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Revision 530

VegBIEN: Use stem instead of individualplant to store diameter/dbh

View differences:

test/accepted_output/SALVIAS.organisms.VegBIEN.xml
22 22
        <aggregateoccurrence>
23 23
            <count>1</count>
24 24
            <individualplant>
25
                <diameter>662</diameter>
26 25
                <specimen>
27 26
                    <reference_id>
28 27
                        <reference/>
......
36 35
                    <sourceaccessionnumber>607771</sourceaccessionnumber>
37 36
                </specimen>
38 37
                <stem>
38
                    <diameter>662</diameter>
39 39
                    <sourceid>8</sourceid>
40 40
                </stem>
41 41
                <sourceid>607771</sourceid>
......
291 291
        <aggregateoccurrence>
292 292
            <count>1</count>
293 293
            <individualplant>
294
                <diameter>215</diameter>
295 294
                <specimen>
296 295
                    <reference_id>
297 296
                        <reference/>
......
305 304
                    <sourceaccessionnumber>607722</sourceaccessionnumber>
306 305
                </specimen>
307 306
                <stem>
307
                    <diameter>215</diameter>
308 308
                    <sourceid>91</sourceid>
309 309
                </stem>
310 310
                <sourceid>607722</sourceid>
inputs/SALVIAS/maps/VegBIEN.organisms.csv
3 3
NoInd,/aggregateoccurrence/count/_alt/1,"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."
4 4
cover_percent,/aggregateoccurrence/cover,
5 5
intercept_cm,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@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."
6
temp_dbh,/aggregateoccurrence/individualplant/diameter,
7 6
height_m,/aggregateoccurrence/individualplant/height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
8 7
coll_number,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string
9 8
census_date,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/collectiondate/_date/date,
10 9
coll_firstname,"/aggregateoccurrence/individualplant/specimen:[*_id/reference]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}",Brad: See comment above
11 10
coll_lastname,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/collector_id/party/{surname},"Brad: Correct for VegBank. This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
12 11
ht_first_branch_m,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
12
temp_dbh,/aggregateoccurrence/individualplant/stem/diameter,
13 13
tag2,/aggregateoccurrence/individualplant/stem/sourceid/_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."
14 14
tag1,/aggregateoccurrence/individualplant/stem/sourceid/_alt/2,"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."
15 15
x_position,/aggregateoccurrence/individualplant/stem/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."
schemas/vegbien.sql
1055 1055
CREATE TABLE individualplant (
1056 1056
    individualplant_id integer NOT NULL,
1057 1057
    aggregateoccurrence_id integer NOT NULL,
1058
    diameter double precision,
1059
    diameteraccuracy double precision,
1060 1058
    height double precision,
1061 1059
    heightaccuracy double precision,
1062 1060
    emb_individualplant integer,
mappings/SALVIAS_db-VegBIEN.organisms.csv
3 3
NoInd,/aggregateoccurrence/count/_alt/1,"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."
4 4
cover_percent,/aggregateoccurrence/cover,
5 5
intercept_cm,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@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."
6
temp_dbh,/aggregateoccurrence/individualplant/diameter,
7 6
height_m,/aggregateoccurrence/individualplant/height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
8 7
coll_number,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string
9 8
census_date,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/collectiondate/_date/date,
10 9
coll_firstname,"/aggregateoccurrence/individualplant/specimen:[*_id/reference]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}",Brad: See comment above
11 10
coll_lastname,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/collector_id/party/{surname},"Brad: Correct for VegBank. This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
12 11
ht_first_branch_m,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
12
temp_dbh,/aggregateoccurrence/individualplant/stem/diameter,
13 13
tag2,/aggregateoccurrence/individualplant/stem/sourceid/_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."
14 14
tag1,/aggregateoccurrence/individualplant/stem/sourceid/_alt/2,"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."
15 15
x_position,/aggregateoccurrence/individualplant/stem/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."
mappings/VegX-VegBIEN.organisms.csv
53 53
/simpleUserdefined[name=count]/value,/aggregateoccurrence/count/_alt/1
54 54
/simpleUserdefined[name=coverPercent]/value,/aggregateoccurrence/cover
55 55
/simpleUserdefined[name=interceptCm]/value,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
56
/diameterBaseDistance[baseDistance/value=1.37]/diameter,/aggregateoccurrence/individualplant/diameter
57 56
/height,/aggregateoccurrence/individualplant/height
58 57
/simpleUserdefined[name=stemHeightM]/value,/aggregateoccurrence/individualplant/height
59 58
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/authorCode,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/catalognumber_dwc
......
85 84
/simpleUserdefined[name=substrate]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=substrate]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
86 85
/simpleUserdefined[name=vegetation]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=vegetation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
87 86
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance[!complexUserDefined/method]/value=1.37]/diameter,/aggregateoccurrence/individualplant/stem/diameter
87
/diameterBaseDistance[baseDistance/value=1.37]/diameter,/aggregateoccurrence/individualplant/stem/diameter
88 88
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=stemHeightM]/value,/aggregateoccurrence/individualplant/stem/height
89 89
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/*ID->/*s/individualOrganism/identificationLabel,/aggregateoccurrence/individualplant/stem/sourceid
90 90
/*ID->/*s/individualOrganism/identificationLabel,/aggregateoccurrence/individualplant/stem/sourceid
mappings/for_review/SALVIAS_db-VegBIEN.organisms.csv
3 3
NoInd,//aggregateoccurrence/count/_alt/1,"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."
4 4
cover_percent,//aggregateoccurrence/cover,
5 5
intercept_cm,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]/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."
6
temp_dbh,//individualplant/diameter,
7 6
height_m,//individualplant/height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
8 7
coll_number,//specimen/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string
9 8
census_date,//specimen/collectiondate/_date/date,
10 9
coll_firstname,"/aggregateoccurrence/individualplant/specimen/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}",Brad: See comment above
11 10
coll_lastname,/aggregateoccurrence/individualplant/specimen/collector_id/party/{surname},"Brad: Correct for VegBank. This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
12 11
ht_first_branch_m,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
12
temp_dbh,//stem/diameter,
13 13
tag2,//stem/sourceid/_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."
14 14
tag1,//stem/sourceid/_alt/2,"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."
15 15
x_position,//stem/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."
mappings/for_review/VegX-VegBIEN.organisms.csv
53 53
/simpleUserdefined[name=count]/value,//aggregateoccurrence/count/_alt/1
54 54
/simpleUserdefined[name=coverPercent]/value,//aggregateoccurrence/cover
55 55
/simpleUserdefined[name=interceptCm]/value,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]/definedvalue"
56
/diameterBaseDistance[value=1.37]/diameter,//individualplant/diameter
57 56
/height,//individualplant/height
58 57
/simpleUserdefined[name=stemHeightM]/value,//individualplant/height
59 58
//taxonNameUsageConcept/authorCode,//specimen/catalognumber_dwc
......
85 84
/simpleUserdefined[name=substrate]/value,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=substrate]]/definedvalue"
86 85
/simpleUserdefined[name=vegetation]/value,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=vegetation]]/definedvalue"
87 86
//*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance[]/value=1.37]/diameter,//stem/diameter
87
/diameterBaseDistance[value=1.37]/diameter,//stem/diameter
88 88
//*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=stemHeightM]/value,//stem/height
89 89
//individualOrganism/identificationLabel,//stem/sourceid
90 90
//individualOrganism/identificationLabel,//stem/sourceid
mappings/for_review/SALVIAS-VegBIEN.organisms.csv
5 5
no_of_individuals,//aggregateoccurrence/count/_alt/1,"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."
6 6
cover_percent,//aggregateoccurrence/cover,
7 7
intercept_cm,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]/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."
8
stem_dbh,//individualplant/diameter,
9 8
height_m,//individualplant/height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
10 9
stem_height_m,//individualplant/height,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
11 10
coll_number,//specimen/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string
......
17 16
ht_first_branch_m,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
18 17
stem_height_first_branch_m,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]/definedvalue","Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
19 18
stem_liana_infestation,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=lianaInfestation]]/definedvalue",Brad: Should also be userDefined for VegBank. 
19
stem_dbh,//stem/diameter,
20 20
stem_tag1,//stem/sourceid,"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."
21 21
stem_tag2,//stem/sourceid,Brad: see above
22 22
tag2,//stem/sourceid/_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."
mappings/SALVIAS-VegBIEN.organisms.csv
5 5
no_of_individuals,/aggregateoccurrence/count/_alt/1,"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."
6 6
cover_percent,/aggregateoccurrence/cover,
7 7
intercept_cm,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@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."
8
stem_dbh,/aggregateoccurrence/individualplant/diameter,
9 8
height_m,/aggregateoccurrence/individualplant/height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
10 9
stem_height_m,/aggregateoccurrence/individualplant/height,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
11 10
coll_number,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string
......
17 16
ht_first_branch_m,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
18 17
stem_height_first_branch_m,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
19 18
stem_liana_infestation,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=lianaInfestation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. 
19
stem_dbh,/aggregateoccurrence/individualplant/stem/diameter,
20 20
stem_tag1,/aggregateoccurrence/individualplant/stem/sourceid,"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."
21 21
stem_tag2,/aggregateoccurrence/individualplant/stem/sourceid,Brad: see above
22 22
tag2,/aggregateoccurrence/individualplant/stem/sourceid/_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."

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