This is the documentation of the Ecological Traitdata Standard (ETS), version 0.4

This defined vocabulary aims at providing all essential columns for raw data of functional trait measurements for ecological research. Most terms relate to terms from the Darwin Core Standard and it’s Extensions (terms of DWC are referenced thus in field ‘Refines’; the full Darwin Core Standard can be found here: http://rs.tdwg.org/dwc/terms/index.htm)

The glossary of terms is ordered into a core section with essential columns for trait data, extensions which are allowing to provide additional layers of information, as well as a vocabulary for metadata information of particular importance for trait data. A final section provides defined terms for lists of trait definitions, also termed a Trait Thesaurus.

Extensions:

We provide three extensions of the vocabulary, that allow for additional information on the trait measurement.

the Occurrence extension contains information on the level of individual specimens, such as date and location and method of sampling and preservation, or physiological specifications of the phenotype, such as sex, life stage or age.
the MeasurementOrFact extension takes information at the level of single measurements or reported values, such as the original literature from where the value is cited, the method of measurement or statistical method of aggregation.
The BiodiversityExploratories extension provides columns for localisation for trait data from the Biodiversity Exploratories sites (www.biodiversity-exploratories.de).

Structure of trait data:

The traitdata standard implies that the trait data should be stored in a long table format containing one measurement per row described by the column terms provided in the core section. (see our Methods paper for further considerations on data structure and format).

There are two ways of integrating the information provided by the extensions:

within the same data file: additional columns are provided to describe the properties concerning the measurement or the occurrence of the specimen. The output file may be stored as a csv or txt table or an excel spreadsheet.
in separate data files: the main file refers to additional data files in the fields measurementID or occurrenceID. This is usually the case if the occurrences are externally documented, for instance as specimens from a museum. This also applies if the data are stored as an Excel spreadsheet or as a Darwin Core Archive (as proposed for TraitBank).

The R package ‘traitdataform’ (https://www.github.com/fdschneider/traitdataform) provides tools to transfer heterogeneous datasets into a longtable format and to create standardized taxa and trait columns, based on public ontologies.

This list of terms will also be available as

a csv/txt/xlsx table file which will be provided for download on BExIS including full documentation in the metadata (for manual use, this may be uploaded to BExIs as soon it’s ready), and
a machine readable glossary of terms compliant with semantic web standards (OWL format) and accessible via an API (hosted on GFBio Terminology Server).

defined terms:

Core traitdata columns

For the essential primary data (trait value, taxon assignment, trait name), the trait data standard recommends to report the original naming and value scheme as used by the data provider. However, to ensure compatibility with other datasets, the original data provider’s information should be doubled into standardized columns indexed by appending Std to the column name. This ensures compatibility on the provider’s side and transparency for data users on the reported measurements and facts, and enables checking for inconsistencies and misspellings in the complete dataset provided by the author. If provided, the standardized fields allow merging heterogeneous data sources into a single table to perform further analyses. This practice of double bookkeeping of trait data has successfully established for the TRY database on plant traits, for instance (Kattge ..).

By linking to (public) ontologies via the field taxonID, further taxonomic information can be extracted for analysis. Alternatively, taxonID may also link to an accompanying datasheet that contains information on the taxonomic resolution or specification of the observation.

Similarly, linking to trait terminologies (a ‘Thesaurus’) via the field traitID allows an unambiguous interpretation of the trait measurement. If no online ontology is available, an accompanying dataset should specify the trait definition. For setting up such a Thesaurus, we propose the use of terms provided in section ‘Traitlist’ below.

	scientificName
valueType	character
vocabulary
Identifier	http://ecologicaltraitdata.github.io/TraitDataStandard/#scientificname
Refines	http://rs.tdwg.org/dwc/terms/scientificName
Replaces	NA
Version	v0.3
DateIssued	7/7/2017
DateModified
Definition	Original character string provided as species name by the data owner (kept for reference and continueity)
Comment	Can be equal to scientificNameStd. Authors may use abbreviations, or use underscores to separate genus and species name.

	traitID
valueType	factor
vocabulary
Identifier	http://ecologicaltraitdata.github.io/TraitDataStandard/#traitid
Refines
Replaces	NA
Version	v0.3
DateIssued	7/7/2017
DateModified
Definition	Unique identifier of the trait following a public or user-provided thesaurus of traits.
Comment

	measurementDeterminedDate
valueType	Date
vocabulary
Identifier	http://ecologicaltraitdata.github.io/TraitDataStandard/#measurementDeterminedDate
Refines	http://rs.tdwg.org/dwc/terms/measurementDeterminedDate
Replaces	NA
Version	v0.3
DateIssued	7/7/2017
DateModified
Definition	The date of the measurement. Also kept as a co-factor. Use format “YYYY-MM-DD hh:mm TIMEZONE”. Not to confuse with year, month, day columns which are reserved for the date of sampling (may be identical, though).
Comment	Examples: “1963-03-08T14:07-0600” is 8 Mar 1963 2:07pm in the time zone six hours earlier than UTC, “2009-02-20T08:40Z” is 20 Feb 2009 8:40am UTC, “1809-02-12” is 12 Feb 1809, “1906-06” is Jun 1906, “1971” is just that year, “2007-03-01T13:00:00Z/2008-05-11T15:30:00Z” is the interval between 1 Mar 2007 1pm UTC and 11 May 2008 3:30pm UTC, “2007-11-13/15” is the interval between 13 Nov 2007 and 15 Nov 2007. For discussion see http://terms.tdwg.org/wiki/dwc:measurementDeterminedDate

	aggregateMeasure
valueType	logical
vocabulary
Identifier	http://ecologicaltraitdata.github.io/TraitDataStandard/#aggregateMeasure
Refines
Replaces	NA
Version	v0.3
DateIssued	7/7/2017
DateModified
Definition	Is measurementValue reporting an individual measurement or an aggregate Measure? Takes a binary entry: TRUE or FALSE
Comment	This is flagging aggregate data in an unambiguous way. Aggregate measures are often reported for repeated measures, e.g. replicate measurements of leaf size from a single plant individual or for grouped measurement, e.g. for weightings of a counted number of specimens (e.g. leaves or small organisms).

	individualCount
valueType	integer
vocabulary
Identifier	http://ecologicaltraitdata.github.io/TraitDataStandard/#individualCount
Refines	http://rs.tdwg.org/dwc/terms/individualCount
Replaces	NA
Version	v0.3
DateIssued	7/7/2017
DateModified
Definition	If measurement is an aggregate measure of multiple individuals or specimens, report number of specimens as count, i.e. integer number. Defaults to 1
Comment	Examples: “1”, “25”. For discussion see http://terms.tdwg.org/wiki/dwc:individualCount

	dispersion
valueType	numeric
vocabulary
Identifier	http://ecologicaltraitdata.github.io/TraitDataStandard/#dispersion
Refines
Replaces	NA
Version	v0.3
DateIssued	7/7/2017
DateModified
Definition	If aggregate measure of multiple individuals or specimens, the numeric value of dispersion (variance or standard deviation) for the mean value reported in measurementValue_user (no unit conversion is provided by the R-package!). Defaults to 0. If a value is provided, report the statistical method in the field statisticalMethod.
Comment

	traitUnit
valueType	character
vocabulary
Identifier	http://ecologicaltraitdata.github.io/TraitDataStandard/#traitunit
Refines	http://rs.tdwg.org/dwc/terms/measurementUnit
Replaces	NA
Version	v0.3
DateIssued	7/7/2017
DateModified
Definition	Reports the unit that the author’s raw data were measured in, if applicable (only for numeric values). For unitless numerical values, use ‘unitless’ in this field. For factorial values, leave empty or provide NA.
Comment	For numerical values report unit in format for lengths “mm”, for volumes “mm3” / “mm^3”, areas “mm2” / “mm^2”, for movement “m/s”, or for volume to surface ratios: “mm3/mm2”

	scientificNameStd
valueType	character
vocabulary
Identifier	http://ecologicaltraitdata.github.io/TraitDataStandard/#scientificnamestd
Refines	http://rs.tdwg.org/dwc/terms/scientificName
Replaces	NA
Version	v0.3
DateIssued	7/7/2017
DateModified
Definition	Full scientific name (with authorship and date information if known). It should be an accepted taxon name according to a published taxonomy (provided in taxonID).
Comment	Provide reference taxonomy in metadata of the dataset. Examples: “Coleoptera” (order), “Vespertilionidae” (family), “Manis” (genus), “Ctenomys sociabilis” (genus + specificEpithet), “Ambystoma tigrinum diaboli” (genus + specificEpithet + infraspecificEpithet), “Roptrocerus typographi (Györfi, 1952)” (genus + specificEpithet + scientificNameAuthorship), “Quercus agrifolia var. oxyadenia (Torr.) J.T. Howell” (genus + specificEpithet + taxonRank + infraspecificEpithet + scientificNameAuthorship). For discussion see http://terms.tdwg.org/wiki/dwc:scientificName

	traitValueStd
valueType	character
vocabulary
Identifier	http://ecologicaltraitdata.github.io/TraitDataStandard/#traitvaluestd
Refines	http://rs.tdwg.org/dwc/terms/measurementValue
Replaces	NA
Version	v0.3
DateIssued	7/7/2017
DateModified
Definition	Standardised measured value or factor level for this species trait. Numerical values must use the correct unit. Factor levels must be compliant with the thesaurus of traits.
Comment	Using “.” as a decimal separator! The standardized data values or factor levels must correspond to the expected units and factor levels of the trait thesaurus, e.g. “32.423”, “female”, “apter”, “3”

	taxonRank
valueType	factor
vocabulary	domain; kingdom; subkingdom; superphylum; phylum; subphylum; superclass; class; subclass; supercohort; cohort; subcohort; superorder; order; subordern; infraorder; superfamily; family; subfamily; tribe; subtribe; genus; subgenus; section; subsection; series; subseries; speciesAggregate; species; subspecificAggregate; subspecies; variety; cultivar; strain
Identifier	http://ecologicaltraitdata.github.io/TraitDataStandard/#taxonrank
Refines	http://rs.tdwg.org/dwc/terms/taxonRank
Replaces	NA
Version	v0.3
DateIssued	7/7/2017
DateModified
Definition	The taxonomic rank of the most specific name in the scientificName. Recommended best practice is to use a controlled vocabulary.
Comment	This is to clarify cases where information is not given on a species level. Examples: “subspecies”, “varietas”, “forma”, “species”, “genus”.

Ecological Traitdata Standard

Florian D. Schneider, Nadja K. Simons, Caterina Penone, Andreas Ostrowski

12 Mai 2017

Extensions:

Structure of trait data:

defined terms:

Core traitdata columns

scientificName

traitName

traitID

traitValue

traitUnit

scientificNameStd

traitNameStd

traitValueStd

traitUnitStd

taxonRank

kingdom

order

taxonID

measurementID

occurrenceID

warnings

Extension: Measurement or Fact

basisOfRecord

basisOfRecordDescription

references

measurementResolution

measurementMethod

measurementDeterminedBy

measurementDeterminedDate

measurementRemarks

aggregateMeasure

individualCount

dispersion

measurementValue_min

measurementValue_max

measurementAccuracy

statisticalMethod

Extension: Occurrence

sex

lifeStage

age

morphotype

eventID

preparations

samplingProtocol

year

month

day

eventDate

locationID

habitat

decimalLongitude

decimalLatitude

elevation

geodeticDatum

verbatimLocality

country

countryCode

occurenceRemarks

Extension: Biodiversity Exploratories

OriginExploratories

ExploratoriesPlotID

Exploratory

ExploType

Metadata vocabulary

rightsHolder

bibliographicCitation

license

datasetID

datasetName

author

version

Terms for Traitlists (a ‘Trait Thesaurus’)

traitID

traitName

broaderTerm

narrowerTerm

valueType

`scientificName`

`traitName`

`traitID`

`traitValue`

`traitUnit`

`scientificNameStd`

`traitNameStd`

`traitValueStd`

`traitUnitStd`

`taxonRank`

`kingdom`

`order`

`taxonID`

`measurementID`

`occurrenceID`

`warnings`

`basisOfRecord`

`basisOfRecordDescription`

`references`

`measurementResolution`

`measurementMethod`

`measurementDeterminedBy`

`measurementDeterminedDate`

`measurementRemarks`

`aggregateMeasure`

`individualCount`

`dispersion`

`measurementValue_min`

`measurementValue_max`

`measurementAccuracy`

`statisticalMethod`

`sex`

`lifeStage`

`age`

`morphotype`

`eventID`

`preparations`

`samplingProtocol`

`year`

`month`

`day`

`eventDate`

`locationID`

`habitat`

`decimalLongitude`

`decimalLatitude`

`elevation`

`geodeticDatum`

`verbatimLocality`

`country`

`countryCode`

`occurenceRemarks`

`OriginExploratories`

`ExploratoriesPlotID`

`Exploratory`

`ExploType`

`rightsHolder`

`bibliographicCitation`

`license`

`datasetID`

`datasetName`

`author`

`version`

`traitID`

`traitName`

`broaderTerm`

`narrowerTerm`

`valueType`

`traitUnit`

`factorLevels`

`maxAllowedValue`

`minAllowedValue`

`factorLevels`

`traitDescription`

`Comments`

`relationSource`

`source`