SALVIAS,VegCore,Filter,Comments

PlotObsID,individualID,,"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."

PlotID,locationID,,

PlotCode,locationName,,

census_no,censusNumber,,"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."

census_date,eventDate,,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:

-----

SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count

FROM ""SALVIAS"".organisms

WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL

GROUP BY ""PlotID"", ""Line""

HAVING count(DISTINCT census_date) > 1

-----"

OrigRecordID,*OrigRecordID,,

Line,subplot,,

Ind,individualCode,,"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."

ind_id,*ind_id,,Brad: OMIT

tag1,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."

tag2,tag,/_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."

x_position,organismX_m,,"""x coordinate in meters"" (x_position definition at <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data>). Brad: These are important, fundamental values of many tree plots"

y_position,organismY_m,,"""y coordinate in meters"" (y_position definition at <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data>). Brad: See comment above for x_position"

dist,*dist,,

perp_dist,*perp_dist,,

SourceVoucher,recordNumber,/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."

coll_number,recordNumber,/_alt/1,Brad: Map instead as for voucher_string

collector_code,*collector_code,,Brad: OMIT

coll_inits,*coll_inits,,

coll_lastname,recordedBy_surName,,"Brad: This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."

coll_firstname,recordedBy_givenName,,Brad: See comment above

DetType,voucherType,,"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."

det_by,identifiedBy,,

fam_status,OMIT,,Brad: OMIT. This will be determined later by using TNRS.

gen_status,OMIT,,Brad: OMIT. This will be determined later by using TNRS.

name_status,OMIT,,"Brad: OMIT. Except, note that if species_status=3, this indicate that name is a morphospecies and not a standard latin name. Not exactly sure how to use this in BIEN, but could be useful during the name-scrubbing process with TNRS."

SpAuthStatus,*SpAuthStatus,,

Family,family,,

Genus,genus,,

GenAuth,*GenAuth,,

Species,specificEpithet,,

auth,scientificNameAuthorship,,Brad: This is the author of the scientificName.

infra_rank_1,taxonRank,,

infra_ep_1,infraspecificEpithet,,

infra_auth_1,*infra_auth_1,,

common_name,*common_name,,

morphoname,morphoname,,"Not the morphospecies, which is stored in Species"

species_code,*species_code,,

Habit,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."

height_class,*height_class,,

height_m,height_m,,"""Total height of individual, in meters"" (height_m definition at <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data>)"

height_m_commercial,*height_m_commercial,,

ht_first_branch_m,heightFirstBranch,,

NoInd,individualCount,,"Brad: This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."

cover_percent,coverPercent,,

intercept_cm,intercept_cm,,"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."

cfaff,identificationQualifier,,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."

other_annotations,*other_annotations,,

morphocf,*morphocf,,

IsMorpho,*IsMorpho,,

OrigFamily,originalFamily,,Brad: OMIT

OrigGenus,originalGenus,,

OrigSpecies,originalSpecificEpithet,,Brad: OMIT

OrigAuth,*OrigAuth,,

phenology,phenology,,

canopy_position,canopyPosition,,

canopy_form,canopyForm,,

liana_infestation,lianaInfestation,,

Notes,fieldNotes,,

tmp_PlotObsID,*tmp_PlotObsID,,

temp_dbh,diameterBreastHeight_cm,,"Assuming units based on the units for intercept_cm, which measures the same dimension"

temp_liandbh,*temp_liandbh,,

tmp_del,*tmp_del,,

PlotID_index,OMIT,,Placeholder column created by MySQL to PostgreSQL translation

tmp_del_index,OMIT,,Placeholder column created by MySQL to PostgreSQL translation

tmp_PlotObsID_index,OMIT,,Placeholder column created by MySQL to PostgreSQL translation