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Revision 608

VegX-VegBIEN mapping: Take advantage of aggregateoccurrence.count being optional

View differences:

test/accepted_output/SALVIAS_db.organisms.VegBIEN.xml
173 173
            <originaldetermination>true</originaldetermination>
174 174
            <currentdetermination>true</currentdetermination>
175 175
        </taxondetermination>
176
        <specimen>
177
            <reference_id>
178
                <reference/>
179
            </reference_id>
180
            <sourceaccessioncode>1</sourceaccessioncode>
181
        </specimen>
176 182
        <taxondetermination>
177 183
            <role_id>
178 184
                <role>
......
195 201
            <originaldetermination>true</originaldetermination>
196 202
            <currentdetermination>true</currentdetermination>
197 203
        </taxondetermination>
198
        <specimen>
199
            <reference_id>
200
                <reference/>
201
            </reference_id>
202
            <sourceaccessioncode>1</sourceaccessioncode>
203
        </specimen>
204 204
    </taxonoccurrence>
205 205
    <taxonoccurrence id="1">
206 206
        <locationevent_id>
......
375 375
            <originaldetermination>true</originaldetermination>
376 376
            <currentdetermination>true</currentdetermination>
377 377
        </taxondetermination>
378
        <specimen>
379
            <reference_id>
380
                <reference/>
381
            </reference_id>
382
            <sourceaccessioncode>2</sourceaccessioncode>
383
        </specimen>
378 384
        <taxondetermination>
379 385
            <role_id>
380 386
                <role>
......
397 403
            <originaldetermination>true</originaldetermination>
398 404
            <currentdetermination>true</currentdetermination>
399 405
        </taxondetermination>
400
        <specimen>
401
            <reference_id>
402
                <reference/>
403
            </reference_id>
404
            <sourceaccessioncode>2</sourceaccessioncode>
405
        </specimen>
406 406
    </taxonoccurrence>
407 407
</VegBIEN>
test/accepted_output/NYBG.organisms.VegBIEN.xml
63 63
                </stem>
64 64
                <authorplantcode>816590</authorplantcode>
65 65
            </individualplant>
66
            <count>1</count>
67 66
        </aggregateoccurrence>
68 67
        <specimen>
69 68
            <reference_id>
......
374 373
            <currentdetermination>true</currentdetermination>
375 374
        </taxondetermination>
376 375
        <aggregateoccurrence>
377
            <count>1</count>
378 376
            <individualplant>
379 377
                <authorplantcode>220541</authorplantcode>
380 378
            </individualplant>
inputs/SALVIAS/maps/VegBIEN.organisms.csv
1 1
SALVIAS:plotObservations,VegBIEN:/taxonoccurrence,Comments
2 2
PlotID,/*_id/locationevent/authoreventcode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
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."
3
NoInd,/aggregateoccurrence/count,"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]]:[@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 6
height_m,/aggregateoccurrence/individualplant/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
......
27 27
infra_rank_1,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/{*_id/*/plantname/_name/first,*_id/plantconcept/_name/first}",
28 28
infra_ep_1,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept/_name/last",
29 29
OrigFamily,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname",Brad: OMIT
30
PlotObsID,"/{aggregateoccurrence/individualplant/authorplantcode,specimen:[*_id/reference]/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."
30 31
OrigSpecies,"/{taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname/_alt/2,taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname}",Brad: OMIT
31
PlotObsID,":[aggregateoccurrence/count/_alt/2=1]/{aggregateoccurrence/individualplant/authorplantcode,specimen:[*_id/reference]/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."
mappings/SALVIAS_db-VegBIEN.organisms.csv
1 1
SALVIAS:plotObservations,VegBIEN:/taxonoccurrence,Comments
2 2
PlotID,/*_id/locationevent/authoreventcode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
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."
3
NoInd,/aggregateoccurrence/count,"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]]:[@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 6
height_m,/aggregateoccurrence/individualplant/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
......
27 27
infra_rank_1,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/{*_id/*/plantname/_name/first,*_id/plantconcept/_name/first}",
28 28
infra_ep_1,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept/_name/last",
29 29
OrigFamily,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname",Brad: OMIT
30
PlotObsID,"/{aggregateoccurrence/individualplant/authorplantcode,specimen:[*_id/reference]/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."
30 31
OrigSpecies,"/{taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname/_alt/2,taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname}",Brad: OMIT
31
PlotObsID,":[aggregateoccurrence/count/_alt/2=1]/{aggregateoccurrence/individualplant/authorplantcode,specimen:[*_id/reference]/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."
mappings/VegX-VegBIEN.organisms.csv
50 50
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=texture]/value,/*_id/locationevent/soilobs:[soilhorizon=unknown]/soiltexture
51 51
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/maximumDepthInMeters,/*_id/locationevent/waterdepth/max
52 52
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/minimumDepthInMeters,/*_id/locationevent/waterdepth/min
53
/simpleUserdefined[name=count]/value,/aggregateoccurrence/count/_alt/1
53
/simpleUserdefined[name=count]/value,/aggregateoccurrence/count
54 54
/simpleUserdefined[name=coverPercent]/value,/aggregateoccurrence/cover
55 55
/simpleUserdefined[name=interceptCm]/value,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]:[@fkey=tableRecord_ID]/definedvalue"
56 56
/height,/aggregateoccurrence/individualplant/overallheight
......
121 121
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=ord])/Name","/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Order]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname"
122 122
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=phyl_div])/Name","/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname"
123 123
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=ssp])/Name","/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/*_id/plantconcept/*_id/*/plantname"
124
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,"/{aggregateoccurrence/individualplant/authorplantcode,specimen:[*_id/reference]/sourceaccessioncode}"
124 125
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=sp])/Name","/{taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname/_alt/2,taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname}"
125
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,":[aggregateoccurrence/count/_alt/2=1]/{aggregateoccurrence/individualplant/authorplantcode,specimen:[*_id/reference]/sourceaccessioncode}"
mappings/NYBG-VegBIEN.organisms.csv
38 38
Order,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Order]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname",
39 39
Phylum,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname",
40 40
Subspecies,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/*_id/plantconcept/*_id/*/plantname",
41
UniqueNYInternalRecordNumber,"/{aggregateoccurrence/individualplant/authorplantcode,specimen:[*_id/reference]/sourceaccessioncode}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key"
41 42
Species,"/{taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname/_alt/2,taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname}",
42
UniqueNYInternalRecordNumber,":[aggregateoccurrence/count/_alt/2=1]/{aggregateoccurrence/individualplant/authorplantcode,specimen:[*_id/reference]/sourceaccessioncode}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key"
mappings/for_review/SALVIAS_db-VegBIEN.organisms.csv
1 1
SALVIAS:plotObservations,VegBIEN:/taxonoccurrence,Comments
2 2
PlotID,//locationevent/authoreventcode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
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."
3
NoInd,//aggregateoccurrence/count,"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 6
height_m,//individualplant/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
......
27 27
infra_rank_1,"/taxondetermination[rolecode=computer,plantlevel=Subspecies]/{*_id/*/plantname/_name/first,*_id/plantconcept/_name/first}",
28 28
infra_ep_1,"/taxondetermination[rolecode=computer,plantlevel=Subspecies]/*_id/plantconcept/_name/last",
29 29
OrigFamily,"/taxondetermination[rolecode=identifier,plantlevel=Family]/*_id/plantconcept/*_id/*/plantname",Brad: OMIT
30
PlotObsID,"/{aggregateoccurrence/individualplant/authorplantcode,specimen/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."
30 31
OrigSpecies,"/{taxondetermination[rolecode=collector]/*_id/plantconcept/*_id/*/plantname/_alt/2,taxondetermination[rolecode=identifier,plantlevel=Species]/*_id/plantconcept/*_id/*/plantname}",Brad: OMIT
31
PlotObsID,"/{aggregateoccurrence/individualplant/authorplantcode,specimen/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."
mappings/for_review/VegX-VegBIEN.organisms.csv
50 50
//*s/abioticObservation/simpleUserdefined[name=texture]/value,//soilobs/soiltexture
51 51
//geospatial/maximumDepthInMeters,//waterdepth/max
52 52
//geospatial/minimumDepthInMeters,//waterdepth/min
53
/simpleUserdefined[name=count]/value,//aggregateoccurrence/count/_alt/1
53
/simpleUserdefined[name=count]/value,//aggregateoccurrence/count
54 54
/simpleUserdefined[name=coverPercent]/value,//aggregateoccurrence/cover
55 55
/simpleUserdefined[name=interceptCm]/value,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]/definedvalue"
56 56
/height,//individualplant/overallheight
......
121 121
//*s/taxonConcept[@code=ord]/Name,"/taxondetermination[rolecode=identifier,plantlevel=Order]/*_id/plantconcept/*_id/*/plantname"
122 122
//*s/taxonConcept[@code=phyl_div]/Name,"/taxondetermination[rolecode=identifier,plantlevel=Subkingdom]/*_id/plantconcept/*_id/*/plantname"
123 123
//*s/taxonConcept[@code=ssp]/Name,"/taxondetermination[rolecode=identifier,plantlevel=Subspecies]/*_id/plantconcept/*_id/*/plantname"
124
//taxonNameUsageConcept/voucher,"/{aggregateoccurrence/individualplant/authorplantcode,specimen/sourceaccessioncode}"
124 125
//*s/taxonConcept[@code=sp]/Name,"/{taxondetermination[rolecode=collector]/*_id/plantconcept/*_id/*/plantname/_alt/2,taxondetermination[rolecode=identifier,plantlevel=Species]/*_id/plantconcept/*_id/*/plantname}"
125
//taxonNameUsageConcept/voucher,"/{aggregateoccurrence/individualplant/authorplantcode,specimen/sourceaccessioncode}"
mappings/for_review/NYBG-VegBIEN.organisms.csv
38 38
Order,"/taxondetermination[rolecode=identifier,plantlevel=Order]/*_id/plantconcept/*_id/*/plantname",
39 39
Phylum,"/taxondetermination[rolecode=identifier,plantlevel=Subkingdom]/*_id/plantconcept/*_id/*/plantname",
40 40
Subspecies,"/taxondetermination[rolecode=identifier,plantlevel=Subspecies]/*_id/plantconcept/*_id/*/plantname",
41
UniqueNYInternalRecordNumber,"/{aggregateoccurrence/individualplant/authorplantcode,specimen/sourceaccessioncode}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key"
41 42
Species,"/{taxondetermination[rolecode=collector]/*_id/plantconcept/*_id/*/plantname/_alt/2,taxondetermination[rolecode=identifier,plantlevel=Species]/*_id/plantconcept/*_id/*/plantname}",
42
UniqueNYInternalRecordNumber,"/{aggregateoccurrence/individualplant/authorplantcode,specimen/sourceaccessioncode}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key"
mappings/for_review/SALVIAS-VegBIEN.organisms.csv
2 2
subplot,//location/authorlocationcode,
3 3
plot_code,//location/authorlocationcode,"Brad: Same as plotCode, above"
4 4
census_date,//locationevent/obsstartdate/_date/year,
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."
5
no_of_individuals,//aggregateoccurrence/count,"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 8
height_m,//individualplant/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
......
36 36
infra_rank_1,"/taxondetermination[rolecode=computer,plantlevel=Subspecies]/{*_id/*/plantname/_name/first,*_id/plantconcept/_name/first}",
37 37
infra_ep_1,"/taxondetermination[rolecode=computer,plantlevel=Subspecies]/*_id/plantconcept/_name/last",
38 38
orig_family,"/taxondetermination[rolecode=identifier,plantlevel=Family]/*_id/plantconcept/*_id/*/plantname",Brad: OMIT
39
OBSERVATION_ID,"/{aggregateoccurrence/individualplant/authorplantcode,specimen/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."
39 40
orig_species,"/{taxondetermination[rolecode=collector]/*_id/plantconcept/*_id/*/plantname/_alt/2,taxondetermination[rolecode=identifier,plantlevel=Species]/*_id/plantconcept/*_id/*/plantname}",Brad: OMIT
40
OBSERVATION_ID,"/{aggregateoccurrence/individualplant/authorplantcode,specimen/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."
mappings/SALVIAS-VegBIEN.organisms.csv
2 2
subplot,/*_id/locationevent/*_id/location/authorlocationcode,
3 3
plot_code,/*_id/locationevent/*_id/location/parent_id/location/authorlocationcode,"Brad: Same as plotCode, above"
4 4
census_date,/*_id/locationevent/obsstartdate/_date/year,
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."
5
no_of_individuals,/aggregateoccurrence/count,"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]]:[@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 8
height_m,/aggregateoccurrence/individualplant/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
......
36 36
infra_rank_1,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/{*_id/*/plantname/_name/first,*_id/plantconcept/_name/first}",
37 37
infra_ep_1,"/taxondetermination[role_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",currentdetermination=true]/*_id/plantconcept/_name/last",
38 38
orig_family,"/taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname",Brad: OMIT
39
OBSERVATION_ID,"/{aggregateoccurrence/individualplant/authorplantcode,specimen:[*_id/reference]/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."
39 40
orig_species,"/{taxondetermination[role_id/role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname/_alt/2,taxondetermination[role_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true]/*_id/plantconcept/*_id/*/plantname}",Brad: OMIT
40
OBSERVATION_ID,":[aggregateoccurrence/count/_alt/2=1]/{aggregateoccurrence/individualplant/authorplantcode,specimen:[*_id/reference]/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."

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