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Revision 918

Added by Aaron Marcuse-Kubitza almost 13 years ago

DwC mappings: Mapped Notes and PlantFungusDescription to bien.specimenDescription, merged together

View differences:

inputs/NYBG/test/import.specimens.out.ref
1 
Inserted 83 new rows into database
1 
Inserted 81 new rows into database
inputs/NYBG/test/DwC.specimens.xml.ref
27 27 
        <minimumElevationInMeters>350</minimumElevationInMeters>
28 28 
        <maximumElevationInMeters>350</maximumElevationInMeters>
29 29 
        <habitat>Floodplain forest</habitat>
30 
        <bien.plantFungusDescription>with rough brown bark, almost no buttressing, 1 m diam; fallen fruit and leaves</bien.plantFungusDescription>
30 
        <bien.specimenDescription>plant fungus: with rough brown bark, almost no buttressing, 1 m diam; fallen fruit and leaves</bien.specimenDescription>
31 31 
        <occurrenceID>816590</occurrenceID>
32 32 
    </list>
33 33 
    <list id="1">
inputs/NYBG/test/VegBIEN.specimens.xml.ref
54 54 
                                    </userdefined_id>
55 55 
                                    <definedvalue>Floodplain forest</definedvalue>
56 56 
                                </definedvalue>
57 
                                <definedvalue fkey="tableRecord_ID">
58 
                                    <userdefined_id>
59 
                                        <userdefined>
60 
                                            <tablename>stemobservation</tablename>
61 
                                            <userdefinedname>plantFungusDescription</userdefinedname>
62 
                                        </userdefined>
63 
                                    </userdefined_id>
64 
                                    <definedvalue>with rough brown bark, almost no buttressing, 1 m diam; fallen fruit and leaves</definedvalue>
65 
                                </definedvalue>
66 57 
                            </stemobservation>
67 58 
                            <authorplantcode>816590</authorplantcode>
68 59 
                        </plantobservation>
......
153 144 
        <sourceaccessioncode>816590</sourceaccessioncode>
154 145 
        <catalognumber_dwc>00682023</catalognumber_dwc>
155 146 
        <collectionnumber>9877</collectionnumber>
147 
        <description>plant fungus: with rough brown bark, almost no buttressing, 1 m diam; fallen fruit and leaves</description>
156 148 
        <verbatimcollectorname>R. B. Foster</verbatimcollectorname>
157 149 
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
158 150 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
inputs/NYBG/maps/DwC.specimens.csv
49 49 
"PreviousCatalogNumber","previousIdentifications","?"
50 50 
"RelationshipType","relationshipOfResource",
51 51 
"RelatedCatalogItem","relatedResourceID",
52 
"Notes","fieldNotes",
52 
"Notes","bien.specimenDescription/_merge/1",
53 53 
"Habitat","habitat",
54 
"PlantFungusDescription","bien.plantFungusDescription",
54 
"PlantFungusDescription","bien.specimenDescription/_merge/2/_label[label=""plant fungus""]/value",
55 55 
"Substrate",,
56 56 
"Vegetation",,
57 57 
"UniqueNYInternalRecordNumber","occurrenceID",
inputs/NYBG/maps/VegBIEN.specimens.csv
14 14 
MaximumDepth,/*_id/taxonoccurrence/*_id/locationevent/waterdepth/max,,75
15 15 
MinimumDepth,/*_id/taxonoccurrence/*_id/locationevent/waterdepth/min,,74
16 16 
Habitat,"/*_id/taxonoccurrence/aggregateoccurrence/*_id/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=habitat]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
17 
PlantFungusDescription,"/*_id/taxonoccurrence/aggregateoccurrence/*_id/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=plantFungusDescription]]:[@fkey=tableRecord_ID]/definedvalue",,
18 17 
Sex,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,!*_id/plantconcept]/definedvalue[*_id/userdefined[tablename=taxondetermination,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",26
19 18 
IdentifiedDate,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_alt/1/_*/date",,120
20 19 
DayIdentified,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_alt/2/_date/day",,120
......
31 30 
Species,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,149
32 31 
Phylum,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,143
33 32 
Subspecies,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,150
34 
Notes,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=notes]]:[@fkey=tableRecord_ID]/definedvalue","Brad: mapping OK; NY appears to be using this field for almost anything, but mostly internal collections notes",54
35 33 
UniqueNYInternalRecordNumber,"/{:[*_id/reference]/sourceaccessioncode,*_id/taxonoccurrence/aggregateoccurrence/*_id/plantobservation/authorplantcode}","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
36 34 
CatalogNumber,:[*_id/reference]/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
37 35 
CollectorNumber,:[*_id/reference]/collectionnumber/_alt/1,,22
38 36 
FieldNumber,:[*_id/reference]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
37 
Notes,:[*_id/reference]/description/_merge/1,,
38 
PlantFungusDescription,":[*_id/reference]/description/_merge/2/_label[label=""plant fungus""]/value",,
39 39 
Collector,:[*_id/reference]/verbatimcollectorname,,23
40 40 
InstitutionCode,:[*_id/reference]/{museum_id/party/organizationname/_name/first},,11
41 41 
CollectionCode,":[*_id/reference]/{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
mappings/DwC-VegBIEN.specimens.csv
19 19 
maximumDepthInMeters,/*_id/taxonoccurrence/*_id/locationevent/waterdepth/max,,75
20 20 
minimumDepthInMeters,/*_id/taxonoccurrence/*_id/locationevent/waterdepth/min,,74
21 21 
habitat,"/*_id/taxonoccurrence/aggregateoccurrence/*_id/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=habitat]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
22 
bien.plantFungusDescription,"/*_id/taxonoccurrence/aggregateoccurrence/*_id/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=plantFungusDescription]]:[@fkey=tableRecord_ID]/definedvalue",,
23 22 
sex,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,!*_id/plantconcept]/definedvalue[*_id/userdefined[tablename=taxondetermination,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",26
24 23 
dateIdentified,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,!*_id/plantconcept]/determinationdate",,120
25 24 
dateIdentified/_alt/1/_*/date,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,!*_id/plantconcept]/determinationdate/_alt/1/_*/date",,120
......
43 42 
recordNumber,:[*_id/reference]/collectionnumber/_alt/1,,22
44 43 
collectionID,:[*_id/reference]/collectionnumber/_alt/2,,9
45 44 
fieldNumber,:[*_id/reference]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
45 
bien.specimenDescription,:[*_id/reference]/description,,
46 
bien.specimenDescription/_merge/1,:[*_id/reference]/description/_merge/1,,
47 
"bien.specimenDescription/_merge/2/_label[label=""plant fungus""]/value",":[*_id/reference]/description/_merge/2/_label[label=""plant fungus""]/value",,
46 48 
recordedBy,:[*_id/reference]/verbatimcollectorname,,23
47 49 
institutionCode,:[*_id/reference]/{museum_id/party/organizationname/_name/first},,11
48 50 
collectionCode,":[*_id/reference]/{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

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