Table descriptions, relationships, and requirements

Overview

This document describes the eight ecocomDP tables and their contents. Four tables are required (observation, location, taxon, and dataset_summary). Each main table (observation, location, taxon) has an optional ancillary table for additional information. These are included because primary research typically contains related measurements which may be of interest during analysis. The dataset_summary table is populated from the observation table contents, and the variable_mapping table holds URIs and labels for external measurement dictionaries.

An example ecocomDP dataset is here and a graphic showing all tables and their relationships is available here.

Tables

table name required? references tables unique constraints
observation yes location, taxon, dataset_summary observation_id
location yes NA location_id
taxon yes NA taxon_id
dataset_summary yes NA package_id
observation_ancillary no observation observation_id, variable_name
location_ancillary no location location_id, datetime, variable_name
taxon_ancillary no taxon taxon_id, variable_name
variable_mapping no observation, observation_ancillary, location_ancillary, taxon_ancillary table_name, variable_name

Table: observation

Description: This is the core table, which holds the observations being analyzed (e.g. organism abundance or density). Observations must be linked to a taxon and to a location. Linking to ancillary observations is optional.

Columns

column name type not NULL required? references description example
observation_id character yes NA Identifier assigned to each unique observation. 4161
event_id character yes NA Identifier assigned to each unique sampling event. 2009mar03_dive1
package_id character yes /dataset_summary/package_id Identifier of this data package. edi.100001.1
location_id character yes /location/location_id A reference to a location. sbc_ABUR_1
datetime datetime yes NA Date and time of the observation in ISO-8601 format. 2017-08-01, 2017-08-01 14:30:00
taxon_id character yes /taxon/taxon_id A reference to a taxon. sbclter_MAPY
variable_name character yes NA Name of the measured variable. count
value float yes NA Value of the measured variable. 7
unit character yes NA Unit of the measured variable. number

Table: location

Description: Identifying information about a place (longitude, latitude, elevation). The table is self-referencing so that sites can be nested.

Columns

column name type not NULL required? references description example
location_id character yes NA Identifier assigned to each unique location. sbclter_abur_I
location_name character no NA Sampling location full name. Arroyo Burro Reef, transect I
latitude float no NA Latitude in decimal degrees. Latitudes south of the equator are negative. 34.400275
longitude float no NA Longitude in decimal degrees. Longitudes west of the prime meridian are negative. -119.7445915
elevation float no NA Sampling location elevation in meters relative to sea level. Above sea level is positive. Below sea level is negative. -15
parent_location_id character no NA Sampling location identifier from this table for the parent of this sampling location. Presence indicates nested locations. sbclter_abur_I

Table: taxon

Description: Identifying information about a taxon (e.g. name, id, and system).

Columns

column name type not NULL required? references description example
taxon_id character yes NA Identifier assigned to each unique organism. sbclter_MAPY
taxon_rank character no NA Taxonomic rank of the organism. species
taxon_name character yes NA Taxonomic name of the organism. Macrocystis pyrifera
authority_system character no NA Name of the system assigning the authority_taxon_id. ITIS
authority_taxon_id character no NA Identifier in the authority system corresponding to the taxon_name. 11274

Table: dataset_summary

Description: Summary info about the dataset.

Columns

column name type not NULL required? references description example
package_id character yes NA Identifier of this data package. edi.100001.1
original_package_id character no NA Identifier of source data package. knb-lter-sbc.21.17
length_of_survey_years integer yes NA Number of years the study has been ongoing. 17
number_of_years_sampled integer yes NA Number of years within the period of the study that samples were taken. 17
std_dev_interval_betw_years float yes NA Standard deviation of the interval between sampling events. 1.1
max_num_taxa integer yes NA Number of unique values in the taxon table. 10
geo_extent_bounding_box_m2 float no NA Area of the study location. 40

Table: observation_ancillary

Description: Ancillary information about an observational event for context. These are very often environmental driver data in analyses (e.g. water depth, height of a tower, temperature of medium).

Columns

column name type not NULL required? references description example
observation_ancillary_id character yes NA Identifier of the observation ancillary information. TBE01JUN05
observation_id character yes /observation/observation_id A reference to an observation. References the observation_id field of the observation table. 4161
variable_name character yes NA Name of the measured variable. sample_z
value character no NA Value of the measured variable. 5
unit character no NA Unit of the measured variable. meter

Table: location_ancillary

Description: Additional information about a place that does not change frequently (e.g. lake area or depth, experimental treatment). Features that change frequently are more closely related to the observational event, and are thus kept in the observation_ancillary table. Ancillary observations are linked through the location_id, and one location_id may have many ancillary observations about it.

Columns

column name type not NULL required? references description example
location_ancillary_id character yes NA Identifier of the location ancillary information.
location_id character yes /location/location_id A reference to a location. References the location_id field of the location table. sbclter_ABUR_1
datetime datetime no NA Date and time of the ancillary information in ISO-8601 format. 2017-08-01, 2017-08-01 14:30:00
variable_name character yes NA Name of the measured variable. treatment
value character yes NA Value of the measured variable. kelp removal
unit character no NA Unit of the measured variable.

Table: taxon_ancillary

Description: Additional info about an organism that does not change frequently (e.g. trophic level). Features that change frequently are probably observations. Ancillary observations are linked through the taxon_id, which may have many ancillary observations about it.

Columns

column name type not NULL required? references description example
taxon_ancillary_id character yes NA Identifier of the taxon ancillary information.
taxon_id character yes /taxon/taxon_id A reference to a taxon. References the taxon_id field of the taxon table.
datetime datetime no NA Date and time of the ancillary information in ISO-8601 format. 2017-08-01, 2017-08-01 14:30:00
variable_name character yes NA Name of the measured variable. trophic_level
value character yes NA Value of the measured variable. primary producer
unit character no NA Unit of the measured variable.
author character no NA Author associated with identification of the taxon.

Table: variable_mapping

Description: Information linking a variable_name used in a table to an external definition.

This optional table holds mappings (or relations) between variable names in the data tables and measurement definitions external to the data package. This table has multiple uses:

  • provides definitions for variables in the datasets (more extensive than might be found in metadata)
  • code can use this table to to create EML code-definition pairs or annotations in metadata
  • a single column in a data table may have mappings to multiple dictionaries, by including multiple rows for it

Columns

column name type not NULL required? references description example
variable_mapping_id character yes NA Identifier of the variable mapping information. 1
table_name character yes NA Name of the table containing this variable. my_observation
variable_name character yes /table/variable_name Name of the measured variable in another table. sample_z
mapped_system character no NA System defining variable_name. NERC
mapped_id character no NA Identifier of the definition in mapped_system. SDN:P07::CFSN0721
mapped_label character no NA Label for variable_name in mapped_system. depth

Entity Relationship Diagram

Figure 1: The optional tables are partly transparent. The primary key for each table is the id (column named “table_name_id”, with a green background. Columns that (as a group) should be unique within the table, have a yellow background. Many:many relationships are shown with dotted lines (side note: if this model were implemented in a relational database, each many:many relationship would require an intermediate table).