taxon-parser

Taxon parser

This library is a pure Python adaptation of the GBIF Java name-parser library.

It is used to parse any taxonomic name into its elementary components (genus, species, authors...)

It returns a ParsedName object containing the name parts and the original parsed string.

Installation

pip install taxon_parser

Requirements

This library works for Python version 3.4 or higher

The only external package dependancy is the regex package for handling advanced regular expressions.

Usage

basic usage:

from taxon_parser import TaxonParser, UnparsableNameException

parser = TaxonParser("Abies pectinata mill.")
try:
    parsed_name = parser.parse()
    print(parsed_name)
except UnparsableNameException as e:
    print("this name does not seem to be a valid taxon name: \n" + e )

For any name that can not be parsed, an UnparsableNameException is thrown.

ParsedName objects

Results of the parsing are ParsedName objects. These have the following attributes and functions:

• ParsedName.combinationAuthorship: Authorship object with years of the name, but excluding any basionym authorship. For binomials the combination authors.

• ParsedName.basionymAuthorship: basionym Authorship object with years of the name

• ParsedName.sanctioningAuthor: The sanctioning author for sanctioned fungal names. Fr. or Pers.

• ParsedName.rank: Rank of the name from enumeration see the rank.py for description of possible ranks

• ParsedName.uninomial: Represents the monomial for genus, families or names at higher ranks which do not have further epithets.

• ParsedName.genus: The genus part of an infrageneric, bi- or trinomial name. Not used for standalone genus names which are represented as uninomials.

Infrageneric epithets:

• ParsedName.infragenericEpithet

• ParsedName.specificEpithet

• ParsedName.infraspecificEpithet

• ParsedName.cultivarEpithet

• ParsedName.strain

• ParsedName.candidatus: A bacterial candidate name. Candidatus is a provisional status for incompletely described procaryotes (e.g. that cannot be maintained in a Bacteriology Culture Collection) which was published in the January 1995. The category Candidatus is not covered by the Rules of the Bacteriological Code but is a taxonomic assignment. The names included in the category Candidatus are usually written as follows: Candidatus (in italics), the subsequent name(s) in roman type and the entire name in quotation marks. For example, "Candidatus Phytoplasma", "Candidatus Phytoplasma allocasuarinae". See http://www.bacterio.net/-candidatus.html and https://en.wikipedia.org/wiki/Candidatus

• ParsedName.notho: The part of the named hybrid which is considered a hybrid

• ParsedName.taxonomicNotes: Nomenclatural status remarks of the name.

• ParsedName.remarks: Any informal remarks found in the name

• ParsedName.unparsed: Any additional unparsed string found at the end of the name. Only ever set when state=PARTIAL

• ParsedName.type: The kind of name classified in broad catagories based on their syntactical structure

• ParsedName.doubtful: Indicates some doubts that this is a name of the given type. Usually indicates the existance of unusual characters not normally found in scientific names.

• ParsedName.state: Indicates if the full name has been parsed

• ParsedName.getTerminalEpithet(): returns the terminal epithet. Infraspecific epithet if existing, the species epithet or null

• ParsedName.hasName(): return True if the parsed name has non null name properties or a scientific name. Remarks will not count as a name

• ParsedName.hasAuthorship(): return True if any kind of authorship exists

• ParsedName.isBinomial(): return True if the name is a bi- or trinomial with at least a genus and species epithet given.

• ParsedName.isTrinomial(): return true if the name is a trinomial with at least a genus, species and infraspecific epithet given.

• ParsedName.isIndetermined(): Checks if a parsed name is missing final epithets compared to what is indicated by its rank. Returns True if the name is not fully determined.

• ParsedName.isIncomplete(): returns True if some "higher" epithet of a name is missing, e.g. the genus in case of a species.

• ParsedName.isAbbreviated(): returns True if the name contains an abbreviated genus or uninomial.

• ParsedName.canonicalName(): A full scientific name with authorship from the individual properties in its canonical form. Autonyms are rendered without authorship and subspecies are using the subsp rank marker unless a name is assigned to the zoological code.

• ParsedName.canonicalName(): A full scientific name just as canonicalName, but without any authorship.

• ParsedName.canonicalComplete(): Assembles a full name with all details including non code compliant, informal remarks.

• ParsedName.nameMinimal(): returns a minimal canonical name with nothing else but the 3 main name parts (genus, species, infraspecific). No rank or hybrid markers and no authorship, cultivar or strain information is rendered. Infrageneric names are represented without a leading genus. Unicode characters will be replaced by their matching ASCII characters. For example:

  • Abies alba
  • Abies alba alpina
  • Bracteata

• ParsedName.authorshipComplete(): returns the full concatenated authorship for parsed names including the sanctioning author.