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Revision 1108

Added by Aaron Marcuse-Kubitza about 13 years ago

DwC-VegBIEN mapping: Map datasource name via DwC institutionCode

View differences:

inputs/NYBG/test/import.specimens.out.ref
1 
Inserted 79 new rows into database
1 
Inserted 78 new rows into database
inputs/NYBG/test/DwC.specimens.xml.ref
1 1 
<?xml version="1.0" ?>
2 2 
<DwC xmlns:dcterms="http://purl.org/dc/terms/">
3 3 
    <list id="0">
4 
        <bien.datasource>NYBG</bien.datasource>
4 
        <institutionCode>NYBG</institutionCode>
5 5 
        <dcterms:modified>2005-2-22T14:47:32.000EST</dcterms:modified>
6 
        <institutionCode>NY</institutionCode>
7 6 
        <collectionCode>Herbarium</collectionCode>
8 7 
        <catalogNumber>00682023</catalogNumber>
9 8 
        <scientificName>Cariniana estrellensis (Raddi) Kuntze</scientificName>
......
32 31 
        <occurrenceID>816590</occurrenceID>
33 32 
    </list>
34 33 
    <list id="1">
35 
        <bien.datasource>NYBG</bien.datasource>
34 
        <institutionCode>NYBG</institutionCode>
36 35 
        <dcterms:modified>2004-1-13T00:00EST</dcterms:modified>
37 
        <institutionCode>NY</institutionCode>
38 36 
        <collectionCode>Herbarium</collectionCode>
39 37 
        <catalogNumber>200996</catalogNumber>
40 38 
        <scientificName>Scrophulariaceae</scientificName>
inputs/NYBG/test/VegBIEN.specimens.xml.ref
128 128 
                <verbatimcollectorname>R. B. Foster</verbatimcollectorname>
129 129 
            </taxonoccurrence>
130 130 
        </taxonoccurrence_id>
131 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
131 132 
        <description>plant fungus: with rough brown bark, almost no buttressing, 1 m diam; fallen fruit and leaves</description>
132 
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
133 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
134 133 
        <datasource_id><party><organizationname>NYBG</organizationname></party></datasource_id>
135 134 
        <catalognumber_dwc>00682023</catalognumber_dwc>
136 135 
        <collectionnumber>9877</collectionnumber>
......
219 218 
                <verbatimcollectorname>J. B. Walker</verbatimcollectorname>
220 219 
            </taxonoccurrence>
221 220 
        </taxonoccurrence_id>
222 
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
223 221 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
224 222 
        <datasource_id><party><organizationname>NYBG</organizationname></party></datasource_id>
225 223 
        <catalognumber_dwc>200996</catalognumber_dwc>
inputs/NYBG/maps/DwC.specimens.csv
1 
"NYBG:nybg_raw","DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[bien.datasource=$/_ignore/inLabel]/","Comments"
1 
"NYBG:nybg_raw","DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionCode=$/_ignore/inLabel]/","Comments"
2 2 
"key",,
3 3 
"DateLastModified","dcterms:modified",
4 
"InstitutionCode","institutionCode",
4 
"InstitutionCode",,
5 5 
"CollectionCode","collectionCode",
6 6 
"CatalogNumber","catalogNumber",
7 7 
"ScientificName","scientificName",
inputs/NYBG/maps/VegBIEN.specimens.csv
35 35 
Phylum,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,143
36 36 
Subspecies,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,150
37 37 
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
38 
CollectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
38 39 
Notes,/description/_merge/1,,
39 40 
PlantFungusDescription,"/description/_merge/2/_label[label=""plant fungus""]/value",,
40 
InstitutionCode,/{museum_id/party/organizationname/_name/first},,11
41 
CollectionCode,"/{museum_id/party/organizationname/_name/last,collectioncode_dwc}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
42 41 
CatalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
43 42 
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
44 43 
FieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
......
47 46 
ContinentOcean,,Brad: OMIT,59
48 47 
DateLastModified,,"Brad: Mapping to VegX is incorrect. I think is this merely an internal timestamp indicated when record last modified, not necessarily when determination (taxon name) last modified. Probably we should omit this field, although might be useful for updating changed records from this source.",1
49 48 
IndividualCount,,Brad: OMIT; not relevant for DwC plant specimen data.,25
49 
InstitutionCode,,
50 50 
JulianDay,,Brad: OMIT,50
51 51 
PreparationType,,Brad: OMIT,32
52 52 
PreviousCatalogNumber,,?; Brad: OMIT,35
inputs/NYBG-CSV/test/import.specimens.out.ref
1 
Inserted 79 new rows into database
1 
Inserted 78 new rows into database
inputs/NYBG-CSV/test/DwC.specimens.xml.ref
1 1 
<?xml version="1.0" ?>
2 2 
<DwC xmlns:dcterms="http://purl.org/dc/terms/">
3 3 
    <list id="0">
4 
        <bien.datasource>NYBG</bien.datasource>
4 
        <institutionCode>NYBG</institutionCode>
5 5 
        <dcterms:modified>2005-2-22T14:47:32.000EST</dcterms:modified>
6 
        <institutionCode>NY</institutionCode>
7 6 
        <collectionCode>Herbarium</collectionCode>
8 7 
        <catalogNumber>00682023</catalogNumber>
9 8 
        <scientificName>Cariniana estrellensis (Raddi) Kuntze</scientificName>
......
32 31 
        <occurrenceID>816590</occurrenceID>
33 32 
    </list>
34 33 
    <list id="1">
35 
        <bien.datasource>NYBG</bien.datasource>
34 
        <institutionCode>NYBG</institutionCode>
36 35 
        <dcterms:modified>2004-1-13T00:00EST</dcterms:modified>
37 
        <institutionCode>NY</institutionCode>
38 36 
        <collectionCode>Herbarium</collectionCode>
39 37 
        <catalogNumber>200996</catalogNumber>
40 38 
        <scientificName>Scrophulariaceae</scientificName>
inputs/NYBG-CSV/test/VegBIEN.specimens.xml.ref
128 128 
                <verbatimcollectorname>R. B. Foster</verbatimcollectorname>
129 129 
            </taxonoccurrence>
130 130 
        </taxonoccurrence_id>
131 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
131 132 
        <description>plant fungus: with rough brown bark, almost no buttressing, 1 m diam; fallen fruit and leaves</description>
132 
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
133 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
134 133 
        <datasource_id><party><organizationname>NYBG</organizationname></party></datasource_id>
135 134 
        <catalognumber_dwc>00682023</catalognumber_dwc>
136 135 
        <collectionnumber>9877</collectionnumber>
......
219 218 
                <verbatimcollectorname>J. B. Walker</verbatimcollectorname>
220 219 
            </taxonoccurrence>
221 220 
        </taxonoccurrence_id>
222 
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
223 221 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
224 222 
        <datasource_id><party><organizationname>NYBG</organizationname></party></datasource_id>
225 223 
        <catalognumber_dwc>200996</catalognumber_dwc>
inputs/NYBG-CSV/maps/DwC.specimens.csv
1 
"NYBG","DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[bien.datasource=$/_ignore/inLabel]/","Comments"
1 
"NYBG","DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionCode=$/_ignore/inLabel]/","Comments"
2 2 
"key",,
3 3 
"DateLastModified","dcterms:modified",
4 
"InstitutionCode","institutionCode",
4 
"InstitutionCode",,
5 5 
"CollectionCode","collectionCode",
6 6 
"CatalogNumber","catalogNumber",
7 7 
"ScientificName","scientificName",
inputs/NYBG-CSV/maps/VegBIEN.specimens.csv
33 33 
Phylum,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,143
34 34 
Subspecies,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,150
35 35 
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
36 
CollectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
36 37 
Notes,/description/_merge/1,,
37 38 
PlantFungusDescription,"/description/_merge/2/_label[label=""plant fungus""]/value",,
38 
InstitutionCode,/{museum_id/party/organizationname/_name/first},,11
39 
CollectionCode,"/{museum_id/party/organizationname/_name/last,collectioncode_dwc}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
40 39 
CatalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
41 40 
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
42 41 
FieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
......
45 44 
ContinentOcean,,Brad: OMIT,59
46 45 
DateLastModified,,"Brad: Mapping to VegX is incorrect. I think is this merely an internal timestamp indicated when record last modified, not necessarily when determination (taxon name) last modified. Probably we should omit this field, although might be useful for updating changed records from this source.",1
47 46 
IndividualCount,,Brad: OMIT; not relevant for DwC plant specimen data.,25
47 
InstitutionCode,,
48 48 
JulianDay,,Brad: OMIT,50
49 49 
PreparationType,,Brad: OMIT,32
50 50 
PreviousCatalogNumber,,?; Brad: OMIT,35
mappings/for_review/DwC-VegBIEN.specimens.csv
1 
"DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[bien.datasource=$/_ignore/inLabel]/",VegBIEN:/specimenreplicate,Comments,Order
1 
"DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionCode=$/_ignore/inLabel]/",VegBIEN:/specimenreplicate,Comments,Order
2 2 
country,"//*_id/namedplace[placesystem=""area|country|territory""]/placename",Brad: Required; reject record if this field NULL,63
3 3 
stateProvince,"//*_id/namedplace[placesystem=""region|state|province""]/placename",,65
4 4 
county,//*_id/namedplace[placesystem=county]/placename,,66
......
42 42 
phylum,"//taxonoccurrence/taxondetermination[rolecode=identifier,plantlevel=Subkingdom]/*_id/plantconcept/*_id/*/plantname",,143
43 43 
infraspecificEpithet,"//taxonoccurrence/taxondetermination[rolecode=identifier,plantlevel=Subspecies]/*_id/plantconcept/*_id/*/plantname",,150
44 44 
recordedBy,//taxonoccurrence/verbatimcollectorname,,23
45 
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
45 46 
fieldNotes,/description,,
46 47 
fieldNotes/_merge/1,/description/_merge/1,,
47 48 
"fieldNotes/_merge/2/_label[label=""plant fungus""]/value","/description/_merge/2/_label[label=""plant fungus""]/value",,
48 
institutionCode,/{museum_id/party/organizationname/_name/first},,11
49 
collectionCode,"/{museum_id/party/organizationname/_name/last,collectioncode_dwc}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
50 49 
catalogNumber,/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
51 50 
recordNumber,/collectionnumber/_alt/1,,22
52 51 
collectionID,/collectionnumber/_alt/2,,9
53 52 
fieldNumber,/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
54 
bien.datasource,//party/organizationname/_alt/1,,
53 
institutionCode,//party/organizationname/_alt/1,,
55 54 
occurrenceID,/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
56 55 
acceptedNameUsage,,,135
57 56 
acceptedNameUsageID,,,128
mappings/DwC-VegBIEN.specimens.csv
1 
"DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[bien.datasource=$/_ignore/inLabel]/",VegBIEN:/specimenreplicate,Comments,Order
1 
"DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionCode=$/_ignore/inLabel]/",VegBIEN:/specimenreplicate,Comments,Order
2 2 
country,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=""area|country|territory""])/placename",Brad: Required; reject record if this field NULL,63
3 3 
stateProvince,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=""region|state|province""])/placename",,65
4 4 
county,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=county])/placename,,66
......
42 42 
phylum,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,143
43 43 
infraspecificEpithet,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,150
44 44 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
45 
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
45 46 
fieldNotes,/description,,
46 47 
fieldNotes/_merge/1,/description/_merge/1,,
47 48 
"fieldNotes/_merge/2/_label[label=""plant fungus""]/value","/description/_merge/2/_label[label=""plant fungus""]/value",,
48 
institutionCode,/{museum_id/party/organizationname/_name/first},,11
49 
collectionCode,"/{museum_id/party/organizationname/_name/last,collectioncode_dwc}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
50 49 
catalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
51 50 
recordNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
52 51 
collectionID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/2,,9
53 52 
fieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
54 
bien.datasource,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1,,
53 
institutionCode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1,,
55 54 
occurrenceID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
56 55 
acceptedNameUsage,,,135
57 56 
acceptedNameUsageID,,,128

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