Download names and the currently accepted national taxonomy
Exports are available at:
APNI/APC : biodiversity.org.au/nsl/services/api/export/index
AusMoss : moss.biodiversity.org.au/nsl/services/api/export/index
Algae: algae.biodiversity.org.au/nsl/services/api/export/index
Lichen : lichen.biodiversity.org.au/nsl/services/api/export/index (currently will export the ABRS Lichen taxonomy, this is not a consensus taxonomy)
Fungi: fungi.biodiversity.org.au/nsl/services/api/export/index
Attribute description
A description of the attributes provided in the Darwin Core(DwC)/CSV Output definition file/s:
Name file : Output Name DwC Name Alternative Name ( TCS, TDWG, LinneCore, NSL) example: Name record example: Name record Explanation scientificName Persoonia glaucescens Sieber ex Spreng. Persoonia glaucescens Sieber ex Schult. & Schult. The name and author in full. scientificNameHTML scientificNameHTML <scientific><name id='112770'><scientific><name id='111160'><element><i>Persoonia</i></element></name></scientific> <element><i>glaucescens</i></element> <authors><ex id='9121' title='Sieber, F.W.'>Sieber</ex> ex <author id='6882' title='Sprengel, C.P.J.'>Spreng.</author></authors></name></scientific> <scientific><name id='112735'><scientific><name id='111160'><element><i>Persoonia</i></element></name></scientific> <element><i>glaucescens</i></element> <authors><ex id='9121' title='Sieber, F.W.'>Sieber</ex> ex <author id='10071' title='J.A. & J.H. Schultes'>Schult. & Schult.f.</author></authors></name></scientific> HTML version of the name with authorship. canonicalName canonicalName Persoonia glaucescens Persoonia glaucescens The name without authorship. canonicalNameHTML canonicalNameHTML <scientific><name id='112770'><scientific><name id='111160'><element><i>Persoonia</i></element></name></scientific> <element><i>glaucescens</i></element></name></scientific> <scientific><name id='112735'><scientific><name id='111160'><element><i>Persoonia</i></element></name></scientific> <element><i>glaucescens</i></element></name></scientific> HTML version of the name without authoriship. nameElement glaucescens glaucescens The component of the name at the lowest rank.ie. dealbata scientificNameID The identifier of this name. nameType nameType scientific scientific A categorisation of the name in the National Species List to indicate the structure and rules applied to this name ie. scientific, named hybrid, cultivar etc. taxonomicStatus accepted included The taxonomic status of the name in regard to the 'accepted taxonomy' for this dataset for example the Australian Plant Census (APC). nomenclaturalStatus legitimate nom. illeg., nom. superfl. The nomencultural status of this name. scientificNameAuthorship Sieber ex Spreng. Sieber ex Schult. & Schult.f. Authorship of the name, optionally :sanctioning author when appropriate. cultivarEpithet cultivarEpithet For cultivars, the cultivar name part of the name. autonym f f A flag indicating if this name is a autonym. hybrid f f A flag indicating if this is a hybrid name. cultivar f f A flag indicating if this is a cultivar name. formula f f A flag indicating if this is a formula name. scientific t t A flag indicating if this is a scientific name. nomInval f f A flag indicating if this name is nom. inval. nomIlleg f t A flag indicating if this name is nom. illeg. namePublishedIn Curae Posteriores. Systema Vegetabilium 4(2) Mantissa in Volumen ... Systematis Vegetabilium Edn. 16, 3: 271 The Protologue reference. Equivalent to nameAccordingTo namePublishedInYear 1827 1827 The year the protologue was published. nameInstanceType tax. nov. tax. nov. Status of this name in this work. tax. nov.; nom. nov.; primary reference etc. nameAccordingToID An identifier for the source in which the specific taxon concept circumscription is defined or implied. nameAccordingTo Sprengel, C.P.J. (1827) Endlicher, S.F.L. (1848) The reference to the source in which the specific taxon concept circumscription is defined or implied originalNameUsage The basionym or replaced synonym if a new combination or name. originalNameUsageID basionymID The scientificNameID of the basionym or replaced synonym if a new combination or name. originalNameUsageYear 1827 The year the original name usage was published. typeCitation Nov. Holl. Sieb. Herb. nov. Holl. No. 57. The type citation if this is the original name. ie. If this record is for Doodia media subsp. australis Parris then the citation would be "HOLOTYPE: CHR 202053; Kitekite Falls, Piha, North Auckland, B.S.Parris, 26.5.1966. Isotypes; Parris 683, 684." kingdom Plantae The full scientific name of the kingdom based on the classification being used in this output. family Proteaceae Proteaceae The full scientific name of the family based on the classification being used in this output. The Family is not provided for unplaced names. genericName Persoonia Persoonia The full scientific name of the genus based on the classification being used in this output. specificEpithet glaucescens glaucescens The name of the first or species epithet of the scientificName, based on the classification being used in this output. infraspecificEpithet The name of the lowest or terminal infraspecific epithet of the scientificName, excluding any rank designation, based on the classification being used in this output. taxonRank Species The taxonomic rank of the most specific name in the scientificName. taxonRankSortOrder taxonRankSortOrder 190 A sort order that can be applied to the rank. taxonRankAbbreviation taxonRankAbbreviation sp. The abbreviated taxonomic rank of this name. firstHybridParentName firstHybridParentName scientificName for the first hybrid parent. firstHybridParentNameID firstHybridParentNameID scientificNameID of the first hybrid parent. secondHybridParentName secondHybridParentName scientificName for the second hybrid parent (if known). secondHybridParentNameID secondHybridParentNameId scientificNameID of the second hybrid parent (if known). created created Date the record for this name was created. modified Date of the most recent change across all elements that make up a name. nomenclaturalCode ICN ICN The nomenclatural code under which this name is constructed. datasetName APNI The name of the dataset that this name came from. license ccLicense License by which this data is provide. ccAttributionIRI The attribution to be used when citing this name.
Values: accepted, included, excluded, unplaced.
http://rs.gbif.org/vocabulary/gbif/nomenclatural_status.xml
Synonyms in the accepted classification are placed in the family of the accepted name.
Taxon file : NOTE: All attributes are extracted based on the selected ‘tree’ or classification. By default the selected tree is the nationally accepted taxonomy. Attribute DwC Name Alternative Name ( TCS, TDWG, LinneCore, NSL) Example: accepted name record Example: synonym (relationship instance) Explaination taxonID https://id.biodiversity.org.au/node/apni/2908545 or a newer format https://id.biodiversity.org.au/taxon/apni/51434310 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. The taxon identifier for the accepted name is the nodeID in the NSL. The taxonID provides for read consistency within a classification at the point in time the taxon extract is taken. It is not a global identifier. nameType nameType scientific scientific A categorisation of the name in the National Species List to indicate the structure and rules applied to this name ie. scientific, named hybrid, cultivar etc. acceptedNameUsageID The taxonID associated with the accepted concept for this name according to the classification being exported. eg. APC. acceptedNameUsage Persoonia glaucescens Sieber ex Spreng. Persoonia glaucescens Sieber ex. Spreng The scientific name of the accepted concept for this name. nomenclaturalStatus legitimate nom. illeg., nom. superfl. The nomenclatural status of this name. taxonomicStatus accepted nomenclatural synonym The status of this name in this classification. Accepted names are indicated as such and names that are mentioned in the accepted taxonomy have the relationship of that name to the accepted name. proParte proParteRelationship f f For names that are not the accepted name, a flag that indicates this name is applied to this accepted name in part. If a name is 'pro parte' then the name will have more than 1 accepted name. t=true, f=false scientificName Persoonia glaucescens Sieber ex Spreng. Persoonia glaucescens Sieber ex Schult. & Schult.f The name and author in full. scientificNameID The identifier of this name. Unique within the Australian National Species infrastructure. canonicalName canonicalName Persoonia glaucescens Persoonia glaucescens The name without authorship scientificNameAuthorship Sieber ex Spreng. Sieber ex Schult. & Schult.f. Authorship of the name, optionally :sanctioning author when appropriate. parentNameUsageID For accepted names: The taxonID of the direct, most proximate higher-rank parent taxon (in a classification) of the most specific element of the scientificName. taxonRank Species Species The taxonomic rank of the most specific name in the scientificName. taxonRankSortOrder taxonRankSortOrder 190 190 A sort order that can be applied to the rank. kingdom Plantae Plantae The full scientific name of the kingdom based on the classification being used in this output. class Magnoliopsida Magnoliopsida The full scientific name of the class, based on the classification being used in this output.. subclass subclass Rosidae Rosidae The full scientific name of the subclass, based on the classification being used in this output. family Proteaceae Proteaceae The full scientific name of the family based on the classification being used in this output. created created 2005-11-22 14:51:45+11 2005-06-20 14:27:23+10 Date the record for this concept was created. Format ISO:86 01 modified 2005-11-22 14:51:45+11 2005-06-20 14:27:23+10 Date of the most recent change across all elements that make up a concept. Format ISO:86 01 datasetName classification APC APC Name of the taxonomy (tree) that contains this concept. ie. APC, AusMoss etc taxonConceptID An identifier for the taxonomic concept to which the record refers. The identifier for the accepted name is the instance.instanceID in the NSL. The taxonConceptId is persistent across extracts and will be consistent for the time for which a concept is accepted. Changes in the circumscription of a taxon that occur through the publication of a new taxon concept will result in a new identifier. nameAccordingTo CHAH (2005), Australian Plant Census Schultes, J.A. & Schultes, J.H. (1827) The reference citation for this name. nameAccordingToID The identifier associated with the reference in which this name is described. taxonRemarks Comments made specifically about this name in the classification being referenced. taxonDistribution taxonDistribution NSW States/Territory distribution of the accepted name higherClassification Plantae|Charophyta|Equisetopsida| Magnoliidae|Proteanaea|Proteales|Proteaceae| Persoonia| A list (concatenated and separated) of taxa names terminating at the rank immediately superior to the taxon referenced in this record. Based on the classification being used in this output. firstHybridParentName firstHybridParentName scientificName for the first hybrid parent. firstHybridParentNameID firstHybridParentNameID scientificNameID of the first hybrid parent. secondHybridParentName secondHybridParentName scientificName for the second hybrid parent (if known). secondHybridParentNameID secondHybridParentNameId scientificNameID of the second hybrid parent (if known). nomenclaturalCode ICN ICN The nomenclatural code under which this name is constructed. license ccLicense The license by which this data is being made available ccAttributionIRI The attribution to be used when citing this concept.
The taxon identifier for a synonym is the relationshipID in the NSL.
https://rs.gbif.org/vocabulary/gbif/nomenclatural_status.xml
https://rs.gbif.org/vocabulary/gbif/taxonomic_status.xml
The identifier for a synonym is the instance.citesID in the NSL.
Notes & Caveats
Extracts are provided in CSV format, using DwC attribute names where possible.
All object identifiers are actionable IRI.
Additional attribute names are taken from the DwC issue tracker or from the NSL schema.
These flattened extracts are a high level abstraction from the underlying data objects. The queries are complex and subject to frequent review so please report errors and discrepancies if they are found.
These datasets are incomplete, works in progress - for details of the specific status of each, please contact the custodian.
Specific information in regards to APNI / APC
APNI Names Extract
Additional caveats:
- these data are not (yet) filtered to correctly limit APNI's taxonomic scope so there will be some overlap with names from other NSL shards, such as Mosses, Fungi, etc.;
not every name will have a protologue, some trees remain un-rooted, there are still several families missing.
Includes names:
- that have been used in APC including phrase names, common names and hybrid names;
- that have not yet treated in APC such as the Orchids;
- cultivars;
- Algae, Fungi and Bryophytes (these will be replaced with the names from their source datasets when they are incorporated into the NSL)
- hybrid formulae.
The extract now includes many names (such as isonyms) that may seem superfluous or unnecessary complications outside of their nomenclatural or taxonomic context. The solution here may be to provide a number of expurgated editions, tailoring to particular use cases.
APC Taxon Extract
APC is incomplete. This is most noticeable in the taxonomic arrangement. Parent taxa with taxonomic status 'DeclaredBT' are hypothetical entries (for the purpose of maintaining the tree - then mostly for excluded taxa) that should be removed from this extract. They will disappear as the APC coverage incorporates these taxa.