Revision 1061
Added by Aaron Marcuse-Kubitza almost 13 years ago
| inputs/SALVIAS/test/VegX.organisms.xml.ref | ||
|---|---|---|
| 3 | 3 |
<individualOrganismObservations> |
| 4 | 4 |
<individualOrganismObservation id="0"> |
| 5 | 5 |
<individualOrganismID>0</individualOrganismID> |
| 6 |
<simpleUserdefined> |
|
| 7 |
<name>sourceaccessioncode</name> |
|
| 8 |
<value>1</value> |
|
| 9 |
</simpleUserdefined> |
|
| 6 | 10 |
<plotObservationID>0</plotObservationID> |
| 7 | 11 |
<simpleUserdefined> |
| 8 | 12 |
<name>censusNo</name> |
| ... | ... | |
| 23 | 27 |
</individualOrganismObservation> |
| 24 | 28 |
<individualOrganismObservation id="1"> |
| 25 | 29 |
<individualOrganismID>1</individualOrganismID> |
| 30 |
<simpleUserdefined> |
|
| 31 |
<name>sourceaccessioncode</name> |
|
| 32 |
<value>2</value> |
|
| 33 |
</simpleUserdefined> |
|
| 26 | 34 |
<plotObservationID>1</plotObservationID> |
| 27 | 35 |
<simpleUserdefined> |
| 28 | 36 |
<name>censusNo</name> |
| ... | ... | |
| 49 | 57 |
<taxonNameUsageConcepts> |
| 50 | 58 |
<taxonNameUsageConcept id="0"> |
| 51 | 59 |
<partyWithRole><partyID>0</partyID></partyWithRole> |
| 52 |
<voucher>1</voucher> |
|
| 60 |
<voucher>931</voucher>
|
|
| 53 | 61 |
</taxonNameUsageConcept> |
| 54 | 62 |
<taxonNameUsageConcept id="1"> |
| 55 | 63 |
<partyWithRole><partyID>2</partyID></partyWithRole> |
| 56 |
<voucher>2</voucher>
|
|
| 64 |
<voucher>933</voucher>
|
|
| 57 | 65 |
</taxonNameUsageConcept> |
| 58 | 66 |
</taxonNameUsageConcepts> |
| 59 | 67 |
<parties> |
| inputs/SALVIAS/test/VegBIEN.organisms.xml.ref | ||
|---|---|---|
| 8 | 8 |
</locationevent> |
| 9 | 9 |
</locationevent_id> |
| 10 | 10 |
<aggregateoccurrence> |
| 11 |
<plantobservation_id><plantobservation><authorplantcode>1</authorplantcode></plantobservation></plantobservation_id>
|
|
| 11 |
<plantobservation_id><plantobservation><sourceaccessioncode>1</sourceaccessioncode></plantobservation></plantobservation_id>
|
|
| 12 | 12 |
<count>1</count> |
| 13 | 13 |
</aggregateoccurrence> |
| 14 | 14 |
<definedvalue fkey="tableRecord_ID"> |
| ... | ... | |
| 47 | 47 |
</userdefined_id> |
| 48 | 48 |
<definedvalue>direct</definedvalue> |
| 49 | 49 |
</definedvalue> |
| 50 |
<specimenreplicate> |
|
| 51 |
<datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id> |
|
| 52 |
<catalognumber_dwc>931</catalognumber_dwc> |
|
| 53 |
</specimenreplicate> |
|
| 50 | 54 |
<taxondetermination> |
| 51 | 55 |
<role_id><role><rolecode>computer</rolecode></role></role_id> |
| 52 | 56 |
<plantconcept_id> |
| ... | ... | |
| 124 | 128 |
</locationevent> |
| 125 | 129 |
</locationevent_id> |
| 126 | 130 |
<aggregateoccurrence> |
| 127 |
<plantobservation_id><plantobservation><authorplantcode>2</authorplantcode></plantobservation></plantobservation_id>
|
|
| 131 |
<plantobservation_id><plantobservation><sourceaccessioncode>2</sourceaccessioncode></plantobservation></plantobservation_id>
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|
| 128 | 132 |
<count>1</count> |
| 129 | 133 |
</aggregateoccurrence> |
| 130 | 134 |
<definedvalue fkey="tableRecord_ID"> |
| ... | ... | |
| 163 | 167 |
</userdefined_id> |
| 164 | 168 |
<definedvalue>direct</definedvalue> |
| 165 | 169 |
</definedvalue> |
| 170 |
<specimenreplicate> |
|
| 171 |
<datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id> |
|
| 172 |
<catalognumber_dwc>933</catalognumber_dwc> |
|
| 173 |
</specimenreplicate> |
|
| 166 | 174 |
<taxondetermination> |
| 167 | 175 |
<role_id><role><rolecode>computer</rolecode></role></role_id> |
| 168 | 176 |
<plantconcept_id> |
| inputs/SALVIAS/test/import.organisms.out.ref | ||
|---|---|---|
| 1 |
Inserted 85 new rows into database |
|
| 1 |
Inserted 87 new rows into database |
|
| inputs/SALVIAS/maps/VegX.organisms.csv | ||
|---|---|---|
| 1 | 1 |
"SALVIAS:plotObservations","VegX:/*s/individualOrganismObservation","Comments" |
| 2 |
"PlotObsID","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
|
|
| 2 |
"PlotObsID",":[*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/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."
|
|
| 3 | 3 |
"PlotID","/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=authorCode]/value","Brad: Not sure why this is repeated? This field and plotCode, as the same as above." |
| 4 | 4 |
"PlotCode",,"Brad: Same as plotCode, above" |
| 5 | 5 |
"census_no","/simpleUserdefined[name=censusNo]/value","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not." |
| ... | ... | |
| 14 | 14 |
"y_position","/simpleUserdefined[name=yPosition]/value","Brad: See comment above for x_position" |
| 15 | 15 |
"dist",, |
| 16 | 16 |
"perp_dist",, |
| 17 |
"SourceVoucher",,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
|
| 18 |
"coll_number","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/authorCode","Brad: Incorrect. Map instead as for voucher_string"
|
|
| 17 |
"SourceVoucher","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
|
|
| 18 |
"coll_number","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher/_alt/1","Brad: Incorrect. Map instead as for voucher_string"
|
|
| 19 | 19 |
"collector_code",,"Brad: OMIT" |
| 20 | 20 |
"coll_inits",, |
| 21 | 21 |
"coll_lastname","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/partyWithRole/*ID->/parties/party/individualName/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." |
| inputs/SALVIAS/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 1 | 1 |
SALVIAS:plotObservations,VegBIEN:/taxonoccurrence,Comments |
| 2 | 2 |
PlotID,/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authoreventcode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above." |
| 3 |
PlotObsID,/aggregateoccurrence/*_id/plantobservation/authorplantcode,"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." |
|
| 4 | 3 |
height_m,/aggregateoccurrence/*_id/plantobservation/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
| 4 |
PlotObsID,/aggregateoccurrence/*_id/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." |
|
| 5 | 5 |
ht_first_branch_m,"/aggregateoccurrence/*_id/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
| 6 | 6 |
temp_dbh,/aggregateoccurrence/*_id/plantobservation/stemobservation/diameter, |
| 7 | 7 |
tag1,"/aggregateoccurrence/*_id/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" |
| ... | ... | |
| 19 | 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 |
coll_number,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string |
|
| 22 |
coll_number,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/1,Brad: Incorrect. Map instead as for voucher_string |
|
| 23 |
SourceVoucher,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
|
| 23 | 24 |
census_date,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate/_*/date, |
| 24 | 25 |
auth,"/taxondetermination[*_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=""Computer (automated)"",iscurrent=true]/*_id/plantconcept/*_id/*/plantname",Brad: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss. |
| 25 | 26 |
Family,"/taxondetermination[*_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=""Computer (automated)"",iscurrent=true]/*_id/plantconcept/*_id/*/plantname", |
| ... | ... | |
| 39 | 40 |
OrigAuth,, |
| 40 | 41 |
OrigRecordID,, |
| 41 | 42 |
PlotCode,,"Brad: Same as plotCode, above" |
| 42 |
SourceVoucher,,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
|
| 43 | 43 |
SpAuthStatus,, |
| 44 | 44 |
coll_inits,, |
| 45 | 45 |
collector_code,,Brad: OMIT |
| inputs/SALVIAS-CSV/test/VegX.organisms.xml.ref | ||
|---|---|---|
| 3 | 3 |
<individualOrganismObservations> |
| 4 | 4 |
<individualOrganismObservation id="0"> |
| 5 | 5 |
<individualOrganismID>0</individualOrganismID> |
| 6 |
<simpleUserdefined> |
|
| 7 |
<name>sourceaccessioncode</name> |
|
| 8 |
<value>607771</value> |
|
| 9 |
</simpleUserdefined> |
|
| 6 | 10 |
<plotObservationID>0</plotObservationID> |
| 7 | 11 |
<simpleUserdefined> |
| 8 | 12 |
<name>censusNo</name> |
| ... | ... | |
| 31 | 35 |
</individualOrganismObservation> |
| 32 | 36 |
<individualOrganismObservation id="1"> |
| 33 | 37 |
<individualOrganismID>1</individualOrganismID> |
| 38 |
<simpleUserdefined> |
|
| 39 |
<name>sourceaccessioncode</name> |
|
| 40 |
<value>607722</value> |
|
| 41 |
</simpleUserdefined> |
|
| 34 | 42 |
<plotObservationID>1</plotObservationID> |
| 35 | 43 |
<simpleUserdefined> |
| 36 | 44 |
<name>censusNo</name> |
| ... | ... | |
| 71 | 79 |
<taxonNameUsageConcepts> |
| 72 | 80 |
<taxonNameUsageConcept id="0"> |
| 73 | 81 |
<partyWithRole><partyID>0</partyID></partyWithRole> |
| 74 |
<voucher>607771</voucher> |
|
| 75 |
<authorCode>14598</authorCode> |
|
| 82 |
<voucher>14598</voucher> |
|
| 76 | 83 |
</taxonNameUsageConcept> |
| 77 | 84 |
<taxonNameUsageConcept id="1"> |
| 78 | 85 |
<partyWithRole><partyID>3</partyID></partyWithRole> |
| 79 |
<voucher>607722</voucher> |
|
| 80 |
<authorCode>14669</authorCode> |
|
| 86 |
<voucher>14669</voucher> |
|
| 81 | 87 |
</taxonNameUsageConcept> |
| 82 | 88 |
</taxonNameUsageConcepts> |
| 83 | 89 |
<parties> |
| inputs/SALVIAS-CSV/test/VegBIEN.organisms.xml.ref | ||
|---|---|---|
| 17 | 17 |
<aggregateoccurrence> |
| 18 | 18 |
<plantobservation_id> |
| 19 | 19 |
<plantobservation> |
| 20 |
<authorplantcode>607771</authorplantcode>
|
|
| 20 |
<sourceaccessioncode>607771</sourceaccessioncode>
|
|
| 21 | 21 |
<stemobservation> |
| 22 | 22 |
<diameter>662</diameter> |
| 23 | 23 |
<stemtag> |
| ... | ... | |
| 140 | 140 |
<aggregateoccurrence> |
| 141 | 141 |
<plantobservation_id> |
| 142 | 142 |
<plantobservation> |
| 143 |
<authorplantcode>607722</authorplantcode>
|
|
| 143 |
<sourceaccessioncode>607722</sourceaccessioncode>
|
|
| 144 | 144 |
<stemobservation> |
| 145 | 145 |
<diameter>215</diameter> |
| 146 | 146 |
<stemtag> |
| inputs/SALVIAS-CSV/maps/VegX.organisms.csv | ||
|---|---|---|
| 1 | 1 |
"SALVIAS","VegX:/*s/individualOrganismObservation","Comments" |
| 2 |
"OBSERVATION_ID","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher","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."
|
|
| 2 |
"OBSERVATION_ID",":[*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceaccessioncode]/value","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
|
|
| 3 | 3 |
"PLOT_ID","/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=authorCode]/value","Brad: Not sure why this is repeated? This field and plotCode, as the same as above." |
| 4 | 4 |
"plot_code","/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/relatedSpatialItem/relatedItem[relationshipType=parentPlot]/relatedItemID->/*s/plot/plotUniqueIdentifier","Brad: Same as plotCode, above" |
| 5 | 5 |
"census_no","/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." |
| ... | ... | |
| 11 | 11 |
"tag2","/simpleUserdefined[name=tag2]/value","Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other." |
| 12 | 12 |
"x_position","/simpleUserdefined[name=xPosition]/value","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." |
| 13 | 13 |
"y_position","/simpleUserdefined[name=yPosition]/value","Brad: See comment above for x_position" |
| 14 |
"voucher_string",,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
|
| 15 |
"coll_number","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/authorCode","Brad: Incorrect. Map instead as for voucher_string"
|
|
| 14 |
"voucher_string","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
|
|
| 15 |
"coll_number","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher/_alt/1","Brad: Incorrect. Map instead as for voucher_string"
|
|
| 16 | 16 |
"collector_code",,"Brad: OMIT" |
| 17 | 17 |
"coll_lastname","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/partyWithRole/*ID->/parties/party/individualName/surName","Brad: Correct for VegBank. This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick." |
| 18 | 18 |
"coll_firstname","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/partyWithRole/*ID->/parties/party/individualName/givenName","Brad: See comment above" |
| inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 3 | 3 |
plot_code,/*_id/locationevent/*_id/location/parent_id/location/authorlocationcode,"Brad: Same as plotCode, above" |
| 4 | 4 |
census_date,/*_id/locationevent/obsstartdate/_date/year, |
| 5 | 5 |
PLOT_ID,/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authoreventcode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above." |
| 6 |
OBSERVATION_ID,/aggregateoccurrence/*_id/plantobservation/authorplantcode,"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." |
|
| 7 | 6 |
height_m,/aggregateoccurrence/*_id/plantobservation/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
| 8 | 7 |
stem_height_m,/aggregateoccurrence/*_id/plantobservation/overallheight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare." |
| 8 |
OBSERVATION_ID,/aggregateoccurrence/*_id/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." |
|
| 9 | 9 |
basal_diam,"/aggregateoccurrence/*_id/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=basalDiameter]]:[@fkey=tableRecord_ID]/definedvalue", |
| 10 | 10 |
stem_canopy_form,"/aggregateoccurrence/*_id/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. |
| 11 | 11 |
stem_canopy_position,"/aggregateoccurrence/*_id/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. |
| ... | ... | |
| 27 | 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 |
coll_number,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string |
|
| 30 |
coll_number,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/1,Brad: Incorrect. Map instead as for voucher_string |
|
| 31 |
voucher_string,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
|
| 31 | 32 |
specific_authority,"/taxondetermination[*_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=""Computer (automated)"",iscurrent=true]/*_id/plantconcept/*_id/*/plantname",Brad: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss. |
| 32 | 33 |
family,"/taxondetermination[*_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=""Computer (automated)"",iscurrent=true]/*_id/plantconcept/*_id/*/plantname", |
| 33 | 34 |
genus,"/taxondetermination[*_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=""Computer (automated)"",iscurrent=true]/*_id/plantconcept/*_id/*/plantname", |
| ... | ... | |
| 45 | 46 |
gen_status,,Brad: OMIT. This will be determined later by using TNRS. |
| 46 | 47 |
ind_id,,Brad: OMIT |
| 47 | 48 |
species_status,,"Brad: OMIT. Except, note that if species_status=3, this indicate that name is a morphospecies and not a standard latin name. Not exactly sure how to use this in BIEN, but could be useful during the name-scrubbing process with TNRS." |
| 48 |
voucher_string,,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
|
| mappings/VegX-VegBIEN.organisms.csv | ||
|---|---|---|
| 50 | 50 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/minimumDepthInMeters,/*_id/locationevent/waterdepth/min, |
| 51 | 51 |
/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=authorCode]/value,/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authoreventcode, |
| 52 | 52 |
/*ID->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1, |
| 53 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher,/aggregateoccurrence/*_id/plantobservation/authorplantcode, |
|
| 54 | 53 |
/height,/aggregateoccurrence/*_id/plantobservation/overallheight, |
| 55 | 54 |
/simpleUserdefined[name=stemHeightM]/value,/aggregateoccurrence/*_id/plantobservation/overallheight, |
| 55 |
:[*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceaccessioncode]/value,/aggregateoccurrence/*_id/plantobservation/sourceaccessioncode, |
|
| 56 | 56 |
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/relatedItem[relationshipType=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,/aggregateoccurrence/*_id/plantobservation/stemobservation/*_id/plantobservation/authorplantcode, |
| 57 | 57 |
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=count]/value,/aggregateoccurrence/*_id/plantobservation/stemobservation/*_id/plantobservation/stemcount, |
| 58 | 58 |
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance/value=0]/diameter,"/aggregateoccurrence/*_id/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=basalDiameter]]:[@fkey=tableRecord_ID]/definedvalue", |
| ... | ... | |
| 88 | 88 |
/simpleUserdefined[name=growthForm]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=growthForm]]:[@fkey=tableRecord_ID]/definedvalue", |
| 89 | 89 |
/simpleUserdefined[name=individualCode]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=individualCode]]:[@fkey=tableRecord_ID]/definedvalue", |
| 90 | 90 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/groupType","/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=voucherType]]:[@fkey=tableRecord_ID]/definedvalue", |
| 91 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/authorCode,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc, |
|
| 91 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc, |
|
| 92 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher/_alt/1,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/1, |
|
| 93 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher/_alt/2,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/2, |
|
| 92 | 94 |
/simpleUserdefined[name=collectionDate]/value,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate, |
| 93 | 95 |
/simpleUserdefined[name=collectionDate]/value/_*/date,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate/_*/date, |
| 94 | 96 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1, |
| mappings/for_review/VegX-VegBIEN.organisms.csv | ||
|---|---|---|
| 50 | 50 |
//geospatial/minimumDepthInMeters,//waterdepth/min, |
| 51 | 51 |
//plotObservation/simpleUserdefined[name=authorCode]/value,//locationevent/authoreventcode, |
| 52 | 52 |
//party/organizationName,//party/organizationname/_alt/1, |
| 53 |
//taxonNameUsageConcept/voucher,//plantobservation/authorplantcode, |
|
| 54 | 53 |
/height,//plantobservation/overallheight, |
| 55 | 54 |
/simpleUserdefined[name=stemHeightM]/value,//plantobservation/overallheight, |
| 55 |
/simpleUserdefined[name=sourceaccessioncode]/value,//plantobservation/sourceaccessioncode, |
|
| 56 | 56 |
//taxonNameUsageConcept/voucher,//plantobservation/authorplantcode, |
| 57 | 57 |
//*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=count]/value,//plantobservation/stemcount, |
| 58 | 58 |
//*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[value=0]/diameter,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=basalDiameter]]/definedvalue", |
| ... | ... | |
| 88 | 88 |
/simpleUserdefined[name=growthForm]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=growthForm]]/definedvalue", |
| 89 | 89 |
/simpleUserdefined[name=individualCode]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=individualCode]]/definedvalue", |
| 90 | 90 |
//*s/taxonDetermination[role=collector]/groupType,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=voucherType]]/definedvalue", |
| 91 |
//taxonNameUsageConcept/authorCode,//specimenreplicate/catalognumber_dwc, |
|
| 91 |
//taxonNameUsageConcept/voucher,//specimenreplicate/catalognumber_dwc, |
|
| 92 |
//taxonNameUsageConcept/voucher/_alt/1,//specimenreplicate/catalognumber_dwc/_alt/1, |
|
| 93 |
//taxonNameUsageConcept/voucher/_alt/2,//specimenreplicate/catalognumber_dwc/_alt/2, |
|
| 92 | 94 |
/simpleUserdefined[name=collectionDate]/value,//specimenreplicate/collectiondate, |
| 93 | 95 |
/simpleUserdefined[name=collectionDate]/value/_*/date,//specimenreplicate/collectiondate/_*/date, |
| 94 | 96 |
//party/organizationName,//party/organizationname/_alt/1, |
Also available in: Unified diff
VegX-VegBIEN mapping: Map sourceaccessioncode and voucher (catalognumber_dwc) to correct place. SALVIAS mappings: Map SourceVoucher as an alternative to coll_number.