checklist module

class pyobis.checklist.ChecklistResponse(url, args, paginate)[source]

An OBIS Checklist Response Object

Usage

from pyobis import checklist

query = checklist.list(taxonid=127405, **kwargs)
query.api_url  # Returns the API URL
query.to_pandas()  # Returns a pandas DataFrame object

Methods:

pyobis.checklist.list(scientificname=None, taxonid=None, nodeid=None, startdate=None, enddate=None, startdepth=None, enddepth=None, geometry=None, flags=None, **kwargs)[source]

Generate an OBIS checklist

Parameters:

  • taxonid – [Fixnum] A obis occurrence identifier

  • scientificname – [String,Array] One or more scientific names from the OBIS backbone. All included and synonym taxa are included in the search.

  • geometry – [String] Well Known Text (WKT). A WKT shape written as either POINT, LINESTRING, LINEARRING or POLYGON. Example of a polygon: ((30.1 10.1, 10 20, 20 40, 40 40, 30.1 10.1)) would be queried as https://api.obis.org/v3/occurrence?geometry=POLYGON%28%2830.1+10.1%2C+10+20%2C+20+40%2C+40+40%2C+30.1+10.1%29%29

  • nodeid – [Fixnum] Node UUID.

  • startdate – [String] Start date YYYY-MM-DD

  • enddate – [String] End date YYYY-MM-DD

  • startdepth – [Fixnum] Start depth, in meters. Depth below sea level are treated as positive numbers.

  • enddepth – [Fixnum] End depth, in meters. Depth below sea level are treated as positive numbers.

  • flags – [String] Comma separated list of quality flags which need to be set

Returns:

A dictionary

Usage:

from pyobis import checklist
checklist.list(scientificname = 'Mola mola').execute()

# taxonid of 3013
checklist.list(taxonid = 3013).execute()
pyobis.checklist.redlist(scientificname=None, taxonid=None, nodeid=None, startdate=None, enddate=None, startdepth=None, enddepth=None, geometry=None, flags=None, **kwargs)[source]

Generate a checklist of IUCN Red List species.

Parameters:

  • scientificname – [String] Scientific name. Leave empty to include all taxa.

  • taxonid – [String] Taxon AphiaID.

  • nodeid – [String] Node UUID.

  • startdate – [String] Start date formatted as YYYY-MM-DD.

  • enddate – [String] End date formatted as YYYY-MM-DD.

  • startdepth – [Fixnum] Start depth, in meters. Depth below sea level are treated as positive numbers.

  • enddepth – [Fixnum] End depth, in meters. Depth below sea level are treated as positive numbers.

  • geometry – [String] Geometry, formatted as WKT or GeoHash.

  • flags – [String] Comma separated list of quality flags which need to be set.

Returns:

A dictionary

Usage:

from pyobis import checklist
checklist.redlist(scientificname='Abra Alba').execute()
pyobis.checklist.newest(scientificname=None, taxonid=None, nodeid=None, startdate=None, enddate=None, startdepth=None, enddepth=None, geometry=None, flags=None, **kwargs)[source]

Generate a checklist of most recently added species.

Parameters:

  • scientificname – [String] Scientific name. Leave empty to include all taxa.

  • taxonid – [String] Taxon AphiaID.

  • nodeid – [String] Node UUID.

  • startdate – [String] Start date formatted as YYYY-MM-DD.

  • enddate – [String] End date formatted as YYYY-MM-DD.

  • startdepth – [Fixnum] Start depth, in meters. Depth below sea level are treated as positive numbers.

  • enddepth – [Fixnum] End depth, in meters. Depth below sea level are treated as positive numbers.

  • geometry – [String] Geometry, formatted as WKT or GeoHash.

  • flags – [String] Comma separated list of quality flags which need to be set.

Returns:

A dictionary

Usage:

from pyobis import checklist
checklist.newest(scientificname='Abra Alba')