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Revision 3829

inputs/SALVIAS*/maps/VegX.organisms.csv: Fixed missing join mappings for stemobservation-related fields

View differences:

inputs/SALVIAS-CSV/test/import.organisms.xml.ref
81 81
                        </overallheight>
82 82
                        <sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode>
83 83
                        <stemobservation>
84
                            <basaldiameter>$basal_diam</basaldiameter>
85
                            <definedvalue fkey="tablerecord_id">
86
                                <userdefined_id>
87
                                    <userdefined>
88
                                        <tablename>stemobservation</tablename>
89
                                        <userdefinedname>canopyForm</userdefinedname>
90
                                    </userdefined>
91
                                </userdefined_id>
92
                                <definedvalue>$stem_canopy_form</definedvalue>
93
                            </definedvalue>
94
                            <definedvalue fkey="tablerecord_id">
95
                                <userdefined_id>
96
                                    <userdefined>
97
                                        <tablename>stemobservation</tablename>
98
                                        <userdefinedname>canopyPosition</userdefinedname>
99
                                    </userdefined>
100
                                </userdefined_id>
101
                                <definedvalue>$stem_canopy_position</definedvalue>
102
                            </definedvalue>
103
                            <definedvalue fkey="tablerecord_id">
104
                                <userdefined_id>
105
                                    <userdefined>
106
                                        <tablename>stemobservation</tablename>
107
                                        <userdefinedname>lianaInfestation</userdefinedname>
108
                                    </userdefined>
109
                                </userdefined_id>
110
                                <definedvalue>$stem_liana_infestation</definedvalue>
111
                            </definedvalue>
112
                            <definedvalue fkey="tablerecord_id">
113
                                <userdefined_id>
114
                                    <userdefined>
115
                                        <tablename>stemobservation</tablename>
116
                                        <userdefinedname>notes</userdefinedname>
117
                                    </userdefined>
118
                                </userdefined_id>
119
                                <definedvalue>$notes</definedvalue>
120
                            </definedvalue>
121
                            <diameterbreastheight>$stem_dbh</diameterbreastheight>
122
                            <heightfirstbranch>
123
                                <_alt>
124
                                    <0>$ht_first_branch_m</0>
125
                                    <1>$stem_height_first_branch_m</1>
126
                                </_alt>
127
                            </heightfirstbranch>
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
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
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,
40
basal_diam,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/diameterBaseDistance[baseDistance/value=0]/diameter,
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,
40
basal_diam,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance/value=0]/diameter,
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."
43
stem_canopy_form,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=canopyForm]/value,Brad: Should also be userDefined for VegBank. 
44
stem_canopy_position,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=canopyPosition]/value,Brad: Should also be userDefined for VegBank. 
45
stem_liana_infestation,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/simpleUserdefined[name=lianaInfestation]/value,Brad: Should also be userDefined for VegBank. 
46
notes,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/note/text,
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."
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. 
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. 
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. 
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,
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
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,
3
basal_diam,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]->/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance/value=0]/diameter,
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,
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. 
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. 
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
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."
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. 
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,
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,
23
stem_dbh,/*s/plot->/*s/plotObservation[*UniqueIdentifierID]->/*s/individualOrganismObservation[*ID]/diameterBaseDistance[baseDistance/value=1.37]/diameter,
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
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
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,
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. 
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. 
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. 
25
notes,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=notes]]:[@fkey=tablerecord_id]/definedvalue",
26
stem_dbh,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight,
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