Revision 4638
Added by Aaron Marcuse-Kubitza about 12 years ago
| inputs/ACAD/Specimen/map.full.csv | ||
|---|---|---|
| 1 | 1 |
ACAD[Veg+],Veg+,Comments |
| 2 |
catalogNumber,catalogNumber |
|
| 3 |
class,class |
|
| 4 |
collectionCode,collectionCode |
|
| 5 |
collectionID,collectionID |
|
| 6 |
continent,continent |
|
| 7 |
country,country |
|
| 8 |
county,county |
|
| 9 |
dateIdentified,dateIdentified |
|
| 10 |
decimalLatitude,decimalLatitude |
|
| 11 |
decimalLongitude,decimalLongitude |
|
| 12 |
eventDate,eventDate |
|
| 13 |
family,family |
|
| 14 |
genus,genus |
|
| 15 |
habitat,habitat |
|
| 16 |
id,id |
|
| 17 |
identifiedBy,identifiedBy |
|
| 18 |
infraspecificEpithet,infraspecificEpithet |
|
| 19 |
institutionCode,institutionCode |
|
| 20 |
kingdom,kingdom |
|
| 21 |
locality,locality |
|
| 22 |
order,order |
|
| 23 |
phylum,phylum |
|
| 24 |
recordNumber,recordNumber |
|
| 25 |
recordedBy,recordedBy |
|
| 26 |
scientificName,scientificName |
|
| 27 |
scientificNameAuthorship,scientificNameAuthorship |
|
| 28 |
specificEpithet,specificEpithet |
|
| 29 |
stateProvince,stateProvince |
|
| 30 |
taxonRank,taxonRank |
|
| 31 |
verbatimElevation,verbatimElevation |
|
| 2 |
basisOfRecord,basisOfRecord, |
|
| 3 |
catalogNumber,catalogNumber, |
|
| 4 |
class,class, |
|
| 5 |
collectionCode,collectionCode, |
|
| 6 |
collectionID,collectionID, |
|
| 7 |
continent,continent, |
|
| 8 |
country,country, |
|
| 9 |
county,county, |
|
| 10 |
dateIdentified,dateIdentified, |
|
| 11 |
bibliographicCitation,dcterms:bibliographicCitation, |
|
| 12 |
language,dcterms:language, |
|
| 13 |
modified,dcterms:modified, |
|
| 14 |
rights,dcterms:rights, |
|
| 15 |
rightsHolder,dcterms:rightsHolder, |
|
| 16 |
type,dcterms:type, |
|
| 17 |
decimalLatitude,decimalLatitude, |
|
| 18 |
decimalLongitude,decimalLongitude, |
|
| 19 |
dynamicProperties,dynamicProperties, |
|
| 20 |
eventDate,eventDate, |
|
| 21 |
family,family, |
|
| 22 |
genus,genus, |
|
| 23 |
geodeticDatum,geodeticDatum, |
|
| 24 |
georeferenceSources,georeferenceSources, |
|
| 25 |
georeferenceVerificationStatus,georeferenceVerificationStatus, |
|
| 26 |
habitat,habitat, |
|
| 27 |
identificationRemarks,identificationRemarks, |
|
| 28 |
identifiedBy,identifiedBy, |
|
| 29 |
infraspecificEpithet,infraspecificEpithet, |
|
| 30 |
institutionCode,institutionCode, |
|
| 31 |
kingdom,kingdom, |
|
| 32 |
locality,locality, |
|
| 33 |
locationRemarks,locationRemarks, |
|
| 34 |
municipality,municipality, |
|
| 35 |
id,occurrenceID, |
|
| 36 |
occurrenceRemarks,occurrenceRemarks, |
|
| 37 |
order,order, |
|
| 38 |
ownerInstitutionCode,ownerInstitutionCode, |
|
| 39 |
phylum,phylum, |
|
| 40 |
recordNumber,recordNumber, |
|
| 41 |
recordedBy,recordedBy, |
|
| 42 |
reproductiveCondition,reproductiveCondition, |
|
| 43 |
scientificName,scientificName, |
|
| 44 |
scientificNameAuthorship,scientificNameAuthorship, |
|
| 45 |
specificEpithet,specificEpithet, |
|
| 46 |
stateProvince,stateProvince, |
|
| 47 |
taxonRank,taxonRank, |
|
| 48 |
verbatimDepth,verbatimDepth, |
|
| 49 |
verbatimElevation,verbatimElevation, |
|
| inputs/SALVIAS-CSV/Organism/map.full.csv | ||
|---|---|---|
| 5 | 5 |
coll_number,catalogNumber/_alt/1,Brad: Map instead as for voucher_string |
| 6 | 6 |
voucher_string,catalogNumber/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
| 7 | 7 |
census_no,censusNumber,"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." |
| 8 |
collector_code,collector_code,Brad: OMIT |
|
| 9 |
comments,comments,Brad: OMIT |
|
| 8 | 10 |
cover_percent,coverPercent, |
| 9 | 11 |
stem_dbh,diameterBreastHeight, |
| 10 | 12 |
census_date,eventDate,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows: |
| ... | ... | |
| 15 | 17 |
GROUP BY ""PLOT_ID"", subplot |
| 16 | 18 |
HAVING count(DISTINCT census_date) > 1 |
| 17 | 19 |
-----" |
| 20 |
fam_status,fam_status,Brad: OMIT. This will be determined later by using TNRS. |
|
| 18 | 21 |
family,family, |
| 22 |
gen_status,gen_status,Brad: OMIT. This will be determined later by using TNRS. |
|
| 19 | 23 |
genus,genus, |
| 20 | 24 |
stem_height_m,height/_alt/1,"Brad: Same as for height, but applies to individuals stems, not trees. Rare." |
| 21 | 25 |
height_m,height/_alt/2, |
| 22 | 26 |
ht_first_branch_m,heightFirstBranch, |
| 23 | 27 |
stem_height_first_branch_m,heightFirstBranch,"Brad: Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare." |
| 24 | 28 |
cf_aff,identificationQualifier,"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." |
| 29 |
ind_id,ind_id,Brad: OMIT |
|
| 25 | 30 |
no_of_individuals,individualCount,"Brad: 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." |
| 26 | 31 |
OBSERVATION_ID,individualID,"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." |
| 27 | 32 |
infra_ep_1,infraspecificEpithet, |
| ... | ... | |
| 36 | 41 |
coll_firstname,recordedBy.givenName,Brad: See comment above |
| 37 | 42 |
coll_lastname,recordedBy.surName,"Brad: 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." |
| 38 | 43 |
specific_authority,scientificNameAuthorship,Brad: This is the author of the scientificName. |
| 44 |
species_status,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." |
|
| 39 | 45 |
specific_epithet,specificEpithet, |
| 40 | 46 |
notes,stemNotes, |
| 41 | 47 |
subplot,subplot, |
| inputs/SALVIAS-CSV/Organism/unmapped_terms.csv | ||
|---|---|---|
| 1 |
""
|
|
| 1 |
ind_id
|
|
| 2 | 2 |
tag/_alt/1 |
| 3 | 3 |
previousTag/_alt/1 |
| 4 | 4 |
catalogNumber/_alt/2 |
| 5 | 5 |
catalogNumber/_alt/1 |
| 6 |
""
|
|
| 7 |
""
|
|
| 8 |
""
|
|
| 9 |
""
|
|
| 10 |
""
|
|
| 6 |
collector_code
|
|
| 7 |
fam_status
|
|
| 8 |
gen_status
|
|
| 9 |
species_status
|
|
| 10 |
comments
|
|
| 11 | 11 |
height/_alt/2 |
| 12 | 12 |
tag/_alt/2 |
| 13 | 13 |
previousTag/_alt/2 |
| inputs/SALVIAS-CSV/Plot/VegBIEN.csv | ||
|---|---|---|
| 47 | 47 |
locality_description,/location/locationnarrative/_merge/1,"Brad: No; this is free text description of locality where plot was situated, same as for DwC. Not a description of vegetation. Most likely='namedPlace.placeDescription' in VB; not sure about VX, again need to ask Nick where locality descriptions live in VX" |
| 48 | 48 |
slope_aspect,/location/slopeaspect/_alt/1/_compass/value, |
| 49 | 49 |
slope_gradient,/location/slopegradient/_alt/1, |
| 50 |
observation_type,,"** No join mapping for observation_type ** Brad: SALVIAS internal metadata indicating whether the record represents an individual or aggregate observation. Rather than storing, use to decide where to store in VegX.; Aaron: VegX aggregateOrganismObservation table is missing many fields available in individualOrganismObservation, so we're mapping to individualOrganismObservation regardless of observation type" |
|
| 51 |
recensused,,"** No join mapping for recensused ** Brad: This is a 0/1 value, internal to SALVIAS. 1 indicates that a plot has >1 set of values, from different census events.; Aaron: Different censuses are distinguished in organisms data by different census_no values" |
|
| inputs/MT/Specimen/map.csv | ||
|---|---|---|
| 1 | 1 |
MT[Veg+],Veg+,Comments |
| 2 |
id,, |
|
| 3 |
establishmentMeans,, |
|
| 4 |
locality,, |
|
| 5 |
language,, |
|
| 6 |
collectionID,, |
|
| 7 |
occurrenceRemarks,, |
|
| 8 |
type,, |
|
| 9 |
institutionCode,, |
|
| 10 |
rights,, |
|
| 11 |
family,, |
|
| 12 |
continent,, |
|
| 13 |
collectionCode,, |
|
| 14 |
datasetName,, |
|
| 15 |
rightsHolder,, |
|
| 16 |
genus,, |
|
| 17 |
basisOfRecord,, |
|
| 18 |
individualCount,, |
|
| 19 |
countryCode,, |
|
| 2 |
id,occurrenceID, |
|
| 3 |
establishmentMeans,establishmentMeans, |
|
| 4 |
locality,locality, |
|
| 5 |
language,dcterms:language, |
|
| 6 |
collectionID,collectionID, |
|
| 7 |
occurrenceRemarks,occurrenceRemarks, |
|
| 8 |
type,dcterms:type, |
|
| 9 |
institutionCode,institutionCode, |
|
| 10 |
rights,dcterms:rights, |
|
| 11 |
family,family, |
|
| 12 |
continent,continent, |
|
| 13 |
collectionCode,collectionCode, |
|
| 14 |
datasetName,datasetName, |
|
| 15 |
rightsHolder,dcterms:rightsHolder, |
|
| 16 |
genus,genus, |
|
| 17 |
basisOfRecord,basisOfRecord, |
|
| 18 |
individualCount,individualCount, |
|
| 19 |
countryCode,countryCode, |
|
| inputs/MT/Specimen/map.full.csv | ||
|---|---|---|
| 1 | 1 |
MT[Veg+],Veg+,Comments |
| 2 |
collectionCode,collectionCode |
|
| 3 |
collectionID,collectionID |
|
| 4 |
continent,continent |
|
| 5 |
establishmentMeans,establishmentMeans |
|
| 6 |
family,family |
|
| 7 |
genus,genus |
|
| 8 |
id,id |
|
| 9 |
individualCount,individualCount |
|
| 10 |
institutionCode,institutionCode |
|
| 11 |
locality,locality |
|
| 2 |
basisOfRecord,basisOfRecord, |
|
| 3 |
collectionCode,collectionCode, |
|
| 4 |
collectionID,collectionID, |
|
| 5 |
continent,continent, |
|
| 6 |
countryCode,countryCode, |
|
| 7 |
datasetName,datasetName, |
|
| 8 |
language,dcterms:language, |
|
| 9 |
rights,dcterms:rights, |
|
| 10 |
rightsHolder,dcterms:rightsHolder, |
|
| 11 |
type,dcterms:type, |
|
| 12 |
establishmentMeans,establishmentMeans, |
|
| 13 |
family,family, |
|
| 14 |
genus,genus, |
|
| 15 |
individualCount,individualCount, |
|
| 16 |
institutionCode,institutionCode, |
|
| 17 |
locality,locality, |
|
| 18 |
id,occurrenceID, |
|
| 19 |
occurrenceRemarks,occurrenceRemarks, |
|
| inputs/MT/Specimen/VegBIEN.csv | ||
|---|---|---|
| 14 | 14 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname", |
| 15 | 15 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname", |
| 16 | 16 |
locality,/location/locationnarrative/_merge/1, |
| 17 |
basisOfRecord,,** No join mapping for basisOfRecord ** |
|
| 18 |
countryCode,,** No join mapping for countryCode ** |
|
| 19 |
datasetName,,** No join mapping for datasetName ** |
|
| 20 |
language,,** No join mapping for dcterms:language ** |
|
| 21 |
occurrenceRemarks,,** No join mapping for occurrenceRemarks ** |
|
| 22 |
rights,,** No join mapping for dcterms:rights ** |
|
| 23 |
rightsHolder,,** No join mapping for dcterms:rightsHolder ** |
|
| 24 |
type,,** No join mapping for dcterms:type ** |
|
| inputs/TEAM/VL/map.csv | ||
|---|---|---|
| 1 | 1 |
TEAM[Veg+],Veg+,Comments |
| 2 |
ID,, |
|
| 2 |
ID,occurrenceID,
|
|
| 3 | 3 |
SiteName,projectName, |
| 4 | 4 |
1haPlotCode,plotName, |
| 5 | 5 |
ObservationDate,eventDate, |
| 6 |
Family,, |
|
| 7 |
Genus,, |
|
| 8 |
SpecificEpithet,, |
|
| 6 |
Family,family,
|
|
| 7 |
Genus,genus,
|
|
| 8 |
SpecificEpithet,specificEpithet,
|
|
| 9 | 9 |
Collectors,recordedBy, |
| 10 |
dbh,, |
|
| 11 |
max_diam,, |
|
| 12 |
max_diam_pom,, |
|
| 13 |
ConditionCodes,, |
|
| 14 |
LocationCodes,, |
|
| 15 |
SamplingPeriod,, |
|
| 16 |
Comments,, |
|
| 17 |
SamplingUnitName,, |
|
| 18 |
Latitude,, |
|
| 19 |
Longitude,, |
|
| 10 |
dbh,diameterBreastHeight,
|
|
| 11 |
max_diam,max_diam,
|
|
| 12 |
max_diam_pom,max_diam_pom,
|
|
| 13 |
ConditionCodes,ConditionCodes,
|
|
| 14 |
LocationCodes,LocationCodes,
|
|
| 15 |
SamplingPeriod,SamplingPeriod,
|
|
| 16 |
Comments,Comments,
|
|
| 17 |
SamplingUnitName,SamplingUnitName,
|
|
| 18 |
Latitude,verbatimLatitude,
|
|
| 19 |
Longitude,verbatimLongitude,
|
|
| 20 | 20 |
Method,samplingProtocol, |
| 21 |
Subplot,, |
|
| 21 |
Subplot,subplot,
|
|
| 22 | 22 |
X_1haPlot,organismX, |
| 23 | 23 |
Y_1haPlot,organismY, |
| 24 | 24 |
TreeNumber,tag, |
| 25 |
ProtocolVersion,, |
|
| 26 |
ResponsibleInstitution,, |
|
| 27 |
ProtocolLeadScientist,, |
|
| 28 |
ProtocolLeadScientistInstitution,, |
|
| 25 |
ProtocolVersion,ProtocolVersion, |
|
| 26 |
ResponsibleInstitution,ResponsibleInstitution, |
|
| 27 |
ProtocolLeadScientist,ProtocolLeadScientist, |
|
| 28 |
ProtocolLeadScientistInstitution,ProtocolLeadScientistInstitution, |
|
| inputs/TEAM/VL/map.full.csv | ||
|---|---|---|
| 1 | 1 |
TEAM[Veg+],Veg+,Comments |
| 2 |
DBH,DBH |
|
| 2 |
Comments,Comments, |
|
| 3 |
ConditionCodes,ConditionCodes, |
|
| 4 |
LocationCodes,LocationCodes, |
|
| 5 |
ProtocolLeadScientist,ProtocolLeadScientist, |
|
| 6 |
ProtocolLeadScientistInstitution,ProtocolLeadScientistInstitution, |
|
| 7 |
ProtocolVersion,ProtocolVersion, |
|
| 8 |
ResponsibleInstitution,ResponsibleInstitution, |
|
| 9 |
SamplingPeriod,SamplingPeriod, |
|
| 10 |
SamplingUnitName,SamplingUnitName, |
|
| 11 |
dbh,diameterBreastHeight, |
|
| 3 | 12 |
ObservationDate,eventDate, |
| 4 |
family,family
|
|
| 5 |
genus,genus
|
|
| 6 |
id,id
|
|
| 7 |
latitude,latitude
|
|
| 8 |
longitude,longitude
|
|
| 13 |
Family,family,
|
|
| 14 |
Genus,genus,
|
|
| 15 |
max_diam,max_diam,
|
|
| 16 |
max_diam_pom,max_diam_pom,
|
|
| 17 |
ID,occurrenceID,
|
|
| 9 | 18 |
X_1haPlot,organismX, |
| 10 | 19 |
Y_1haPlot,organismY, |
| 11 | 20 |
1haPlotCode,plotName, |
| 12 | 21 |
SiteName,projectName, |
| 13 | 22 |
Collectors,recordedBy, |
| 14 | 23 |
Method,samplingProtocol, |
| 15 |
specificEpithet,specificEpithet
|
|
| 16 |
subplot,subplot
|
|
| 24 |
SpecificEpithet,specificEpithet,
|
|
| 25 |
Subplot,subplot,
|
|
| 17 | 26 |
TreeNumber,tag, |
| 27 |
Latitude,verbatimLatitude, |
|
| 28 |
Longitude,verbatimLongitude, |
|
| inputs/TEAM/VL/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
TEAM[Veg+],VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
subplot,"/location/_if[@name=""if subplot""]/cond/_exists/_first/2",
|
|
| 2 |
Subplot,"/location/_if[@name=""if subplot""]/cond/_exists/_first/2",
|
|
| 3 | 3 |
1haPlotCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 4 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1",
|
|
| 4 |
ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1",
|
|
| 5 | 5 |
1haPlotCode,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
| 6 |
subplot,/location/authorlocationcode,
|
|
| 7 |
latitude,"/location/locationdetermination/latitude/_alt/2/_nullIf:[null=0,type=float]/value",
|
|
| 8 |
longitude,"/location/locationdetermination/longitude/_alt/2/_nullIf:[null=0,type=float]/value",
|
|
| 6 |
Subplot,/location/authorlocationcode,
|
|
| 7 |
Latitude,"/location/locationdetermination/latitude/_alt/2/_nullIf:[null=0,type=float]/value",
|
|
| 8 |
Longitude,"/location/locationdetermination/longitude/_alt/2/_nullIf:[null=0,type=float]/value",
|
|
| 9 | 9 |
Method,/location/locationevent/*_id/method/name, |
| 10 | 10 |
SiteName,/location/locationevent/*_id/project/projectname, |
| 11 |
subplot,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists/_first/2",
|
|
| 11 |
Subplot,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists/_first/2",
|
|
| 12 | 12 |
1haPlotCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/authorlocationcode", |
| 13 | 13 |
ObservationDate,/location/locationevent/obsenddate/_*/date/_alt/2/_dateRangeEnd/value, |
| 14 | 14 |
ObservationDate,/location/locationevent/obsstartdate/_*/date/_alt/2/_dateRangeStart/value, |
| 15 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
|
|
| 16 |
DBH,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight,
|
|
| 15 |
ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
|
|
| 16 |
dbh,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight,
|
|
| 17 | 17 |
TreeNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2 |
| 18 | 18 |
X_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition, |
| 19 | 19 |
Y_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition, |
| 20 |
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname",
|
|
| 21 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname",
|
|
| 22 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",
|
|
| 20 |
SpecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname",
|
|
| 21 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname",
|
|
| 22 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",
|
|
| 23 | 23 |
Collectors,/location/locationevent/taxonoccurrence/verbatimcollectorname, |
| 24 |
Comments,,** No join mapping for Comments ** |
|
| 25 |
ConditionCodes,,** No join mapping for ConditionCodes ** |
|
| 26 |
LocationCodes,,** No join mapping for LocationCodes ** |
|
| 27 |
ProtocolLeadScientist,,** No join mapping for ProtocolLeadScientist ** |
|
| 28 |
ProtocolLeadScientistInstitution,,** No join mapping for ProtocolLeadScientistInstitution ** |
|
| 29 |
ProtocolVersion,,** No join mapping for ProtocolVersion ** |
|
| 30 |
ResponsibleInstitution,,** No join mapping for ResponsibleInstitution ** |
|
| 31 |
SamplingPeriod,,** No join mapping for SamplingPeriod ** |
|
| 32 |
SamplingUnitName,,** No join mapping for SamplingUnitName ** |
|
| 33 |
max_diam,,** No join mapping for max_diam ** |
|
| 34 |
max_diam_pom,,** No join mapping for max_diam_pom ** |
|
| inputs/TEAM/VL/new_terms.csv | ||
|---|---|---|
| 3 | 3 |
ObservationDate |
| 4 | 4 |
Collectors |
| 5 | 5 |
max_diam |
| 6 |
max_diam_pom |
|
| 7 |
ConditionCodes |
|
| 8 |
LocationCodes |
|
| 9 |
SamplingPeriod |
|
| 10 |
Comments |
|
| 11 |
SamplingUnitName |
|
| 12 | 6 |
Method |
| 13 | 7 |
X_1haPlot |
| 14 | 8 |
Y_1haPlot |
| 15 | 9 |
TreeNumber |
| 16 |
ProtocolVersion |
|
| 17 |
ResponsibleInstitution |
|
| 18 |
ProtocolLeadScientist |
|
| 19 |
ProtocolLeadScientistInstitution |
|
| inputs/TEAM/VL/unmapped_terms.csv | ||
|---|---|---|
| 1 |
"" |
|
| 2 |
"" |
|
| 3 |
"" |
|
| 4 |
"" |
|
| 5 |
"" |
|
| 6 |
"" |
|
| 7 |
"" |
|
| 8 |
"" |
|
| 9 |
"" |
|
| 10 |
"" |
|
| 11 |
"" |
|
| 12 |
"" |
|
| 13 |
"" |
|
| 14 |
"" |
|
| 15 |
"" |
|
| 16 |
"" |
|
| 17 |
"" |
|
| 18 |
"" |
|
| 19 |
"" |
|
| 1 |
max_diam |
|
| 2 |
max_diam_pom |
|
| 3 |
ConditionCodes |
|
| 4 |
LocationCodes |
|
| 5 |
SamplingPeriod |
|
| 6 |
Comments |
|
| 7 |
SamplingUnitName |
|
| 8 |
ProtocolVersion |
|
| 9 |
ResponsibleInstitution |
|
| 10 |
ProtocolLeadScientist |
|
| 11 |
ProtocolLeadScientistInstitution |
|
| inputs/TEAM/VT/map.csv | ||
|---|---|---|
| 1 | 1 |
TEAM[Veg+],Veg+,Comments |
| 2 | 2 |
ID,occurrenceID, |
| 3 | 3 |
ObservationDate,eventDate, |
| 4 |
Family,, |
|
| 5 |
Genus,, |
|
| 6 |
SpecificEpithet,, |
|
| 4 |
Family,family,
|
|
| 5 |
Genus,genus,
|
|
| 6 |
SpecificEpithet,specificEpithet,
|
|
| 7 | 7 |
Collectors,recordedBy, |
| 8 | 8 |
dbh,diameterBreastHeight, |
| 9 |
dbh_pom,, |
|
| 10 |
dbh_new,, |
|
| 11 |
dbh_new_pom,, |
|
| 12 |
ConditionCodes,, |
|
| 13 |
SamplingPeriod,, |
|
| 14 |
Comments,, |
|
| 15 |
SamplingUnitName,, |
|
| 16 |
Latitude,, |
|
| 17 |
Longitude,, |
|
| 9 |
dbh_pom,dbh_pom,
|
|
| 10 |
dbh_new,dbh_new,
|
|
| 11 |
dbh_new_pom,dbh_new_pom,
|
|
| 12 |
ConditionCodes,ConditionCodes,
|
|
| 13 |
SamplingPeriod,SamplingPeriod,
|
|
| 14 |
Comments,Comments,
|
|
| 15 |
SamplingUnitName,SamplingUnitName,
|
|
| 16 |
Latitude,verbatimLatitude,
|
|
| 17 |
Longitude,verbatimLongitude,
|
|
| 18 | 18 |
Method,samplingProtocol, |
| 19 |
Subplot,, |
|
| 19 |
Subplot,subplot,
|
|
| 20 | 20 |
X_1haPlot,organismX, |
| 21 | 21 |
Y_1haPlot,organismY, |
| 22 | 22 |
TreeNumber,tag, |
| 23 | 23 |
SiteName,projectName, |
| 24 | 24 |
1haPlotCode,plotName, |
| 25 |
ProtocolVersion,, |
|
| 26 |
ResponsibleInstitution,, |
|
| 27 |
ProtocolLeadScientist,, |
|
| 28 |
ProtocolLeadScientistInstitution,, |
|
| 25 |
ProtocolVersion,ProtocolVersion, |
|
| 26 |
ResponsibleInstitution,ResponsibleInstitution, |
|
| 27 |
ProtocolLeadScientist,ProtocolLeadScientist, |
|
| 28 |
ProtocolLeadScientistInstitution,ProtocolLeadScientistInstitution, |
|
| inputs/TEAM/VT/map.full.csv | ||
|---|---|---|
| 1 | 1 |
TEAM[Veg+],Veg+,Comments |
| 2 |
Comments,Comments, |
|
| 3 |
ConditionCodes,ConditionCodes, |
|
| 4 |
ProtocolLeadScientist,ProtocolLeadScientist, |
|
| 5 |
ProtocolLeadScientistInstitution,ProtocolLeadScientistInstitution, |
|
| 6 |
ProtocolVersion,ProtocolVersion, |
|
| 7 |
ResponsibleInstitution,ResponsibleInstitution, |
|
| 8 |
SamplingPeriod,SamplingPeriod, |
|
| 9 |
SamplingUnitName,SamplingUnitName, |
|
| 10 |
dbh_new,dbh_new, |
|
| 11 |
dbh_new_pom,dbh_new_pom, |
|
| 12 |
dbh_pom,dbh_pom, |
|
| 2 | 13 |
dbh,diameterBreastHeight, |
| 3 | 14 |
ObservationDate,eventDate, |
| 4 |
family,family |
|
| 5 |
genus,genus |
|
| 6 |
latitude,latitude |
|
| 7 |
longitude,longitude |
|
| 15 |
Family,family, |
|
| 16 |
Genus,genus, |
|
| 8 | 17 |
ID,occurrenceID, |
| 9 | 18 |
X_1haPlot,organismX, |
| 10 | 19 |
Y_1haPlot,organismY, |
| ... | ... | |
| 12 | 21 |
SiteName,projectName, |
| 13 | 22 |
Collectors,recordedBy, |
| 14 | 23 |
Method,samplingProtocol, |
| 15 |
specificEpithet,specificEpithet
|
|
| 16 |
subplot,subplot
|
|
| 24 |
SpecificEpithet,specificEpithet,
|
|
| 25 |
Subplot,subplot,
|
|
| 17 | 26 |
TreeNumber,tag, |
| 27 |
Latitude,verbatimLatitude, |
|
| 28 |
Longitude,verbatimLongitude, |
|
| inputs/TEAM/VT/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
TEAM[Veg+],VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
subplot,"/location/_if[@name=""if subplot""]/cond/_exists/_first/2",
|
|
| 2 |
Subplot,"/location/_if[@name=""if subplot""]/cond/_exists/_first/2",
|
|
| 3 | 3 |
1haPlotCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 4 | 4 |
ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 5 | 5 |
1haPlotCode,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
| 6 |
subplot,/location/authorlocationcode,
|
|
| 7 |
latitude,"/location/locationdetermination/latitude/_alt/2/_nullIf:[null=0,type=float]/value",
|
|
| 8 |
longitude,"/location/locationdetermination/longitude/_alt/2/_nullIf:[null=0,type=float]/value",
|
|
| 6 |
Subplot,/location/authorlocationcode,
|
|
| 7 |
Latitude,"/location/locationdetermination/latitude/_alt/2/_nullIf:[null=0,type=float]/value",
|
|
| 8 |
Longitude,"/location/locationdetermination/longitude/_alt/2/_nullIf:[null=0,type=float]/value",
|
|
| 9 | 9 |
Method,/location/locationevent/*_id/method/name, |
| 10 | 10 |
SiteName,/location/locationevent/*_id/project/projectname, |
| 11 |
subplot,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists/_first/2",
|
|
| 11 |
Subplot,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists/_first/2",
|
|
| 12 | 12 |
1haPlotCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/authorlocationcode", |
| 13 | 13 |
ObservationDate,/location/locationevent/obsenddate/_*/date/_alt/2/_dateRangeEnd/value, |
| 14 | 14 |
ObservationDate,/location/locationevent/obsstartdate/_*/date/_alt/2/_dateRangeStart/value, |
| ... | ... | |
| 17 | 17 |
TreeNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2 |
| 18 | 18 |
X_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition, |
| 19 | 19 |
Y_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition, |
| 20 |
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname",
|
|
| 21 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname",
|
|
| 22 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",
|
|
| 20 |
SpecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname",
|
|
| 21 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname",
|
|
| 22 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",
|
|
| 23 | 23 |
Collectors,/location/locationevent/taxonoccurrence/verbatimcollectorname, |
| 24 |
Comments,,** No join mapping for Comments ** |
|
| 25 |
ConditionCodes,,** No join mapping for ConditionCodes ** |
|
| 26 |
ProtocolLeadScientist,,** No join mapping for ProtocolLeadScientist ** |
|
| 27 |
ProtocolLeadScientistInstitution,,** No join mapping for ProtocolLeadScientistInstitution ** |
|
| 28 |
ProtocolVersion,,** No join mapping for ProtocolVersion ** |
|
| 29 |
ResponsibleInstitution,,** No join mapping for ResponsibleInstitution ** |
|
| 30 |
SamplingPeriod,,** No join mapping for SamplingPeriod ** |
|
| 31 |
SamplingUnitName,,** No join mapping for SamplingUnitName ** |
|
| 32 |
dbh_new,,** No join mapping for dbh_new ** |
|
| 33 |
dbh_new_pom,,** No join mapping for dbh_new_pom ** |
|
| 34 |
dbh_pom,,** No join mapping for dbh_pom ** |
|
| inputs/TEAM/VT/new_terms.csv | ||
|---|---|---|
| 1 | 1 |
ObservationDate |
| 2 | 2 |
Collectors |
| 3 | 3 |
dbh_pom |
| 4 |
dbh_new |
|
| 5 |
dbh_new_pom |
|
| 6 |
ConditionCodes |
|
| 7 |
SamplingPeriod |
|
| 8 |
Comments |
|
| 9 |
SamplingUnitName |
|
| 10 | 4 |
Method |
| 11 | 5 |
X_1haPlot |
| 12 | 6 |
Y_1haPlot |
| 13 | 7 |
TreeNumber |
| 14 | 8 |
SiteName |
| 15 | 9 |
1haPlotCode |
| 16 |
ProtocolVersion |
|
| 17 |
ResponsibleInstitution |
|
| 18 |
ProtocolLeadScientist |
|
| 19 |
ProtocolLeadScientistInstitution |
|
| inputs/TEAM/VT/unmapped_terms.csv | ||
|---|---|---|
| 1 |
"" |
|
| 2 |
"" |
|
| 3 |
"" |
|
| 4 |
"" |
|
| 5 |
"" |
|
| 6 |
"" |
|
| 7 |
"" |
|
| 8 |
"" |
|
| 9 |
"" |
|
| 10 |
"" |
|
| 11 |
"" |
|
| 12 |
"" |
|
| 13 |
"" |
|
| 14 |
"" |
|
| 15 |
"" |
|
| 16 |
"" |
|
| 17 |
"" |
|
| 1 |
dbh_pom |
|
| 2 |
dbh_new |
|
| 3 |
dbh_new_pom |
|
| 4 |
ConditionCodes |
|
| 5 |
SamplingPeriod |
|
| 6 |
Comments |
|
| 7 |
SamplingUnitName |
|
| 8 |
ProtocolVersion |
|
| 9 |
ResponsibleInstitution |
|
| 10 |
ProtocolLeadScientist |
|
| 11 |
ProtocolLeadScientistInstitution |
|
| inputs/NY/Specimen/map.csv | ||
|---|---|---|
| 1 | 1 |
NY[Veg+],Veg+,Comments |
| 2 |
key,,Not used because UniqueNYInternalRecordNumber is a better pkey |
|
| 3 |
DateLastModified,, |
|
| 4 |
InstitutionCode,, |
|
| 5 |
CollectionCode,, |
|
| 6 |
CatalogNumber,, |
|
| 7 |
ScientificName,, |
|
| 8 |
BasisOfRecord,, |
|
| 9 |
Kingdom,, |
|
| 10 |
Phylum,, |
|
| 11 |
Class,, |
|
| 12 |
Order,, |
|
| 13 |
Family,, |
|
| 14 |
Genus,, |
|
| 15 |
Species,, |
|
| 16 |
Subspecies,, |
|
| 17 |
ScientificNameAuthor,, |
|
| 18 |
IdentifiedBy,, |
|
| 19 |
YearIdentified,, |
|
| 20 |
MonthIdentified,, |
|
| 21 |
DayIdentified,, |
|
| 22 |
TypeStatus,, |
|
| 2 |
key,key,Not used because UniqueNYInternalRecordNumber is a better pkey
|
|
| 3 |
DateLastModified,dcterms:modified,
|
|
| 4 |
InstitutionCode,institutionCode,
|
|
| 5 |
CollectionCode,collectionCode,
|
|
| 6 |
CatalogNumber,catalogNumber,
|
|
| 7 |
ScientificName,scientificName,
|
|
| 8 |
BasisOfRecord,BasisOfRecord,
|
|
| 9 |
Kingdom,kingdom,
|
|
| 10 |
Phylum,phylum,
|
|
| 11 |
Class,class,
|
|
| 12 |
Order,order,
|
|
| 13 |
Family,family,
|
|
| 14 |
Genus,genus,
|
|
| 15 |
Species,specificEpithet,
|
|
| 16 |
Subspecies,infraspecificEpithet,
|
|
| 17 |
ScientificNameAuthor,scientificNameAuthorship,
|
|
| 18 |
IdentifiedBy,identifiedBy,
|
|
| 19 |
YearIdentified,yearIdentified,
|
|
| 20 |
MonthIdentified,monthIdentified,
|
|
| 21 |
DayIdentified,dayIdentified,
|
|
| 22 |
TypeStatus,TypeStatus,
|
|
| 23 | 23 |
CollectorNumber,OMIT,"Not used [1], so does not need to be mapped. |
| 24 | 24 |
|
| 25 | 25 |
[1] The following query returns no rows: SELECT * FROM ""NY"".""Specimen"" WHERE ""CollectorNumber"" IS NOT NULL" |
| 26 | 26 |
FieldNumber,recordNumber,Usage inconsistent with DwC definition |
| 27 |
Collector,, |
|
| 28 |
YearCollected,, |
|
| 29 |
MonthCollected,, |
|
| 30 |
DayCollected,, |
|
| 31 |
JulianDay,, |
|
| 32 |
TimeOfDay,, |
|
| 33 |
ContinentOcean,, |
|
| 34 |
Country,, |
|
| 35 |
StateProvince,, |
|
| 36 |
County,, |
|
| 27 |
Collector,recordedBy,
|
|
| 28 |
YearCollected,yearCollected,
|
|
| 29 |
MonthCollected,monthCollected,
|
|
| 30 |
DayCollected,dayCollected,
|
|
| 31 |
JulianDay,day,
|
|
| 32 |
TimeOfDay,eventTime,
|
|
| 33 |
ContinentOcean,continent,
|
|
| 34 |
Country,country,
|
|
| 35 |
StateProvince,stateProvince,
|
|
| 36 |
County,county,
|
|
| 37 | 37 |
Locality,Locality/_merge/1, |
| 38 |
Longitude,, |
|
| 39 |
Latitude,, |
|
| 40 |
CoordinatePrecision,, |
|
| 41 |
BoundingBox,, |
|
| 38 |
Longitude,verbatimLongitude,
|
|
| 39 |
Latitude,verbatimLatitude,
|
|
| 40 |
CoordinatePrecision,coordinatePrecision,
|
|
| 41 |
BoundingBox,footprintWKT,
|
|
| 42 | 42 |
MinimumElevation,MinimumElevation/_nullIf:[null=.]/value, |
| 43 |
MaximumElevation,, |
|
| 44 |
MinimumDepth,, |
|
| 45 |
MaximumDepth,, |
|
| 46 |
Sex,, |
|
| 47 |
PreparationType,, |
|
| 48 |
IndividualCount,, |
|
| 49 |
PreviousCatalogNumber,, |
|
| 50 |
RelationshipType,, |
|
| 51 |
RelatedCatalogItem,, |
|
| 43 |
MaximumElevation,maximumElevationInMeters,
|
|
| 44 |
MinimumDepth,minimumDepthInMeters,
|
|
| 45 |
MaximumDepth,maximumDepthInMeters,
|
|
| 46 |
Sex,sex,
|
|
| 47 |
PreparationType,preparations,
|
|
| 48 |
IndividualCount,individualCount,
|
|
| 49 |
PreviousCatalogNumber,otherCatalogNumbers,
|
|
| 50 |
RelationshipType,relationshipOfResource,
|
|
| 51 |
RelatedCatalogItem,relatedResourceID,
|
|
| 52 | 52 |
Notes,Notes/_merge/1, |
| 53 |
Habitat,, |
|
| 53 |
Habitat,habitat,
|
|
| 54 | 54 |
PlantFungusDescription,"Notes/_merge/2/_label[label=""plant fungus""]/value", |
| 55 | 55 |
Substrate,"Locality/_merge/2/_label[label=""substrate""]/value", |
| 56 | 56 |
Vegetation,"Locality/_merge/3/_label[label=""vegetation""]/value", |
| inputs/NY/Specimen/map.full.csv | ||
|---|---|---|
| 1 | 1 |
NY[Veg+],Veg+,Comments |
| 2 |
BasisOfRecord,BasisOfRecord, |
|
| 2 | 3 |
Locality,Locality/_merge/1, |
| 3 | 4 |
Substrate,"Locality/_merge/2/_label[label=""substrate""]/value", |
| 4 | 5 |
Vegetation,"Locality/_merge/3/_label[label=""vegetation""]/value", |
| ... | ... | |
| 8 | 9 |
CollectorNumber,OMIT,"Not used [1], so does not need to be mapped. |
| 9 | 10 |
|
| 10 | 11 |
[1] The following query returns no rows: SELECT * FROM ""NY"".""Specimen"" WHERE ""CollectorNumber"" IS NOT NULL" |
| 11 |
boundingBox,boundingBox |
|
| 12 |
catalogNumber,catalogNumber |
|
| 13 |
class,class |
|
| 14 |
collectionCode,collectionCode |
|
| 15 |
collector,collector |
|
| 16 |
continentOcean,continentOcean |
|
| 17 |
coordinatePrecision,coordinatePrecision |
|
| 18 |
country,country |
|
| 19 |
county,county |
|
| 20 |
dayCollected,dayCollected |
|
| 21 |
dayIdentified,dayIdentified |
|
| 22 |
family,family |
|
| 23 |
genus,genus |
|
| 24 |
habitat,habitat |
|
| 25 |
identifiedBy,identifiedBy |
|
| 26 |
individualCount,individualCount |
|
| 27 |
institutionCode,institutionCode |
|
| 28 |
kingdom,kingdom |
|
| 29 |
latitude,latitude |
|
| 30 |
longitude,longitude |
|
| 31 |
maximumDepth,maximumDepth |
|
| 32 |
maximumElevation,maximumElevation |
|
| 33 |
minimumDepth,minimumDepth |
|
| 34 |
monthCollected,monthCollected |
|
| 35 |
monthIdentified,monthIdentified |
|
| 12 |
TypeStatus,TypeStatus, |
|
| 13 |
CatalogNumber,catalogNumber, |
|
| 14 |
Class,class, |
|
| 15 |
CollectionCode,collectionCode, |
|
| 16 |
ContinentOcean,continent, |
|
| 17 |
CoordinatePrecision,coordinatePrecision, |
|
| 18 |
Country,country, |
|
| 19 |
County,county, |
|
| 20 |
JulianDay,day, |
|
| 21 |
DayCollected,dayCollected, |
|
| 22 |
DayIdentified,dayIdentified, |
|
| 23 |
DateLastModified,dcterms:modified, |
|
| 24 |
TimeOfDay,eventTime, |
|
| 25 |
Family,family, |
|
| 26 |
BoundingBox,footprintWKT, |
|
| 27 |
Genus,genus, |
|
| 28 |
Habitat,habitat, |
|
| 29 |
IdentifiedBy,identifiedBy, |
|
| 30 |
IndividualCount,individualCount, |
|
| 31 |
Subspecies,infraspecificEpithet, |
|
| 32 |
InstitutionCode,institutionCode, |
|
| 33 |
key,key,Not used because UniqueNYInternalRecordNumber is a better pkey |
|
| 34 |
Kingdom,kingdom, |
|
| 35 |
MaximumDepth,maximumDepthInMeters, |
|
| 36 |
MaximumElevation,maximumElevationInMeters, |
|
| 37 |
MinimumDepth,minimumDepthInMeters, |
|
| 38 |
MonthCollected,monthCollected, |
|
| 39 |
MonthIdentified,monthIdentified, |
|
| 36 | 40 |
UniqueNYInternalRecordNumber,occurrenceID, |
| 37 |
order,order |
|
| 38 |
phylum,phylum |
|
| 41 |
Order,order, |
|
| 42 |
PreviousCatalogNumber,otherCatalogNumbers, |
|
| 43 |
Phylum,phylum, |
|
| 44 |
PreparationType,preparations, |
|
| 39 | 45 |
FieldNumber,recordNumber,Usage inconsistent with DwC definition |
| 40 |
scientificName,scientificName |
|
| 41 |
scientificNameAuthor,scientificNameAuthor |
|
| 42 |
sex,sex |
|
| 43 |
species,species |
|
| 44 |
stateProvince,stateProvince |
|
| 45 |
subspecies,subspecies |
|
| 46 |
yearCollected,yearCollected |
|
| 47 |
yearIdentified,yearIdentified |
|
| 46 |
Collector,recordedBy, |
|
| 47 |
RelatedCatalogItem,relatedResourceID, |
|
| 48 |
RelationshipType,relationshipOfResource, |
|
| 49 |
ScientificName,scientificName, |
|
| 50 |
ScientificNameAuthor,scientificNameAuthorship, |
|
| 51 |
Sex,sex, |
|
| 52 |
Species,specificEpithet, |
|
| 53 |
StateProvince,stateProvince, |
|
| 54 |
Latitude,verbatimLatitude, |
|
| 55 |
Longitude,verbatimLongitude, |
|
| 56 |
YearCollected,yearCollected, |
|
| 57 |
YearIdentified,yearIdentified, |
|
| inputs/NY/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
NY[Veg+],VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments |
| 2 | 2 |
UniqueNYInternalRecordNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 |
institutionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_join/1",
|
|
| 4 |
collectionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_join/2/_join/1",
|
|
| 5 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_join/3/_if[@name=""if indirect voucher""]/else",
|
|
| 6 |
maximumElevation,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
|
|
| 3 |
InstitutionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_join/1",
|
|
| 4 |
CollectionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_join/2/_join/1",
|
|
| 5 |
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_join/3/_if[@name=""if indirect voucher""]/else",
|
|
| 6 |
MaximumElevation,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
|
|
| 7 | 7 |
MinimumElevation,"/location/elevation/_alt/2/_avg/min/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value/_nullIf:[null=.]/value", |
| 8 | 8 |
MinimumElevation,"/location/elevationrange/_range/from/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value/_nullIf:[null=.]/value", |
| 9 |
maximumElevation,"/location/elevationrange/_range/to/_units:[default=m,to=m,to=]/value/_alt/1/_replace:[""\bca\.?""=]/value",
|
|
| 9 |
MaximumElevation,"/location/elevationrange/_range/to/_units:[default=m,to=m,to=]/value/_alt/1/_replace:[""\bca\.?""=]/value",
|
|
| 10 | 10 |
MinimumElevation,"/location/elevationrange/_range/to/_units:[default=m,to=m,to=]/value/_alt/2/_rangeEnd/value/_replace:[""\bca\.?""=]/value/_nullIf:[null=.]/value", |
| 11 |
coordinatePrecision,/location/locationdetermination/coordsaccuracy/_noCV/value/_alt/2,
|
|
| 12 |
boundingBox,/location/locationdetermination/footprintgeometry_dwc,
|
|
| 13 |
latitude,"/location/locationdetermination/latitude/_alt/2/_nullIf:[null=0,type=float]/value",
|
|
| 14 |
longitude,"/location/locationdetermination/longitude/_alt/2/_nullIf:[null=0,type=float]/value",
|
|
| 15 |
county,"/location/locationdetermination/namedplace_id/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",
|
|
| 16 |
stateProvince,"/location/locationdetermination/namedplace_id/_forEach:[in:[county,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=stateProvince]/placename",
|
|
| 17 |
country,"/location/locationdetermination/namedplace_id/_forEach:[in:[county,stateProvince,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=country]/placename",
|
|
| 18 |
continentOcean,"/location/locationdetermination/namedplace_id/_forEach:[in:[county,stateProvince,country,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=continent]/placename",
|
|
| 19 |
dayCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
|
|
| 20 |
monthCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
|
|
| 21 |
yearCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
|
|
| 22 |
individualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,
|
|
| 11 |
CoordinatePrecision,/location/locationdetermination/coordsaccuracy/_noCV/value/_alt/2,
|
|
| 12 |
BoundingBox,/location/locationdetermination/footprintgeometry_dwc,
|
|
| 13 |
Latitude,"/location/locationdetermination/latitude/_alt/2/_nullIf:[null=0,type=float]/value",
|
|
| 14 |
Longitude,"/location/locationdetermination/longitude/_alt/2/_nullIf:[null=0,type=float]/value",
|
|
| 15 |
County,"/location/locationdetermination/namedplace_id/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",
|
|
| 16 |
StateProvince,"/location/locationdetermination/namedplace_id/_forEach:[in:[county,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=stateProvince]/placename",
|
|
| 17 |
Country,"/location/locationdetermination/namedplace_id/_forEach:[in:[county,stateProvince,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=country]/placename",
|
|
| 18 |
ContinentOcean,"/location/locationdetermination/namedplace_id/_forEach:[in:[county,stateProvince,country,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=continent]/placename",
|
|
| 19 |
DayCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
|
|
| 20 |
MonthCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
|
|
| 21 |
YearCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
|
|
| 22 |
IndividualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,
|
|
| 23 | 23 |
Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/1, |
| 24 | 24 |
PlantFungusDescription,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/2/_label[label=""plant fungus""]/value", |
| 25 | 25 |
FieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,Usage inconsistent with DwC definition |
| 26 |
sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections"
|
|
| 27 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
|
|
| 28 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
|
|
| 29 |
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
|
|
| 26 |
Sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections"
|
|
| 27 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
|
|
| 28 |
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
|
|
| 29 |
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
|
|
| 30 | 30 |
UniqueNYInternalRecordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 31 | 31 |
FieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1,Usage inconsistent with DwC definition |
| 32 |
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
|
|
| 33 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first,
|
|
| 34 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle,
|
|
| 35 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/surname/_namePart/last,
|
|
| 36 |
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname",
|
|
| 37 |
scientificNameAuthor,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname",
|
|
| 38 |
subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/last",
|
|
| 39 |
species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname",
|
|
| 40 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname",
|
|
| 41 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",
|
|
| 42 |
order,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,family,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=order]/plantname",
|
|
| 43 |
class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=class]/plantname",
|
|
| 44 |
phylum,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subkingdom]/plantname",
|
|
| 45 |
kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,subkingdom,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",
|
|
| 46 |
dayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
|
|
| 47 |
monthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
|
|
| 48 |
yearIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
|
|
| 49 |
collector,/location/locationevent/taxonoccurrence/verbatimcollectorname,
|
|
| 50 |
catalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
|
|
| 51 |
maximumDepth,"/location/locationevent/waterdepth/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
|
|
| 52 |
minimumDepth,"/location/locationevent/waterdepth/_avg/min/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
|
|
| 32 |
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
|
|
| 33 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first,
|
|
| 34 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle,
|
|
| 35 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/surname/_namePart/last,
|
|
| 36 |
ScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname",
|
|
| 37 |
ScientificNameAuthor,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname",
|
|
| 38 |
Subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/last",
|
|
| 39 |
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname",
|
|
| 40 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname",
|
|
| 41 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",
|
|
| 42 |
Order,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,family,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=order]/plantname",
|
|
| 43 |
Class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=class]/plantname",
|
|
| 44 |
Phylum,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subkingdom]/plantname",
|
|
| 45 |
Kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,subkingdom,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",
|
|
| 46 |
DayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
|
|
| 47 |
MonthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
|
|
| 48 |
YearIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
|
|
| 49 |
Collector,/location/locationevent/taxonoccurrence/verbatimcollectorname,
|
|
| 50 |
CatalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
|
|
| 51 |
MaximumDepth,"/location/locationevent/waterdepth/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
|
|
| 52 |
MinimumDepth,"/location/locationevent/waterdepth/_avg/min/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
|
|
| 53 | 53 |
Locality,/location/locationnarrative/_merge/1/_merge/1, |
| 54 | 54 |
Substrate,"/location/locationnarrative/_merge/1/_merge/2/_label[label=""substrate""]/value", |
| 55 | 55 |
Vegetation,"/location/locationnarrative/_merge/1/_merge/3/_label[label=""vegetation""]/value", |
| 56 |
habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?" |
|
| 56 |
Habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?" |
|
| 57 |
BasisOfRecord,,** No join mapping for BasisOfRecord ** |
|
| 57 | 58 |
CollectorNumber,,"** No join mapping for OMIT ** Not used [1], so does not need to be mapped. |
| 58 | 59 |
|
| 59 | 60 |
[1] The following query returns no rows: SELECT * FROM ""NY"".""Specimen"" WHERE ""CollectorNumber"" IS NOT NULL" |
| 61 |
DateLastModified,,** No join mapping for dcterms:modified ** |
|
| 62 |
JulianDay,,** No join mapping for day ** |
|
| 63 |
PreparationType,,** No join mapping for preparations ** |
|
| 64 |
PreviousCatalogNumber,,** No join mapping for otherCatalogNumbers ** |
|
| 65 |
RelatedCatalogItem,,** No join mapping for relatedResourceID ** |
|
| 66 |
RelationshipType,,** No join mapping for relationshipOfResource ** |
|
| 67 |
TimeOfDay,,** No join mapping for eventTime ** |
|
| 68 |
TypeStatus,,** No join mapping for TypeStatus ** |
|
| 69 |
key,,** No join mapping for key ** Not used because UniqueNYInternalRecordNumber is a better pkey |
|
| inputs/NY/Specimen/new_terms.csv | ||
|---|---|---|
| 1 | 1 |
key |
| 2 |
BasisOfRecord |
|
| 3 |
TypeStatus |
|
| 4 | 2 |
PlantFungusDescription |
| 5 | 3 |
Substrate |
| 6 | 4 |
Vegetation |
| inputs/NY/Specimen/unmapped_terms.csv | ||
|---|---|---|
| 1 |
"" |
|
| 2 |
"" |
|
| 3 |
"" |
|
| 4 |
"" |
|
| 5 |
"" |
|
| 6 |
"" |
|
| 7 |
"" |
|
| 8 |
"" |
|
| 9 |
"" |
|
| 10 |
"" |
|
| 11 |
"" |
|
| 12 |
"" |
|
| 13 |
"" |
|
| 14 |
"" |
|
| 15 |
"" |
|
| 16 |
"" |
|
| 17 |
"" |
|
| 18 |
"" |
|
| 19 |
"" |
|
| 20 |
"" |
|
| 21 |
"" |
|
| 1 |
key |
|
| 2 |
dcterms:modified |
|
| 3 |
BasisOfRecord |
|
| 4 |
TypeStatus |
|
| 22 | 5 |
OMIT |
| 23 |
"" |
|
| 24 |
"" |
|
| 25 |
"" |
|
| 26 |
"" |
|
| 27 |
"" |
|
| 28 |
"" |
|
| 29 |
"" |
|
| 30 |
"" |
|
| 31 |
"" |
|
| 32 |
"" |
|
| 6 |
day |
|
| 7 |
eventTime |
|
| 33 | 8 |
Locality/_merge/1 |
| 34 |
"" |
|
| 35 |
"" |
|
| 36 |
"" |
|
| 37 |
"" |
|
| 38 | 9 |
MinimumElevation/_nullIf:[null=.]/value |
| 39 |
"" |
|
| 40 |
"" |
|
| 41 |
"" |
|
| 42 |
"" |
|
| 43 |
"" |
|
| 44 |
"" |
|
| 45 |
"" |
|
| 46 |
"" |
|
| 47 |
"" |
|
| 10 |
preparations |
|
| 11 |
otherCatalogNumbers |
|
| 12 |
relationshipOfResource |
|
| 13 |
relatedResourceID |
|
| 48 | 14 |
Notes/_merge/1 |
| 49 |
"" |
|
| 50 | 15 |
"Notes/_merge/2/_label[label=""plant fungus""]/value" |
| 51 | 16 |
"Locality/_merge/2/_label[label=""substrate""]/value" |
| 52 | 17 |
"Locality/_merge/3/_label[label=""vegetation""]/value" |
| inputs/Madidi/Organism/map.csv | ||
|---|---|---|
| 1 | 1 |
Madidi[Veg+],Veg+,Comments |
| 2 | 2 |
Expedition,projectName, |
| 3 | 3 |
Inventory name,plotName, |
| 4 |
Number of inventory (general),, |
|
| 5 |
Number of inventory (expedition),, |
|
| 6 |
"Type Inventory (C, PP, TP)",, |
|
| 4 |
Number of inventory (general),Number of inventory (general),
|
|
| 5 |
Number of inventory (expedition),Number of inventory (expedition),
|
|
| 6 |
"Type Inventory (C, PP, TP)","Type Inventory (C, PP, TP)",
|
|
| 7 | 7 |
Inventory code,locationID, |
| 8 | 8 |
Tag number,tag, |
| 9 | 9 |
Tree number,recordNumber, |
| 10 | 10 |
Number of subplot,subplot, |
| 11 | 11 |
Index collector,recordedBy, |
| 12 | 12 |
Specimen,catalogNumber, |
| 13 |
Similar specimen,, |
|
| 14 |
Plot specimen,, |
|
| 15 |
Expedition specimen,, |
|
| 16 |
Project specimen,, |
|
| 13 |
Similar specimen,Similar specimen,
|
|
| 14 |
Plot specimen,Plot specimen,
|
|
| 15 |
Expedition specimen,Expedition specimen,
|
|
| 16 |
Project specimen,Project specimen,
|
|
| 17 | 17 |
Field family,verbatimFamily, |
| 18 | 18 |
Field name,verbatimGenus,Often = Genera |
| 19 | 19 |
Family (revised),family, |
| 20 | 20 |
Specie+autor,scientificName, |
| 21 | 21 |
Genera,genus, |
| 22 | 22 |
Specific epithet,specificEpithet, |
| 23 |
Species and morphotypes,,"Contains less than ""Specie+autor""" |
|
| 23 |
Species and morphotypes,Species and morphotypes,"Contains less than ""Specie+autor"""
|
|
| 24 | 24 |
Autor (revised),scientificNameAuthorship, |
| 25 | 25 |
Determined by,identifiedBy, |
| 26 | 26 |
Qualifier,identificationQualifier, |
| 27 |
Common name,, |
|
| 28 |
Circumference,, |
|
| 27 |
Common name,Common name,
|
|
| 28 |
Circumference,Circumference,
|
|
| 29 | 29 |
Diameter,diameterBreastHeight, |
| 30 | 30 |
Trunk,authorStemCode, |
| 31 | 31 |
Total height,height, |
| 32 |
Bole height,,trunk height |
|
| 33 |
Habit,, |
|
| 34 |
Phenology,, |
|
| 35 |
Crown position,, |
|
| 36 |
Crown shape,, |
|
| 32 |
Bole height,Bole height,trunk height
|
|
| 33 |
Habit,verbatimGrowthForm,
|
|
| 34 |
Phenology,Phenology,
|
|
| 35 |
Crown position,Crown position,
|
|
| 36 |
Crown shape,Crown shape,
|
|
| 37 | 37 |
Liana presence,lianaInfestation, |
| 38 |
Basal area,,"Would be basalDiameter, but need formula to translate" |
|
| 38 |
Basal area,Basal area,"Would be basalDiameter, but need formula to translate"
|
|
| 39 | 39 |
Subplot X,organismX, |
| 40 | 40 |
Subplot Y,organismY, |
| 41 |
Plot X,, |
|
| 42 |
Plot Y,, |
|
| 41 |
Plot X,Plot X,
|
|
| 42 |
Plot Y,Plot Y,
|
|
| 43 | 43 |
Observations,fieldNotes, |
| inputs/Madidi/Organism/map.full.csv | ||
|---|---|---|
| 1 | 1 |
Madidi[Veg+],Veg+,Comments |
| 2 |
Basal area,Basal area,"Would be basalDiameter, but need formula to translate" |
|
| 3 |
Bole height,Bole height,trunk height |
|
| 4 |
Circumference,Circumference, |
|
| 5 |
Common name,Common name, |
|
| 6 |
Crown position,Crown position, |
|
| 7 |
Crown shape,Crown shape, |
|
| 8 |
Expedition specimen,Expedition specimen, |
|
| 9 |
Number of inventory (expedition),Number of inventory (expedition), |
|
| 10 |
Number of inventory (general),Number of inventory (general), |
|
| 11 |
Phenology,Phenology, |
|
| 12 |
Plot X,Plot X, |
|
| 13 |
Plot Y,Plot Y, |
|
| 14 |
Plot specimen,Plot specimen, |
|
| 15 |
Project specimen,Project specimen, |
|
| 16 |
Similar specimen,Similar specimen, |
|
| 17 |
Species and morphotypes,Species and morphotypes,"Contains less than ""Specie+autor""" |
|
| 18 |
"Type Inventory (C, PP, TP)","Type Inventory (C, PP, TP)", |
|
| 2 | 19 |
Trunk,authorStemCode, |
| 3 | 20 |
Specimen,catalogNumber, |
| 4 | 21 |
Diameter,diameterBreastHeight, |
| 5 | 22 |
Family (revised),family, |
| 6 | 23 |
Observations,fieldNotes, |
| 7 | 24 |
Genera,genus, |
| 8 |
habit,habit |
|
| 9 | 25 |
Total height,height, |
| 10 | 26 |
Qualifier,identificationQualifier, |
| 11 | 27 |
Determined by,identifiedBy, |
| ... | ... | |
| 24 | 40 |
Tag number,tag, |
| 25 | 41 |
Field family,verbatimFamily, |
| 26 | 42 |
Field name,verbatimGenus,Often = Genera |
| 43 |
Habit,verbatimGrowthForm, |
|
| inputs/Madidi/Organism/VegBIEN.csv | ||
|---|---|---|
| 23 | 23 |
Subplot Y,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition, |
| 24 | 24 |
Tree number,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1, |
| 25 | 25 |
Specie+autor,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2, |
| 26 |
habit,"/location/locationevent/taxonoccurrence/growthform/_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","According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>"
|
|
| 26 |
Habit,"/location/locationevent/taxonoccurrence/growthform/_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","According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>"
|
|
| 27 | 27 |
Determined by,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first, |
| 28 | 28 |
Determined by,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle, |
| 29 | 29 |
Determined by,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/surname/_namePart/last, |
| ... | ... | |
| 37 | 37 |
Field family,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname", |
| 38 | 38 |
Index collector,/location/locationevent/taxonoccurrence/verbatimcollectorname, |
| 39 | 39 |
Specimen,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
| 40 |
Basal area,,"** No join mapping for Basal area ** Would be basalDiameter, but need formula to translate" |
|
| 41 |
Bole height,,** No join mapping for Bole height ** trunk height |
|
| 42 |
Circumference,,** No join mapping for Circumference ** |
|
| 43 |
Common name,,** No join mapping for Common name ** |
|
| 44 |
Crown position,,** No join mapping for Crown position ** |
|
| 45 |
Crown shape,,** No join mapping for Crown shape ** |
|
| 46 |
Expedition specimen,,** No join mapping for Expedition specimen ** |
|
| 47 |
Number of inventory (expedition),,** No join mapping for Number of inventory (expedition) ** |
|
| 48 |
Number of inventory (general),,** No join mapping for Number of inventory (general) ** |
|
| 49 |
Phenology,,** No join mapping for Phenology ** |
|
| 50 |
Plot X,,** No join mapping for Plot X ** |
|
| 51 |
Plot Y,,** No join mapping for Plot Y ** |
|
| 52 |
Plot specimen,,** No join mapping for Plot specimen ** |
|
| 53 |
Project specimen,,** No join mapping for Project specimen ** |
|
| 54 |
Similar specimen,,** No join mapping for Similar specimen ** |
|
| 55 |
Species and morphotypes,,"** No join mapping for Species and morphotypes ** Contains less than ""Specie+autor""" |
|
| 56 |
"Type Inventory (C, PP, TP)",,"** No join mapping for Type Inventory (C, PP, TP) ** " |
|
| inputs/Madidi/Organism/new_terms.csv | ||
|---|---|---|
| 1 | 1 |
Expedition |
| 2 | 2 |
Inventory name |
| 3 | 3 |
Number of inventory (general) |
| 4 |
Number of inventory (expedition) |
|
| 5 |
"Type Inventory (C, PP, TP)" |
|
| 6 | 4 |
Inventory code |
| 7 | 5 |
Tag number |
| 8 | 6 |
Tree number |
| 9 | 7 |
Number of subplot |
| 10 | 8 |
Index collector |
| 11 | 9 |
Specimen |
| 12 |
Similar specimen |
|
| 13 |
Plot specimen |
|
| 14 |
Expedition specimen |
|
| 15 |
Project specimen |
|
| 16 | 10 |
Field family |
| 17 | 11 |
Field name |
| 18 | 12 |
Family (revised) |
| 19 | 13 |
Specie+autor |
| 20 | 14 |
Genera |
| 21 |
Species and morphotypes |
|
| 22 | 15 |
Autor (revised) |
| 23 | 16 |
Determined by |
| 24 | 17 |
Qualifier |
| 25 |
Common name |
|
| 26 |
Circumference |
|
| 27 | 18 |
Diameter |
| 28 | 19 |
Trunk |
| 29 | 20 |
Total height |
| 30 |
Bole height |
|
| 31 |
Phenology |
|
| 32 |
Crown position |
|
| 33 |
Crown shape |
|
| 34 | 21 |
Liana presence |
| 35 |
Basal area |
|
| 36 |
Plot X |
|
| 37 |
Plot Y |
|
| 38 | 22 |
Observations |
| inputs/Madidi/Organism/unmapped_terms.csv | ||
|---|---|---|
| 1 |
"" |
|
| 2 |
"" |
|
| 3 |
"" |
|
| 4 |
"" |
|
| 5 |
"" |
|
| 6 |
"" |
|
| 7 |
"" |
|
| 8 |
"" |
|
| 9 |
"" |
|
| 10 |
"" |
|
| 11 |
"" |
|
| 12 |
"" |
|
| 13 |
"" |
|
| 14 |
"" |
|
| 15 |
"" |
|
| 16 |
"" |
|
| 17 |
"" |
|
| 18 |
"" |
|
| 1 |
Number of inventory (general) |
|
| 2 |
Number of inventory (expedition) |
|
| 3 |
"Type Inventory (C, PP, TP)" |
|
| 4 |
Similar specimen |
|
| 5 |
Plot specimen |
|
| 6 |
Expedition specimen |
|
| 7 |
Project specimen |
|
| 8 |
Species and morphotypes |
|
| 9 |
Common name |
|
| 10 |
Circumference |
|
| 11 |
Bole height |
|
| 12 |
Phenology |
|
| 13 |
Crown position |
|
| 14 |
Crown shape |
|
| 15 |
Basal area |
|
| 16 |
Plot X |
|
| 17 |
Plot Y |
|
| inputs/Madidi/Plot/map.csv | ||
|---|---|---|
| 1 | 1 |
Madidi[Veg+],Veg+,Comments |
| 2 |
Inventory number,,Not globally unique |
|
| 2 |
Inventory number,Inventory number,Not globally unique
|
|
| 3 | 3 |
Expedition number,projectID,Consistent (globally unique) between PPM and PT data |
| 4 | 4 |
Expedition name,projectName,Consistent (globally unique) between PPM and PT data |
| 5 |
Number of inventory (expedition),,The number of the event within the project |
|
| 5 |
Number of inventory (expedition),Number of inventory (expedition),The number of the event within the project
|
|
| 6 | 6 |
Inventory name,plotName, |
| 7 | 7 |
Inventory code,locationID, |
| 8 | 8 |
First evaluation,eventDate, |
| 9 |
Installed and evaluated by,,"Need a way to store a verbatim list of people, or a function to parse it and insert it iteratively into party" |
|
| 10 |
Collaborators,,"Need a way to store a verbatim list of people, or a function to parse it and insert it iteratively into party" |
|
| 11 |
Related Epilocs,,"It appears to be a list of people, some with #s after them. It doesn't seem like the definition of Epiloc at <http://rithm.wikispaces.com/Tropicos.Epiloc>, which relates to individual specimens, not whole plots." |
|
| 9 |
Installed and evaluated by,Installed and evaluated by,"Need a way to store a verbatim list of people, or a function to parse it and insert it iteratively into party"
|
|
| 10 |
Collaborators,Collaborators,"Need a way to store a verbatim list of people, or a function to parse it and insert it iteratively into party"
|
|
| 11 |
Related Epilocs,Related Epilocs,"It appears to be a list of people, some with #s after them. It doesn't seem like the definition of Epiloc at <http://rithm.wikispaces.com/Tropicos.Epiloc>, which relates to individual specimens, not whole plots."
|
|
| 12 | 12 |
Area,plotArea, |
| 13 |
Number of stems,,Do we want to store this data? |
|
| 14 |
Number of trees,,Do we want to store this data? |
|
| 15 |
Coordinates,,Concatenation of Latitude (DMS) and Longitude (DMS) |
|
| 13 |
Number of stems,Number of stems,Do we want to store this data?
|
|
| 14 |
Number of trees,Number of trees,Do we want to store this data?
|
|
| 15 |
Coordinates,Coordinates,Concatenation of Latitude (DMS) and Longitude (DMS)
|
|
| 16 | 16 |
Latitude,decimalLatitude, |
| 17 | 17 |
Longitude,decimalLongitude, |
| 18 | 18 |
Latitude (DMS),verbatimLatitude, |
| ... | ... | |
| 25 | 25 |
Vegetation type,communityID, |
| 26 | 26 |
Topographical situation,landform, |
| 27 | 27 |
Slope,slopeGradient, |
| 28 |
Soil sample,,Always empty |
|
| 28 |
Soil sample,Soil sample,Always empty
|
|
| 29 | 29 |
pH acuoso (ISRIC 4–– 1 - 14),ph, |
| 30 | 30 |
Conductividad electrica (ASPT 6–µS/cm– 1 - 10000),conductivity, |
| 31 | 31 |
Nitrógeno total (ISRIC 6–%–0.0014),nitrogen, |
| inputs/Madidi/Plot/map.full.csv | ||
|---|---|---|
| 1 | 1 |
Madidi[Veg+],Veg+,Comments |
| 2 |
Collaborators,Collaborators,"Need a way to store a verbatim list of people, or a function to parse it and insert it iteratively into party" |
|
| 3 |
Coordinates,Coordinates,Concatenation of Latitude (DMS) and Longitude (DMS) |
|
| 4 |
Installed and evaluated by,Installed and evaluated by,"Need a way to store a verbatim list of people, or a function to parse it and insert it iteratively into party" |
|
| 5 |
Inventory number,Inventory number,Not globally unique |
|
| 6 |
Number of inventory (expedition),Number of inventory (expedition),The number of the event within the project |
|
| 7 |
Number of stems,Number of stems,Do we want to store this data? |
|
| 8 |
Number of trees,Number of trees,Do we want to store this data? |
|
| 9 |
Related Epilocs,Related Epilocs,"It appears to be a list of people, some with #s after them. It doesn't seem like the definition of Epiloc at <http://rithm.wikispaces.com/Tropicos.Epiloc>, which relates to individual specimens, not whole plots." |
|
| 10 |
Soil sample,Soil sample,Always empty |
|
| 2 | 11 |
Acidez intercambiable (ISRIC 11–cmolc/Kg–0.05),acidity, |
| 3 | 12 |
"Calcio intercambiable (WSP S-5,10–cmolc/Kg–0.016)",calcium, |
| 4 | 13 |
"Carbón Orgánico (WSP S-9,10–%–0.06)",carbon, |
| inputs/Madidi/Plot/new_terms.csv | ||
|---|---|---|
| 1 | 1 |
Inventory number |
| 2 | 2 |
Expedition number |
| 3 | 3 |
Expedition name |
| 4 |
Number of inventory (expedition) |
|
| 5 | 4 |
Inventory name |
| 6 | 5 |
Inventory code |
| 7 | 6 |
First evaluation |
| 8 |
Installed and evaluated by |
|
| 9 |
Collaborators |
|
| 10 |
Related Epilocs |
|
| 11 | 7 |
Area |
| 12 |
Number of stems |
|
| 13 |
Number of trees |
|
| 14 |
Coordinates |
|
| 15 | 8 |
Latitude (DMS) |
| 16 | 9 |
Longitude (DMS) |
| 17 | 10 |
Altitude |
| ... | ... | |
| 21 | 14 |
Vegetation type |
| 22 | 15 |
Topographical situation |
| 23 | 16 |
Slope |
| 24 |
Soil sample |
|
| 25 | 17 |
pH acuoso (ISRIC 4–– 1 - 14) |
| 26 | 18 |
Conductividad electrica (ASPT 6–µS/cm– 1 - 10000) |
| 27 | 19 |
Nitrógeno total (ISRIC 6–%–0.0014) |
| inputs/UNCC/Specimen/map.csv | ||
|---|---|---|
| 1 | 1 |
UNCC[Veg+],Veg+,Comments |
| 2 | 2 |
accession,occurrenceID, |
| 3 | 3 |
herbarium,institutionCode, |
| 4 |
family,, |
|
| 5 |
genus,, |
|
| 6 |
species,, |
|
| 4 |
family,family,
|
|
| 5 |
genus,genus,
|
|
| 6 |
species,specificEpithet,
|
|
| 7 | 7 |
usdaRank,taxonRank/_alt/1, |
| 8 | 8 |
infrarank,taxonRank/_alt/2, |
| 9 | 9 |
infraname,infraspecificEpithet, |
| ... | ... | |
| 17 | 17 |
collmonth,monthCollected, |
| 18 | 18 |
collday,dayCollected, |
| 19 | 19 |
collyear,yearCollected, |
| 20 |
country,, |
|
| 21 |
state,, |
|
| 22 |
county,, |
|
| 20 |
country,country,
|
|
| 21 |
state,stateProvince,
|
|
| 22 |
county,county,
|
|
| 23 | 23 |
campus,"fieldNotes/_merge/5/_label[label=""campus""]/value", |
| 24 | 24 |
leaves,"reproductiveCondition/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?" |
| 25 | 25 |
flower,"reproductiveCondition/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?" |
| 26 | 26 |
fruit,"reproductiveCondition/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?" |
| 27 | 27 |
root,"reproductiveCondition/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?" |
| 28 |
locality,, |
|
| 29 |
habitat,, |
|
| 28 |
locality,locality,
|
|
| 29 |
habitat,habitat,
|
|
| 30 | 30 |
comment1,fieldNotes/_merge/1, |
| 31 | 31 |
comment2,fieldNotes/_merge/2, |
| 32 | 32 |
comment3,fieldNotes/_merge/3, |
| ... | ... | |
| 35 | 35 |
inorout,"fieldNotes/_merge/7/_label[label=""in or out""]/value", |
| 36 | 36 |
sheetno,associatedMedia,? |
| 37 | 37 |
cultivated,cultivated,Ignore other values |
| 38 |
filler,,"Where used, same as family" |
|
| 38 |
filler,filler,"Where used, same as family" |
|
| inputs/UNCC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 34 | 34 |
collector3,/location/locationevent/taxonoccurrence/verbatimcollectorname/_merge/4, |
| 35 | 35 |
locality,/location/locationnarrative/_merge/1, |
| 36 | 36 |
habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?" |
| 37 |
filler,,"** No join mapping for filler ** Where used, same as family" |
|
| 37 | 38 |
flower,,"** No join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?" |
| 38 | 39 |
fruit,,"** No join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?" |
| 39 | 40 |
leaves,,"** No join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?" |
| inputs/UNCC/Specimen/unmapped_terms.csv | ||
|---|---|---|
| 1 |
"" |
|
| 2 |
"" |
|
| 3 |
"" |
|
| 4 | 1 |
taxonRank/_alt/1 |
| 5 | 2 |
taxonRank/_alt/2 |
| 6 | 3 |
Collector/_merge/1 |
| 7 | 4 |
Collector/_merge/2 |
| 8 | 5 |
Collector/_merge/3 |
| 9 | 6 |
Collector/_merge/4 |
| 10 |
"" |
|
| 11 |
"" |
|
| 12 |
"" |
|
| 13 | 7 |
"fieldNotes/_merge/5/_label[label=""campus""]/value" |
| 14 | 8 |
"reproductiveCondition/_map:[A=*,I=*,M=*]/value" |
| 15 | 9 |
"reproductiveCondition/_map:[A=*,I=*,M=*]/value" |
| 16 | 10 |
"reproductiveCondition/_map:[A=*,I=*,M=*]/value" |
| 17 | 11 |
"reproductiveCondition/_map:[A=*,I=*,M=*]/value" |
| 18 |
"" |
|
| 19 |
"" |
|
| 20 | 12 |
fieldNotes/_merge/1 |
| 21 | 13 |
fieldNotes/_merge/2 |
| 22 | 14 |
fieldNotes/_merge/3 |
| ... | ... | |
| 24 | 16 |
"fieldNotes/_merge/6/_label[label=""loaned to""]/value" |
| 25 | 17 |
"fieldNotes/_merge/7/_label[label=""in or out""]/value" |
| 26 | 18 |
associatedMedia |
| 27 |
"" |
|
| 19 |
filler |
|
| inputs/ACAD/Specimen/VegBIEN.csv | ||
|---|---|---|
| 40 | 40 |
catalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
| 41 | 41 |
locality,/location/locationnarrative/_merge/1, |
| 42 | 42 |
habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?" |
| 43 |
basisOfRecord,,** No join mapping for basisOfRecord ** |
|
| 44 |
bibliographicCitation,,** No join mapping for dcterms:bibliographicCitation ** |
|
| 45 |
dynamicProperties,,** No join mapping for dynamicProperties ** |
|
| 46 |
geodeticDatum,,** No join mapping for geodeticDatum ** |
|
| 47 |
georeferenceSources,,** No join mapping for georeferenceSources ** |
|
| 48 |
georeferenceVerificationStatus,,** No join mapping for georeferenceVerificationStatus ** |
|
| 49 |
identificationRemarks,,** No join mapping for identificationRemarks ** |
|
| 50 |
language,,** No join mapping for dcterms:language ** |
|
| 51 |
locationRemarks,,** No join mapping for locationRemarks ** |
|
| 52 |
modified,,** No join mapping for dcterms:modified ** |
|
| 53 |
municipality,,** No join mapping for municipality ** |
|
| 54 |
occurrenceRemarks,,** No join mapping for occurrenceRemarks ** |
|
| 55 |
ownerInstitutionCode,,** No join mapping for ownerInstitutionCode ** |
|
| 56 |
reproductiveCondition,,** No join mapping for reproductiveCondition ** |
|
| 57 |
rights,,** No join mapping for dcterms:rights ** |
|
| 58 |
rightsHolder,,** No join mapping for dcterms:rightsHolder ** |
|
| 59 |
type,,** No join mapping for dcterms:type ** |
|
| 60 |
verbatimDepth,,** No join mapping for verbatimDepth ** |
|
| inputs/SALVIAS-CSV/Organism/VegBIEN.csv | ||
|---|---|---|
| 70 | 70 |
det_type,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","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." |
| 71 | 71 |
coll_number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then/_alt/1",Brad: Map instead as for voucher_string |
| 72 | 72 |
voucher_string,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
| 73 |
collector_code,,** No join mapping for collector_code ** Brad: OMIT |
|
| 74 |
comments,,** No join mapping for comments ** Brad: OMIT |
|
| 75 |
fam_status,,** No join mapping for fam_status ** Brad: OMIT. This will be determined later by using TNRS. |
|
| 76 |
gen_status,,** No join mapping for gen_status ** Brad: OMIT. This will be determined later by using TNRS. |
|
| 77 |
ind_id,,** No join mapping for ind_id ** Brad: OMIT |
|
| 78 |
species_status,,"** No join mapping for 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." |
|
| inputs/SALVIAS-CSV/Plot/map.csv | ||
|---|---|---|
| 35 | 35 |
soil_texture,texture, |
| 36 | 36 |
holdridge_life_zone,communityID, |
| 37 | 37 |
life_zone_code,communityName, |
| 38 |
observation_type,,"Brad: SALVIAS internal metadata indicating whether the record represents an individual or aggregate observation. Rather than storing, use to decide where to store in VegX.; Aaron: VegX aggregateOrganismObservation table is missing many fields available in individualOrganismObservation, so we're mapping to individualOrganismObservation regardless of observation type" |
|
| 38 |
observation_type,observation_type,"Brad: SALVIAS internal metadata indicating whether the record represents an individual or aggregate observation. Rather than storing, use to decide where to store in VegX.; Aaron: VegX aggregateOrganismObservation table is missing many fields available in individualOrganismObservation, so we're mapping to individualOrganismObservation regardless of observation type"
|
|
| 39 | 39 |
plot_methodology,samplingProtocol, |
| 40 | 40 |
plot_area_ha,plotArea,"Brad: Area in hectares. Is there any way to store units?; Aaron: VegX plot area annotation says ""Total area of the plot in square meters."" so units are fixed" |
| 41 |
recensused,,"Brad: This is a 0/1 value, internal to SALVIAS. 1 indicates that a plot has >1 set of values, from different census events.; Aaron: Different censuses are distinguished in organisms data by different census_no values" |
|
| 41 |
recensused,recensused,"Brad: This is a 0/1 value, internal to SALVIAS. 1 indicates that a plot has >1 set of values, from different census events.; Aaron: Different censuses are distinguished in organisms data by different census_no values"
|
|
| 42 | 42 |
date_start,startDate, |
| 43 | 43 |
date_finish,endDate, |
Also available in: Unified diff
inputs/*/*/map.csv: Changed empty mappings to self mappings, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Map_refactoring#Change-empty-mappings-to-self-mappings>. Note that in map.full.csv and VegBIEN.csv, lines that have changed are always the result of the input field's case being changed to match the case of the datasource's actual column name.