestation,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=lianaInfestation]]:[@fkey=tablerecord_id]/definedvalue",Brad: Should also be userDefined for VegBank. |
|
24 |
Notes,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=notes]]:[@fkey=tablerecord_id]/definedvalue", |
|
25 |
temp_dbh,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight, |
|
26 |
ht_first_branch_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/heightfirstbranch,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
|
21 | 27 |
tag1,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag","Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once.; Quotes sort it before tag2" |
22 | 28 |
tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other." |
23 | 29 |
x_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX." |
... | ... | |
45 | 51 |
Line,/location/sourceaccessioncode/_merge/2/_alt/2, |
46 | 52 |
GenAuth,,** No input mapping for GenAuth ** |
47 | 53 |
IsMorpho,,** No input mapping for IsMorpho ** |
48 |
Notes,,** No join mapping for /*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/note/text ** |
|
49 | 54 |
OrigAuth,,** No input mapping for OrigAuth ** |
50 | 55 |
OrigRecordID,,** No input mapping for OrigRecordID ** |
51 | 56 |
SpAuthStatus,,** No input mapping for SpAuthStatus ** |
52 |
canopy_form,,** No join mapping for /*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=canopyForm]/value ** Brad: Should also be userDefined for VegBank. |
|
53 |
canopy_position,,** No join mapping for /*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=canopyPosition]/value ** Brad: Should also be userDefined for VegBank. |
|
54 | 57 |
coll_inits,,** No input mapping for coll_inits ** |
55 | 58 |
collector_code,,Brad: OMIT |
56 | 59 |
common_name,,** No input mapping for common_name ** |
... | ... | |
60 | 63 |
gen_status,,Brad: OMIT. This will be determined later by using TNRS. |
61 | 64 |
height_class,,** No input mapping for height_class ** |
62 | 65 |
height_m_commercial,,** No input mapping for height_m_commercial ** |
63 |
ht_first_branch_m,,** No join mapping for /*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=heightFirstBranch]/value ** Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
|
64 | 66 |
ind_id,,Brad: OMIT |
65 | 67 |
infra_auth_1,,** No input mapping for infra_auth_1 ** |
66 |
liana_infestation,,** No join mapping for /*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=lianaInfestation]/value ** Brad: Should also be userDefined for VegBank. |
|
67 | 68 |
morphocf,,** No input mapping for morphocf ** |
68 | 69 |
morphoname,,** No input mapping for morphoname ** |
69 | 70 |
name_status,,"Brad: OMIT. Except, note that if species_status=3, this indicate that name is a morphospecies and not a standard latin name. Not exactly sure how to use this in BIEN, but could be useful during the name-scrubbing process with TNRS." |
... | ... | |
71 | 72 |
perp_dist,,** No input mapping for perp_dist ** |
72 | 73 |
phenology,,** No input mapping for phenology ** |
73 | 74 |
species_code,,** No input mapping for species_code ** |
74 |
temp_dbh,,** No join mapping for /*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/diameterBaseDistance[baseDistance/value=1.37]/diameter ** |
|
75 | 75 |
temp_liandbh,,** No input mapping for temp_liandbh ** |
76 | 76 |
tmp_del,,** No input mapping for tmp_del ** |
Also available in: Unified diff
inputs/SALVIAS*/maps/VegX.organisms.csv: Fixed missing join mappings for stemobservation-related fields