Revision 7000
Added by Aaron Marcuse-Kubitza about 12 years ago
inputs/CTFS/StemObservation/VegBIEN.csv | ||
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12 | 12 |
QuadratID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/cond/_first/2",Not globally unique; unique only within Site |
13 | 13 |
PlotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
14 | 14 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/sourceaccessioncode", |
15 |
MeasureID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
15 |
MeasureID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/2,
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|
16 | 16 |
StemID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode, |
17 | 17 |
DBH,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,Assuming units based on the range and precision of values. Not documented in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>. |
18 | 18 |
StemTag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
... | ... | |
25 | 25 |
StemTag,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
26 | 26 |
Tag,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
27 | 27 |
MeasureID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
28 |
MeasureID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else", |
|
28 |
MeasureID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/2",
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|
29 | 29 |
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/_nullIf/value", |
30 | 30 |
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", |
31 | 31 |
SpeciesName,"/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", |
inputs/CTFS/StemObservation/test.xml.ref | ||
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43 | 43 |
</stemobservation> |
44 | 44 |
</plantobservation> |
45 | 45 |
</aggregateoccurrence> |
46 |
<authortaxoncode> |
|
47 |
<_alt> |
|
48 |
<0>$StemTag</0> |
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49 |
<1>$Tag</1> |
|
50 |
</_alt> |
|
51 |
</authortaxoncode> |
|
52 | 46 |
<sourceaccessioncode>$MeasureID</sourceaccessioncode> |
53 | 47 |
<taxondetermination> |
54 | 48 |
<taxonverbatim_id> |
inputs/SALVIAS/stems/VegBIEN.csv | ||
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1 | 1 |
SALVIAS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
2 | 2 |
PlotObsID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
3 |
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
3 |
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/2,
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|
4 | 4 |
NoInd,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount, |
5 | 5 |
basal_diam,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter_m, |
6 | 6 |
stem_canopy_form,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue", |
... | ... | |
19 | 19 |
stem_tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2/_alt/1","The second tag supercedes the first. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other." |
20 | 20 |
stem_tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2/_alt/2","The second tag supercedes the first. 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." |
21 | 21 |
PlotObsID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
22 |
PlotObsID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else", |
|
22 |
PlotObsID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/2",
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|
23 | 23 |
origrecord_id_stems,,** No join mapping for *origrecord_id_stems ** |
24 | 24 |
plotobs_id_index,,** No non-empty join mapping for OMIT ** Placeholder column created by MySQL to PostgreSQL translation |
25 | 25 |
tmp_del,,** No join mapping for *tmp_del ** |
inputs/SALVIAS/plotObservations/VegBIEN.csv | ||
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68 | 68 |
intercept_cm,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover_m/_cm_to_m/value,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance." |
69 | 69 |
Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
70 | 70 |
Ind,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,"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." |
71 |
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
|
71 |
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/2,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
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72 | 72 |
DetType,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_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." |
73 | 73 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string |
74 | 74 |
SourceVoucher,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_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." |
... | ... | |
95 | 95 |
Habit,"/location/locationevent/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=*]/value","Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait." |
96 | 96 |
Ind,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","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." |
97 | 97 |
PlotObsID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
98 |
PlotObsID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
|
98 |
PlotObsID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/2","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
|
|
99 | 99 |
det_by,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
100 | 100 |
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/_nullIf/value", |
101 | 101 |
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", |
inputs/SALVIAS/plotObservations/test.xml.ref | ||
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117 | 117 |
</stemobservation> |
118 | 118 |
</plantobservation> |
119 | 119 |
</aggregateoccurrence> |
120 |
<authortaxoncode>$Ind</authortaxoncode> |
|
121 | 120 |
<collector_id> |
122 | 121 |
<party> |
123 | 122 |
<fullname> |
inputs/SALVIAS-CSV/Organism/VegBIEN.csv | ||
---|---|---|
67 | 67 |
census_no,"/location/locationevent/taxonoccurrence/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]:[@fkey=tablerecord_id]/definedvalue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not." |
68 | 68 |
intercept_cm,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover_m/_cm_to_m/value,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance." |
69 | 69 |
individual_code,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,"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." |
70 |
OBSERVATION_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
|
70 |
OBSERVATION_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/2,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
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71 | 71 |
det_type,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_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." |
72 | 72 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string |
73 | 73 |
voucher_string,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_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." |
... | ... | |
102 | 102 |
habit,"/location/locationevent/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=*]/value","Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait." |
103 | 103 |
OBSERVATION_ID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
104 | 104 |
individual_code,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","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." |
105 |
OBSERVATION_ID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
|
105 |
OBSERVATION_ID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/2","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
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106 | 106 |
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/_nullIf/value", |
107 | 107 |
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", |
108 | 108 |
specific_epithet,"/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", |
inputs/SALVIAS-CSV/Organism/test.xml.ref | ||
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146 | 146 |
</stemobservation> |
147 | 147 |
</plantobservation> |
148 | 148 |
</aggregateoccurrence> |
149 |
<authortaxoncode>$individual_code</authortaxoncode> |
|
150 | 149 |
<collector_id> |
151 | 150 |
<party> |
152 | 151 |
<fullname> |
inputs/CVS/stemLocation_/VegBIEN.csv | ||
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1 | 1 |
CVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
2 | 2 |
STEMLOCATION_ID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
3 | 3 |
stemCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
4 |
STEMLOCATION_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
4 |
STEMLOCATION_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/2,
|
|
5 | 5 |
stemCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode, |
6 | 6 |
stemDiameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value, |
7 | 7 |
stemHeight,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m, |
... | ... | |
12 | 12 |
STEMLOCATION_ID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_if[@name=""if individual""]/cond/_exists", |
13 | 13 |
STEMLOCATION_ID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
14 | 14 |
STEMCOUNT_ID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/cond/_exists", |
15 |
STEMLOCATION_ID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else", |
|
15 |
STEMLOCATION_ID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/2",
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|
16 | 16 |
cust_cvs_ddh,,** No join mapping for *cust_cvs_ddh ** |
17 | 17 |
cust_cvs_ddhAccuracy,,** No join mapping for *cust_cvs_ddhAccuracy ** |
18 | 18 |
cust_cvs_isPlanted,,** No join mapping for *cust_cvs_isPlanted ** |
inputs/CVS/taxonObservation_/test.xml.ref | ||
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18 | 18 |
<stemobservation><sourceaccessioncode>$stemLocation_ID</sourceaccessioncode></stemobservation> |
19 | 19 |
</plantobservation> |
20 | 20 |
</aggregateoccurrence> |
21 |
<authortaxoncode>$authorPlantName</authortaxoncode> |
|
22 | 21 |
<collector_id> |
23 | 22 |
<party> |
24 | 23 |
<fullname> |
inputs/VegBank/stemlocation_/VegBIEN.csv | ||
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1 | 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
2 | 2 |
stemlocation_id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
3 | 3 |
stemcount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
4 |
stemlocation_id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
4 |
stemlocation_id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/2,
|
|
5 | 5 |
stemcode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode, |
6 | 6 |
stemdiameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,"""The diameter of the stem in centimeters"" (stemDiameter definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
7 | 7 |
stemheight,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m,"""The measured height of the stem in meters"" (stemHeight definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
... | ... | |
12 | 12 |
stemlocation_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_if[@name=""if individual""]/cond/_exists", |
13 | 13 |
stemlocation_id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
14 | 14 |
stemcount_id,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/cond/_exists", |
15 |
stemlocation_id,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else", |
|
15 |
stemlocation_id,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/2",
|
|
16 | 16 |
emb_stemcount,,** No join mapping for *emb_stemcount ** |
17 | 17 |
emb_stemlocation,,** No join mapping for *emb_stemlocation ** |
18 | 18 |
stemdiameteraccuracy,,** No join mapping for *stemdiameteraccuracy ** |
mappings/VegCore-VegBIEN.csv | ||
---|---|---|
38 | 38 |
verbatimElevation_m,/location/elevationrange_m/_range/from/_rangeStart/value, |
39 | 39 |
verbatimElevation_m,/location/elevationrange_m/_range/to/_rangeEnd/value, |
40 | 40 |
individualID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
41 |
individualObservationID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
41 | 42 |
occurrenceID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
42 | 43 |
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
43 | 44 |
taxonOccurrenceID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
... | ... | |
110 | 111 |
fieldNotes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
111 | 112 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber, |
112 | 113 |
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" |
113 |
individualID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
114 |
individualObservationID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/1, |
|
115 |
individualID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/2, |
|
114 | 116 |
voucherType,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left", |
115 | 117 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
116 | 118 |
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 |
... | ... | |
144 | 146 |
locationID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
145 | 147 |
locationName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
146 | 148 |
individualID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_if[@name=""if individual""]/cond/_exists", |
149 |
individualObservationID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_if[@name=""if individual""]/cond/_exists", |
|
147 | 150 |
stemID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_if[@name=""if individual""]/cond/_exists", |
148 | 151 |
authorTaxonCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_if[@name=""if individual""]/else", |
149 | 152 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/1", |
... | ... | |
156 | 159 |
recordedBy_surName,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join_words/2, |
157 | 160 |
growthForm,/location/locationevent/taxonoccurrence/growthform, |
158 | 161 |
individualID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
162 |
individualObservationID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
159 | 163 |
occurrenceID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
160 | 164 |
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
161 | 165 |
taxonOccurrenceID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
... | ... | |
165 | 169 |
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
166 | 170 |
taxonOccurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1, |
167 | 171 |
aggregateOccurrenceID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/cond/_exists", |
168 |
individualID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else", |
|
172 |
individualObservationID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/1", |
|
173 |
individualID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/2", |
|
169 | 174 |
occurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
170 | 175 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
171 | 176 |
taxonNameOrEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/cond/_exists", |
mappings/for_review/VegCore-VegBIEN.csv | ||
---|---|---|
38 | 38 |
verbatimElevation_m,//location/elevationrange_m, |
39 | 39 |
verbatimElevation_m,//location/elevationrange_m, |
40 | 40 |
individualID,"//location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
41 |
individualObservationID,"//location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
41 | 42 |
occurrenceID,"//location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
42 | 43 |
recordNumber,"//location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
43 | 44 |
taxonOccurrenceID,"//location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
... | ... | |
110 | 111 |
fieldNotes,//aggregateoccurrence/notes, |
111 | 112 |
recordNumber,//plantobservation/collectionnumber, |
112 | 113 |
sex,"//plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,userdefinedname=sex]]/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" |
114 |
individualObservationID,//plantobservation/sourceaccessioncode, |
|
113 | 115 |
individualID,//plantobservation/sourceaccessioncode, |
114 | 116 |
voucherType,"//specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond", |
115 | 117 |
catalogNumber,"//specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
... | ... | |
144 | 146 |
locationID,"//taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
145 | 147 |
locationName,"//taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
146 | 148 |
individualID,"//taxonoccurrence/authortaxoncode/_if[@name=""if individual""]/cond/_exists", |
149 |
individualObservationID,"//taxonoccurrence/authortaxoncode/_if[@name=""if individual""]/cond/_exists", |
|
147 | 150 |
stemID,"//taxonoccurrence/authortaxoncode/_if[@name=""if individual""]/cond/_exists", |
148 | 151 |
authorTaxonCode,"//taxonoccurrence/authortaxoncode/_if[@name=""if individual""]/else", |
149 | 152 |
recordNumber,"//taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then", |
... | ... | |
156 | 159 |
recordedBy_surName,//party/fullname, |
157 | 160 |
growthForm,//taxonoccurrence/growthform, |
158 | 161 |
individualID,"//taxonoccurrence/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
162 |
individualObservationID,"//taxonoccurrence/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
159 | 163 |
occurrenceID,"//taxonoccurrence/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
160 | 164 |
recordNumber,"//taxonoccurrence/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
161 | 165 |
taxonOccurrenceID,"//taxonoccurrence/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
... | ... | |
165 | 169 |
establishmentMeans,//taxonoccurrence/isnative, |
166 | 170 |
taxonOccurrenceID,//taxonoccurrence/sourceaccessioncode, |
167 | 171 |
aggregateOccurrenceID,"//taxonoccurrence/sourceaccessioncode/_if[@name=""if organism in AggregateOccurrence""]/cond/_exists", |
172 |
individualObservationID,"//taxonoccurrence/sourceaccessioncode/_if[@name=""if organism in AggregateOccurrence""]/else", |
|
168 | 173 |
individualID,"//taxonoccurrence/sourceaccessioncode/_if[@name=""if organism in AggregateOccurrence""]/else", |
169 | 174 |
occurrenceID,//taxonoccurrence/sourceaccessioncode, |
170 | 175 |
identifiedBy,//taxonoccurrence/taxondetermination[]/*_id/party/fullname, |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: authortaxoncode mappings: Only using authorTaxonCode if there is no plant ID: Added individualID, stemID to the terms that cause authorTaxonCode not to be mapped to VegBIEN authortaxoncode