ITIS

itis.itis_ping(**kwargs)

Ping the ITIS API

Usage:

import pytaxize
pytaxize.itis_ping()
itis.getacceptednamesfromtsn(tsn, **kwargs)

Get accepted names from tsn

Parameters:tsn – taxonomic serial number (TSN) (character or numeric)

Usage:

# TSN accepted - good name
pytaxize.getacceptednamesfromtsn('208527')
# TSN not accepted - input TSN is old name
pytaxize.getacceptednamesfromtsn('504239')
itis.getanymatchcount(x, **kwargs)

Get any match count.

Parameters:
  • x – text or taxonomic serial number (TSN) (character or numeric)
  • **kwargs

    Curl options passed on to requests.get

Usage:

pytaxize.getanymatchcount(x=202385)
pytaxize.getanymatchcount(x="dolphin")
itis.getcommentdetailfromtsn(tsn, **kwargs)

Get comment detail from TSN

Parameters:
  • tsn – TSN for a taxonomic group (numeric)
  • **kwargs

    Curl options passed on to requests.get

Usage:

pytaxize.getcommentdetailfromtsn(tsn=180543)
itis.getcommonnamesfromtsn(tsn, **kwargs)

Get common names from tsn

Parameters:
  • tsn – TSN for a taxonomic group (numeric)
  • **kwargs

    Curl options passed on to requests.get

Usage:

pytaxize.getcommonnamesfromtsn(tsn=183833)
itis.getcoremetadatafromtsn(tsn, **kwargs)

Get core metadata from tsn

Usage:

# coverage and currrency data
pytaxize.getcoremetadatafromtsn(tsn=28727)
# no coverage or currrency data
pytaxize.getcoremetadatafromtsn(tsn=183671)
itis.getcoveragefromtsn(tsn, **kwargs)

Get coverge from tsn

Usage:

# coverage data
pytaxize.getcoveragefromtsn(tsn=28727)
# no coverage data
pytaxize.getcoveragefromtsn(526852)
itis.getcredibilityratingfromtsn(tsn, **kwargs)

Get credibility rating from tsn

Usage:

pytaxize.getcredibilityratingfromtsn(526852)
pytaxize.getcredibilityratingfromtsn(28727)
itis.getcredibilityratings(**kwargs)

Get possible credibility ratings

Parameters:**kwargs

Curl options passed on to requests.get

Usage:

pytaxize.getcredibilityratings()
itis.getcurrencyfromtsn(tsn, **kwargs)

Get currency from tsn

Usage:

# currency data
pytaxize.getcurrencyfromtsn(28727)
# no currency dat
pytaxize.getcurrencyfromtsn(526852)
itis.getdatedatafromtsn(tsn, **kwargs)

Get date data from tsn

Usage:

pytaxize.getdatedatafromtsn(180543)
itis.getexpertsfromtsn(tsn, **kwargs)

Get expert information for the TSN.

Usage:

pytaxize.getexpertsfromtsn(180544)
itis.gettaxonomicranknamefromtsn(tsn, **kwargs)

Returns the kingdom and rank information for the TSN.

Parameters:tsn – TSN for a taxonomic group (numeric)

Usage:

pytaxize.gettaxonomicranknamefromtsn(tsn = 202385)
itis.getfullhierarchyfromtsn(tsn, **kwargs)

Get full hierarchy from ts

Parameters:tsn – TSN for a taxonomic group (numeric)

Usage:

pytaxize.getfullhierarchyfromtsn(tsn = 37906)
pytaxize.getfullhierarchyfromtsn(tsn = 100800)
itis.getfullrecordfromlsid(lsid, **kwargs)

Returns the full ITIS record for the TSN in the LSID, found by comparing the TSN in the search key to the TSN field. Returns an empty result set if there is no match or the TSN is invalid.

Parameters:
  • lsid – lsid for a taxonomic group (character)
  • **kwargs

    Curl options passed on to requests.get

Usage:

pytaxize.getfullrecordfromlsid("urn:lsid:itis.gov:itis_tsn:180543")
pytaxize.getfullrecordfromlsid("urn:lsid:itis.gov:itis_tsn:37906")
pytaxize.getfullrecordfromlsid("urn:lsid:itis.gov:itis_tsn:100800")
itis.getfullrecordfromtsn(tsn, **kwargs)

Returns the full ITIS record for a TSN

Parameters:
  • tsn – tsn for a taxonomic group (character)
  • **kwargs

    Curl options passed on to requests.get

Usage:

pytaxize.getfullrecordfromtsn("504239")
pytaxize.getfullrecordfromtsn("202385")
pytaxize.getfullrecordfromtsn("183833")
itis.getgeographicdivisionsfromtsn(tsn, **kwargs)

Get geographic divisions from tsn

Usage:

pytaxize.getgeographicdivisionsfromtsn(180543)
itis.getgeographicvalues(**kwargs)

Get all possible geographic values

Parameters:**kwargs

Curl options passed on to requests.get

Usage:

pytaxize.getgeographicvalues()
itis.getglobalspeciescompletenessfromtsn(tsn, **kwargs)

Get global species completeness from tsn

Usage:

pytaxize.getglobalspeciescompletenessfromtsn(180541)
itis.gethierarchydownfromtsn(tsn, **kwargs)

Get hierarchy down from tsn

Parameters:tsn – TSN for a taxonomic group (numeric)

Usage:

pytaxize.gethierarchydownfromtsn(tsn = 161030)
itis.gethierarchyupfromtsn(tsn, **kwargs)

Get hierarchy up from tsn

Parameters:tsn – TSN for a taxonomic group (numeric)

Usage:

pytaxize.gethierarchyupfromtsn(tsn = 36485)
pytaxize.gethierarchyupfromtsn(tsn = 37906)
itis.getitistermsfromcommonname(x, **kwargs)

Get itis terms from common names

Usage:

pytaxize.getitistermsfromcommonname("buya")
itis.getitisterms(x, **kwargs)

Get itis terms

Usage:

# fails
pytaxize.getitisterms("bear")
itis.getitistermsfromscientificname(x, **kwargs)

Get itis terms from scientific names

Usage:

pytaxize.getitistermsfromscientificname("ursidae")
pytaxize.getitistermsfromscientificname("Ursus")
itis.itis_hierarchy(tsn=None, what='full')

Get hierarchies from TSN values, full, upstream only, or immediate downstream only. Uses the ITIS database.

Parameters:
  • tsn – One or more TSN’s (taxonomic serial number)
  • what – One of full (full hierarchy), up (immediate upstream), or down (immediate downstream)
Details Note that pytaxize.itis_downstream gets taxa downstream to a particular
rank, whilc this function only gets immediate names downstream.

Usage:

# Get full hierarchy
pytaxize.itis_hierarchy(tsn=180543)

# Get hierarchy upstream
pytaxize.itis_hierarchy(tsn=180543, "up")

# Get hierarchy downstream
pytaxize.itis_hierarchy(tsn=180543, "down")

# Many tsn's
pytaxize.itis_hierarchy(tsn=[180543,41074,36616])
itis.getjurisdictionaloriginfromtsn(tsn, **kwargs)

Get jurisdictional origin from tsn

Usage:

pytaxize.getjurisdictionaloriginfromtsn(180543)
itis.getjurisdictionoriginvalues(**kwargs)

Get jurisdiction origin values

Usage:

pytaxize.getjurisdictionoriginvalues()
itis.getjurisdictionvalues(**kwargs)

Get possible jurisdiction values

Usage:

pytaxize.getjurisdictionvalues()
itis.getkingdomnamefromtsn(tsn, **kwargs)

Get kingdom names from tsn

Usage:

pytaxize.getkingdomnamefromtsn(202385)
itis.getkingdomnames(**kwargs)

Get all possible kingdom names

Usage:

pytaxize.getkingdomnames()
itis.getlastchangedate(**kwargs)

Provides the date the ITIS database was last updated.

Usage:

pytaxize.getlastchangedate()
itis.getlsidfromtsn(tsn, **kwargs)

Gets the unique LSID for the TSN, or an empty result if there is no match.

Usage:

# valid TSN
pytaxize.getlsidfromtsn(155166)
# invalid TSN, returns nothing
pytaxize.getlsidfromtsn(0)
itis.getothersourcesfromtsn(tsn, **kwargs)

Returns a list of the other sources used for the TSN.

Usage:

pytaxize.getothersourcesfromtsn(182662)
itis.getparenttsnfromtsn(tsn, **kwargs)

Returns the parent TSN for the entered TSN.

Usage:

pytaxize.getparenttsnfromtsn(202385)
itis.getpublicationsfromtsn(tsn, **kwargs)

Returns a list of the pulications used for the TSN.

Usage:

pytaxize.getpublicationsfromtsn(70340)
itis.getranknames(**kwargs)

Provides a list of all the unique rank names contained in the database and their kingdom and rank ID values.

Usage:

pytaxize.getranknames()
itis.getrecordfromlsid(lsid, **kwargs)

Gets the partial ITIS record for the TSN in the LSID, found by comparing the TSN in the search key to the TSN field. Returns an empty result set if there is no match or the TSN is invalid.

Usage:

pytaxize.getrecordfromlsid("urn:lsid:itis.gov:itis_tsn:180543")
itis.getreviewyearfromtsn(tsn, **kwargs)

Returns the review year for the TSN.

Usage:

pytaxize.getreviewyearfromtsn(180541)
itis.getscientificnamefromtsn(tsn, **kwargs)

Returns the scientific name for the TSN. Also returns the component parts (names and indicators) of the scientific name.

Usage:

pytaxize.getscientificnamefromtsn(531894)
itis.gettaxonauthorshipfromtsn(tsn, **kwargs)

Returns the author information for the TSN.

Usage:

pytaxize.gettaxonauthorshipfromtsn(183671)
itis.gettaxonomicranknamefromtsn(tsn, **kwargs)

Returns the kingdom and rank information for the TSN.

Parameters:tsn – TSN for a taxonomic group (numeric)

Usage:

pytaxize.gettaxonomicranknamefromtsn(tsn = 202385)
itis.gettaxonomicusagefromtsn(tsn, **kwargs)

Returns the usage information for the TSN.

Usage:

pytaxize.gettaxonomicusagefromtsn(526852)
itis.gettsnbyvernacularlanguage(language, **kwargs)

Get tsn by vernacular language not the international language code (character)

Usage:

pytaxize.gettsnbyvernacularlanguage("french")
itis.gettsnfromlsid(lsid, **kwargs)

Gets the TSN corresponding to the LSID, or an empty result if there is no match.

Usage:

pytaxize.gettsnfromlsid(lsid="urn:lsid:itis.gov:itis_tsn:28726")
pytaxize.gettsnfromlsid("urn:lsid:itis.gov:itis_tsn:0")
itis.getunacceptabilityreasonfromtsn(tsn, **kwargs)

Returns the unacceptability reason, if any, for the TSN.

Usage:

pytaxize.getunacceptabilityreasonfromtsn(183671)
itis.getvernacularlanguages(**kwargs)

Provides a list of the unique languages used in the vernacular table.

Usage:

pytaxize.getvernacularlanguages()
itis.searchbycommonname(x, **kwargs)

Search for tsn by common name

Usage:

pytaxize.searchbycommonname(x="american bullfrog")
pytaxize.searchbycommonname("ferret-badger")
pytaxize.searchbycommonname("polar bear")
itis.searchbycommonnamebeginswith(x, **kwargs)

Search for tsn by common name beginning with

Usage:

pytaxize.searchbycommonnamebeginswith("inch")
itis.searchbycommonnameendswith(x, **kwargs)

Search for tsn by common name ending with

Usage:

pytaxize.searchbycommonnameendswith("snake")
itis.itis_searchcommon(x, which='begin', **kwargs)

Searches common name and acts as thin wrapper around pytaxize.searchbycommonnamebeginswith and pytaxize.searchbycommonnameendswith

Usage:

pytaxize.itis_searchcommon("inch")
pytaxize.itis_searchcommon("inch", which = "end")
itis.searchbyscientificname(x, **kwargs)

Search by scientific name

Usage:

pytaxize.searchbyscientificname(x="Tardigrada")
pytaxize.searchbyscientificname("Quercus douglasii")
itis.searchforanymatch(x, **kwargs)

Search for any match

Usage:

pytaxize.searchforanymatch(x=202385)
pytaxize.searchforanymatch(x="dolphin")
itis.searchforanymatchpaged(x, pagesize, pagenum, ascend, **kwargs)

Search for any matched page for descending (logical)

Usage:

pytaxize.searchforanymatchpaged(x=202385, pagesize=100, pagenum=1, ascend=False)
pytaxize.searchforanymatchpaged("Zy", pagesize=100, pagenum=1, ascend=False)