Revision 1754
Added by Aaron Marcuse-Kubitza almost 13 years ago
inputs/SALVIAS-CSV/maps/VegX.organisms.csv | ||
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31 | 31 |
"habit","/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 | 32 |
"no_of_individuals","/*ID->/*s/individualOrganism/*sID->/*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." |
33 | 33 |
"cover_percent","/volumeCanopy/*ID->/*s/attribute/ordinal/coverPercent", |
34 |
"intercept_cm","/simpleUserdefined[name=lineCover]/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."
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34 |
"intercept_cm","/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."
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35 | 35 |
"height_m","/height","Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob" |
36 | 36 |
"ht_first_branch_m","/simpleUserdefined[name=heightFirstBranch]/value","Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob" |
37 | 37 |
"stem_tag1","/*ID->/*s/individualOrganism/identificationLabel","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." |
inputs/SALVIAS-CSV/maps/VegX.organisms.full.csv | ||
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31 | 31 |
"habit","/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 | 32 |
"no_of_individuals","/*ID->/*s/individualOrganism/*sID->/*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." |
33 | 33 |
"cover_percent","/volumeCanopy/*ID->/*s/attribute/ordinal/coverPercent", |
34 |
"intercept_cm","/simpleUserdefined[name=lineCover]/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."
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34 |
"intercept_cm","/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."
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35 | 35 |
"height_m","/height","Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob" |
36 | 36 |
"ht_first_branch_m","/simpleUserdefined[name=heightFirstBranch]/value","Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob" |
37 | 37 |
"stem_tag1","/*ID->/*s/individualOrganism/identificationLabel","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." |
inputs/SALVIAS/maps/VegX.organisms.csv | ||
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44 | 44 |
"ht_first_branch_m","/simpleUserdefined[name=heightFirstBranch]/value","Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob" |
45 | 45 |
"NoInd","/*ID->/*s/individualOrganism/*sID->/*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","/volumeCanopy/*ID->/*s/attribute/ordinal/coverPercent", |
47 |
"intercept_cm","/simpleUserdefined[name=lineCover]/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."
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47 |
"intercept_cm","/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."
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48 | 48 |
"cfaff","/*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." |
49 | 49 |
"other_annotations",, |
50 | 50 |
"morphocf",, |
inputs/SALVIAS/maps/VegX.organisms.full.csv | ||
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44 | 44 |
"ht_first_branch_m","/simpleUserdefined[name=heightFirstBranch]/value","Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob" |
45 | 45 |
"NoInd","/*ID->/*s/individualOrganism/*sID->/*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","/volumeCanopy/*ID->/*s/attribute/ordinal/coverPercent", |
47 |
"intercept_cm","/simpleUserdefined[name=lineCover]/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."
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47 |
"intercept_cm","/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."
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48 | 48 |
"cfaff","/*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." |
49 | 49 |
"other_annotations",, |
50 | 50 |
"morphocf",, |
mappings/VegX-VegBIEN.organisms.csv | ||
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86 | 86 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/aggregateOrganismObservation[*ID]/*/aggregateValue/value,/aggregateoccurrence/count, |
87 | 87 |
/volumeCanopy/*ID->/*s/attribute/ordinal/coverPercent,/aggregateoccurrence/cover, |
88 | 88 |
/simpleUserdefined[name=censusNo]/value,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]:[@fkey=tablerecord_id]/definedvalue", |
89 |
/simpleUserdefined[name=lineCover]/value,/aggregateoccurrence/linecover,
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89 |
/volumeCanopy/value,/aggregateoccurrence/linecover,
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90 | 90 |
/simpleUserdefined[name=growthForm]/value,/growthform, |
91 | 91 |
/simpleUserdefined[name=collectionDate]/value,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate, |
92 | 92 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=TaxonomicRankBelowSubspeciesEnum])/Rank","/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/first", |
mappings/for_review/VegX-VegBIEN.organisms.csv | ||
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86 | 86 |
//*s/aggregateOrganismObservation/*/aggregateValue/value,//aggregateoccurrence/count, |
87 | 87 |
//ordinal/coverPercent,//aggregateoccurrence/cover, |
88 | 88 |
/simpleUserdefined[name=censusNo]/value,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]/definedvalue", |
89 |
/simpleUserdefined[name=lineCover]/value,//aggregateoccurrence/linecover,
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89 |
//volumeCanopy/value,//aggregateoccurrence/linecover,
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90 | 90 |
/simpleUserdefined[name=growthForm]/value,/growthform, |
91 | 91 |
/simpleUserdefined[name=collectionDate]/value,//specimenreplicate/collectiondate, |
92 | 92 |
//*s/taxonConcept[@code=TaxonomicRankBelowSubspeciesEnum]/Rank,"/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath/path/_forEach:[do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/first", |
Also available in: Unified diff
VegX-VegBIEN.organisms.csv: Re-mapped individualOrganismObservation user-defined field lineCover to already existing volumeCanopy