Revision 4233
Added by Aaron Marcuse-Kubitza over 12 years ago
inputs/SALVIAS-CSV/1.organisms/map.csv | ||
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11 | 11 |
GROUP BY ""PLOT_ID"", subplot |
12 | 12 |
HAVING count(DISTINCT census_date) > 1 |
13 | 13 |
-----" |
14 |
subplot,plotName,
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|
14 |
subplot,subplot,
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|
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 | ||
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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 | ||
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1 | 1 |
SALVIAS-CSV,VegBIEN:,Comments |
2 |
subplot,/location/authorlocationcode/_alt/1/_alt/2,
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2 |
subplot,/location/authorlocationcode/_alt/1/_alt/1,
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|
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",
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57 |
subplot,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/cond",
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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 | ||
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12 | 12 |
HAVING count(DISTINCT census_date) > 1 |
13 | 13 |
-----" |
14 | 14 |
OrigRecordID,, |
15 |
Line,plotName,
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|
15 |
Line,subplot,
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|
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 | ||
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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 | ||
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1 | 1 |
SALVIAS,VegBIEN:,Comments |
2 |
Line,/location/authorlocationcode/_alt/1/_alt/2,
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2 |
Line,/location/authorlocationcode/_alt/1/_alt/1,
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|
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",
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61 |
Line,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/cond",
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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", |
Also available in: Unified diff
inputs/SALVIAS*/1.organisms/map.csv: Mapped subplot, Line to new subplot VegCore term