Revision 4976
Added by Aaron Marcuse-Kubitza over 12 years ago
| inputs/SALVIAS-CSV/Organism/VegBIEN.csv | ||
|---|---|---|
| 63 | 63 |
tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then/_alt/2/_alt/1","The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other." |
| 64 | 64 |
tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then/_alt/2/_alt/2","The second tag supercedes the first. The stem tag supercedes the tree 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." |
| 65 | 65 |
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.; According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>"
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| 66 |
OBSERVATION_ID,/location/locationevent/taxonoccurrence/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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| 66 |
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."
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| 67 | 67 |
specific_authority,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/author,Brad: This is the author of the scientificName. |
| 68 | 68 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 69 | 69 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| inputs/CTFS/StemObservation/VegBIEN.csv | ||
|---|---|---|
| 19 | 19 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists", |
| 20 | 20 |
StemTag,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then", |
| 21 | 21 |
Tag,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then", |
| 22 |
MeasureID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2,
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| 22 |
MeasureID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else",
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| 23 | 23 |
SpeciesAuthority,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/author, |
| 24 | 24 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 25 | 25 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| inputs/SALVIAS/stems/VegBIEN.csv | ||
|---|---|---|
| 15 | 15 |
stem_tag1,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag/_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." |
| 16 | 16 |
stem_tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then/_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." |
| 17 | 17 |
stem_tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then/_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." |
| 18 |
PlotObsID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2,
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| 18 |
PlotObsID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else",
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| 19 | 19 |
origrecord_id_stems,,** No join mapping for origrecord_id_stems ** |
| 20 | 20 |
plotobs_id_index,,** No join mapping for plotobs_id_index ** |
| 21 | 21 |
tmp_del,,** No join mapping for tmp_del ** |
| inputs/SALVIAS/plotObservations/VegBIEN.csv | ||
|---|---|---|
| 56 | 56 |
tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then/_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." |
| 57 | 57 |
tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then/_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." |
| 58 | 58 |
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.; According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>"
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| 59 |
PlotObsID,/location/locationevent/taxonoccurrence/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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| 59 |
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."
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| 60 | 60 |
auth,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/author,Brad: This is the author of the scientificName. |
| 61 | 61 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 62 | 62 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| inputs/VegBank/stemcount/VegBIEN.csv | ||
|---|---|---|
| 4 | 4 |
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>)" |
| 5 | 5 |
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>)" |
| 6 | 6 |
taxonimportance_id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1, |
| 7 |
stemcount_id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2,
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| 7 |
stemcount_id,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else",
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| 8 | 8 |
emb_stemcount,,** No join mapping for emb_stemcount ** |
| 9 | 9 |
stemdiameteraccuracy,,** No join mapping for stemdiameteraccuracy ** |
| 10 | 10 |
stemheightaccuracy,,** No join mapping for stemheightaccuracy ** |
| inputs/VegBank/stemlocation/VegBIEN.csv | ||
|---|---|---|
| 4 | 4 |
stemlocation_id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/sourceaccessioncode, |
| 5 | 5 |
stemxposition,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m, |
| 6 | 6 |
stemyposition,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m, |
| 7 |
stemcount_id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2,
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stemcount_id,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else",
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| 8 | 8 |
emb_stemlocation,,** No join mapping for emb_stemlocation ** |
| 9 | 9 |
stemhealth,,** No join mapping for stemhealth ** |
| inputs/VegBank/taxonimportance/VegBIEN.csv | ||
|---|---|---|
| 2 | 2 |
cover,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover_fraction/_percent_to_fraction/value, |
| 3 | 3 |
taxonimportance_id,/location/locationevent/taxonoccurrence/aggregateoccurrence/sourceaccessioncode, |
| 4 | 4 |
taxonobservation_id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1, |
| 5 |
taxonimportance_id,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/cond/_exists", |
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| 5 | 6 |
basalarea,,** No join mapping for basalarea ** |
| 6 | 7 |
biomass,,** No join mapping for biomass ** |
| 7 | 8 |
covercode,,** No join mapping for covercode ** |
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 122 | 122 |
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_alt/2/_map:[cultivated=t,wild=f,*=]/value", |
| 123 | 123 |
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
| 124 | 124 |
taxonOccurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1, |
| 125 |
individualID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2, |
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| 125 |
aggregateOccurrenceID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/cond/_exists", |
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| 126 |
individualID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else", |
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| 126 | 127 |
occurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 127 | 128 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first, |
| 128 | 129 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle, |
| mappings/for_review/VegCore-VegBIEN.csv | ||
|---|---|---|
| 122 | 122 |
establishmentMeans,//taxonoccurrence/iscultivated, |
| 123 | 123 |
establishmentMeans,//taxonoccurrence/isnative, |
| 124 | 124 |
taxonOccurrenceID,//taxonoccurrence/sourceaccessioncode, |
| 125 |
individualID,//taxonoccurrence/sourceaccessioncode, |
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| 125 |
aggregateOccurrenceID,"//taxonoccurrence/sourceaccessioncode/_if[@name=""if organism in AggregateOccurrence""]/cond/_exists", |
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| 126 |
individualID,"//taxonoccurrence/sourceaccessioncode/_if[@name=""if organism in AggregateOccurrence""]/else", |
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| 126 | 127 |
occurrenceID,//taxonoccurrence/sourceaccessioncode, |
| 127 | 128 |
identifiedBy,//taxonoccurrence/taxondetermination[]/*_id/party/givenname, |
| 128 | 129 |
identifiedBy,//taxonoccurrence/taxondetermination[]/*_id/party/middlename, |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: Don't forward individualID to taxonoccurrence.sourceaccessioncode when aggregateOccurrenceID is present