JBM,VegCore,Filter,Comments

id,occurrenceID,,

minimumElevationInMeters,minimumElevationInMeters,,

verbatimLatitude,verbatimLatitude,,

modified,dcterms:modified,,

recordNumber,recordNumber,,

recordedBy,recordedBy,,

ownerInstitutionCode,ownerInstitutionCode,,

language,dcterms:language,,

genus,genus,,

specificEpithet,specificEpithet,,

coordinateUncertaintyInMeters,coordinateUncertaintyInMeters,,

decimalLatitude,decimalLatitude,,

basisOfRecord,basisOfRecord,,

geodeticDatum,geodeticDatum,,

stateProvince,stateProvince,,

locality,locality,,

collectionID,collectionID,,

rightsHolder,dcterms:rightsHolder,,

verbatimLongitude,verbatimLongitude,,

nomenclaturalCode,nomenclaturalCode,,

county,county,,

dynamicProperties,dynamicProperties,,

sex,sex,,

family,family,,

datasetName,datasetName,,

scientificName,scientificName,,

eventDate,eventDate,,

habitat,habitat,,

country,country,,

rights,dcterms:rights,,

decimalLongitude,decimalLongitude,,

collectionCode,collectionCode,,

type,dcterms:type,,

order,order,,

kingdom,kingdom,,

institutionCode,institutionCode,,

datasetID,datasetID,,

countryCode,countryCode,,

catalogNumber,catalogNumber,,

JBM,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments

id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1",

catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists",

institutionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1",

collectionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1",

collectionID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2",

catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else",

minimumElevationInMeters,/location/elevation_m/_alt/2/_avg/min,

id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists",

recordNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists",

eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists",

eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value",

eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value",

eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value,

eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value,

recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,

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"

catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",

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

collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2,

institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name,

id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,

recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",

scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2",

recordedBy,/location/locationevent/taxonoccurrence/collector_id/party/fullname,

id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",

recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",

id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,

family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family",

scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/1",

genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2",

specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",

specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",

genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",

genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",

family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",

family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet",

order,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=order]/taxonepithet",

kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet",

family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family,

scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/1,

genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2,

specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,

family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,

genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,

specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,

scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname,

catalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",

locality,/location/locationnarrative/_merge/1,

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?"

coordinateUncertaintyInMeters,/location/locationplace/*_id/place/*_id/coordinates/coordsaccuracy_m/_noCV/value,

decimalLatitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value",

decimalLongitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value",

verbatimLatitude,/location/locationplace/*_id/place/*_id/coordinates/verbatimlatitude,

verbatimLongitude,/location/locationplace/*_id/place/*_id/coordinates/verbatimlongitude,

country,/location/locationplace/*_id/place/country,

county,/location/locationplace/*_id/place/county,

decimalLatitude,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings"

decimalLongitude,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings"

country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2,

county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2,

stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2,

stateProvince,/location/locationplace/*_id/place/stateprovince,

basisOfRecord,,** No join mapping for basisOfRecord ** 

countryCode,,** No join mapping for countryCode ** 

datasetID,,** No join mapping for datasetID ** 

datasetName,,** No join mapping for datasetName ** 

dynamicProperties,,** No join mapping for dynamicProperties ** 

geodeticDatum,,** No join mapping for geodeticDatum ** 

language,,** No join mapping for dcterms:language ** 

modified,,** No join mapping for dcterms:modified ** 

nomenclaturalCode,,** No join mapping for nomenclaturalCode ** 

ownerInstitutionCode,,** No join mapping for ownerInstitutionCode ** 

rights,,** No join mapping for dcterms:rights ** 

rightsHolder,,** No join mapping for dcterms:rightsHolder ** 

type,,** No join mapping for dcterms:type ** 

Put template:

<VegBIEN>

    <_simplifyPath id="-1">

        <next>parent_id</next>

        <path>

            <location>

                <authorlocationcode>

                    <_alt>

                        <1>$id</1>

                        <2>

                            <_join>

                                <1>$institutionCode</1>

                                <2>

                                    <_join>

                                        <1>$collectionCode</1>

                                        <2>$collectionID</2>

                                    </_join>

                                </2>

                                <3>$catalogNumber</3>

                            </_join>

                        </2>

                    </_alt>

                </authorlocationcode>

                <elevation_m><_avg><min>$minimumElevationInMeters</min></_avg></elevation_m>

                <locationevent>

                    <obsenddate><_dateRangeEnd><value>$eventDate</value></_dateRangeEnd></obsenddate>

                    <obsstartdate><_dateRangeStart><value>$eventDate</value></_dateRangeStart></obsstartdate>

                    <taxonoccurrence>

                        <aggregateoccurrence>

                            <plantobservation>

                                <collectionnumber>$recordNumber</collectionnumber>

                                <definedvalue fkey="tablerecord_id">

                                    <userdefined_id>

                                        <userdefined>

                                            <tablename>plantobservation</tablename>

                                            <userdefinedname>sex</userdefinedname>

                                        </userdefined>

                                    </userdefined_id>

                                    <definedvalue>$sex</definedvalue>

                                </definedvalue>

                                <specimenreplicate>

                                    <catalognumber_dwc>$catalogNumber</catalognumber_dwc>

                                    <collectioncode_dwc>

                                        <_join>

                                            <1>$collectionCode</1>

                                            <2>$collectionID</2>

                                        </_join>

                                    </collectioncode_dwc>

                                    <institution_id><sourcename><name>$institutionCode</name></sourcename></institution_id>

                                    <sourceaccessioncode>$id</sourceaccessioncode>

                                </specimenreplicate>

                            </plantobservation>

                        </aggregateoccurrence>

                        <collector_id><party><fullname>$recordedBy</fullname></party></collector_id>

                        <sourceaccessioncode>$id</sourceaccessioncode>

                        <taxondetermination>

                            <taxonverbatim_id>

                                <taxonverbatim>

                                    <taxonlabel_id>

                                        <taxonlabel>

                                            <matched_label_id>

                                                <taxonlabel>

                                                    <source_id><source><shortname>TNRS</shortname></source></source_id>

                                                    <taxonomicname>

                                                        <_join_words>

                                                            <1><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></1>

                                                            <2>

                                                                <_alt>

                                                                    <1>$scientificName</1>

                                                                    <2>

                                                                        <_join_words>

                                                                            <2>$genus</2>

                                                                            <3>$specificEpithet</3>

                                                                        </_join_words>

                                                                    </2>

                                                                </_alt>

                                                            </2>

                                                        </_join_words>

                                                    </taxonomicname>

                                                </taxonlabel>

                                            </matched_label_id>

                                            <parent_id>

                                                <taxonlabel>

                                                    <parent_id>

                                                        <taxonlabel>

                                                            <rank>cultivar</rank>

                                                            <parent_id>

                                                                <taxonlabel>

                                                                    <rank>forma</rank>

                                                                    <parent_id>

                                                                        <taxonlabel>

                                                                            <rank>variety</rank>

                                                                            <parent_id>

                                                                                <taxonlabel>

                                                                                    <rank>subspecies</rank>

                                                                                    <parent_id>

                                                                                        <taxonlabel>

                                                                                            <rank>species</rank>

                                                                                            <taxonepithet>$specificEpithet</taxonepithet>

                                                                                            <parent_id>

                                                                                                <taxonlabel>

                                                                                                    <rank>genus</rank>

                                                                                                    <taxonepithet>$genus</taxonepithet>

                                                                                                    <parent_id>

                                                                                                        <taxonlabel>

                                                                                                            <rank>family</rank>

                                                                                                            <taxonepithet>$family</taxonepithet>

                                                                                                            <parent_id>

                                                                                                                <taxonlabel>

                                                                                                                    <rank>order</rank>

                                                                                                                    <taxonepithet>$order</taxonepithet>

                                                                                                                    <parent_id>

                                                                                                                        <taxonlabel>

                                                                                                                            <rank>class</rank>

                                                                                                                            <parent_id>

                                                                                                                                <taxonlabel>

                                                                                                                                    <rank>phylum</rank>

                                                                                                                                    <parent_id>

                                                                                                                                        <taxonlabel>

                                                                                                                                            <rank>kingdom</rank>

                                                                                                                                            <taxonepithet>$kingdom</taxonepithet>

                                                                                                                                        </taxonlabel>

                                                                                                                                    </parent_id>

                                                                                                                                </taxonlabel>

                                                                                                                            </parent_id>

                                                                                                                        </taxonlabel>

                                                                                                                    </parent_id>

                                                                                                                </taxonlabel>

                                                                                                            </parent_id>

                                                                                                        </taxonlabel>

                                                                                                    </parent_id>

                                                                                                </taxonlabel>

                                                                                            </parent_id>

                                                                                        </taxonlabel>

                                                                                    </parent_id>

                                                                                </taxonlabel>

                                                                            </parent_id>

                                                                        </taxonlabel>

                                                                    </parent_id>

                                                                </taxonlabel>

                                                            </parent_id>

                                                        </taxonlabel>

                                                    </parent_id>

                                                </taxonlabel>

                                            </parent_id>

                                            <taxonomicname>

                                                <_join_words>

                                                    <1><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></1>

                                                    <2>

                                                        <_alt>

                                                            <1>$scientificName</1>

                                                            <2>

                                                                <_join_words>

                                                                    <2>$genus</2>

                                                                    <3>$specificEpithet</3>

                                                                </_join_words>

                                                            </2>

                                                        </_alt>

                                                    </2>

                                                </_join_words>

                                            </taxonomicname>

                                        </taxonlabel>

                                    </taxonlabel_id>

                                    <family>$family</family>

                                    <genus>$genus</genus>

                                    <specific_epithet>$specificEpithet</specific_epithet>

                                    <taxonomicname>$scientificName</taxonomicname>

                                </taxonverbatim>

                            </taxonverbatim_id>

                        </taxondetermination>

                    </taxonoccurrence>

                </locationevent>

                <locationnarrative>

                    <_merge>

                        <1>$locality</1>

                        <3>

                            <_label>

                                <label>habitat</label>

                                <value>$habitat</value>

                            </_label>

                        </3>

                    </_merge>

                </locationnarrative>

                <locationplace>

                    <place_id>

                        <place>

                            <coordinates_id>

                                <coordinates>

                                    <coordsaccuracy_m><_noCV><value>$coordinateUncertaintyInMeters</value></_noCV></coordsaccuracy_m>

                                    <latitude_deg>

                                        <_nullIf>

                                            <null>0</null>

                                            <type>float</type>

                                            <value>$decimalLatitude</value>

                                        </_nullIf>

                                    </latitude_deg>

                                    <longitude_deg>

                                        <_nullIf>

                                            <null>0</null>

                                            <type>float</type>

                                            <value>$decimalLongitude</value>

                                        </_nullIf>

                                    </longitude_deg>

                                    <verbatimlatitude>$verbatimLatitude</verbatimlatitude>

                                    <verbatimlongitude>$verbatimLongitude</verbatimlongitude>

                                </coordinates>

                            </coordinates_id>

                            <country>$country</country>

                            <county>$county</county>

                            <matched_place_id>

                                <place>

                                    <source_id><source><shortname>geoscrub</shortname></source></source_id>

                                    <coordinates_id>

                                        <coordinates>

                                            <source_id><source><shortname>geoscrub</shortname></source></source_id>

                                            <latitude_deg>

                                                <_nullIf>

                                                    <null>0</null>

                                                    <type>float</type>

                                                    <value>$decimalLatitude</value>

                                                </_nullIf>

                                            </latitude_deg>

                                            <longitude_deg>

                                                <_nullIf>

                                                    <null>0</null>

                                                    <type>float</type>

                                                    <value>$decimalLongitude</value>

                                                </_nullIf>

                                            </longitude_deg>

                                        </coordinates>

                                    </coordinates_id>

                                    <country>$country</country>

                                    <county>$county</county>

                                    <stateprovince>$stateProvince</stateprovince>

                                </place>

                            </matched_place_id>

                            <stateprovince>$stateProvince</stateprovince>

                        </place>

                    </place_id>

                </locationplace>

            </location>

        </path>

    </_simplifyPath>

</VegBIEN>

Inserted 37 new rows into database

dcterms:modified

ownerInstitutionCode

dcterms:language

basisOfRecord

geodeticDatum

dcterms:rightsHolder

nomenclaturalCode

dynamicProperties

datasetName

dcterms:rights

dcterms:type

datasetID

countryCode