traits.build Data Model

Release 1.2.0

Latest version:
https://w3id.org/traits.build/index.html
This version:
https://w3id.org/traits.build/release/1.2.0/index.html
Previous version:
https://w3id.org/traits.build/release/1.1.0/index.html
Authors:
Elizabeth Wenk, Daniel Falster
Contributors:
David Coleman, Sophie Yang
Serializations:
JSON-LD N-Triples N-Quads TTL
License:
http://purl.org/NET/rdflicense/cc-by4.0
Source:

10.5281/zenodo.8040789

JSON-LD

Contributing:
contributions welcome
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. Since release 1.2.0 every OBOE relation is also expressed against SOSA/SSN and the TERN Ontology, and measurement terms are matched to the Darwin Core MeasurementOrFact and Assertion terms used by the Darwin Core Data Package.

Table of Contents

  1. Introduction
  2. traits.build data model: The terms within the formal traits.build ontology
  3. 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. Each OBOE class used is also matched to its counterpart in SOSA/SSN (following the published SOSA-to-OBOE alignment) and in the TERN Ontology, the SOSA profile used by TERN and the Australian Biodiversity Information Standard; trait-measurement terms are additionally matched to the Darwin Core MeasurementOrFact terms (used by Darwin Core Archives) and Assertion terms (used by the Darwin Core Data Package), and the ETS terms statisticalMethod and aggregateMeasure are recorded as the only published counterparts of value_type. Where a term has no counterpart in any of these standards, its comment says so. Where the strength of a match is not obvious from the two definitions, the term’s editorial note gives the reason. 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:

  1. 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
  2. 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
  3. 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
  4. 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.
  5. 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 traits.build database
creator Daniel Falster
creator Elizabeth Wenk
creator Sophie Yang
created 2024-02-01

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.
comment A traits.build database as a whole; no single counterpart in Darwin Core, DwC-DP, ETS, SOSA or TERN. See the dataset term for the observation-collection reading.
created 2024-02-01
is in scheme traits.build
is top concept in scheme traits.build

Database Tables

The traits.build output tables

traits table

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
location
Site
created 2024-02-01
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
has related match Attribute
Measurement Or Fact
created 2024-02-01
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
Protocol
Procedure
created 2024-02-01
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.
comment Same structure as the traits table plus an error column; no counterpart in Darwin Core, DwC-DP, ETS, SOSA or TERN.
computational entity database table
organizedInClass traits.build database
has related match traits table
created 2024-02-01
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
has related match Identification
Verbatim Identification
created 2024-02-01
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
has close match Taxon
created 2024-02-01
is in scheme w3id.org/traits.build

contributors table

identifiers table

Property Value
URI w3id.org/traits.build#traits.build-identifiers
preferred label identifiers table
alternative label identifiers
description A table containing details on identifiers that cross-references observations between the two dataframes using combinations of the variables dataset_id and observation_id.
comment Includes information about specimen identifiers
computational entity database table
organizedInClass traits.build database
has related match identifier
created 2025-06-08
is in scheme w3id.org/traits.build

sources table

definitions table

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.
comment Internal to traits.build; no counterpart in Darwin Core, DwC-DP, ETS, SOSA or TERN.
computational entity metadata
organizedInClass traits.build database
created 2024-02-01
is in scheme w3id.org/traits.build

metadata table

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.
comment Internal to traits.build; no counterpart in Darwin Core, DwC-DP, ETS, SOSA or TERN.
computational entity metadata
organizedInClass traits.build database
created 2024-02-01
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
identifiers table
has exact match Dataset ID
dataset ID
has broader Identifier
is unique identifier for observations from dataset
created 2024-02-01
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.
editorial note Related to dwc:scientificName and ets:scientificName, which carry authorship where taxon_name does not; scientific_name in the taxa table is the exact match to dwc:scientificName. Close to dwc:acceptedNameUsage, as in 1.1.0: where possible taxon_name is the currently accepted name, which is what acceptedNameUsage holds, without its authorship. Reviewed on #276.
computational entity database column
organizedInClass traits table
taxa table
taxonomic updates table
has close match acceptedNameUsage
has related match Scientific Name
scientific name
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 2024-02-01
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
identifiers table
has related match Parent Measurement ID
has broader Identifier
is unique identifier for observation
created 2024-02-01
is in scheme w3id.org/traits.build

trait name

value

Property Value
URI w3id.org/traits.build#trait_value
preferred label value
alternative label value
description The measured value of a trait.
editorial note Exact to dwc:measurementValue, although Darwin Core measurements are often read as species-level. The term is defined as the value of the measurement, fact, characteristic, or assertion, and a MeasurementOrFact record can attach to an Occurrence (one organism) as well as to a Taxon. Questioned and kept on #276.
computational entity database column
organizedInClass traits table
has exact match traitValue
measurementValue
Assertion Value
has close match has simple result
has broader Measured Value
Result
Value
created 2024-02-01
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.
editorial note Close to tern:unit, which takes a QUDT unit IRI where unit holds the unit as text. dwc:measurementUnit and dwc:assertionUnit hold text and are exact matches. Reviewed on #276.
computational entity database column
organizedInClass traits table
has exact match Unit
traitUnit
Measurement Unit
Assertion Unit
has close match Unit
unit
created 2024-02-01
is in scheme w3id.org/traits.build

entity type

value type

basis of value

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
has close match Individual Count
created 2024-02-01
is in scheme w3id.org/traits.build
datatype integer

basis of record

life stage

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 related match Organism ID
has broader Identifier
is unique identifier for observations of population
created 2024-02-01
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.
editorial note Close, not exact, to dwc:organismID: a Darwin Core organism may be a group of organisms (see dwc:Organism), where individual_id identifies one. Reviewed on #276.
computational entity database column
organizedInClass traits table
has close match Organism ID
has broader Identifier
is unique identifier for observations of individual
created 2024-02-01
is in scheme w3id.org/traits.build
datatype integer

repeat measurements id

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 2024-02-01
is in scheme w3id.org/traits.build
datatype integer

source id

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 exact match Location ID
has broader Identifier
is unique identifier for observations at location
created 2024-02-01
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 2024-02-01
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 2024-02-01
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
locations table
has broader Identifier
is unique identifier for measurement of treatment context property
created 2024-02-01
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
editorial note Close, not exact, to dwc:eventDate, ets:eventDate and the other date terms: when the sampling date is unknown, collection_date holds the publication date, which is not when the event occurred. Reviewed on #276.
computational entity database column
organizedInClass traits table
has close match Measurement Determined Date
Assertion Effective Date
phenomenon time
result date time
Event Date
eventDate
has broader Measured Value
measurementValue
characteristic for observation
created 2024-02-01
is in scheme w3id.org/traits.build
datatype date

measurement remarks

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 related match Protocol ID
has broader Identifier
is unique identifier for methods
is specialisation of methods
created 2024-02-01
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 2024-02-01
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.
editorial note Exact to dwc:verbatimIdentification. Close, not related, to ets:verbatimScientificName, the species name or taxon identifier as originally supplied by the data provider: unlike dwc:scientificName its definition does not call for authorship. Reviewed on #276.
computational entity database column
organizedInClass traits table
taxonomic updates table
has exact match Verbatim Identification
has close match verbatim scientific name
has broader label
preferred label
created 2024-02-01
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 close match Locality
has broader label
preferred label
created 2024-02-01
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.
editorial note dwc:measurementType is broader: it names the type of any measurement, where location_property names only a property of a location. Reviewed on #276.
computational entity database column
organizedInClass locations table
has broader Characteristic
Observable Property
Measurement Type
has value location property value
characteristic for location
created 2024-02-01
is in scheme w3id.org/traits.build
datatype string

location property value

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 Decimal Latitude
has broader Measured Value
measurementValue
characteristic for location
is specialisation of location property
created 2024-02-01
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 Decimal Longitude
has broader Measured Value
measurementValue
characteristic for location
is specialisation of location property
created 2024-02-01
is in scheme w3id.org/traits.build
datatype decimal

elevation (m)

contexts table

context property

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 2024-02-01
is in scheme w3id.org/traits.build
datatype string

context property value

context property value description

treatment context property

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 close match Attribute
has broader Characteristic
has unique identifier plot context id
is specialisation of context property
created 2024-02-01
is in scheme w3id.org/traits.build
datatype string

entity context property

temporal context property

method context property

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 exact match Measurement Method
measurement method
has close match Protocol
Assertion Protocols
Protocol
Procedure
Method
has broader Protocol
created 2024-02-01
is in scheme w3id.org/traits.build
datatype string

dataset description

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 Sampling Protocol
has broader Procedure
refers to observations from dataset
created 2024-02-01
is in scheme w3id.org/traits.build
datatype string

source primary key

source primary citation

source secondary key

source secondary citation

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 2024-02-01
is in scheme w3id.org/traits.build
datatype string

source original dataset citation

data collectors

assistants

dataset curators

contributor

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 2024-02-01
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 Taxon Rank
is property of aligned name
created 2024-02-01
is in scheme w3id.org/traits.build
datatype string

taxa table

taxonomic dataset

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 Taxon Rank
is property of taxon name
created 2024-02-01
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 Infraspecific Epithet
has broader label
preferred label
is identifier for taxon
created 2024-02-01
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 Specific Epithet
has broader label
preferred label
is identifier for taxon
created 2024-02-01
is in scheme w3id.org/traits.build
datatype string

genus

family

taxon distribution

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.
editorial note Close, not exact, to dwc:establishmentMeans: Darwin Core applies establishmentMeans to an organism at a place and time; a traits.build database records it once per taxon.
computational entity database column
organizedInClass taxa table
has close match Establishment Means
is property of taxon
created 2024-02-01
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 Taxonomic Status
is property of taxon name
created 2024-02-01
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 Taxon ID
has broader Identifier
is unique identifier for taxon name
created 2024-02-01
is in scheme w3id.org/traits.build
datatype anyURI

scientific name

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 Scientific Name ID
has broader Identifier
is unique identifier for scientific name
created 2024-02-01
is in scheme w3id.org/traits.build
datatype anyURI

taxon

Property Value
URI w3id.org/traits.build#taxon
preferred label taxon
alternative label taxon
description A group of organisms (sensu http://purl.obolibrary.org/obo/OBI_0100026) considered by taxonomists to form a homogeneous unit.
editorial note Close, not exact, to tern:Taxon. TERN takes the Darwin Core definition but makes tern:Taxon a subclass of tern:Value: a taxon is the result of an identification. Here a taxon is the thing observed, a feature of interest. The meaning is the same, the role in the model is different. dwc:Taxon has no such role and is the exact match. Reviewed on #276.
computational entity database entry
organizedInClass taxa table
has exact match Taxon
has close match Taxon
has broader Entity
Feature of Interest
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 2024-02-01
is in scheme w3id.org/traits.build

contributors table

last name

given name

ORCID identifier

affiliation

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 2024-02-01
is in scheme w3id.org/traits.build
datatype string

identifiers table

identifier type

institution code

identifier value

Property Value
URI w3id.org/traits.build#identifier_value
preferred label identifier value
alternative label identifier_value
description A sequence of characters that links an observation within a traits.build database to additional information about observed entity in another database.
computational entity database column
organizedInClass identifiers table
has close match identifier
has broader Identifier
has identifier identifier type
institution code
created 2025-06-08
is in scheme w3id.org/traits.build
datatype string

definitions table

trait concept

trait identifier

label

description

comments

max allowed values

min allowed values

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
has close match Measurement Unit
has related match Unit
is property of trait concept
created 2024-02-01
is in scheme w3id.org/traits.build
datatype string

allowed categorical values

type

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 close match Attribute
has broader Entity
created 2024-02-01
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.
editorial note Exact to sosa:FeatureOfInterest but close to tern:FeatureOfInterest. TERN’s SHACL shapes (TERN Ontology 0.9.0) require every tern:FeatureOfInterest to have a tern:featureType and a dataset; an entity requires neither. Reviewed on #276.
computational entity database entry
has exact match Entity
Feature of Interest
has close match Feature of Interest
created 2024-02-01
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.
editorial note Close to dwc:Organism, which is a particular organism or defined group of organisms considered to be taxonomically homogeneous, where an individual is one organism. individual_id is close to dwc:organismID for the same reason.
computational entity database entry
has exact match organism
has close match Organism
plant individual
has broader Entity
Feature of Interest
has context life stage
created 2024-02-01
is in scheme w3id.org/traits.build

location

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.
editorial note Related, not close, to sosa:Procedure and tern:Procedure. A method context is one component of a protocol that varies between measurements; the procedure itself is recorded in methods, which is the close match to both. Reviewed on #276.
computational entity database entry
has related match Procedure
Procedure
has broader Entity
contexts table
created 2024-02-01
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 related match Site
has broader Entity
contexts table
Feature of Interest
created 2024-02-01
is in scheme w3id.org/traits.build

population

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 related match Site Visit
has broader Entity
contexts table
created 2024-02-01
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
Feature of Interest
created 2024-02-01
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

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.
editorial note Exact to sosa:Observation but close to tern:Observation. TERN’s SHACL shapes (TERN Ontology 0.9.0) require every tern:Observation to have a dataset, procedure, phenomenon time, result date-time, observed property, result and feature of interest. A measurement requires none of these (many records have no date), so it is as general as the SOSA class and broader than the TERN one. Reviewed on #276.
computational entity database row
has exact match Measurement
Observation
Measurement Or Fact
has close match Observation
has broader Assertion
created 2024-02-01
is in scheme w3id.org/traits.build

measurement of entity context property

measurement of location property

measurement of plot context property

measurement of temporal context property

measurement of treatment context property

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
Observation Collection
has close match Observation Collection
has related match Parent Measurement ID
has unique identifier observation id
created 2024-02-01
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
Observation Collection
has unique identifier entity context id
of entity individual
population
taxon
has measurement measurement of entity context property
characteristic for entity context property
created 2024-02-01
is in scheme w3id.org/traits.build

observation of location

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
Observation Collection
has unique identifier plot context id
of entity plot context
has measurement measurement of plot context property
characteristic for plot context property
created 2024-02-01
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
Observation Collection
has unique identifier temporal context id
of entity temporal context
has measurement measurement of temporal context property
characteristic for temporal context property
created 2024-02-01
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
Observation Collection
has unique identifier treatment context id
of entity treatment context
has measurement measurement of treatment context property
characteristic for treatment context property
created 2024-02-01
is in scheme w3id.org/traits.build

observations at location

observations from dataset

observations from source

observations of individual

observations of population

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
Observation Collection
has unique identifier taxon name
of entity taxon
has measurement trait measurement
created 2024-02-01
is in scheme w3id.org/traits.build

trait measurement

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).