traits.build Data Model

Release 0.1.0

Latest version:

https://w3id.org/traits.build/index.html

This version:

https://w3id.org/traits.build/release/0.1.0/index.html

Previous version:

https://w3id.org/traits.build/release/0.1.0/index.html

Authors:

Elizabeth Wenk, Daniel Falster

Contributors:

David Coleman, Sophie Yang

Serializations:

License:

Source:

Contributing:

Cite as:

Wenk, Elizabeth H., Payal Bal, David Coleman, Rachael V. Gallagher, Sophie Yang, and Daniel S. Falster. “Traits.Build: A Data Model, Workflow and R Package for Building Harmonised Ecological Trait Databases.” bioRxiv, February 12, 2024. doi.org/10.1101/2024.02.11.579848

Abstract

This document presents the traits.build data model (data standard), formally published within the w3id.org/traits.build namespace. The traits.build ontology documents the output structure of a database built using the {traits.build} R package. It terms are both the output variables in each of the databases’s relational tables and additional conceptual terms inherent to the database structure. The ontology describes these terms and the semantic relationships between them. The traits.build data model adheres to the OBOE ontology and draws upon previously published terms whenever possible, especially DarwinCore and the Ecological Trait-data Standard.

Introduction
traits.build data model: The terms within the formal traits.build ontology
Acknowledgements

1. Introduction

A database must be accompanied by a published data model to be: 1) efficiently and accurately interpreted and used by researchers; and 2) easily integrated with other databases. A published data model should be machine-readable for easy integration into future data products, yet also tractable to human readers. A data model (a.k.a. data standard, ontology) must document the meanings behind each database output variable and should also record the semantic relationships between columns. For instance, within the traits.build ontology, indicating that observation_id is an identifier for a unique observation.

To the extent possible, a data model should draw upon previously published vocabularies and ontologies, explicitly indicating when terms within the data model are identical to those used by other databases (or other bioinformatics outputs). For instance, the traits.build data standard maps terms related to taxonomy and species occurrences to DarwinCore and terms related to trait measurements to the Ecological Trait-data Standard. The semantic relationships between terms adhere to the OBOE ontology, a generic relational ontology developed explicitly for documenting ecological trait observations and the context properties that are essential to document for ecological data. It further draws upon properties defined by the Semanticscience Integrated Ontology (https://bioportal.bioontology.org/ontologies/SIO) to describe relationships between terms.

Within the traits.build ontology, there are 5 main categories of terms, differentiated based on whether they are database tables, rows, or columns:

Database tables: The relational tables (traits, contexts, locations, methods, taxa, contributors, taxonomic_updates). These terms are all mapped as having the property computational entity = database table
Database table columns: The columns within these relational tables, all mapped as being organised into one (or more) of the tables using dwc-attributes:organisedInClass. These terms are all mapped as having the property computational entity = database column
Database table entries: Single, implicitly structured data items in a table. These terms are all types of oboe-core:Entity, objects that are the foci for an oboe-core:observation. These terms are all mapped as having the property computational entity = database entry
Clusters of rows within a database table: Collections of rows within a table that represent either observations or observation collections. These terms are all mapped as having the property computational entity = database table.
Individual rows within a database table: Individual rows within a table that are measurements. These terms are all mapped as having the property computational entity = database row.

2. Traits.build data model

The traits.build resource

Property	Value
URI	w3id.org/traits.build
description	The traits.build ontology documents the output structure of a database built using the {traits.build} R package.
license	https://creativecommons.org/licenses/by/4.0/
publisher	https://austraits.org/
type	concept scheme
label	traits.build
has top concept	https://w3id.org/traits.build-database
creator	Daniel Falster
creator	Elizabeth Wenk
creator	Sophie Yang
created	01 February 2024

Database

A traits.build database

Property	Value
URI	w3id.org/traits.build#traits.build-database
alternative label	traits.build_database
computational entity	database
label	traits.build database
description	A database of 13 relational tables build using the {traits.build} R-package for harmonizing trait data.
created	01 February 2024
is in scheme	traits.build

Database Tables

The traits.build output tables

traits table

Property	Value
URI	w3id.org/traits.build#traits.build-traits
preferred label	traits table
alternative label	traits
description	A table containing measurements of traits.
comment	Includes information that must be recorded at the Measurement or Observation level.
computational entity	database table
organizedInClass	traits.build database
has exact match	Traitdata
has related match	MeasurementOrFact Occurrence
created	01 February 2024
is in scheme	w3id.org/traits.build

locations table

Property	Value
URI	w3id.org/traits.build#traits.build-locations
preferred label	locations table
alternative label	locations
description	A table containing observations of location/site characteristics associated with information in `traits`. Cross referencing between the two dataframes is possible using combinations of the variables `dataset_id`, `location_name`.
comment	Includes information about Location properties.
computational entity	database table
organizedInClass	traits.build database
has related match	Occurrence
created	01 February 2024
is in scheme	w3id.org/traits.build

contexts table

Property	Value
URI	w3id.org/traits.build#traits.build-contexts
preferred label	contexts table
alternative label	contexts
description	A table containing observations of contextual characteristics associated with information in `traits`. Cross referencing between the two dataframes is possible using combinations of the variables `dataset_id`, `link_id`, and `link_vals`.
computational entity	database table
organizedInClass	traits.build database
created	01 February 2024
is in scheme	w3id.org/traits.build

methods table

Property	Value
URI	w3id.org/traits.build#traits.build-methods
preferred label	methods table
alternative label	methods
description	A table containing details on methods with which data were collected, including time frame and source. Cross referencing with the `traits` table is possible using combinations of the variables `dataset_id`, `trait_name`.
computational entity	database table
organizedInClass	traits.build database
has related match	MeasurementOrFact
created	01 February 2024
is in scheme	w3id.org/traits.build

excluded data table

Property	Value
URI	w3id.org/traits.build#traits.build-excluded_data
preferred label	excluded data table
alternative label	excluded_data
description	A table of data that did not pass quality tests and so were excluded from the master dataset. The structure is identical to that presented in the `traits` table, only with an extra column called `error` indicating why the record was excluded. Common reasons are missing_unit_conversions, missing_value, and unsupported_trait_value.
computational entity	database table
organizedInClass	traits.build database
created	01 February 2024
is in scheme	w3id.org/traits.build

taxonomic updates table

Property	Value
URI	w3id.org/traits.build#traits.build-taxonomic_updates
preferred label	taxonomic updates table
alternative label	taxonomic_updates
description	A table of all taxonomic changes implemented in the construction of AusTraits. Changes are determined by comparing the originally submitted taxon name against the taxonomic names listed in the taxonomic reference files, best placed in a subfolder in the `config` folder . Cross referencing with the `traits` table is possible using combinations of the variables `dataset_id` and `taxon_name`.
computational entity	database table
organizedInClass	traits.build database
created	01 February 2024
is in scheme	w3id.org/traits.build

taxa table

Property	Value
URI	w3id.org/traits.build#traits.build-taxa
preferred label	taxa table
alternative label	taxa
description	A table containing details on taxa associated with information in `traits`. Whenever possible, this information is sourced from curated taxon lists that include identifiers for each taxon. The information compiled in this table is released under a CC-BY3 license. Cross referencing between the two dataframes is possible using combinations of the variable `taxon_name`.
computational entity	database table
organizedInClass	traits.build database
has exact match	Taxon
created	01 February 2024
is in scheme	w3id.org/traits.build

contributors table

Property	Value
URI	w3id.org/traits.build#traits.build-contributors
preferred label	contributors table
alternative label	contributors
description	A table of people contributing to each study.
computational entity	database table
organizedInClass	traits.build database
created	01 February 2024
is in scheme	w3id.org/traits.build

sources table

Property	Value
URI	w3id.org/traits.build#traits.build-sources
preferred label	sources table
alternative label	sources
description	A list containing citation details for all database sources.
computational entity	database table
organizedInClass	traits.build database
created	01 February 2024
is in scheme	w3id.org/traits.build

definitions table

Property	Value
URI	w3id.org/traits.build#traits.build-definitions
preferred label	definitions table
alternative label	definitions
description	A list containing trait concept descriptions used to build the database.
computational entity	database table
organizedInClass	traits.build database
has exact match	Traitdata
created	01 February 2024
is in scheme	w3id.org/traits.build

schema

Property	Value
URI	w3id.org/traits.build#traits.build-schema
preferred label	schema
alternative label	schema
description	A copy of the schema for all tables and terms. Information included here was used to process data and generate any documentation for the study.
computational entity	metadata
organizedInClass	traits.build database
created	01 February 2024
is in scheme	w3id.org/traits.build

metadata table

Property	Value
URI	w3id.org/traits.build#traits.build-metadata
preferred label	metadata table
alternative label	metadata
description	A list containing database metadata.
computational entity	metadata
organizedInClass	traits.build database
has close match	Metadata
created	01 February 2024
is in scheme	w3id.org/traits.build

build info

Property	Value
URI	w3id.org/traits.build#traits.build-build_info
preferred label	build info
alternative label	build_info
description	A description of the computing environment used to create this version of the dataset, including version number, git commit and R session_info.
computational entity	metadata
organizedInClass	traits.build database
created	01 February 2024
is in scheme	w3id.org/traits.build

Database Table Columns

Columns within the traits.build output tables

traits table

dataset id

Property	Value
URI	w3id.org/traits.build#dataset_id
preferred label	dataset id
alternative label	dataset_id
description	Primary identifier for each study contributed to AusTraits, most often these are scientific papers, books, or online resources. By default this should be the name of the first author and year of publication, e.g. `Falster_2005`.
computational entity	database column
organizedInClass	traits table locations table contexts table methods table taxonomic updates table contributors table sources table
has broader	Identifier
is unique identifier for	observations from dataset
created	01 February 2024
is in scheme	w3id.org/traits.build

taxon name

Property	Value
URI	w3id.org/traits.build#taxon_name
preferred label	taxon name
alternative label	taxon_name
description	Scientific name of the taxon on which traits were sampled, without authorship. When possible, this is the currently accepted (botanical) or valid (zoological) scientific name, but might also be a higher taxonomic level.
computational entity	database column
organizedInClass	traits table taxa table taxonomic updates table
has close match	acceptedNameUsage
has broader	label preferred label
has unique identifier	taxon id
is unique identifier for	observations of taxon
has basis	aligned name original taxon name
has property	taxonomic dataset taxon rank taxonomic status
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

observation id

Property	Value
URI	w3id.org/traits.build#observation_id
preferred label	observation id
alternative label	observation_id
description	A unique integral identifier for the observation, where an observation is all measurements made on an individual at a single point in time. It is important for joining traits coming from the same `observation_id`. Within each dataset, observation_id’s are unique combinations of `taxon_name`, `population_id`, `individual_id`, and `temporal_context_id`.
computational entity	database column
organizedInClass	traits table
has broader	Identifier
is unique identifier for	observation
created	01 February 2024
is in scheme	w3id.org/traits.build

trait name

Property	Value
URI	w3id.org/traits.build#trait_name
preferred label	trait name
alternative label	trait_name
description	Name of the trait sampled. Allowable values specified in the table `definitions`.
computational entity	database column
organizedInClass	traits table methods table definitions table
has exact match	alternative label label
created	01 February 2024
is in scheme	w3id.org/traits.build

value

Property	Value
URI	w3id.org/traits.build#trait_value
preferred label	value
alternative label	value
description	The measured value of a trait.
computational entity	database column
organizedInClass	traits table
has exact match	traitValue
has broader	Measured Value measurementValue
created	01 February 2024
is in scheme	w3id.org/traits.build

unit

Property	Value
URI	w3id.org/traits.build#unit
preferred label	unit
alternative label	unit
description	Units of the sampled trait value after aligning with AusTraits standards.
computational entity	database column
organizedInClass	traits table
has exact match	Unit traitUnit
created	01 February 2024
is in scheme	w3id.org/traits.build

entity type

Property	Value
URI	w3id.org/traits.build#entity_type
preferred label	entity type
alternative label	entity_type
description	A categorical variable specifying the entity corresponding to the trait values recorded.
computational entity	database column
organizedInClass	traits table
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

value type

Property	Value
URI	w3id.org/traits.build#value_type
preferred label	value type
alternative label	value_type
description	A categorical variable describing the statistical nature of the trait value recorded.
computational entity	database column
organizedInClass	traits table
has exact match	Base Characteristic Qualifier
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

basis of value

Property	Value
URI	w3id.org/traits.build#basis_of_value
preferred label	basis of value
alternative label	basis_of_value
description	A categorical variable describing how the trait value was obtained.
computational entity	database column
organizedInClass	traits table
has exact match	Measurement Type
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

replicates

Property	Value
URI	w3id.org/traits.build#replicates
preferred label	replicates
alternative label	replicates
description	Number of replicate measurements that comprise a recorded trait measurement. A numeric value (or range) is ideal and appropriate if the value type is a `mean`, `median`, `min` or `max`. For these value types, if replication is unknown the entry should be `unknown`. If the value type is `raw_value` the replicate value should be 1. If the trait is categorical or the value indicates a measurement for an entire species (or other taxon) replicate value should be `.na`.
computational entity	database column
organizedInClass	traits table
has exact match	individualCount
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	integer

basis of record

Property	Value
URI	w3id.org/traits.build#basis_of_record
preferred label	basis of record
alternative label	basis_of_record
description	A categorical variable specifying from which kind of specimen traits were recorded.
computational entity	database column
organizedInClass	traits table
has close match	basisOfRecord
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

life stage

Property	Value
URI	w3id.org/traits.build#life_stage
preferred label	life stage
alternative label	life_stage
description	A field to indicate the life stage or age class of the entity measured. Standard values are `adult`, `sapling`, `seedling` and `juvenile`.
computational entity	database column
organizedInClass	traits table
has exact match	lifeStage
has broader	Measured Value measurementValue
characteristic for	observation of entity context
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

population id

Property	Value
URI	w3id.org/traits.build#population_id
preferred label	population id
alternative label	population_id
description	A unique integer identifier for a population, where a population is defined as individuals growing in the same location (location_id /location_name) and plot (plot_context_id, a context category) and being subjected to the same treatment (treatment_context_id, a context category).
computational entity	database column
organizedInClass	traits table
has broader	Identifier
is unique identifier for	observations of population
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	integer

individual id

Property	Value
URI	w3id.org/traits.build#individual_id
preferred label	individual id
alternative label	individual_id
description	A unique integer identifier for an individual, with individuals numbered sequentially within each dataset by taxon by population grouping. Most often each row of data represents an individual, but in some datasets trait data collected on a single individual is presented across multiple rows of data, such as if the same trait is measured using different methods or the same individual is measured repeatedly across time.
computational entity	database column
organizedInClass	traits table
has broader	Identifier
is unique identifier for	observations of individual
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	integer

repeat measurements id

Property	Value
URI	w3id.org/traits.build#repeat_measurements_id
preferred label	repeat measurements id
alternative label	repeat_measurements_id
description	A unique integer identifier for repeat measurements of a trait that comprise a single observation, such as a response curve.
computational entity	database column
organizedInClass	traits table
has broader	Identifier
is unique identifier for	observations of individual collection date
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	integer

temporal context id

Property	Value
URI	w3id.org/traits.build#temporal_context_id
preferred label	temporal context id
alternative label	temporal_context_id
description	A unique integer identifier assigned where repeat observations are made on the same individual (or population, or taxon) across time. The identifier links to specific information in the context table.
computational entity	database column
organizedInClass	traits table contexts table
has broader	Identifier
is unique identifier for	measurement of temporal context property
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	integer

source id

Property	Value
URI	w3id.org/traits.build#source_id
preferred label	source id
alternative label	source_id
description	For datasets that are compilations, an identifier for the original data source.
computational entity	database column
organizedInClass	traits table sources table
has broader	Identifier
is unique identifier for	observations from source
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

location id

Property	Value
URI	w3id.org/traits.build#location_id
preferred label	location id
alternative label	location_id
description	A unique integer identifier for a location, with locations numbered sequentially within a dataset. The identifier links to specific information in the location table.
computational entity	database column
organizedInClass	traits table locations table
has broader	Identifier
is unique identifier for	observations at location
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	integer

entity context id

Property	Value
URI	w3id.org/traits.build#entity_context_id
preferred label	entity context id
alternative label	entity_context_id
description	A unique integer identifier indicating specific contextual properties of an individual, possibly including the individual’s sex or caste (for social insects).
computational entity	database column
organizedInClass	traits table contexts table
has broader	Identifier
is unique identifier for	measurement of entity context property
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	integer

plot context id

Property	Value
URI	w3id.org/traits.build#plot_context_id
preferred label	plot context id
alternative label	plot_context_id
description	A unique integer identifier for a plot, where a plot is a distinct collection of organisms within a single geographic location, such as plants growing on different aspects or blocks in an experiment. The identifier links to specific information in the context table.
computational entity	database column
organizedInClass	traits table contexts table
has broader	Identifier
is unique identifier for	measurement of plot context property
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	integer

treatment context id

Property	Value
URI	w3id.org/traits.build#treatment_context_id
preferred label	treatment context id
alternative label	treatment_context_id
description	A unique integer identifier for a treatment, where a treatment is any experimental manipulation to an organism’s growing/living conditions. The identifier links to specific information in the context table.
computational entity	database column
organizedInClass	traits table contexts table
has broader	Identifier
is unique identifier for	measurement of treatment context property
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	integer

collection date

Property	Value
URI	w3id.org/traits.build#collection_date
preferred label	collection date
alternative label	collection_date
description	Date sample was taken, in the format `yyyy-mm-dd`, `yyyy-mm` or `yyyy`, depending on the resoluton specified. Alternatively an overall range for the study can be indicating, with the starting and ending sample date sepatated by a `/`, as in 2010-10/2011-03
computational entity	database column
organizedInClass	traits table
has exact match	eventDate
has broader	Measured Value measurementValue
characteristic for	observation
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	date

measurement remarks

Property	Value
URI	w3id.org/traits.build#measurement_remarks
preferred label	measurement remarks
alternative label	measurement_remarks
description	Brief comments or notes accompanying the trait measurement.
computational entity	database column
organizedInClass	traits table
has broader	comment
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

method id

Property	Value
URI	w3id.org/traits.build#method_id
preferred label	method id
alternative label	method_id
description	A unique integer identifier to distinguish between multiple sets of methods used to measure a single trait within the same dataset. The identifier links to specific information in the methods table.
computational entity	database column
organizedInClass	traits table methods table
has broader	Identifier
is unique identifier for	methods
is specialisation of	methods
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	integer

method context id

Property	Value
URI	w3id.org/traits.build#method_context_id
preferred label	method context id
alternative label	method_context_id
description	A unique integer identifier indicating a trait is measured multiple times on the same entity, with different methods used for each entry. This field is only used if a single trait is measured using multiple methods within the same dataset. The identifier links to specific information in the context table.
computational entity	database column
organizedInClass	traits table contexts table
has broader	Identifier
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	integer

original taxon name

Property	Value
URI	w3id.org/traits.build#original_name
preferred label	original taxon name
alternative label	original_name
description	Name given to taxon in the original data supplied by the authors.
computational entity	database column
organizedInClass	traits table taxonomic updates table
has broader	label preferred label
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

locations table

location name

Property	Value
URI	w3id.org/traits.build#location_name
preferred label	location name
alternative label	location_name
description	The location name used by the data contributor or a generic location name designated by AusTraits when one is not provided.
computational entity	database column
organizedInClass	locations table
has broader	label preferred label
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

location property

Property	Value
URI	w3id.org/traits.build#location_property
preferred label	location property
alternative label	location_property
description	The location characteristic being recorded. The name should include units of measurement, e.g. `MAT (C)`. Ideally we have at least the following variables for each location, `longitude (deg)`, `latitude (deg)`, `description`.
computational entity	database column
organizedInClass	locations table
has broader	Characteristic
has value	location property value
characteristic for	location
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

location property value

Property	Value
URI	w3id.org/traits.build#locations_value
preferred label	location property value
alternative label	value
description	The measured value of a location property.
computational entity	database column
organizedInClass	locations table
has broader	Measured Value measurementValue
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

latitude (deg)

Property	Value
URI	w3id.org/traits.build#latitude
preferred label	latitude (deg)
alternative label	latitude
description	The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are north of the Equator, negative values are south of it. Legal values lie between -90 and 90, inclusive.
computational entity	database column
organizedInClass	locations table
has exact match	decimalLatitude
has broader	Measured Value measurementValue
characteristic for	location
is specialisation of	location property
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	decimal

longitude (deg)

Property	Value
URI	w3id.org/traits.build#longitude
preferred label	longitude (deg)
alternative label	longitude
description	The geographic longitude (in decimal degrees, using the spatial reference system given in dwc:geodeticDatum) of the geographic center of a dcterms:Location. Positive values are east of the Greenwich Meridian, negative values are west of it. Legal values lie between -180 and 180, inclusive.
computational entity	database column
organizedInClass	locations table
has exact match	decimalLongitude
has broader	Measured Value measurementValue
characteristic for	location
is specialisation of	location property
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	decimal

elevation (m)

Property	Value
URI	w3id.org/traits.build#elevation
preferred label	elevation (m)
alternative label	elevation
description	The elevation above mean sea level in meters.
computational entity	database column
organizedInClass	locations table
has exact match	verbatimElevation
has broader	Measured Value measurementValue
characteristic for	location
is specialisation of	location property
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	decimal

contexts table

context property

Property	Value
URI	w3id.org/traits.build#context_property
preferred label	context property
alternative label	context_property
description	The contextual characteristic being recorded. If applicable, name should include units of measurement, e.g. `CO2 concentration (ppm)`.
computational entity	database column
organizedInClass	contexts table
has exact match	context property value
has broader	Characteristic
characteristic for	context
has annotation	context property category
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

context property category

Property	Value
URI	w3id.org/traits.build#contexts_category
preferred label	context property category
alternative label	category
description	The category of context property, with options being `plot`, `treatment`, `individual_context`, `temporal` and `method`.
computational entity	database column
organizedInClass	contexts table
has broader	scope note
is annotation of	context property
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

context property value

Property	Value
URI	w3id.org/traits.build#contexts_value
preferred label	context property value
alternative label	value
description	The measured value of a context property.
computational entity	database column
organizedInClass	contexts table
has broader	Measured Value measurementValue
measurement for	context property
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

context property value description

Property	Value
URI	w3id.org/traits.build#contexts_description
preferred label	context property value description
alternative label	description
description	Description of a specific context property value.
computational entity	database column
organizedInClass	contexts table
has broader	description
refers to	context property
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

context propety link id

Property	Value
URI	w3id.org/traits.build#contexts_link_id
preferred label	context propety link id
alternative label	link_id
description	Variable indicating which identifier column in the traits table contains the specified `link_vals`.
computational entity	database column
organizedInClass	contexts table
has broader	Identifier
refers to	treatment context id plot context id entity context id temporal context id method context id
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	integer

context propety link vals

Property	Value
URI	w3id.org/traits.build#contexts_link_vals
preferred label	context propety link vals
alternative label	link_vals
description	Unique integer identifiers that link between identifier columns in the `traits` table and the contextual properties/values in the `contexts` table.
computational entity	database column
organizedInClass	contexts table
has broader	Identifier
is unique identifier for	treatment context property plot context property entity context property temporal context property method context property
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	integer

treatment context property

Property	Value
URI	w3id.org/traits.build#treatment_context_property
preferred label	treatment context property
alternative label	treatment_context_property
description	A context characteristic indicating stratified treatments that might affect the trait values measured on an individual or population-level entity.
computational entity	database column
organizedInClass	contexts table
has exact match	context property value
has broader	Characteristic
has unique identifier	treatment context id
is specialisation of	context property
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

plot context property

Property	Value
URI	w3id.org/traits.build#plot_context_property
preferred label	plot context property
alternative label	plot_context_property
description	A context characteristic indicating stratified variation within a location that might affect the trait values measured on an individual or population-level entity.
computational entity	database column
organizedInClass	contexts table
has exact match	context property value
has broader	Characteristic
has unique identifier	plot context id
is specialisation of	context property
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

entity context property

Property	Value
URI	w3id.org/traits.build#entity_context_property
preferred label	entity context property
alternative label	entity_context_property
description	A context characteristic indicating stratified variation across individuals or populations might affect the trait values measured.
computational entity	database column
organizedInClass	contexts table
has exact match	context property value
has broader	Characteristic
has unique identifier	entity context id
is specialisation of	context property
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

temporal context property

Property	Value
URI	w3id.org/traits.build#temporal_context_property
preferred label	temporal context property
alternative label	temporal_context_property
description	A context characteristic indicating stratified variation across time might affect the trait values measured.
computational entity	database column
organizedInClass	contexts table
has exact match	context property value
has broader	Characteristic
has unique identifier	temporal context id
is specialisation of	context property
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

method context property

Property	Value
URI	w3id.org/traits.build#method_context_property
preferred label	method context property
alternative label	method_context_property
description	A context characteristic indicating stratified variation in the protocol used to measure traits might affect the trait values measured.
computational entity	database column
organizedInClass	contexts table
has exact match	context property value
has broader	Characteristic
has unique identifier	method context id
is specialisation of	context property
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

methods table

methods

Property	Value
URI	w3id.org/traits.build#methods_methods
preferred label	methods
alternative label	methods
description	A textual description of the methods used to collect the trait data. Whenever available, methods are taken near-verbatim from the referenced source. Methods can include descriptions such as ‘measured on botanical collections’, ‘data from the literature’, or a detailed description of the field or lab methods used to collect the data.
computational entity	database column
organizedInClass	methods table
has close match	Protocol
has broader	Protocol
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

dataset description

Property	Value
URI	w3id.org/traits.build#methods_description
preferred label	dataset description
alternative label	description
description	A 1-2 sentence description of the purpose of the study.
computational entity	database column
organizedInClass	methods table
has exact match	datasetDescription
has broader	description
refers to	methods
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

dataset sampling strategy

Property	Value
URI	w3id.org/traits.build#sampling_strategy
preferred label	dataset sampling strategy
alternative label	sampling_strategy
description	When available, this information is lifted verbatim from a published manuscript. For preserved specimens, this field ideally indicates which records were ‘sampled’ to measure a specific trait.
computational entity	database column
organizedInClass	methods table
has exact match	samplingProtocol
refers to	observations from dataset
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

source primary key

Property	Value
URI	w3id.org/traits.build#source_primary_key
preferred label	source primary key
alternative label	source_primary_key
description	Citation key for the primary source in `sources`. The key is typically formatted as `Surname_year`.
computational entity	database column
organizedInClass	methods table
has exact match	dataset id
has broader	Identifier
is unique identifier for	source primary citation
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

source primary citation

Property	Value
URI	w3id.org/traits.build#source_primary_citation
preferred label	source primary citation
alternative label	source_primary_citation
description	Citation for the primary source. This detail is generated from the primary source in the metadata.
computational entity	database column
organizedInClass	methods table
has broader	bibliographic citation
has unique identifier	source primary key
cites	dataset
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

source secondary key

Property	Value
URI	w3id.org/traits.build#source_secondary_key
preferred label	source secondary key
alternative label	source_secondary_key
description	Citation key for the secondary source in `sources`. The key is typically formatted as `Surname_year`.
computational entity	database column
organizedInClass	methods table
has broader	Identifier
is unique identifier for	source secondary citation
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

source secondary citation

Property	Value
URI	w3id.org/traits.build#source_secondary_citation
preferred label	source secondary citation
alternative label	source_secondary_citation
description	Citations for the secondary source. This detail is generated from the secondary source in the metadata.
computational entity	database column
organizedInClass	methods table
has broader	bibliographic citation
has unique identifier	source secondary key
cites	dataset
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

source original dataset key

Property	Value
URI	w3id.org/traits.build#source_original_dataset_key
preferred label	source original dataset key
alternative label	source_original_dataset_key
description	Citation key for the original dataset_id in sources, for compilations. The key is typically formatted as `Surname_year`.
computational entity	database column
organizedInClass	methods table
has exact match	source id
has broader	Identifier
is unique identifier for	source original dataset citation
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

source original dataset citation

Property	Value
URI	w3id.org/traits.build#source_original_dataset_citation
preferred label	source original dataset citation
alternative label	source_original_dataset_citation
description	Citations for the original dataset_id in sources, for compilationse. This detail is generated from the original source in the metadata.
computational entity	database column
organizedInClass	methods table
has broader	bibliographic citation
has unique identifier	source original dataset key
cites	observations from source
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

data collectors

Property	Value
URI	w3id.org/traits.build#data_collectors
preferred label	data collectors
alternative label	data_collectors
description	Person contributing to a dataset as a data collector.
computational entity	database column
organizedInClass	contributors table methods table
has exact match	Data Collector
has broader	contributor
has unique identifier	ORCID identifier given name last name
is specialisation of	contributor
has annotation	affiliation additional role
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

assistants

Property	Value
URI	w3id.org/traits.build#assistants
preferred label	assistants
alternative label	assistants
description	People who played a more minor role in data collection for the study.
computational entity	database column
organizedInClass	methods table
has exact match	Related Person
has broader	contributor
is specialisation of	contributor
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

dataset curators

Property	Value
URI	w3id.org/traits.build#dataset_curators
preferred label	dataset curators
alternative label	dataset_curators
description	Database team member(s) who contacted the data collectors and added the study to the database repository.
computational entity	database column
organizedInClass	methods table
has exact match	Data Curator
has broader	contributor
is specialisation of	contributor
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

contributor

Property	Value
URI	w3id.org/traits.build#contributor
preferred label	contributor
alternative label	contributor
description	A person contributing to a dataset.
computational entity	database column
organizedInClass	contributors table methods table
has exact match	contributor
refers to	observations from dataset
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

taxonomic updates table

aligned name

Property	Value
URI	w3id.org/traits.build#aligned_name
preferred label	aligned name
alternative label	aligned_name
description	The taxon name without authorship after implementing automated syntax standardisation and spelling changes as well as manually encoded syntax alignments for this taxon in the metadata file for the corresponding `dataset_id`. This name has not yet been matched to the currently accepted (botanical) or valid (zoological) taxon name in cases where there are taxonomic synonyms, isonyms, orthographic variants, etc.
computational entity	database column
organizedInClass	taxonomic updates table
has broader	label preferred label
has basis	original taxon name
is base for	taxon name
has property	taxonomic resolution
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

taxonomic resolution

Property	Value
URI	w3id.org/traits.build#taxonomic_resolution
preferred label	taxonomic resolution
alternative label	taxonomic_resolution
description	The rank of the most specific taxon name (or scientific name) to which a submitted orignal name resolves.
computational entity	database column
organizedInClass	taxonomic updates table
has related match	taxonRank
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

taxa table

taxonomic dataset

Property	Value
URI	w3id.org/traits.build#taxonomic_dataset
preferred label	taxonomic dataset
alternative label	taxonomic_dataset
description	Name of the taxonomy (tree) that contains this concept. ie. APC, AusMoss etc.
computational entity	database column
organizedInClass	taxa table
has exact match	nomenclaturalCode
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

taxon rank

Property	Value
URI	w3id.org/traits.build#taxon_rank
preferred label	taxon rank
alternative label	taxon_rank
description	The taxonomic rank of the most specific name in the scientific name.
comment	This is to clarify cases where information is not given on a species level.
computational entity	database column
organizedInClass	taxa table
has exact match	taxonRank
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

trinomial

Property	Value
URI	w3id.org/traits.build#trinomial
preferred label	trinomial
alternative label	trinomial
description	The infraspecific taxon name match for an original name. This column is assigned `na` for taxon name that are at a broader taxonomic_resolution.
computational entity	database column
organizedInClass	taxa table
has related match	infraspecificEpithet
has broader	label preferred label
is identifier for	taxon
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

binomial

Property	Value
URI	w3id.org/traits.build#binomial
preferred label	binomial
alternative label	binomial
description	The species-level taxon name match for an original name. This column is assigned `na` for taxon name that are at a broader taxonomic_resolution.
computational entity	database column
organizedInClass	taxa table
has related match	specificEpithet
has broader	label preferred label
is identifier for	taxon
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

genus

Property	Value
URI	w3id.org/traits.build#genus
preferred label	genus
alternative label	genus
description	Genus of the taxon without authorship.
computational entity	database column
organizedInClass	taxa table
has exact match	genus
has broader	label preferred label
is identifier for	taxon
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

family

Property	Value
URI	w3id.org/traits.build#family
preferred label	family
alternative label	family
description	Family of the taxon.
computational entity	database column
organizedInClass	taxa table
has exact match	family
has broader	label preferred label
is identifier for	taxon
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

taxon distribution

Property	Value
URI	w3id.org/traits.build#taxon_distribution
preferred label	taxon distribution
alternative label	taxon_distribution
description	Known distribution of the taxon, by Australian state.
computational entity	database column
organizedInClass	taxa table
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

establishment means

Property	Value
URI	w3id.org/traits.build#establishment_means
preferred label	establishment means
alternative label	establishment_means
description	Statement about whether an organism or organisms have been introduced to a given place and time through the direct or indirect activity of modern humans.
computational entity	database column
organizedInClass	taxa table
has exact match	establishmentMeans
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

taxonomic status

Property	Value
URI	w3id.org/traits.build#taxonomic_status
preferred label	taxonomic status
alternative label	taxonomic_status
description	The status of the use of the scientificName as a label for the taxon in regard to the ‘accepted (or valid) taxonomy’. The assigned taxonomic status must be linked to a specific taxonomic reference that defines the concept.
computational entity	database column
organizedInClass	taxa table
has exact match	taxonomicStatus
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

taxon id

Property	Value
URI	w3id.org/traits.build#taxon_id
preferred label	taxon id
alternative label	taxon_id
description	An identifier for the set of taxon information (data associated with the taxon class). May be a global unique identifier or an identifier specific to the data set. Must be resolvable within this dataset.
computational entity	database column
organizedInClass	taxa table
has exact match	taxonID
has broader	Identifier
is unique identifier for	taxon name
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	anyURI

scientific name

Property	Value
URI	w3id.org/traits.build#scientific_name
preferred label	scientific name
alternative label	scientific_name
description	The full scientific name, with authorship and date information if known.
computational entity	database column
organizedInClass	taxa table
has exact match	scientificName
has unique identifier	scientific name id
is unique identifier for	taxon
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

scientific name id

Property	Value
URI	w3id.org/traits.build#scientific_name_id
preferred label	scientific name id
alternative label	scientific_name_id
description	An identifier for the set of taxon information (data associated with the taxon class). May be a global unique identifier or an identifier specific to the data set. Must be resolvable within this dataset.
computational entity	database column
organizedInClass	taxa table
has exact match	scientificNameID
has broader	Identifier
is unique identifier for	scientific name
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	anyURI

taxon

Property	Value
URI	w3id.org/traits.build#taxon
preferred label preferred label	taxon taxon
alternative label alternative label	taxon taxon
description description	A circumscribed set of organisms. A group of organisms assumed to form a homogeneous unit with regard to associated trait measurements.
computational entity computational entity	database entry database column
organizedInClass	taxa table
has exact match	Taxon
has broader	Entity Characteristic
has unique identifier	taxon name scientific name scientific name id taxon id
has identifier	original taxon name trinomial binomial genus family
has property	taxon distribution establishment means
created created	01 February 2024 01 February 2024
is in scheme is in scheme	w3id.org/traits.build
datatype	string

contributors table

last name

Property	Value
URI	w3id.org/traits.build#last_name
preferred label	last name
alternative label	last_name
description	Last name of the data collector.
computational entity	database column
organizedInClass	contributors table
has exact match	family name
has broader	Identifier
is unique identifier for	contributor
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	Name

given name

Property	Value
URI	w3id.org/traits.build#given_name
preferred label	given name
alternative label	given_name
description	Given names of the data collector.
computational entity	database column
organizedInClass	contributors table
has exact match	given name
has broader	Identifier
is unique identifier for	contributor
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	Name

ORCID identifier

Property	Value
URI	w3id.org/traits.build#ORCID
preferred label	ORCID identifier
alternative label	ORCID
description	ORCID (Open Researcher and Contributor ID) for the data collector, if available.
computational entity	database column
organizedInClass	contributors table
has exact match	ORCID identifier
has broader	Identifier
is unique identifier for	contributor
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	anyURI

affiliation

Property	Value
URI	w3id.org/traits.build#affiliation
preferred label	affiliation
alternative label	affiliation
description	Affiliation of data collector.
computational entity	database column
organizedInClass	contributors table
has exact match	has Contributor Affiliation
is annotation of	contributor
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

additional role

Property	Value
URI	w3id.org/traits.build#additional_role
preferred label	additional role
alternative label	additional_role
description	Any additional roles the data collector had in the study, a field most frequently used to identify which data contributor is the contact person for the dataset.
computational entity	database column
organizedInClass	contributors table
has exact match	Contributor Role
is annotation of	contributor
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

definitions table

trait concept

Property	Value
URI	w3id.org/traits.build#trait
preferred label	trait concept
alternative label	trait
description	A collection of trait values pertaining to a distinct characteristic of a specific part of an organism (cell, tissue, organ, or whole organism).
computational entity	database column
organizedInClass	definitions table
has exact match	Standard
has unique identifier	trait identifier
has annotation	trait name label
has property	max allowed values min allowed values allowed categorical values units type
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

trait identifier

Property	Value
URI	w3id.org/traits.build#trait_concept_URI
preferred label	trait identifier
alternative label	trait_concept_URI
description	Unique identifier of the trait according to a public ontology, or a user-provided thesaurus of traits.
computational entity	database column
organizedInClass	definitions table
has exact match	traitID identifier
is unique identifier for	trait concept
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	anyURI

label

Property	Value
URI	w3id.org/traits.build#label
preferred label	label
alternative label	label
description	A concise English label for the trait.
computational entity	database column
organizedInClass	definitions table
has exact match	label preferred label trait
refers to	trait concept
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

description

Property	Value
URI	w3id.org/traits.build#description
preferred label	description
alternative label	description
description	A short description, generally ranging from 1-3 sentences that clearly indicates the trait’s scope.
computational entity	database column
organizedInClass	definitions table
has exact match	traitDescription description
is annotation of	trait concept
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

comments

Property	Value
URI	w3id.org/traits.build#comments
preferred label	comments
alternative label	comments
description	Additional notes about the scope of the trait or acceptable methods.
computational entity	database column
organizedInClass	definitions table
has exact match	comment comments
is annotation of	trait concept
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

max allowed values

Property	Value
URI	w3id.org/traits.build#allowed_values_max
preferred label	max allowed values
alternative label	allowed_values_max
description	An upper boundary for accepted numerical values.
computational entity	database column
organizedInClass	definitions table
has exact match	maxAllowedValue
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	decimal

min allowed values

Property	Value
URI	w3id.org/traits.build#allowed_values_min
preferred label	min allowed values
alternative label	allowed_values_min
description	A lower boundary for accepted numerical values.
computational entity	database column
organizedInClass	definitions table
has exact match	minAllowedValue
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	decimal

units

Property	Value
URI	w3id.org/traits.build#units
preferred label	units
alternative label	units
description	The preferred units for the trait, conforming to the Unified Code for Units of Measure (UCUM). There are often two entries for units, one that is a string and the second which links to a units of measurement axiom.
computational entity	database column
organizedInClass	definitions table
has exact match	expectedUnit
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

allowed categorical values

Property	Value
URI	w3id.org/traits.build#allowed_values_levels
preferred label	allowed categorical values
alternative label	allowed_values_levels
description	Allowed trait values for a categorical trait, including a brief description of the value.
computational entity	database column
organizedInClass	definitions table
has exact match	has narrower factorLevels
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

type

Property	Value
URI	w3id.org/traits.build#type
preferred label	type
alternative label	type
description	Type of trait, specifying if traits are categorical, numeric, or ordinal.
computational entity	database column
organizedInClass	definitions table
has exact match	valueType
created	01 February 2024
is in scheme	w3id.org/traits.build
datatype	string

Database Table Entries

Single, implicitly structured data items in a table.

context

Property	Value
URI	w3id.org/traits.build#context
preferred label	context
alternative label	context
description	The situation within which a trait measurement is made, which can help explain the measured trait value.
computational entity	database entry
has broader	Entity
created	01 February 2024
is in scheme	w3id.org/traits.build

entity

Property	Value
URI	w3id.org/traits.build#entity
preferred label	entity
alternative label	entity
description	An entity is an object (e.g., a tree, a community, an ecological process). Entities constitute the foci of observations, i.e., every observation is of exactly one entity.
computational entity	database entry
has exact match	Entity
created	01 February 2024
is in scheme	w3id.org/traits.build

individual

Property	Value
URI	w3id.org/traits.build#individual
preferred label	individual
alternative label	individual
description	An individual living organism.
computational entity	database entry
has exact match	organism
has broader	Entity
has context	life stage
created	01 February 2024
is in scheme	w3id.org/traits.build

location

Property	Value
URI	w3id.org/traits.build#location
preferred label	location
alternative label	location
description	A spatial region or named place.
computational entity	database entry
has exact match	location
has broader	Entity
has unique identifier	location id
created	01 February 2024
is in scheme	w3id.org/traits.build

method context

Property	Value
URI	w3id.org/traits.build#method_context
preferred label	method context
alternative label	method_context
description	A compment of a trait measurement protocol that is changed between individual trait measurements and might cause the measured trait values of individuals or populations to change.
computational entity	database entry
has broader	Entity contexts table
created	01 February 2024
is in scheme	w3id.org/traits.build

plot context

Property	Value
URI	w3id.org/traits.build#plot
preferred label	plot context
alternative label	plot
description	A subdivision of a location, designated because some properties differ across plots within a location, which might cause differences in measured trait values between plots.
computational entity	database entry
has broader	Entity contexts table
created	01 February 2024
is in scheme	w3id.org/traits.build

population

Property	Value
URI	w3id.org/traits.build#population
preferred label	population
alternative label	population
description	A collection of organisms, all of the same species, that live in the same place.
computational entity	database entry
has exact match	population
has broader	Entity
has context	life stage
created	01 February 2024
is in scheme	w3id.org/traits.build

temporal context

Property	Value
URI	w3id.org/traits.build#temporal_context
preferred label	temporal context
alternative label	temporal_context
description	A situation or process that varies across time and might cause the measured trait values of individuals or populations to change across time.
computational entity	database entry
has broader	Entity contexts table
created	01 February 2024
is in scheme	w3id.org/traits.build

treatment context

Property	Value
URI	w3id.org/traits.build#treatment
preferred label	treatment context
alternative label	treatment
description	An experimental manipulation that subjects different individuals or populations to different conditions, which can lead to differences in measured trait values across treatments.
computational entity	database entry
has broader	Entity contexts table
created	01 February 2024
is in scheme	w3id.org/traits.build

Rows within a database table

Rows or clusters of rows within a database table that represent measurements, observations or observation collections.

dataset

Property	Value
URI	w3id.org/traits.build#dataset
preferred label	dataset
alternative label	dataset
description	13 relational tables and lists containing all data about a dataset.
computational entity	database
has exact match	Observation Collection
has unique identifier	dataset id
created	01 February 2024
is in scheme	w3id.org/traits.build

measurement

Property	Value
URI	w3id.org/traits.build#measurement
preferred label	measurement
alternative label	measurement
description	A measurement is an assertion that a characteristic of an entity had a particular value with respect to an observation event.
computational entity	database row
has exact match	Measurement
created	01 February 2024
is in scheme	w3id.org/traits.build

measurement of entity context property

Property	Value
URI	w3id.org/traits.build#measurement_of_entity_context_property
preferred label	measurement of entity context property
alternative label	measurement_of_entity_context_property
description	A measurement made on an entity context property.
computational entity	database row
has broader	Measurement
has unique identifier	entity context id
measurement for	observation of entity context
created	01 February 2024
is in scheme	w3id.org/traits.build

measurement of location property

Property	Value
URI	w3id.org/traits.build#measurement_of_location_property
preferred label	measurement of location property
alternative label	measurement_of_location_property
description	A measurement made on a location property.
computational entity	database row
has broader	Measurement
has value	location property value
measurement for	observation of location observations at location
created	01 February 2024
is in scheme	w3id.org/traits.build

measurement of plot context property

Property	Value
URI	w3id.org/traits.build#measurement_of_plot_context_property
preferred label	measurement of plot context property
alternative label	measurement_of_plot_context_property
description	A measurement made on a plot context property.
computational entity	database row
has broader	Measurement
has unique identifier	plot context id
measurement for	observation of plot context
created	01 February 2024
is in scheme	w3id.org/traits.build

measurement of temporal context property

Property	Value
URI	w3id.org/traits.build#measurement_of_temporal_context_property
preferred label	measurement of temporal context property
alternative label	measurement_of_temporal_context_property
description	A measurement made on a temporal context property.
computational entity	database row
has broader	Measurement
has unique identifier	temporal context id
measurement for	observation of temporal context
created	01 February 2024
is in scheme	w3id.org/traits.build

measurement of treatment context property

Property	Value
URI	w3id.org/traits.build#measurement_of_treatment_context_property
preferred label	measurement of treatment context property
alternative label	measurement_of_treatment_context_property
description	A measurement made on a treatment context property.
computational entity	database row
has broader	Measurement
has unique identifier	treatment context id
has value	context property value
measurement for	observation of a treatment context
created	01 February 2024
is in scheme	w3id.org/traits.build

observation

Property	Value
URI	w3id.org/traits.build#observation
preferred label	observation
alternative label	observation
description	An Observation is a collection of measurements made at a single point in time. In traits.build it is the subset of rows within the traits data that are made on the same entity and share the same observation_id.
comment	An observation is an assertion that an entity (e.g., biological organisms, geographic locations, or environmental features, among others) was observed by an observer. An observation primarily serves to group a set of measurements together into a single "observation event". Observations are often made within a broader context. The context of an observation is given by other observations, implying that an observed entity (and specifically each corresponding measurement) contextualizes another observed entity (and its corresponding measurements). For example, an observation associated with a location may serve as context for an observation associated with an organism. In this case, the observed characteristic values of the location (such as humidity) are assumed constant for the corresponding measurements of the organism.
computational entity	database table
has exact match	Observation
has unique identifier	observation id
created	01 February 2024
is in scheme	w3id.org/traits.build

observation of entity context

Property	Value
URI	w3id.org/traits.build#observation_of_entity_context
preferred label	observation of entity context
alternative label	observation_of_entity_context
description	Observation where entity is a category of context indicating repeat observations have been made on an individual, population or species-level entity across time which might affect the entity’s measured trait values.
computational entity	database table
has broader	Observation
has unique identifier	entity context id
of entity	individual population taxon
has measurement	measurement of entity context property
characteristic for	entity context property
created	01 February 2024
is in scheme	w3id.org/traits.build

observation of location

Property	Value
URI	w3id.org/traits.build#observation_of_location
preferred label	observation of location
alternative label	observation_of_location
description	Observation of location properties at a single location.
computational entity	database table
has broader	Observation
has unique identifier	location id
of entity	location
has measurement	measurement of location property
created	01 February 2024
is in scheme	w3id.org/traits.build

observation of plot context

Property	Value
URI	w3id.org/traits.build#observation_of_plot_context
preferred label	observation of plot context
alternative label	observation_of_plot_context
description	Observation where entity is a category of context indicating variation across plots at a single location might affect the trait values measured on individual or population-level entities.
computational entity	database table
has broader	Observation
has unique identifier	plot context id
of entity	plot context
has measurement	measurement of plot context property
characteristic for	plot context property
created	01 February 2024
is in scheme	w3id.org/traits.build

observation of temporal context

Property	Value
URI	w3id.org/traits.build#observation_of_temporal_context
preferred label	observation of temporal context
alternative label	observation_of_temporal_context
description	Observation where entity is a category of context indicating repeat observations have been made on a plot, which might affect the trait values measured on individual or population-level entities.
comment	Examples of temporal contexts are `sampling season`, `sampling time of day`, and sequential `observation numbers` without any linked categorical description.
computational entity	database table
has broader	Observation
has unique identifier	temporal context id
of entity	temporal context
has measurement	measurement of temporal context property
characteristic for	temporal context property
created	01 February 2024
is in scheme	w3id.org/traits.build

observation of a treatment context

Property	Value
URI	w3id.org/traits.build#observation_of_treatment_context
preferred label	observation of a treatment context
alternative label	observation_of_treatment_context
description	Observation where entity is a context indicating experimental manipulations that might affect the trait values measured on an individual, population or species-level entities.
comment	Examples include growing temperature, growing CO2 concentrations, and nutrient amendments.
computational entity	database table
has broader	Observation
has unique identifier	treatment context id
of entity	treatment context
has measurement	measurement of treatment context property
characteristic for	treatment context property
created	01 February 2024
is in scheme	w3id.org/traits.build

observations at location

Property	Value
URI	w3id.org/traits.build#observations_at_location
preferred label	observations at location
alternative label	observations_at_location
description	Observation collection of location properties and organismal traits at a single location.
computational entity	database table
has broader	Observation Collection
has unique identifier	location id
of entity	location population individual
has measurement	measurement of location property trait measurement
created	01 February 2024
is in scheme	w3id.org/traits.build

observations from dataset

Property	Value
URI	w3id.org/traits.build#observations_from_dataset
preferred label	observations from dataset
alternative label	observations_from_dataset
description	Observation collection encompassing all observations that comprise a dataset.
computational entity	database table
has broader	Observation Collection
has unique identifier	dataset id
of entity	dataset
has measurement	trait measurement measurement of location property measurement of treatment context property measurement of plot context property measurement of entity context property measurement of temporal context property
created	01 February 2024
is in scheme	w3id.org/traits.build

observations from source

Property	Value
URI	w3id.org/traits.build#observations_from_source
preferred label	observations from source
alternative label	observations_from_source
description	Observation collection encompassing all observations for a single published or unpublished source.
computational entity	database table
has broader	Observation Collection
has unique identifier	source id
of entity	source primary citation
has measurement	trait measurement measurement of location property measurement of treatment context property measurement of plot context property measurement of entity context property measurement of temporal context property
created	01 February 2024
is in scheme	w3id.org/traits.build

observations of individual

Property	Value
URI	w3id.org/traits.build#observations_of_individual
preferred label	observations of individual
alternative label	observations_of_individual
description	Observation collection encompassing all observations on a single individual.
computational entity	database table
has broader	Observation Collection
has unique identifier	individual id
of entity	individual
has measurement	trait measurement
created	01 February 2024
is in scheme	w3id.org/traits.build

observations of population

Property	Value
URI	w3id.org/traits.build#observations_of_population
preferred label	observations of population
alternative label	observations_of_population
description	Observation collection encompassing all observations on a single population.
computational entity	database table
has broader	Observation Collection
has unique identifier	population id
of entity	population
has measurement	trait measurement
created	01 February 2024
is in scheme	w3id.org/traits.build

observations of taxon

Property	Value
URI	w3id.org/traits.build#observations_of_taxon
preferred label	observations of taxon
alternative label	observations_of_taxon
description	Observation collection encompassing all observations on a single taxon within a single dataset.
comment	An observation collection is a container for a set of observations.
computational entity	database table
has broader	Observation Collection
has unique identifier	taxon name
of entity	taxon
has measurement	trait measurement
created	01 February 2024
is in scheme	w3id.org/traits.build

trait measurement

Property	Value
URI	w3id.org/traits.build#trait_measurement
preferred label	trait measurement
alternative label	trait_measurement
description	A measurement made on a trait.
computational entity	database row
has broader	Measurement
has value	value
measurement for	observation observations from dataset observations from source observations of taxon observations at location observations of population observations of individual
created	01 February 2024
is in scheme	w3id.org/traits.build

3. Acknowledgements

We are grateful to S Cox, J Smillie, K Levett, M Barlow, and C Brady for useful conversations. The AusTraits project received investment (https://doi.org/10.47486/TD044, https://doi.org/10.47486/DP720) from the Australian Research Data Commons (ARDC). The ARDC is funded by the National Collaborative Research Infrastructure Strategy (NCRIS).

Release 0.1.0

Abstract

Table of Contents

1. Introduction

2. Traits.build data model

Database

Database Tables

traits table

locations table

contexts table

methods table

excluded data table

taxonomic updates table

taxa table

contributors table

sources table

definitions table

schema

metadata table

build info

Database Table Columns

traits table

dataset id

taxon name

observation id

trait name

value

unit

entity type

value type

basis of value

replicates

basis of record

life stage

population id

individual id

repeat measurements id

temporal context id

source id

location id

entity context id

plot context id

treatment context id

collection date

measurement remarks

method id

method context id

original taxon name

locations table

location name

location property

location property value

latitude (deg)

longitude (deg)

elevation (m)

contexts table

context property

context property category

context property value

context property value description

context propety link id

context propety link vals

treatment context property

plot context property

entity context property

temporal context property

method context property

methods table

methods

dataset description

dataset sampling strategy

source primary key

source primary citation

source secondary key

source secondary citation

source original dataset key

source original dataset citation

data collectors

assistants

dataset curators