SALVIAS DATA DICTIONARY


last updated: 7 sep 2005


Plot metadata

The following fields are downloaded when you select “download plot metadata”.  These fields contain information pertaining to entire plots, such as locality, climate, soil, and methodology.  Please pay particular attention to the field observation_type: values in this field affect intepretation of fields downloaded as plot data (from the PlotObservations table).  See discussion below.  Values from this table can be linked to the plot data (see next table) either using PLOT_ID or plot_code.  PLOT_ID is preferable, however, as plot_code may repeat among different projects.


Field_name

Data_type

Value_list

Can be null?

Standardized_by_SALVIAS?

Comments

PLOT_ID
Integer
Autoincrement
No Added by database
Primary key; unique number for each plot
plot_code
Text


No

Yes (original codes supplied by user may be modified to avoid naming conflicts with other data sets)
Short code for plot; combination of project+plot_code is unique, but plot_code may repeat among different projects

major_geo

Text

Closed pick list (see Comments)

No
Yes
Values as follows: "South America", "Europe", "Africa", "Trop.Asia, Oceania", "North America", "Central America" (includes Mexico), "Caribbean", "Temperate Asia". Based on values in Missouri Botanical Garden version of the "Alwyn Gentry 0.1 ha Transect Dataset"
country
Text
Closed pick list
No
Yes
Modified to correspond to names in SALVIAS lookup tables
pol1
Text

Yes
No
Next political division below country; i.e., state, province, or department. As provided by original data provider, but may be modified to correspond to names in SALVIAS lookup tables
pol2
Text

Yes
No
Next political division below pol1, i.e., county, district, municipio, depending on country. As provided by original data provider, but may be modified to correspond to names in SALVIAS lookup tables
locality_description
Text

Yes
No
Detailed description of locality
lat_decimal
Decimal

Yes
Yes
Latitude, in decimal degrees; may be parsed and converted if original value is text field and/or in different units
long_decimal
Decimal

Yes
Yes
Longitude, in decimal degrees; conversions as for lat_decimal
elev_m
Decimal

Yes
Yes
Elevation in meters; this and following two fields are parsed and converted if original data is text field, range, and/or non-metric
elev_max_m
Decimal

Yes
Yes
Maximum elevation in meters, if a range
elev_min_m
Decimal

Yes
Yes
Minimum elevation in meters, if a range
temp_c
Decimal

Yes
No
Mean annual temperature, in centrigrade
precip_mm
Decimal

Yes
No
Total annual precipitation, in mm
slope_aspect
Decimal

Yes
No
Aspect (compass direction) of slope, in degrees
slope_gradient
Decimal

Yes
No
Steepness of slope, in degrees
clay_percent
Decimal

Yes
No

silt_percent
Decimal

Yes
No

sand_percent
Decimal

Yes
No

soil_pH
Decimal

Yes
No

holdridge_life_zone
Text
Closed pick list
Yes
Yes
Long description of classification within Holdridge Life Zone system
life_zone_code
Text
Closed pick list
Yes
Yes
Short code for Holdridge Life Zone
observation_type
Text
Closed pick list:
"individuals";
"species (individuals)"; “species (stems)” ; "species (percent cover)";
"species (line_intercept)"; "species (presence)"

Yes
Yes
Important!  The value in this field affects interpretation of other fields in the plot data. Values as follows: "individuals": all records in plot data with same OBSERVATION_ID correspond to a single individual; "species (individuals)": all values in plot data with same OBSERVATION_ID represent a record of a single species, with total numbers of individuals recorded in the no_of_individuals field; “species (stems)”: as with  preceding, but may have one or more stem values for each species records, and stems do not map onto specific individuals (this format is unique to the Gentry transect dataset); "species (percent cover)": all values in plot data with same OBSERVATION_ID represent a record of a single species, with proportional coverage of plot area recorded in the cover_percent field; "species (line_intercept)": all values in plot data with same OBSERVATION_ID represent a record of a single species, with linear coverage along a center transect line in cm recorded in the field intercept_cm.  "species (presence)": all values in plot data with same OBSERVATION_ID represent a record of a single species, with no abundance data provided.
plot_methodology
Text
Open pick list
Yes
Partially; user may select from list of standard descriptions, or supply new
"free form" summary of several aspects of methodology; typically a combined description of plot area, plot dimensions, size cufoff (if any), growth forms included or omitted,
plot_area_ha
Decimal

Yes
Yes
Will be NULL if sampling method is dimension less or linear
recensused
Text
"Yes", "No"
Yes
Yes
If yes, then multiple censuses are available in plot data
date_start
Text

Yes
No

date_finish
Text

Yes
No



Plot data

Below are the fields downloaded when you select “download plot data”.  The downloaded table is a single flat file derived principally from two source tables: PlotObservations (containing either species- or individual-level observations, depending on the observation_type; see Plot metadata for more details), and Stems, containing stem-level attributes.  The downloaded table is thus in one-observation-per-stem format.  PlotObservations is linked one-to-many with the Stems table; thus values from field in the PlotObservations table will repeat if more than one record in exists in the Stems table for a given observation  in the PlotObservations table.  Use OBSERVATION_ID field to group stem values for individuals.  In interpreting taxonomy, please pay careful attention to the species_name_status field.

Field name
Data type
Value list
Can be null?
Standardized by SALVIAS?
Comments
OBSERVATION_ID
Integer
Autoincrement
No
Added by database
Primary key for main raw data table (PlotObservations); IMPORTANT: stem measurement are stored in a separate table linked many-to-one with the PlotObservations table; thus, OBSERVATION_ID will repeat if multiple stem values exist for a given individual. 
PLOT_ID
Integer

No
see PlotMetadata table, above
Foreign key, links to PlotMetadata table (table containing plot descriptions); unique number for each plot
plot_code
Text


see PlotMetadata table, above
Short code for plot; combination of project+plot_code is unique, but plot_code may repeat among different projects.  May function as foreign key, but PLOT_ID is safest.
census_no
Integer

Yes
Yes
1 is default; most plots are not recensused. Different censuses for same plot can be distinguished by unique combination of plot_code + census_no
census_date
Text

Yes
No
Date of census, if provided
subplot
Text

Yes
No
Code for subplot, line, or any other subsample  or subdivision of plot
individual_code
Text

Yes
No
Any code for individual, other than tag numbers (see tag1 and tag2, below) provided in original data.
ind_id
Text

Yes
Yes, if not supplied with original data for plots with observation_type = individuals
If observation_type=individuals (see data dictionary for PlotMetadata) this value uniquely identifies each individual.  Different records with same value of ind_id are separate stems for same individual.  If not supplied with original data, this field will be added by SALVIAS upon import to database.
tag1
Text

Yes
No
Original tree tag number
tag2
Text

Yes
No
Most recent tree tag number; if this value is not null, indicates original tag was lost;
x_position
Decimal

Yes
No
x coordinate in meters
y_position
Decimal

Yes
No
y coordinate in meters
voucher_string
Text

Yes
No
Text string for collector name and collector number of voucher specimen, if any, exactly as supplied in source data
coll_number
Text

Yes
Yes.  
Collection number as parsed by SALVIAS from voucher_string
collector_code
Text

Yes
Yes.  
Unique short code for collector, assigned by SALVIAS. (this field may not be populated for all datasets, if original data provider did not provide "key" to abbreviations in original voucher_string)
coll_lastname
Text

Yes
Yes.
 Collector's last name (or names) as parsed by SALVIAS from voucher_string.  Or will be same as original if already stored separately in source database. (this field may not be populated for all datasets, if original data provider did not provide "key" to abbreviations in original voucher_string)
coll_firstname
Text
Open pick list
Yes
Yes
Senior collector's first name, as parsed by SALVIAS (this field may not be populated for all datasets, if original data provider did not provide "key" to abbreviations in original voucher_string)
det_type
Text
Closed pick list:
“direct”, “indirect”, “unvouchered”, “default”
Yes
Yes
Important!  States how reference specimen has been associated with this individual.  Permits each record to be associated with a specimen voucher, and determinations to be updated automatically via herbarium specimens.
“direct” = specimen is collection of this individual; “indirect” = individual was referenced by data provider to specific collection of a different individual; “default” = individual is connected by shared morphospecies name to voucher specimen of a different individual;
“unvouchered” = no specimen vouchers (direct or otherwise) for this individual; species was never collected, and determination is presented as-is.
fam_status
Integer
Closed list: 0, 1
No
Yes
Status of family.  0 = "non-standard"; does not match any family in TROPICOS or IPNI databases.   1 = "standard"; matches to family in TROPICOS and/or IPNI.
gen_status
Integer
Closed list: 0, 1
No
Yes
Status of genus.  0 = "non-standard"; does not match any genus  in TROPICOS or IPNI databases.   1 = "standard"; matches to genus in TROPICOS and/or IPNI.
species_status
Integer
Closed pick list: 0, 1, 2, or 3
Yes
Yes
Important! Gives status of species name (binomial), as determined by SALVIAS TaxonScrubber.  If NULL, name was loaded as-is to database; either not "scrubbed", or scrubbed by status not confirmed by inspection.

0 = "non-standard binomial"; does not match any name within TROPICOS or IPNI database, but apparently a latin binomial; in absence of evidence to contrary, should be assumed to be same species as all other individuals bearing same Genus+species string

1 = "standard binomial"; matches to name in TROPICOS and/or IPNI database. Does not mean names is "correct", simply that it exists in taxonomic database.  User must determine validity of name; 

2 = "indet", undetermined to species and is *not* a morphospecies, therefore does not necesarily match to other individuals bearing the same species string;

3 = "morphospecies"; has not been identified to a standard name, but original determiner asserts that all individuals bearing this species string represent to the same species within a given plot.
family
Text

Yes
Yes
Family name from TROPICOS database; matched by SALVIAS TaxonScrubber based on genus
genus
Text

Yes
Yes

Corrected genus name from SALVIAS TaxonScrubber; may or may not correspond to Genus portion of orig_species
specific_epithet
Text

Yes
Yes

Corrected specific epithet from SALVIAS TaxonScrubber; may or may not correspond to specific epithet in orig_species
specific_authority
Text

Yes
Yes

Corrected authority from SALVIAS TaxonScrubber; this field is usually only populated if original data (see orig_species field) contains authority
infra_rank_1
Text

Yes
Yes

Rank of determination below level of species, if any, as parsed by SALVIAS TaxonScrubber
infra_ep_1
Text

Yes
Yes

Epithet of determination below level of species, if any, as parsed by SALVIAS TaxonScrubber
cf_aff
Text
"cf.", "aff."
Yes
Yes
"cf." or "aff." annotations
habit
Text
Closed pick list; T = tree, H = hemiepiphyte, L = Liana, E = epiphyte, S = shrub, Hb = herb
Yes
Yes

Growth form. May be null, depending on information provided in original data.  Note that many data sets lump S under T.
no_of_individuals
Integer

Yes if observation_type =  "individuals", "species (individuals)", or “species (stems)”; otherwise No
Partially; see Comments

Important!  Number of individuals. Can sum by plot_code, OBSERVATION_ID, or taxon to obtain counts of individuals.  For  observation_type ="species-individuals", equals total individuals for that species within the subplot; if have multiple stem records for each species (Gentry data only) then equals total individuals for first stem record only; for other stem records = 0.  For observation_type = "individuals" will be 1 for first stem for that individual, 0 for remaining stems of same individual.  For all other observation_type, will be NULL; see data dictionary for PlotMetadata.
cover_percent
Decimal


Yes
No
Percent cover (for observation_type="species (percent cover)" only; see data dictionary for PlotMetadata)
intercept_cm
Decimal


Yes
No
Intercept along center line, in cm (for observation_type="species (point intercept)" only; see data dictionary for PlotMetadata)
height_m
Decimal

Yes
No
Total height of individual, in meters
ht_first_branch_m
Decimal

Yes
No
Height to first branch, in meters
stem_tag1
Text

Yes
No Original stem tag number (if tags provided for individual stems, as opposed to entire tree)
stem_tag2
Text

Yes
No
Most recent stem tag number; if this value is not null, indicates original tag was lost
stem_dbh
Decimal

Yes
No
Diameter at breast height of this stem (usually taken at 1.3 meters, but may vary; see metadata files for this dataset)
basal_diam
Decimal

Yes
No
Diameter at ground level for this stem
stem_height_m
Decimal

Yes
No
Total height of this stem only, in meters. for this stem only.
stem_height_first_
branch_m
Decimal

Yes
No
Height to first branch, in meters. For this stem only.
stem_canopy_form
Text
Open pick list

Yes
No
See accompanying documents for particular dataset. Codes are specific to particular dataset, therefore no standardization enforced. Stem-level attribute.
stem_canopy_position
Text
Open pick list

Yes
No
See accompanying documents for particular dataset. Codes are specific to particular dataset, therefore no standardization enforced. Stem-level attribute.
stem_liana_infestation
Text
Open pick list

Yes
No
See accompanying documents for particular dataset. Codes are specific to particular dataset, therefore no standardization enforced. Stem-level attribute
notes
Text

Yes
No
Miscellaneous comments, relevant to this record
orig_family
Text

Yes
No
Original, unaltered text string of family from original data set, for comparison.  This field may be null if original dataset consisted of species name only
orig_species
Text

Yes
No
Original text string of species name from original dataset. If Genus, specific epithet, and/or authority were in separate fields in original dataset, these will appear concatenated in this field. Provided for comparison.


", "Central America" (includes Mexico),
td valign="top">pol2