From 51b1e8da866ade2b641075b77594e48dbc2fda45 Mon Sep 17 00:00:00 2001 From: Florian Schneider Date: Wed, 21 Nov 2018 11:17:18 +0100 Subject: [PATCH] create release version v0.9.1 --- CONTRIBUTING.md | 4 + ETS.csv | 47 ++++-- README.md | 3 +- VERSIONS.md | 14 ++ ets.owl | 394 ++++++++++++++++++++++++++++++++++++------------ 5 files changed, 351 insertions(+), 111 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 0c507a4..e3e40a8 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -3,6 +3,10 @@ The Ecological Traitdata Standard Vocabulary is under continuous and open community development, hosted on [Github](https://github.com/EcologicalTraitData/ETS). It invites submissions of new terms and extensions, and revisions of existing terms from a wide community of researchers working with trait data. Please refer to the [Github Issues page](https://github.com/EcologicalTraitData/ETS/issues) for discussion and revision of individual terms, and settle the issue here before filing a pull-request that implements an update. +# Name scheme for new terms + +New terms should be labelled using lower camel case (i.e. with a lower case letter at the start and then upper case letters to separate words, e.g. "camelCase"). For new classes, (i.e. names of extensions) use upper camel case (e.g. "Metadata"). This is conventional for ontologies for use in the semantic web. + # File format The original source file is [ETS.csv](https://github.com/EcologicalTraitData/ETS/blob/master/ETS.csv), defining the terms and containing the URIs. When editing this file, make sure it is saved with **comma as field separator**, **decimal points**, and using **double quotes** to envelope long text character strings. Standard Date format is ISO 8601, YYYY-MM-DD. diff --git a/ETS.csv b/ETS.csv index 9771160..778747a 100644 --- a/ETS.csv +++ b/ETS.csv @@ -1,16 +1,16 @@ Namespace,columnName,valueType,Identifier,Refines,Replaces,Deprecated,ReplacedBy,FirstIssuedIn,DateIssued,DateModified,Definition,Comment -Traitdata,scientificName,character,http://terminologies.gfbio.org/terms/ETS/scientificname,http://rs.tdwg.org/dwc/terms/scientificName,,,,v0.8,2017-07-07,2018-05-29,Original character string provided as species name by the data owner (kept for reference and continuity),"Can be equal to scientificNameStd. Authors may use abbreviations, or use underscores to separate genus and species name. " -Traitdata,traitName,character,http://terminologies.gfbio.org/terms/ETS/traitname,http://rs.tdwg.org/dwc/terms/measurementType,,,,v0.8,2017-07-07,,Name of the trait as used by the data provider (kept for compatibility on provider side). ,"This can be a short name or user defined coded trait name. However, it is recommended to provide definition of the user provided trait names in the metadata. " -Traitdata,traitID,factor,http://terminologies.gfbio.org/terms/ETS/traitid,,,,,v0.8,2017-07-07,2018-05-29,"Unique identifier of the trait according to a public ontology, or a user-provided thesaurus of traits. ",Examples: TO:0000181; TOP103; http://top-thesaurus.org/annotationInfo?viz=1&&trait=Seed_mass; -Traitdata,traitValue,character,http://terminologies.gfbio.org/terms/ETS/traitvalue,http://rs.tdwg.org/dwc/terms/measurementValue,,,,v0.8,2017-07-07,,Measured raw value or factor level for this species trait as measured and provided by the author. ,"Must respect the unit given in 'measurementUnit_user' for numerical traits. For categorical traits, the factor levels should be harmonized across the dataset and explained in the metadata. " -Traitdata,traitUnit,character,http://terminologies.gfbio.org/terms/ETS/traitunit,http://rs.tdwg.org/dwc/terms/measurementUnit,,,,v0.8,2017-07-07,,"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. ","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""" -Traitdata,scientificNameStd,character,http://terminologies.gfbio.org/terms/ETS/scientificnamestd,http://rs.tdwg.org/dwc/terms/scientificName,,,,v0.8,2017-07-07,2017-11-01,"The full name, with authorship and date information if known. This should resolve to the currently valid (zoological) or accepted (botanical) taxon.","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" -Traitdata,traitNameStd,factor,http://terminologies.gfbio.org/terms/ETS/traitnamestd,http://rs.tdwg.org/dwc/terms/measurementType,,,,v0.8,2017-07-07,,Descriptive Name of the trait reported. This should follow the controlled vocabulary of a thesaurus of traits available online or published along with the dataset. ,"Accompanying this, the traitID should provide an unambiguous link to the trait definition in the thesaurus or supplementary dataset. " -Traitdata,traitValueStd,character,http://terminologies.gfbio.org/terms/ETS/traitvaluestd,http://rs.tdwg.org/dwc/terms/measurementValue,,,,v0.8,2017-07-07,,Standardized 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. ,"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""" -Traitdata,traitUnitStd,character,http://terminologies.gfbio.org/terms/ETS/traitunitstd,http://rs.tdwg.org/dwc/terms/measurementUnit,,,,v0.8,2017-07-07,,The units associated with the measurementValue. The expected standard unit for this trait as defined in the traitlist/ thesaurus. ,"Recommended best practice is to use the International System of Units (SI). Examples: ""mm"", ""C"", ""km"", ""ha"". For discussion see http://terms.tdwg.org/wiki/dwc:measurementUnit" +Traitdata,scientificName,character,http://terminologies.gfbio.org/terms/ETS/scientificName,http://rs.tdwg.org/dwc/terms/scientificName,http://terminologies.gfbio.org/terms/ETS/scientificname,,,v0.9.1,2018-11-01,,Original character string provided as species name by the data owner (kept for reference and continuity),"Can be equal to scientificNameStd. Authors may use abbreviations, or use underscores to separate genus and species name. " +Traitdata,traitName,character,http://terminologies.gfbio.org/terms/ETS/traitName,http://rs.tdwg.org/dwc/terms/measurementType,http://terminologies.gfbio.org/terms/ETS/traitname,,,v0.9.1,2018-11-01,,Name of the trait as used by the data provider (kept for compatibility on provider side). ,"This can be a short name or user defined coded trait name. However, it is recommended to provide definition of the user provided trait names in the metadata. " +Traitdata,traitID,factor,http://terminologies.gfbio.org/terms/ETS/traitID,,http://terminologies.gfbio.org/terms/ETS/traitid,,,v0.9.1,2018-11-01,,"Unique identifier of the trait according to a public ontology, or a user-provided thesaurus of traits. ",Examples: TO:0000181; TOP103; http://top-thesaurus.org/annotationInfo?viz=1&&trait=Seed_mass; +Traitdata,traitValue,character,http://terminologies.gfbio.org/terms/ETS/traitValue,http://rs.tdwg.org/dwc/terms/measurementValue,http://terminologies.gfbio.org/terms/ETS/traitvalue,,,v0.9.1,2018-11-01,,Measured raw value or factor level for this species trait as measured and provided by the author. ,"Must respect the unit given in 'measurementUnit_user' for numerical traits. For categorical traits, the factor levels should be harmonized across the dataset and explained in the metadata. " +Traitdata,traitUnit,character,http://terminologies.gfbio.org/terms/ETS/traitUnit,http://rs.tdwg.org/dwc/terms/measurementUnit,http://terminologies.gfbio.org/terms/ETS/traitunit,,,v0.9.1,2018-11-01,,"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. ","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""" +Traitdata,scientificNameStd,character,http://terminologies.gfbio.org/terms/ETS/scientificNameStd,http://rs.tdwg.org/dwc/terms/scientificName,http://terminologies.gfbio.org/terms/ETS/scientificnamestd,,,v0.9.1,2018-11-01,,"The full name, with authorship and date information if known. This should resolve to the currently valid (zoological) or accepted (botanical) taxon.","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" +Traitdata,traitNameStd,factor,http://terminologies.gfbio.org/terms/ETS/traitNameStd,http://rs.tdwg.org/dwc/terms/measurementType,http://terminologies.gfbio.org/terms/ETS/traitnamestd,,,v0.9.1,2018-11-01,,Descriptive Name of the trait reported. This should follow the controlled vocabulary of a thesaurus of traits available online or published along with the dataset. ,"Accompanying this, the traitID should provide an unambiguous link to the trait definition in the thesaurus or supplementary dataset. " +Traitdata,traitValueStd,character,http://terminologies.gfbio.org/terms/ETS/traitValueStd,http://rs.tdwg.org/dwc/terms/measurementValue,http://terminologies.gfbio.org/terms/ETS/traitvaluestd,,,v0.9.1,2018-11-01,,Standardized 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. ,"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""" +Traitdata,traitUnitStd,character,http://terminologies.gfbio.org/terms/ETS/traitUnitStd,http://rs.tdwg.org/dwc/terms/measurementUnit,http://terminologies.gfbio.org/terms/ETS/traitunitstd,,,v0.9.1,2018-11-01,,The units associated with the measurementValue. The expected standard unit for this trait as defined in the traitlist/ thesaurus. ,"Recommended best practice is to use the International System of Units (SI). Examples: ""mm"", ""C"", ""km"", ""ha"". For discussion see http://terms.tdwg.org/wiki/dwc:measurementUnit" Traitdata,taxonID,factor,http://rs.tdwg.org/dwc/terms/taxonID,,,,,v0.8,2017-07-07,,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.,"Examples: ""GBIF Backbone Taxonomy:497924"", ""8fa58e08-08de-4ac1-b69c-1235340b7001"", ""32567"", ""http://species.gbif.org/abies_alba_1753"", ""urn:lsid:gbif.org:usages:32567"". For discussion see http://terms.tdwg.org/wiki/dwc:taxonID" -Traitdata,measurementID,character,http://terminologies.gfbio.org/terms/ETS/measurementid,http://rs.tdwg.org/dwc/terms/measurementID,,,,v0.8,2017-07-07,,"An identifier for the MeasurementOrFact (information pertaining to measurements, facts, characteristics, or assertions). May be a global unique identifier or an identifier specific to the data set.","Links multi-value trait measurements, e.g. x-y-z coordinates of a morphometric landmark, biochemical compound quantities for different chainlengths. In this case, the trait names must specify the sub-measurement, e.g. ""landmark32_x"", and must be specified in a reference trait list, given in the field ""measurementMethod"". " -Traitdata,occurrenceID,character,http://terminologies.gfbio.org/terms/ETS/occurrenceid,http://rs.tdwg.org/dwc/terms/occurrenceID,,,,v0.8,2017-07-07,,"An identifier for the Occurrence (as opposed to a particular digital record of the occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the occurrenceID globally unique.","For a specimen in the absence of a bona fide global unique identifier, for example, use the form: ""urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]. Examples: ""urn:lsid:nhm.ku.edu:Herps:32"", ""urn:catalog:FMNH:Mammal:145732"". For discussion see http://terms.tdwg.org/wiki/dwc:occurrenceID. This is important for the analysis of co-variation of morphometric data or intraspecific variation. It also couples multiple measurements on a single specimen, which also could be a leaf or a single bone without an assignment to an individual organism. If available, upload related dataset to describe specimens more precisely, e.g. environmental parameters or identity related information. " +Traitdata,measurementID,character,http://terminologies.gfbio.org/terms/ETS/measurementID,http://rs.tdwg.org/dwc/terms/measurementID,http://terminologies.gfbio.org/terms/ETS/measurementid,,,v0.9.1,2018-11-01,,"An identifier for the MeasurementOrFact (information pertaining to measurements, facts, characteristics, or assertions). May be a global unique identifier or an identifier specific to the data set.","Links multi-value trait measurements, e.g. x-y-z coordinates of a morphometric landmark, biochemical compound quantities for different chainlengths. In this case, the trait names must specify the sub-measurement, e.g. ""landmark32_x"", and must be specified in a reference trait list, given in the field ""measurementMethod"". " +Traitdata,occurrenceID,character,http://terminologies.gfbio.org/terms/ETS/occurrenceID,http://rs.tdwg.org/dwc/terms/occurrenceID,http://terminologies.gfbio.org/terms/ETS/occurrenceid,,,v0.9.1,2018-11-01,,"An identifier for the Occurrence (as opposed to a particular digital record of the occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the occurrenceID globally unique.","For a specimen in the absence of a bona fide global unique identifier, for example, use the form: ""urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]. Examples: ""urn:lsid:nhm.ku.edu:Herps:32"", ""urn:catalog:FMNH:Mammal:145732"". For discussion see http://terms.tdwg.org/wiki/dwc:occurrenceID. This is important for the analysis of co-variation of morphometric data or intraspecific variation. It also couples multiple measurements on a single specimen, which also could be a leaf or a single bone without an assignment to an individual organism. If available, upload related dataset to describe specimens more precisely, e.g. environmental parameters or identity related information. " Traitdata,warnings,character,http://terminologies.gfbio.org/terms/ETS/warnings,,,,,v0.8,2017-07-07,2018-05-29,Warnings on the quality or reliability of the reported trait value. ,"Warnings from autogenerated data should be stored here, e.g. regarding a lack of match between the provided taxonID and the ontology, or the trait names or values, a mismatch in the units provided and the unit expected according to the trait table. User defined warnings and flags can be added as well, e.g. 'NOTUSE' to mark data that are unreliable or erroneous." Taxon,taxonRank,factor,http://rs.tdwg.org/dwc/terms/taxonRank,,,,,v0.8,2017-07-07,2018-03-21,The taxonomic rank of the most specific name in the scientificName. Recommended best practice is to use a controlled vocabulary. ,"This is to clarify cases where information is not given on a species level. Examples: ""subspecies"", ""varietas"", ""forma"", ""species"", ""genus"". For discussion see http://terms.tdwg.org/wiki/dwc:taxonRank" Taxon,kingdom,factor,http://rs.tdwg.org/dwc/terms/kingdom,,,,,v0.8,2017-07-07,2018-03-21,The full scientific name of the kingdom in which the taxon is classified.,"Examples: ""Animalia"", ""Plantae"". For discussion see http://terms.tdwg.org/wiki/dwc:kingdom" @@ -19,8 +19,8 @@ Taxon,class,character,http://rs.tdwg.org/dwc/terms/class,,,,,v0.8,2018-03-21,,Th Taxon,order,factor,http://rs.tdwg.org/dwc/terms/order,,,,,v0.8,2017-07-07,2018-03-21,The full scientific name of the order in which the taxon is classified.,"Examples: ""Carnivora"", ""Monocleales"". For discussion see http://terms.tdwg.org/wiki/dwc:order" Taxon,family,character,http://rs.tdwg.org/dwc/terms/family,,,,,v0.8,2018-03-21,,The full scientific name of the family in which the taxon is classified.,"Examples: ""Felidae"", ""Monocleaceae"". For discussion see http://terms.tdwg.org/wiki/dwc:family" Taxon,genus,character,http://rs.tdwg.org/dwc/terms/genus,,,,,v0.8,2018-03-21,,The full scientific name of the genus in which the taxon is classified.,"Examples: ""Puma"", ""Monoclea"". For discussion see http://terms.tdwg.org/wiki/dwc:genus" -MeasurementOrFact,basisOfRecord,factor,http://terminologies.gfbio.org/terms/ETS/basisofrecord,http://rs.tdwg.org/dwc/terms/basisOfRecord,,,,v0.8,2017-07-07,,How and from which kind of specimen were the data obtained? Make use of controlled vocabulary. Valid entries are: 'LivingSpecimen'; 'PreservedSpecimen'; 'FossilSpecimen'; 'literatureData'; 'traitDatabase'; 'expertKnowledge' (see Comments) ,"Options are: Taken by own measurement (defined in DwC: http://rs.tdwg.org/dwc/terms/LivingSpecimen; http://rs.tdwg.org/dwc/terms/PreservedSpecimen; http://rs.tdwg.org/dwc/terms/FossilSpecimen ) or taken from literature (enter 'literatureData'), from an existing trait database (enter 'traitDatabase'), or expert knowledge (enter 'expertKnowledge'). Provide further information in field 'basisOfRecordDescription' and 'references'. " -MeasurementOrFact,basisOfRecordDescription,character,http://terminologies.gfbio.org/terms/ETS/basisofrecorddescription,,,,,v0.8,2017-07-07,,Adding more detail to the basisOfRecord. ,"If life specimens were sampled, where did they come from? Have they been reared in cultivation? If literature data or online database, provide type of literature, e.g. textbook, website, URL, etc. If preserved specimens were used, which method of preservation? In case of expert knowledge, give the name of the authority. " +MeasurementOrFact,basisOfRecord,factor,http://terminologies.gfbio.org/terms/ETS/basisOfRecord,http://rs.tdwg.org/dwc/terms/basisOfRecord,http://terminologies.gfbio.org/terms/ETS/basisofrecord,,,v0.9.1,2018-11-01,,How and from which kind of specimen were the data obtained? Make use of controlled vocabulary. Valid entries are: 'LivingSpecimen'; 'PreservedSpecimen'; 'FossilSpecimen'; 'literatureData'; 'traitDatabase'; 'expertKnowledge' (see Comments) ,"Options are: Taken by own measurement (defined in DwC: http://rs.tdwg.org/dwc/terms/LivingSpecimen; http://rs.tdwg.org/dwc/terms/PreservedSpecimen; http://rs.tdwg.org/dwc/terms/FossilSpecimen ) or taken from literature (enter 'literatureData'), from an existing trait database (enter 'traitDatabase'), or expert knowledge (enter 'expertKnowledge'). Provide further information in field 'basisOfRecordDescription' and 'references'. " +MeasurementOrFact,basisOfRecordDescription,character,http://terminologies.gfbio.org/terms/ETS/basisOfRecordDescription,,http://terminologies.gfbio.org/terms/ETS/basisofrecorddescription,,,v0.9.1,2018-11-01,,Adding more detail to the basisOfRecord. ,"If life specimens were sampled, where did they come from? Have they been reared in cultivation? If literature data or online database, provide type of literature, e.g. textbook, website, URL, etc. If preserved specimens were used, which method of preservation? In case of expert knowledge, give the name of the authority. " MeasurementOrFact,references,character,http://terminologies.gfbio.org/terms/ETS/references,http://purl.org/dc/terms/references,,,,v0.8,2017-08-24,,"Precise reference to the source. If literature data, this should quote the book or online database. If museum specimen, this should report the name of the collection. If expert knowledge, this should name the authority, preferably using ORCID. If trait database, provide reference to the original publication, DOI or URL of the trait-database. ","Examples: ""http://mvzarctos.berkeley.edu/guid/MVZ:Mamm:165861""; ""http://www.catalogueoflife.org/annual-checklist/show_species_details.php?record_id=6197868"". For discussion see http://terms.tdwg.org/wiki/dwc:references" MeasurementOrFact,measurementResolution,character,http://terminologies.gfbio.org/terms/ETS/measurementResolution,,,,,v0.8,2017-07-07,,If the trait information was originally given on another taxonomic level than species. Applies mainly for literature and expert knowledge data. not applying for measured data. The hierarchical level to which the trait data would refer. ,"For example, information given in literature could state 'most species in this genus are winged', but the trait data could be given for each species in this genus." MeasurementOrFact,measurementMethod,character,http://terminologies.gfbio.org/terms/ETS/measurementMethod,http://rs.tdwg.org/dwc/terms/measurementMethod,,,,v0.8,2017-07-07,,"Applies primarily to measured data. The method, tools and scales used to measure a (numerical) trait value. A description of or reference to (publication, URI) the method or protocol used to determine the measurement, fact, characteristic, or assertion. ","Should be a concise and standardized text entry or reference (publication, URI), referring to a particular method (e.g. 'direct weighing', 'length-mass regression', 'intertegular span', 'length between node X and y' ) and measurement conditions (e.g. certain temperature or humidity, name of device or scale used for measurement). To avoid repetition or lengthy entries, authors should use global identifiers of methodological terms if available, or enter dataset specific identifiers and provide a more detailed description of the method or protocol used to determine the measurement, fact, characteristic, or assertion in the metadata of the dataset. " @@ -54,7 +54,7 @@ Occurrence,geodeticDatum,factor,http://rs.tdwg.org/dwc/terms/geodeticDatum,,,,,v Occurrence,verbatimLocality,character,http://rs.tdwg.org/dwc/terms/verbatimLocality,,,,,v0.8,2017-07-07,,The specific description of the place. ,"Less specific geographic information can be provided in other geographic terms of Darwin Core (higherGeography, continent, country, stateProvince, county, municipality, waterBody, island, islandGroup). This term may contain information modified from the original to correct perceived errors or standardize the description. Example: ""25 km NNE Bariloche por R. Nac. 237"". For discussion see http://terms.tdwg.org/wiki/dwc:verbatimLocality" Occurrence,country,character,http://rs.tdwg.org/dwc/terms/country,,,,,v0.8,2017-07-07,,The name of the country or major administrative unit in which the Location occurs. Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.,"Examples: ""Germany"", ""Denmark"", ""Colombia"", ""España"". For discussion see http://terms.tdwg.org/wiki/dwc:country;" Occurrence,countryCode,factor,http://rs.tdwg.org/dwc/terms/countryCode,,,,,v0.8,2017-07-07,,The standard code for the country in which the Location occurs. Recommended best practice is to use ISO 3166-1-alpha-2 country codes.,"Examples:""DE"" for Germany, ""AR"" for Argentina, ""SV"" for El Salvador. For discussion see http://terms.tdwg.org/wiki/dwc:countryCode" -Occurrence,occurenceRemarks,character,http://rs.tdwg.org/dwc/terms/occurrenceRemarks,,,,,v0.8,2017-07-07,,Comments or notes about the Occurrence.,"Example: ""found dead on road"". For discussion see http://terms.tdwg.org/wiki/dwc:occurrenceRemarks" +Occurrence,occurrenceRemarks,character,http://rs.tdwg.org/dwc/terms/occurrenceRemarks,,,,,v0.8,2017-07-07,2018-11-01,Comments or notes about the Occurrence.,"Example: ""found dead on road"". For discussion see http://terms.tdwg.org/wiki/dwc:occurrenceRemarks" Metadata,rightsHolder,character,http://purl.org/dc/terms/rightsHolder,,,,,v0.8,2017-07-07,,"A person or organization owning or managing rights over the resource, i.e. this dataset.","Example: ""The Regents of the University of California."". For discussion see http://terms.tdwg.org/wiki/dwc:rightsHolder" Metadata,bibliographicCitation,character,http://purl.org/dc/terms/bibliographicCitation,,,,,v0.8,2017-07-07,,A bibliographic reference for the resource as a statement indicating how this record should be cited (attributed) when used. Recommended practice is to include sufficient bibliographic detail to identify the resource as unambiguously as possible.,"Examples: ""Ctenomys sociabilis (MVZ 165861)"" for a specimen, ""Oliver P. Pearson. 1985. Los tuco-tucos (genera Ctenomys) de los Parques Nacionales Lanin y Nahuel Huapi, Argentina Historia Natural, 5(37):337-343."" for a Taxon. For discussion see http://terms.tdwg.org/wiki/dwc:bibliographicCitation" Metadata,license,character,http://purl.org/dc/terms/license,,,,,v0.8,2017-07-07,,A legal document giving official permission to do something with the resource.,"Examples: ""http://creativecommons.org/publicdomain/zero/1.0/legalcode"", ""http://creativecommons.org/licenses/by/4.0/legalcode"". For discussion see http://terms.tdwg.org/wiki/dwc:license" @@ -66,7 +66,7 @@ BiodiversityExploratories,OriginBE,logical,http://terminologies.gfbio.org/terms/ BiodiversityExploratories,BEPlotID,factor,http://terminologies.gfbio.org/terms/ETS/BEPlotID,,,,,v0.8,2017-07-07,2018-03-21,EP plot ID (or also any valid Gridplot ID or MIP ID) where the measured specimen was extracted. ,"Only for specimen that were extracted from the Exploratories directly (or direct offspring, if hatched in the lab). Please also report it, even if this was not part of your research question and provide a Date (a year at last) if available." BiodiversityExploratories,Exploratory,factor,http://terminologies.gfbio.org/terms/ETS/Exploratory,,,,,v0.8,2017-07-07,2017-11-01,"Exploratories Region (Hainich, Schorfheide, Alb) for sorting purpose and readability, or if exact Plot ID is not available.",Use vocabulary: 'HAI'; 'SCH'; 'ALB' BiodiversityExploratories,BEType,factor,http://terminologies.gfbio.org/terms/ETS/BEType,,,,,v0.8,2017-07-07,2018-05-29,Defined code for landscape type of the exploratories plot. ,"Use vocabulary: ""W"" for forest and ""G"" for grassland plot" -Traitlist,identifier,character,http://terminologies.gfbio.org/terms/ETS/Identifier,http://purl.org/dc/terms/identifier,,,,v0.8,2017-10-24,2018-05-29,A unique identifier for the trait; globally unique or dataset-specific,Identifiers are ideally globally unique and stable URIs which link to the source of the trait description in a public ontology or thesaurus of traits; +Traitlist,identifier,character,http://terminologies.gfbio.org/terms/ETS/identifier,http://purl.org/dc/terms/identifier,http://terminologies.gfbio.org/terms/ETS/Identifier,,,v0.9.1,2018-11-01,,A unique identifier for the trait; globally unique or dataset-specific,Identifiers are ideally globally unique and stable URIs which link to the source of the trait description in a public ontology or thesaurus of traits; Traitlist,trait,character,http://terminologies.gfbio.org/terms/ETS/trait,http://purl.org/dc/terms/title,,,,v0.8,2017-10-24,,A descriptive trait name,"Trait names should be unique but intuitively comprehensible. Additional specifications such as unit of measurement can be included in the name. Several words are separated by ""_""." Traitlist,broaderTerm,character,http://terminologies.gfbio.org/terms/ETS/broaderTerm,,,,,v0.8,2017-08-24,2017-11-15,One or several terms that enclose the trait definition. ,The broader term is given as the unique identifier (traitID) of the broader trait. Each trait can only have one broader term. Traitlist,narrowerTerm,character,http://terminologies.gfbio.org/terms/ETS/narrowerTerm,,,,,v0.8,2017-08-24,2017-11-15,One or several terms that are enclosed by the trait definition.,This allows to derive hierarchical trees of traits. Several traits can be listed as narrower terms of one trait. @@ -77,5 +77,20 @@ Traitlist,factorLevels,character,http://terminologies.gfbio.org/terms/ETS/factor Traitlist,maxAllowedValue,character,http://terminologies.gfbio.org/terms/ETS/maxAllowedValue,,,,,v0.8,2017-09-27,,A lower boundary for accepted numerical values.,"May be used for eliminating invalid data. This boundary may constrain a range of values of meaningful orders of magnitude, or constrain entries to positive values. " Traitlist,minAllowedValue,character,http://terminologies.gfbio.org/terms/ETS/minAllowedValue,,,,,v0.8,2017-09-27,,An upper boundary for accepted numerical values.,May be used for eliminating invalid data. This boundary may constrain a range of values of meaningful orders of magnitude. Traitlist,traitDescription,character,http://terminologies.gfbio.org/terms/ETS/traitDescription,http://purl.org/dc/terms/description,,,,v0.8,2017-09-27,2018-05-29,"A short, unambiguous definition of the trait as used in the specific study context; may refer to a method of measurement; may copy the description of a public trait ontology;","The definition should make use of terms provided by existing public ontologies, e.g. 'the mass (PATO:mass), either fresh or dried, of a fruit (PO:fruit)'" -Traitlist,comments,character,http://terminologies.gfbio.org/terms/ETS/Comments,,,,,v0.8,2017-07-07,2017-11-15,Details and Examples for clarification of the trait definition.,Can contain definition of trait levels or requirements for standardized conditions. +Traitlist,comments,character,http://terminologies.gfbio.org/terms/ETS/comments,,http://terminologies.gfbio.org/terms/ETS/Comments,,,v0.9.1,2018-11-01,,Details and Examples for clarification of the trait definition.,Can contain definition of trait levels or requirements for standardized conditions. Traitlist,source,character,http://terminologies.gfbio.org/terms/ETS/source,,,,,v0.9,2018-09-18,,The original source of the trait definition,Can be a DOI or bibliographic reference to the original publication of this trait definition +Traitdata,scientificName,character,http://terminologies.gfbio.org/terms/ETS/scientificname,http://rs.tdwg.org/dwc/terms/scientificName,,TRUE,http://terminologies.gfbio.org/terms/ETS/scientificName,v0.8,2017-07-07,2018-05-29,Original character string provided as species name by the data owner (kept for reference and continuity),"Can be equal to scientificNameStd. Authors may use abbreviations, or use underscores to separate genus and species name. " +Traitdata,traitName,character,http://terminologies.gfbio.org/terms/ETS/traitname,http://rs.tdwg.org/dwc/terms/measurementType,,TRUE,http://terminologies.gfbio.org/terms/ETS/traitName,v0.8,2017-07-07,,Name of the trait as used by the data provider (kept for compatibility on provider side). ,"This can be a short name or user defined coded trait name. However, it is recommended to provide definition of the user provided trait names in the metadata. " +Traitdata,traitID,factor,http://terminologies.gfbio.org/terms/ETS/traitid,,,TRUE,http://terminologies.gfbio.org/terms/ETS/traitID,v0.8,2017-07-07,2018-05-29,"Unique identifier of the trait according to a public ontology, or a user-provided thesaurus of traits. ",Examples: TO:0000181; TOP103; http://top-thesaurus.org/annotationInfo?viz=1&&trait=Seed_mass; +Traitdata,traitValue,character,http://terminologies.gfbio.org/terms/ETS/traitvalue,http://rs.tdwg.org/dwc/terms/measurementValue,,TRUE,http://terminologies.gfbio.org/terms/ETS/traitValue,v0.8,2017-07-07,,Measured raw value or factor level for this species trait as measured and provided by the author. ,"Must respect the unit given in 'measurementUnit_user' for numerical traits. For categorical traits, the factor levels should be harmonized across the dataset and explained in the metadata. " +Traitdata,traitUnit,character,http://terminologies.gfbio.org/terms/ETS/traitunit,http://rs.tdwg.org/dwc/terms/measurementUnit,,TRUE,http://terminologies.gfbio.org/terms/ETS/traitUnit,v0.8,2017-07-07,,"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. ","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""" +Traitdata,scientificNameStd,character,http://terminologies.gfbio.org/terms/ETS/scientificnamestd,http://rs.tdwg.org/dwc/terms/scientificName,,TRUE,http://terminologies.gfbio.org/terms/ETS/scientificNameStd,v0.8,2017-07-07,2017-11-01,"The full name, with authorship and date information if known. This should resolve to the currently valid (zoological) or accepted (botanical) taxon.","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" +Traitdata,traitNameStd,factor,http://terminologies.gfbio.org/terms/ETS/traitnamestd,http://rs.tdwg.org/dwc/terms/measurementType,,TRUE,http://terminologies.gfbio.org/terms/ETS/traitNameStd,v0.8,2017-07-07,,Descriptive Name of the trait reported. This should follow the controlled vocabulary of a thesaurus of traits available online or published along with the dataset. ,"Accompanying this, the traitID should provide an unambiguous link to the trait definition in the thesaurus or supplementary dataset. " +Traitdata,traitValueStd,character,http://terminologies.gfbio.org/terms/ETS/traitvaluestd,http://rs.tdwg.org/dwc/terms/measurementValue,,TRUE,http://terminologies.gfbio.org/terms/ETS/traitValueStd,v0.8,2017-07-07,,Standardized 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. ,"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""" +Traitdata,traitUnitStd,character,http://terminologies.gfbio.org/terms/ETS/traitunitstd,http://rs.tdwg.org/dwc/terms/measurementUnit,,TRUE,http://terminologies.gfbio.org/terms/ETS/traitUnitStd,v0.8,2017-07-07,,The units associated with the measurementValue. The expected standard unit for this trait as defined in the traitlist/ thesaurus. ,"Recommended best practice is to use the International System of Units (SI). Examples: ""mm"", ""C"", ""km"", ""ha"". For discussion see http://terms.tdwg.org/wiki/dwc:measurementUnit" +Traitdata,measurementID,character,http://terminologies.gfbio.org/terms/ETS/measurementid,http://rs.tdwg.org/dwc/terms/measurementID,,TRUE,http://terminologies.gfbio.org/terms/ETS/measurementID,v0.8,2017-07-07,,"An identifier for the MeasurementOrFact (information pertaining to measurements, facts, characteristics, or assertions). May be a global unique identifier or an identifier specific to the data set.","Links multi-value trait measurements, e.g. x-y-z coordinates of a morphometric landmark, biochemical compound quantities for different chainlengths. In this case, the trait names must specify the sub-measurement, e.g. ""landmark32_x"", and must be specified in a reference trait list, given in the field ""measurementMethod"". " +Traitdata,occurrenceID,character,http://terminologies.gfbio.org/terms/ETS/occurrenceid,http://rs.tdwg.org/dwc/terms/occurrenceID,,TRUE,http://terminologies.gfbio.org/terms/ETS/occurrenceID,v0.8,2017-07-07,,"An identifier for the Occurrence (as opposed to a particular digital record of the occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the occurrenceID globally unique.","For a specimen in the absence of a bona fide global unique identifier, for example, use the form: ""urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]. Examples: ""urn:lsid:nhm.ku.edu:Herps:32"", ""urn:catalog:FMNH:Mammal:145732"". For discussion see http://terms.tdwg.org/wiki/dwc:occurrenceID. This is important for the analysis of co-variation of morphometric data or intraspecific variation. It also couples multiple measurements on a single specimen, which also could be a leaf or a single bone without an assignment to an individual organism. If available, upload related dataset to describe specimens more precisely, e.g. environmental parameters or identity related information. " +MeasurementOrFact,basisOfRecord,factor,http://terminologies.gfbio.org/terms/ETS/basisofrecord,http://rs.tdwg.org/dwc/terms/basisOfRecord,,TRUE,http://terminologies.gfbio.org/terms/ETS/basisOfRecord,v0.8,2017-07-07,,How and from which kind of specimen were the data obtained? Make use of controlled vocabulary. Valid entries are: 'LivingSpecimen'; 'PreservedSpecimen'; 'FossilSpecimen'; 'literatureData'; 'traitDatabase'; 'expertKnowledge' (see Comments) ,"Options are: Taken by own measurement (defined in DwC: http://rs.tdwg.org/dwc/terms/LivingSpecimen; http://rs.tdwg.org/dwc/terms/PreservedSpecimen; http://rs.tdwg.org/dwc/terms/FossilSpecimen ) or taken from literature (enter 'literatureData'), from an existing trait database (enter 'traitDatabase'), or expert knowledge (enter 'expertKnowledge'). Provide further information in field 'basisOfRecordDescription' and 'references'. " +MeasurementOrFact,basisOfRecordDescription,character,http://terminologies.gfbio.org/terms/ETS/basisofrecorddescription,,,TRUE,http://terminologies.gfbio.org/terms/ETS/basisOfRecordDescription,v0.8,2017-07-07,,Adding more detail to the basisOfRecord. ,"If life specimens were sampled, where did they come from? Have they been reared in cultivation? If literature data or online database, provide type of literature, e.g. textbook, website, URL, etc. If preserved specimens were used, which method of preservation? In case of expert knowledge, give the name of the authority. " +Traitlist,identifier,character,http://terminologies.gfbio.org/terms/ETS/Identifier,http://purl.org/dc/terms/identifier,,TRUE,http://terminologies.gfbio.org/terms/ETS/identifier,v0.8,2017-10-24,2018-05-29,A unique identifier for the trait; globally unique or dataset-specific,Identifiers are ideally globally unique and stable URIs which link to the source of the trait description in a public ontology or thesaurus of traits; +Traitlist,comments,character,http://terminologies.gfbio.org/terms/ETS/Comments,,,TRUE,http://terminologies.gfbio.org/terms/ETS/comments,v0.8,2017-07-07,2017-11-15,Details and Examples for clarification of the trait definition.,Can contain definition of trait levels or requirements for standardized conditions. diff --git a/README.md b/README.md index 1596f55..06e3118 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,7 @@ The repository contains: - the 'source file' of the ETS (in .csv format), defining the terms and containing the URIs. - the 'release' of the ETS (in .owl format), which is the machine-readable reference for the use in GFBio terminology service, accessible at [https://terminologies.gfbio.org/terminology/?ontology=ETS](https://terminologies.gfbio.org/terminology/?ontology=ETS). +- the source files of the documentation website (.Rmd, .yml), which are parsed in [RStudio as a Rmarkdown Website](http://rmarkdown.rstudio.com/rmarkdown_websites.html) and released as a static website at [GFBio Terminology Service](https://terminologies.gfbio.org/terms/ets/pages/), and as a development preview at https://ecologicaltraitdata.github.io/ETS/. # Use the ETS @@ -41,7 +42,7 @@ The vocabulary contains several fields which are defined as follows: To refer to **this version** of the ETS please cite: -> Schneider, F.D., Jochum, M., Le Provost, G., Ostrowski, A., Penone, C. and Simons, N.K. (2018) Ecological Trait-data Standard Vocabulary, v0.9, URL: https://terminologies.gfbio.org/terms/ets/pages/, DOI: [10.5281/zenodo.1041732](https://doi.org/10.5281/zenodo.1041732) +> Schneider, F.D., Jochum, M., Le Provost, G., Ostrowski, A., Penone, C. and Simons, N.K. (2018) Ecological Trait-data Standard Vocabulary, v0.9.1, URL: https://terminologies.gfbio.org/terms/ets/pages/ , DOI: [10.5281/zenodo.1485739](https://doi.org/10.5281/zenodo.1485739) It is recommended to provide this versioned pointer from the metadata of datasets that apply the ETS. You can cite **all versions** of the ETS by using the DOI [10.5281/zenodo.1041732](https://doi.org/10.5281/zenodo.1041732). This will always resolve to the latest version. diff --git a/VERSIONS.md b/VERSIONS.md index 965f0fc..936aeab 100644 --- a/VERSIONS.md +++ b/VERSIONS.md @@ -12,6 +12,20 @@ Discussions on terms and versions are coordinated in the [Github Issues](https:/ --- +# v0.9.1 (patch), released 13 November 2018 + +Fixing inconsistent URIs and terms. Keeping original terms as deprecated, forwarding to new terms. Defining name scheme for new terms in documentation. + +## major changes + +- new case spelling for following terms: occurrenceRemarks +- new URI for following terms: scientificName, traitName, traitID, traitValue, traitUnit, scientificNameStd, traitNameStd, traitValueStd, traitUnitStd, measurementID, occurrenceID, basisOfRecord, basisOfRecordDescription, identifier, comments + +## minor changes + +- define name scheme for new terms and URIs +- add best-practice guidelines to documentation page + # v0.9, released 27 September 2018 First public release at GFBio Terminology Service: https://terminologies.gfbio.org/terms/ets/pages/ (human readable) and https://terminologies.gfbio.org/terminology/?ontology=ETS (API access). diff --git a/ets.owl b/ets.owl index 39b6940..cadfd51 100644 --- a/ets.owl +++ b/ets.owl @@ -14,27 +14,40 @@ David Fichtmueller GFBio Terminology Service en - 2018-09-17 - 0.9 - + 2018-11-13 + 0.9.1 + + + + + + + + + + @@ -88,104 +101,110 @@ - + scientificName Original character string provided as species name by the data owner (kept for reference and continuity) - Can be equal to scientificNameStd. Authors may use abbreviations, or use underscores to separate genus and species name. + Can be equal to scientificNameStd. Authors may use abbreviations, or use underscores to separate genus and species name. - 2017-07-07 - 2018-05-29 + 2018-11-01 + recommended - + traitName - Name of the trait as used by the data provider (kept for compatibility on provider side). - This can be a short name or user defined coded trait name. However, it is recommended to provide definition of the user provided trait names in the metadata. + Name of the trait as used by the data provider (kept for compatibility on provider side). + This can be a short name or user defined coded trait name. However, it is recommended to provide definition of the user provided trait names in the metadata. - 2017-07-07 + 2018-11-01 + recommended - + traitID - Unique identifier of the trait according to a public ontology, or a user-provided thesaurus of traits. - Examples: TO:0000181; TOP103; http://top-thesaurus.org/annotationInfo?viz=1&&trait=Seed_mass; + Unique identifier of the trait according to a public ontology, or a user-provided thesaurus of traits. + Examples: TO:0000181; TOP103; http://top-thesaurus.org/annotationInfo?viz=1&&trait=Seed_mass; - 2017-07-07 - 2018-05-29 + 2018-11-01 + recommended - + traitValue - Measured raw value or factor level for this species trait as measured and provided by the author. - Must respect the unit given in 'measurementUnit_user' for numerical traits. For categorical traits, the factor levels should be harmonized across the dataset and explained in the metadata. + Measured raw value or factor level for this species trait as measured and provided by the author. + Must respect the unit given in 'measurementUnit_user' for numerical traits. For categorical traits, the factor levels should be harmonized across the dataset and explained in the metadata. - 2017-07-07 + 2018-11-01 + recommended - + traitUnit - 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. + 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. 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" - 2017-07-07 + 2018-11-01 + recommended - + scientificNameStd The full name, with authorship and date information if known. This should resolve to the currently valid (zoological) or accepted (botanical) taxon. 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 - 2017-07-07 - 2017-11-01 + 2018-11-01 + recommended - + traitNameStd - Descriptive Name of the trait reported. This should follow the controlled vocabulary of a thesaurus of traits available online or published along with the dataset. - Accompanying this, the traitID should provide an unambiguous link to the trait definition in the thesaurus or supplementary dataset. + Descriptive Name of the trait reported. This should follow the controlled vocabulary of a thesaurus of traits available online or published along with the dataset. + Accompanying this, the traitID should provide an unambiguous link to the trait definition in the thesaurus or supplementary dataset. - 2017-07-07 + 2018-11-01 + recommended - + traitValueStd - Standardized 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. + Standardized 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. 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" - 2017-07-07 + 2018-11-01 + recommended - + traitUnitStd - The units associated with the measurementValue. The expected standard unit for this trait as defined in the traitlist/ thesaurus. + The units associated with the measurementValue. The expected standard unit for this trait as defined in the traitlist/ thesaurus. Recommended best practice is to use the International System of Units (SI). Examples: "mm", "C", "km", "ha". For discussion see http://terms.tdwg.org/wiki/dwc:measurementUnit - 2017-07-07 + 2018-11-01 + recommended @@ -199,31 +218,33 @@ recommended - + measurementID An identifier for the MeasurementOrFact (information pertaining to measurements, facts, characteristics, or assertions). May be a global unique identifier or an identifier specific to the data set. - Links multi-value trait measurements, e.g. x-y-z coordinates of a morphometric landmark, biochemical compound quantities for different chainlengths. In this case, the trait names must specify the sub-measurement, e.g. "landmark32_x", and must be specified in a reference trait list, given in the field "measurementMethod". + Links multi-value trait measurements, e.g. x-y-z coordinates of a morphometric landmark, biochemical compound quantities for different chainlengths. In this case, the trait names must specify the sub-measurement, e.g. "landmark32_x", and must be specified in a reference trait list, given in the field "measurementMethod". - 2017-07-07 + 2018-11-01 + recommended - + occurrenceID An identifier for the Occurrence (as opposed to a particular digital record of the occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the occurrenceID globally unique. - For a specimen in the absence of a bona fide global unique identifier, for example, use the form: "urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]. Examples: "urn:lsid:nhm.ku.edu:Herps:32", "urn:catalog:FMNH:Mammal:145732". For discussion see http://terms.tdwg.org/wiki/dwc:occurrenceID. This is important for the analysis of co-variation of morphometric data or intraspecific variation. It also couples multiple measurements on a single specimen, which also could be a leaf or a single bone without an assignment to an individual organism. If available, upload related dataset to describe specimens more precisely, e.g. environmental parameters or identity related information. + For a specimen in the absence of a bona fide global unique identifier, for example, use the form: "urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]. Examples: "urn:lsid:nhm.ku.edu:Herps:32", "urn:catalog:FMNH:Mammal:145732". For discussion see http://terms.tdwg.org/wiki/dwc:occurrenceID. This is important for the analysis of co-variation of morphometric data or intraspecific variation. It also couples multiple measurements on a single specimen, which also could be a leaf or a single bone without an assignment to an individual organism. If available, upload related dataset to describe specimens more precisely, e.g. environmental parameters or identity related information. - 2017-07-07 + 2018-11-01 + recommended warnings - Warnings on the quality or reliability of the reported trait value. + Warnings on the quality or reliability of the reported trait value. Warnings from autogenerated data should be stored here, e.g. regarding a lack of match between the provided taxonID and the ontology, or the trait names or values, a mismatch in the units provided and the unit expected according to the trait table. User defined warnings and flags can be added as well, e.g. 'NOTUSE' to mark data that are unreliable or erroneous. 2017-07-07 @@ -234,7 +255,7 @@ taxonRank - The taxonomic rank of the most specific name in the scientificName. Recommended best practice is to use a controlled vocabulary. + The taxonomic rank of the most specific name in the scientificName. Recommended best practice is to use a controlled vocabulary. This is to clarify cases where information is not given on a species level. Examples: "subspecies", "varietas", "forma", "species", "genus". For discussion see http://terms.tdwg.org/wiki/dwc:taxonRank 2017-07-07 @@ -305,30 +326,32 @@ recommended - + basisOfRecord - How and from which kind of specimen were the data obtained? Make use of controlled vocabulary. Valid entries are: 'LivingSpecimen'; 'PreservedSpecimen'; 'FossilSpecimen'; 'literatureData'; 'traitDatabase'; 'expertKnowledge' (see Comments) - Options are: Taken by own measurement (defined in DwC: http://rs.tdwg.org/dwc/terms/LivingSpecimen; http://rs.tdwg.org/dwc/terms/PreservedSpecimen; http://rs.tdwg.org/dwc/terms/FossilSpecimen ) or taken from literature (enter 'literatureData'), from an existing trait database (enter 'traitDatabase'), or expert knowledge (enter 'expertKnowledge'). Provide further information in field 'basisOfRecordDescription' and 'references'. + How and from which kind of specimen were the data obtained? Make use of controlled vocabulary. Valid entries are: 'LivingSpecimen'; 'PreservedSpecimen'; 'FossilSpecimen'; 'literatureData'; 'traitDatabase'; 'expertKnowledge' (see Comments) + Options are: Taken by own measurement (defined in DwC: http://rs.tdwg.org/dwc/terms/LivingSpecimen; http://rs.tdwg.org/dwc/terms/PreservedSpecimen; http://rs.tdwg.org/dwc/terms/FossilSpecimen ) or taken from literature (enter 'literatureData'), from an existing trait database (enter 'traitDatabase'), or expert knowledge (enter 'expertKnowledge'). Provide further information in field 'basisOfRecordDescription' and 'references'. - 2017-07-07 + 2018-11-01 + recommended - + basisOfRecordDescription - Adding more detail to the basisOfRecord. - If life specimens were sampled, where did they come from? Have they been reared in cultivation? If literature data or online database, provide type of literature, e.g. textbook, website, URL, etc. If preserved specimens were used, which method of preservation? In case of expert knowledge, give the name of the authority. + Adding more detail to the basisOfRecord. + If life specimens were sampled, where did they come from? Have they been reared in cultivation? If literature data or online database, provide type of literature, e.g. textbook, website, URL, etc. If preserved specimens were used, which method of preservation? In case of expert knowledge, give the name of the authority. - 2017-07-07 + 2018-11-01 + recommended references - Precise reference to the source. If literature data, this should quote the book or online database. If museum specimen, this should report the name of the collection. If expert knowledge, this should name the authority, preferably using ORCID. If trait database, provide reference to the original publication, DOI or URL of the trait-database. + Precise reference to the source. If literature data, this should quote the book or online database. If museum specimen, this should report the name of the collection. If expert knowledge, this should name the authority, preferably using ORCID. If trait database, provide reference to the original publication, DOI or URL of the trait-database. Examples: "http://mvzarctos.berkeley.edu/guid/MVZ:Mamm:165861"; "http://www.catalogueoflife.org/annual-checklist/show_species_details.php?record_id=6197868". For discussion see http://terms.tdwg.org/wiki/dwc:references 2017-08-24 @@ -339,7 +362,7 @@ measurementResolution - If the trait information was originally given on another taxonomic level than species. Applies mainly for literature and expert knowledge data. not applying for measured data. The hierarchical level to which the trait data would refer. + If the trait information was originally given on another taxonomic level than species. Applies mainly for literature and expert knowledge data. not applying for measured data. The hierarchical level to which the trait data would refer. For example, information given in literature could state 'most species in this genus are winged', but the trait data could be given for each species in this genus. 2017-07-07 @@ -349,8 +372,8 @@ measurementMethod - Applies primarily to measured data. The method, tools and scales used to measure a (numerical) trait value. A description of or reference to (publication, URI) the method or protocol used to determine the measurement, fact, characteristic, or assertion. - Should be a concise and standardized text entry or reference (publication, URI), referring to a particular method (e.g. 'direct weighing', 'length-mass regression', 'intertegular span', 'length between node X and y' ) and measurement conditions (e.g. certain temperature or humidity, name of device or scale used for measurement). To avoid repetition or lengthy entries, authors should use global identifiers of methodological terms if available, or enter dataset specific identifiers and provide a more detailed description of the method or protocol used to determine the measurement, fact, characteristic, or assertion in the metadata of the dataset. + Applies primarily to measured data. The method, tools and scales used to measure a (numerical) trait value. A description of or reference to (publication, URI) the method or protocol used to determine the measurement, fact, characteristic, or assertion. + Should be a concise and standardized text entry or reference (publication, URI), referring to a particular method (e.g. 'direct weighing', 'length-mass regression', 'intertegular span', 'length between node X and y' ) and measurement conditions (e.g. certain temperature or humidity, name of device or scale used for measurement). To avoid repetition or lengthy entries, authors should use global identifiers of methodological terms if available, or enter dataset specific identifiers and provide a more detailed description of the method or protocol used to determine the measurement, fact, characteristic, or assertion in the metadata of the dataset. 2017-07-07 @@ -360,7 +383,7 @@ measurementDeterminedBy - A list (concatenated and separated) of names of people, groups, or organizations who determined the value of the measurement. + A list (concatenated and separated) of names of people, groups, or organizations who determined the value of the measurement. The recommended best practice is to separate the values with a vertical bar (' | '). Examples: "Rob Guralnick", "Julie Woodruff | Eileen Lacey". Can be encoded by dataset-specific identifiers for reasons of privacy. This is kept as a co-factor for repeated measurements. 2017-07-07 @@ -370,7 +393,7 @@ measurementDeterminedDate - The date on which the MeasurementOrFact was made. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E). + The date on which the MeasurementOrFact was made. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E). 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 2017-07-07 @@ -381,7 +404,7 @@ measurementRemarks Remarks concerning a particular measurement, e.g. additional information on the quality and reliability, reference or acknowledgements. - Any particularities about the individual measurement or specimen that might affect trait measuremnt, e.g. 'last antenna segment missing'. + Any particularities about the individual measurement or specimen that might affect trait measuremnt, e.g. 'last antenna segment missing'. 2017-07-07 @@ -392,7 +415,7 @@ aggregateMeasure Is measurementValue reporting an individual measurement or an aggregate Measure? Takes a binary entry: TRUE or FALSE - 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). + 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). 2017-07-07 @@ -421,7 +444,7 @@ measurementValue_min - The lower boundary of observed values. Instead of or in addition to dispersion metric. + The lower boundary of observed values. Instead of or in addition to dispersion metric. 2017-07-07 @@ -430,7 +453,7 @@ measurementValue_max - The upper boundary of observed values. Instead of or in addition to dispersion metric. + The upper boundary of observed values. Instead of or in addition to dispersion metric. 2017-07-07 @@ -451,7 +474,7 @@ statisticalMethod For aggregated measures, the method for data aggregation or averaging as well as the variation or range. - Example: 'mean and standard deviation', 'median and 95% confidence interval', 'mean and variance', 'mean and range of values', 'median and 95% interquantile range' + Example: 'mean and standard deviation', 'median and 95% confidence interval', 'mean and variance', 'mean and range of values', 'median and 95% interquantile range' 2017-07-07 @@ -460,7 +483,7 @@ sex - The sex of the biological individual(s) represented in the Occurrence. Recommended best practice is to use a controlled vocabulary. + The sex of the biological individual(s) represented in the Occurrence. Recommended best practice is to use a controlled vocabulary. Use vocabulary: "male", "female", "subadult", "unknown", "hermaphrodite" (no abbreviations or numerical encodings) 2017-07-07 @@ -472,7 +495,7 @@ lifeStage The age class or life stage of the biological individual(s) at the time the Occurrence was recorded. Recommended best practice is to use a controlled vocabulary. - Recommended factor levels are: seed, seedling, sapling, adult, egg, larval_instar_1, larval_instar_2, larval_instar_3, ... , pupa; For very taxon-specific life stages, it is recommended to provide detailed explanation in the metadata of the dataset. + Recommended factor levels are: seed, seedling, sapling, adult, egg, larval_instar_1, larval_instar_2, larval_instar_3, ... , pupa; For very taxon-specific life stages, it is recommended to provide detailed explanation in the metadata of the dataset. 2017-07-07 @@ -493,7 +516,7 @@ morphotype The morphotype of the observed specimen. - Examples: "worker", "drone", "queen". Since morphotypes can differ between organism groups, provide definition of morphotypes in the metadata of the dataset. + Examples: "worker", "drone", "queen". Since morphotypes can differ between organism groups, provide definition of morphotypes in the metadata of the dataset. 2017-07-07 @@ -503,7 +526,7 @@ eventID The sampling event or campaign. A globally valid URI or user specified character string that links to another table providing detailed information, e.g. environmental or temporal parameters, descriptions on methods etc.. - Examples: a combination of date and sampling region + Examples: a combination of date and sampling region 2017-07-07 @@ -513,7 +536,7 @@ preparations - For preserved specimens, a list (concatenated and separated) of preparations and preservation methods for the occurrence. + For preserved specimens, a list (concatenated and separated) of preparations and preservation methods for the occurrence. Do not report procedures for measurement or sampling here (see samplingProtocol and measurementMethod). The recommended best practice is to separate the values with a vertical bar (' | '). Examples: "fossil", "cast", "photograph", "DNA extract", "skin | "skull | skeleton", "whole animal (ETOH) | tissue (EDTA)". For discussion see http://terms.tdwg.org/wiki/dwc:preparations 2017-07-07 @@ -523,7 +546,7 @@ samplingProtocol - The name of, reference to, or description of the method or protocol used for obtaining the specimen. + The name of, reference to, or description of the method or protocol used for obtaining the specimen. Examples: "UV light trap", "mist net", "bottom trawl", "ad hoc observation", "point count", "Penguins from space: faecal stains reveal the location of emperor penguin colonies, http://dx.doi.org/10.1111/j.1466-8238.2009.00467.x", "Takats et al. 2001. Guidelines for Nocturnal Owl Monitoring in North America. Beaverhill Bird Observatory and Bird Studies Canada, Edmonton, Alberta. 32 pp.", "http://www.bsc-eoc.org/download/Owl.pdf". For discussion see http://terms.tdwg.org/wiki/dwc:samplingProtocol 2017-07-07 @@ -533,7 +556,7 @@ year - The four-digit year, at which the specimens were extracted or sampled. + The four-digit year, at which the specimens were extracted or sampled. Example: "2008". For discussion see http://terms.tdwg.org/wiki/dwc:year 2017-07-07 @@ -543,7 +566,7 @@ month - The ordinal month, in which the specimens were extracted or sampled. + The ordinal month, in which the specimens were extracted or sampled. Examples: "1" (=January), "10" (=October). For discussion see http://terms.tdwg.org/wiki/dwc:month 2017-07-07 @@ -553,7 +576,7 @@ day - The integer day of the month on which the specimens were extracted or sampled. + The integer day of the month on which the specimens were extracted or sampled. Examples: "9", "28". For discussion see http://terms.tdwg.org/wiki/dwc:day 2017-07-07 @@ -636,7 +659,7 @@ verbatimLocality - The specific description of the place. + The specific description of the place. Less specific geographic information can be provided in other geographic terms of Darwin Core (higherGeography, continent, country, stateProvince, county, municipality, waterBody, island, islandGroup). This term may contain information modified from the original to correct perceived errors or standardize the description. Example: "25 km NNE Bariloche por R. Nac. 237". For discussion see http://terms.tdwg.org/wiki/dwc:verbatimLocality 2017-07-07 @@ -665,11 +688,12 @@ - occurenceRemarks + occurrenceRemarks Comments or notes about the Occurrence. Example: "found dead on road". For discussion see http://terms.tdwg.org/wiki/dwc:occurrenceRemarks 2017-07-07 + 2018-11-01 recommended @@ -751,7 +775,7 @@ OriginBE Did measured specimens originate from Exploratories Plots? TRUE or FALSE, defaults to FALSE - As unambiguous flag for data and specimens that are originating from Exploratories sites. + As unambiguous flag for data and specimens that are originating from Exploratories sites. 2017-07-07 @@ -760,7 +784,7 @@ BEPlotID - EP plot ID (or also any valid Gridplot ID or MIP ID) where the measured specimen was extracted. + EP plot ID (or also any valid Gridplot ID or MIP ID) where the measured specimen was extracted. Only for specimen that were extracted from the Exploratories directly (or direct offspring, if hatched in the lab). Please also report it, even if this was not part of your research question and provide a Date (a year at last) if available. 2017-07-07 @@ -782,7 +806,7 @@ BEType - Defined code for landscape type of the exploratories plot. + Defined code for landscape type of the exploratories plot. Use vocabulary: "W" for forest and "G" for grassland plot 2017-07-07 @@ -791,15 +815,15 @@ recommended - + identifier A unique identifier for the trait; globally unique or dataset-specific - Identifiers are ideally globally unique and stable URIs which link to the source of the trait description in a public ontology or thesaurus of traits; + Identifiers are ideally globally unique and stable URIs which link to the source of the trait description in a public ontology or thesaurus of traits; - 2017-10-24 - 2018-05-29 + 2018-11-01 + recommended @@ -816,7 +840,7 @@ broaderTerm - One or several terms that enclose the trait definition. + One or several terms that enclose the trait definition. The broader term is given as the unique identifier (traitID) of the broader trait. Each trait can only have one broader term. 2017-08-24 @@ -839,7 +863,7 @@ relatedTerm One or several terms that relate to this term - This allows to link terms of the same hierarchical level or of other branches of the ontology + This allows to link terms of the same hierarchical level or of other branches of the ontology 2018-09-18 @@ -859,7 +883,7 @@ expectedUnit - The unit expected for measurement entries. + The unit expected for measurement entries. Only applies to numerical traits. Should be given in SI units. 2017-10-24 @@ -871,7 +895,7 @@ factorLevels A comma separated list of terms comprising the constrained vocabulary for categorical traits or ordinal binary traits. - Ordinal traits may be encoded with numerically indexed factor levels; e.g. 1_egg, 2_larvae, 3_pupae, 4_adult; the field traitDescription should define the factor levels; + Ordinal traits may be encoded with numerically indexed factor levels; e.g. 1_egg, 2_larvae, 3_pupae, 4_adult; the field traitDescription should define the factor levels; 2017-09-27 2017-11-15 @@ -882,7 +906,7 @@ maxAllowedValue A lower boundary for accepted numerical values. - May be used for eliminating invalid data. This boundary may constrain a range of values of meaningful orders of magnitude, or constrain entries to positive values. + May be used for eliminating invalid data. This boundary may constrain a range of values of meaningful orders of magnitude, or constrain entries to positive values. 2017-09-27 @@ -892,7 +916,7 @@ minAllowedValue An upper boundary for accepted numerical values. - May be used for eliminating invalid data. This boundary may constrain a range of values of meaningful orders of magnitude. + May be used for eliminating invalid data. This boundary may constrain a range of values of meaningful orders of magnitude. 2017-09-27 @@ -911,14 +935,14 @@ recommended - + comments Details and Examples for clarification of the trait definition. Can contain definition of trait levels or requirements for standardized conditions. - 2017-07-07 - 2017-11-15 + 2018-11-01 + recommended @@ -932,4 +956,186 @@ recommended - \ No newline at end of file + + scientificName + Original character string provided as species name by the data owner (kept for reference and continuity) + Can be equal to scientificNameStd. Authors may use abbreviations, or use underscores to separate genus and species name. + + 2017-07-07 + 2018-05-29 + + + historical + + + + + traitName + Name of the trait as used by the data provider (kept for compatibility on provider side). + This can be a short name or user defined coded trait name. However, it is recommended to provide definition of the user provided trait names in the metadata. + + 2017-07-07 + + + historical + + + + + traitID + Unique identifier of the trait according to a public ontology, or a user-provided thesaurus of traits. + Examples: TO:0000181; TOP103; http://top-thesaurus.org/annotationInfo?viz=1&&trait=Seed_mass; + + 2017-07-07 + 2018-05-29 + + historical + + + + + traitValue + Measured raw value or factor level for this species trait as measured and provided by the author. + Must respect the unit given in 'measurementUnit_user' for numerical traits. For categorical traits, the factor levels should be harmonized across the dataset and explained in the metadata. + + 2017-07-07 + + + historical + + + + + traitUnit + 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. + 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" + + 2017-07-07 + + + historical + + + + + scientificNameStd + The full name, with authorship and date information if known. This should resolve to the currently valid (zoological) or accepted (botanical) taxon. + 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 + + 2017-07-07 + 2017-11-01 + + + historical + + + + + traitNameStd + Descriptive Name of the trait reported. This should follow the controlled vocabulary of a thesaurus of traits available online or published along with the dataset. + Accompanying this, the traitID should provide an unambiguous link to the trait definition in the thesaurus or supplementary dataset. + + 2017-07-07 + + + historical + + + + + traitValueStd + Standardized 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. + 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" + + 2017-07-07 + + + historical + + + + + traitUnitStd + The units associated with the measurementValue. The expected standard unit for this trait as defined in the traitlist/ thesaurus. + Recommended best practice is to use the International System of Units (SI). Examples: "mm", "C", "km", "ha". For discussion see http://terms.tdwg.org/wiki/dwc:measurementUnit + + 2017-07-07 + + + historical + + + + + measurementID + An identifier for the MeasurementOrFact (information pertaining to measurements, facts, characteristics, or assertions). May be a global unique identifier or an identifier specific to the data set. + Links multi-value trait measurements, e.g. x-y-z coordinates of a morphometric landmark, biochemical compound quantities for different chainlengths. In this case, the trait names must specify the sub-measurement, e.g. "landmark32_x", and must be specified in a reference trait list, given in the field "measurementMethod". + + 2017-07-07 + + + historical + + + + + occurrenceID + An identifier for the Occurrence (as opposed to a particular digital record of the occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the occurrenceID globally unique. + For a specimen in the absence of a bona fide global unique identifier, for example, use the form: "urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]. Examples: "urn:lsid:nhm.ku.edu:Herps:32", "urn:catalog:FMNH:Mammal:145732". For discussion see http://terms.tdwg.org/wiki/dwc:occurrenceID. This is important for the analysis of co-variation of morphometric data or intraspecific variation. It also couples multiple measurements on a single specimen, which also could be a leaf or a single bone without an assignment to an individual organism. If available, upload related dataset to describe specimens more precisely, e.g. environmental parameters or identity related information. + + 2017-07-07 + + + historical + + + + + basisOfRecord + How and from which kind of specimen were the data obtained? Make use of controlled vocabulary. Valid entries are: 'LivingSpecimen'; 'PreservedSpecimen'; 'FossilSpecimen'; 'literatureData'; 'traitDatabase'; 'expertKnowledge' (see Comments) + Options are: Taken by own measurement (defined in DwC: http://rs.tdwg.org/dwc/terms/LivingSpecimen; http://rs.tdwg.org/dwc/terms/PreservedSpecimen; http://rs.tdwg.org/dwc/terms/FossilSpecimen ) or taken from literature (enter 'literatureData'), from an existing trait database (enter 'traitDatabase'), or expert knowledge (enter 'expertKnowledge'). Provide further information in field 'basisOfRecordDescription' and 'references'. + + 2017-07-07 + + + historical + + + + + basisOfRecordDescription + Adding more detail to the basisOfRecord. + If life specimens were sampled, where did they come from? Have they been reared in cultivation? If literature data or online database, provide type of literature, e.g. textbook, website, URL, etc. If preserved specimens were used, which method of preservation? In case of expert knowledge, give the name of the authority. + + 2017-07-07 + + historical + + + + + identifier + A unique identifier for the trait; globally unique or dataset-specific + Identifiers are ideally globally unique and stable URIs which link to the source of the trait description in a public ontology or thesaurus of traits; + + 2017-10-24 + 2018-05-29 + + + historical + + + + + comments + Details and Examples for clarification of the trait definition. + Can contain definition of trait levels or requirements for standardized conditions. + + 2017-07-07 + 2017-11-15 + + historical + + + +