traits.build Data Model

Release 1.0.0

Latest version:
https://w3id.org/traits.build/index.html
This version:
https://w3id.org/traits.build/release/1.0.0/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:
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.

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. 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 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
is top concept 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
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
    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
    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
    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
    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
    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
    has exact match
  • Taxon
  • created 01 February 2024
    is in scheme w3id.org/traits.build

    contributors table

    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
    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
    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
    created 01 February 2024
    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.
    computational entity metadata
    organizedInClass
    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
    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
    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
    has broader
  • Identifier
  • is unique identifier for
  • observation
  • created 01 February 2024
    is in scheme w3id.org/traits.build

    trait name

    value

    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
    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
    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
    has exact match
  • Base Characteristic Qualifier
  • created 01 February 2024
    is in scheme w3id.org/traits.build
    datatype string

    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
    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
    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
    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
    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
    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
    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
    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

    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
    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
    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
    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
    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
    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
    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
    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
    has broader
  • Identifier
  • created 01 February 2024
    is in scheme w3id.org/traits.build
    datatype integer

    original taxon name

    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
    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
    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

    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
    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
    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)

    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
    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
    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

    context property value description

    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
    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
    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
    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

    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
    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
    has close match
  • Protocol
  • has broader
  • Protocol
  • created 01 February 2024
    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
    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

    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
    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
    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
    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
    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
    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

    assistants

    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
    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

    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
    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
    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
    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
    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
    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
    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

    family

    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
    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
    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
    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
    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

    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
    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

    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
    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

    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
    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

    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
    has exact match
  • traitDescription
  • description
  • is annotation of
  • trait concept
  • created 01 February 2024
    is in scheme w3id.org/traits.build
    datatype string

    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
    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
    has exact match
  • has narrower
  • factorLevels
  • created 01 February 2024
    is in scheme w3id.org/traits.build
    datatype string

    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 broader
    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
    created 01 February 2024
    is in scheme w3id.org/traits.build

    individual

    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.
    computational entity database entry
    has broader
    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
    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
    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
    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
    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

    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
    created 01 February 2024
    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
    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
    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

    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
    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
    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
    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

    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
    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

    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).