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Revision 1049

SALVIAS mappings: Mapped habit to growthForm (user-defined field) instead of habit

View differences:

inputs/SALVIAS/test/VegX.organisms.xml.ref
13 13
                <value>1</value>
14 14
            </simpleUserdefined>
15 15
            <simpleUserdefined>
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                <name>habit</name>
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                <name>growthForm</name>
17 17
                <value>T</value>
18 18
            </simpleUserdefined>
19 19
            <simpleUserdefined>
......
33 33
                <value>2</value>
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            </simpleUserdefined>
35 35
            <simpleUserdefined>
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                <name>habit</name>
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                <name>growthForm</name>
37 37
                <value>T</value>
38 38
            </simpleUserdefined>
39 39
            <simpleUserdefined>
inputs/SALVIAS/test/VegBIEN.organisms.xml.ref
24 24
            <userdefined_id>
25 25
                <userdefined>
26 26
                    <tablename>taxonoccurrence</tablename>
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                    <userdefinedname>habit</userdefinedname>
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                    <userdefinedname>growthForm</userdefinedname>
28 28
                </userdefined>
29 29
            </userdefined_id>
30 30
            <definedvalue>T</definedvalue>
......
140 140
            <userdefined_id>
141 141
                <userdefined>
142 142
                    <tablename>taxonoccurrence</tablename>
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                    <userdefinedname>habit</userdefinedname>
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                    <userdefinedname>growthForm</userdefinedname>
144 144
                </userdefined>
145 145
            </userdefined_id>
146 146
            <definedvalue>T</definedvalue>
inputs/SALVIAS/maps/VegX.organisms.csv
37 37
"common_name",,
38 38
"morphoname",,
39 39
"species_code",,
40
"Habit","/simpleUserdefined[name=habit]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
40
"Habit","/simpleUserdefined[name=growthForm]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
41 41
"height_class",,
42 42
"height_m","/height","Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob"
43 43
"height_m_commercial",,
inputs/SALVIAS/maps/VegBIEN.organisms.csv
16 16
liana_infestation,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=lianaInfestation]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. 
17 17
Notes,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=notes]]:[@fkey=tableRecord_ID]/definedvalue",
18 18
census_no,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=censusNo]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."
19
Habit,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=habit]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
19
Habit,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=growthForm]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
20 20
Ind,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=individualCode]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
21 21
DetType,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=voucherType]]:[@fkey=tableRecord_ID]/definedvalue","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider  asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen."
22 22
coll_number,/specimenreplicate:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string
inputs/SALVIAS-CSV/test/VegX.organisms.xml.ref
13 13
                <value>10</value>
14 14
            </simpleUserdefined>
15 15
            <simpleUserdefined>
16
                <name>habit</name>
16
                <name>growthForm</name>
17 17
                <value>T</value>
18 18
            </simpleUserdefined>
19 19
            <simpleUserdefined>
......
37 37
                <value>100</value>
38 38
            </simpleUserdefined>
39 39
            <simpleUserdefined>
40
                <name>habit</name>
40
                <name>growthForm</name>
41 41
                <value>T</value>
42 42
            </simpleUserdefined>
43 43
            <simpleUserdefined>
inputs/SALVIAS-CSV/test/VegBIEN.organisms.xml.ref
39 39
            <userdefined_id>
40 40
                <userdefined>
41 41
                    <tablename>taxonoccurrence</tablename>
42
                    <userdefinedname>habit</userdefinedname>
42
                    <userdefinedname>growthForm</userdefinedname>
43 43
                </userdefined>
44 44
            </userdefined_id>
45 45
            <definedvalue>T</definedvalue>
......
155 155
            <userdefined_id>
156 156
                <userdefined>
157 157
                    <tablename>taxonoccurrence</tablename>
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                    <userdefinedname>habit</userdefinedname>
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                    <userdefinedname>growthForm</userdefinedname>
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                </userdefined>
160 160
            </userdefined_id>
161 161
            <definedvalue>T</definedvalue>
inputs/SALVIAS-CSV/maps/VegX.organisms.csv
28 28
"infra_ep_1","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=TaxonomicRankBelowSubspeciesEnum])/Name",
29 29
"cf_aff","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=binom])/{fit,Name/_name/middle}","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."
30 30
"comments",,"Brad: OMIT"
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"habit","/simpleUserdefined[name=habit]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
31
"habit","/simpleUserdefined[name=growthForm]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
32 32
"no_of_individuals","/simpleUserdefined[name=count]/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."
33 33
"cover_percent","/simpleUserdefined[name=coverPercent]/value",
34 34
"intercept_cm","/simpleUserdefined[name=interceptCm]/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
24 24
intercept_cm,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]:[@fkey=tableRecord_ID]/definedvalue","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."
25 25
notes,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=notes]]:[@fkey=tableRecord_ID]/definedvalue",
26 26
census_no,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=censusNo]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."
27
habit,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=habit]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
27
habit,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=growthForm]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
28 28
individual_code,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=individualCode]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
29 29
det_type,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=voucherType]]:[@fkey=tableRecord_ID]/definedvalue","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider  asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen."
30 30
coll_number,/specimenreplicate:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string
mappings/VegX-VegBIEN.organisms.csv
87 87
/simpleUserdefined[name=lianaInfestation]/value,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=lianaInfestation]]:[@fkey=tableRecord_ID]/definedvalue",
88 88
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/note/text,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=notes]]:[@fkey=tableRecord_ID]/definedvalue",
89 89
/simpleUserdefined[name=censusNo]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=censusNo]]:[@fkey=tableRecord_ID]/definedvalue",
90
/simpleUserdefined[name=habit]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=habit]]:[@fkey=tableRecord_ID]/definedvalue",
90
/simpleUserdefined[name=growthForm]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=growthForm]]:[@fkey=tableRecord_ID]/definedvalue",
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/simpleUserdefined[name=individualCode]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=individualCode]]:[@fkey=tableRecord_ID]/definedvalue",
92 92
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/groupType","/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=voucherType]]:[@fkey=tableRecord_ID]/definedvalue",
93 93
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,/specimenreplicate:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/*_id/reference/shortname/_alt/1,
mappings/for_review/VegX-VegBIEN.organisms.csv
87 87
/simpleUserdefined[name=lianaInfestation]/value,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=lianaInfestation]]/definedvalue",
88 88
//note/text,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=notes]]/definedvalue",
89 89
/simpleUserdefined[name=censusNo]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=censusNo]]/definedvalue",
90
/simpleUserdefined[name=habit]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=habit]]/definedvalue",
90
/simpleUserdefined[name=growthForm]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=growthForm]]/definedvalue",
91 91
/simpleUserdefined[name=individualCode]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=individualCode]]/definedvalue",
92 92
//*s/taxonDetermination[role=collector]/groupType,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=voucherType]]/definedvalue",
93 93
//party/organizationName,//reference/shortname/_alt/1,

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