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Revision 4233

inputs/SALVIAS*/1.organisms/map.csv: Mapped subplot, Line to new subplot VegCore term

View differences:

inputs/SALVIAS-CSV/1.organisms/map.csv
11 11
GROUP BY ""PLOT_ID"", subplot
12 12
HAVING count(DISTINCT census_date) > 1
13 13
-----"
14
subplot,plotName,
14
subplot,subplot,
15 15
individual_code,recordNumber,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
16 16
ind_id,,Brad: OMIT
17 17
tag1,tag/_alt/1,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
inputs/SALVIAS-CSV/1.organisms/map.full.csv
29 29
GROUP BY ""PLOT_ID"", subplot
30 30
HAVING count(DISTINCT census_date) > 1
31 31
-----"
32
subplot,plotName,
33 32
tag2,previousTag/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
34 33
stem_tag2,previousTag/_alt/2,Brad: see above
35 34
individual_code,recordNumber,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
......
40 39
specific_authority,scientificNameAuthorship,Brad: This is the author of the scientificName.
41 40
specific_epithet,specificEpithet,
42 41
notes,stemNotes,
42
subplot,subplot,
43 43
tag1,tag/_alt/1,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
44 44
stem_tag1,tag/_alt/2,"Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."
45 45
infra_rank_1,taxonRank,
inputs/SALVIAS-CSV/1.organisms/VegBIEN.csv
1 1
SALVIAS-CSV,VegBIEN:,Comments
2
subplot,/location/authorlocationcode/_alt/1/_alt/2,
2
subplot,/location/authorlocationcode/_alt/1/_alt/1,
3 3
det_type,"/location/authorlocationcode/_alt/4/_merge/3/_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."
4 4
coll_number,"/location/authorlocationcode/_alt/4/_merge/3/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string
5 5
voucher_string,"/location/authorlocationcode/_alt/4/_merge/3/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
......
54 54
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
55 55
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."
56 56
plot_code,/location/parent_id/location/authorlocationcode,
57
subplot,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/then",
57
subplot,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/cond",
58 58
PLOT_ID,/location/parent_id/location/sourceaccessioncode,
59
subplot,"/location/parent_id/location/sourceaccessioncode/_if[@name=""if subplot""]/cond",
60
subplot,"/location/sourceaccessioncode/_if[@name=""if subplot""]/cond",
inputs/SALVIAS/1.organisms/map.csv
12 12
HAVING count(DISTINCT census_date) > 1
13 13
-----"
14 14
OrigRecordID,,
15
Line,plotName,
15
Line,subplot,
16 16
Ind,recordNumber,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
17 17
ind_id,,Brad: OMIT
18 18
tag1,tag,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
inputs/SALVIAS/1.organisms/map.full.csv
27 27
liana_infestation,lianaInfestation,
28 28
PlotID,parentLocationID,
29 29
PlotCode,parentPlotName,
30
Line,plotName,
31 30
tag2,previousTag,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
32 31
Ind,recordNumber,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
33 32
coll_firstname,recordedBy.givenName,Brad: See comment above
......
36 35
y_position,relativePlotY,Brad: See comment above for x_position
37 36
auth,scientificNameAuthorship,Brad: This is the author of the scientificName.
38 37
Species,specificEpithet,
38
Line,subplot,
39 39
tag1,tag,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
40 40
infra_rank_1,taxonRank,
41 41
OrigFamily,verbatimFamily,Brad: OMIT
inputs/SALVIAS/1.organisms/VegBIEN.csv
1 1
SALVIAS,VegBIEN:,Comments
2
Line,/location/authorlocationcode/_alt/1/_alt/2,
2
Line,/location/authorlocationcode/_alt/1/_alt/1,
3 3
DetType,"/location/authorlocationcode/_alt/4/_merge/3/_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."
4 4
coll_number,"/location/authorlocationcode/_alt/4/_merge/3/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string
5 5
SourceVoucher,"/location/authorlocationcode/_alt/4/_merge/3/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
......
58 58
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
59 59
SourceVoucher,"/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."
60 60
PlotCode,/location/parent_id/location/authorlocationcode,
61
Line,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/then",
61
Line,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/cond",
62 62
PlotID,/location/parent_id/location/sourceaccessioncode,
63
Line,"/location/parent_id/location/sourceaccessioncode/_if[@name=""if subplot""]/cond",
64
Line,"/location/sourceaccessioncode/_if[@name=""if subplot""]/cond",

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