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NAME

v.in.pygbif - Search and import GBIF species distribution data

KEYWORDS

vector, geometry

SYNOPSIS

v.in.pygbif
v.in.pygbif --help
v.in.pygbif [-brpigotns] output=name taxa=string [mask=name] [date_from=string] [date_to=string] [basisofrecord=string] rank=string [recordedby=string] [institutioncode=string] [country=string] [continent=string] [--overwrite] [--help] [--verbose] [--quiet] [--ui]

Flags:

-b
Do not build topology
-r
Do not limit import to current region (works only in lat/lon)
-p
Print result from matching taxa names and exit
-i
Produce individual map for each taxon
-g
Print result from matching taxon names in shell script style and exit
-o
Print number of matching occurrences per taxon and exit
-t
Print result of taxon matching in table format and exit
-n
Do not limit search to records with coordinates
-s
Do also import occurrences with spatial issues
--overwrite
Allow output files to overwrite existing files
--help
Print usage summary
--verbose
Verbose module output
--quiet
Quiet module output
--ui
Force launching GUI dialog

Parameters:

output=name [required]
Name of resulting vector map with occurrences
taxa=string [required]
Comma separated list of taxon names or keys to fetch data for
mask=name
Name of input vector map
Vector map that delimits region of interest
date_from=string
Lower bound of acceptable dates (format: yyyy, yyyy-MM, yyyy-MM-dd, or MM-dd)
date_to=string
Upper bound of acceptable dates (format: yyyy, yyyy-MM, yyyy-MM-dd, or MM-dd)
basisofrecord=string
Accepted basis of records
Options: ALL, FOSSIL_SPECIMEN, HUMAN_OBSERVATION, LITERATURE, LIVING_SPECIMEN, MACHINE_OBSERVATION, OBSERVATION, PRESERVED_SPECIMEN, UNKNOWN
Default: ALL
rank=string [required]
Rank of the taxon to search for
Options: class, cultivar, cultivar_group, domain, family, form, genus, informal, infrageneric_name, infraorder, infraspecific_name, infrasubspecific_name, kingdom, order, phylum, section, series, species, strain, subclass, subfamily, subform, subgenus, subkingdom, suborder, subphylum, subsection, subseries, subspecies, subtribe, subvariety, superclass, superfamily, superorder, superphylum, suprageneric_name, tribe, unranked, variety
Default: species
recordedby=string
The person who recorded the occurrence.
institutioncode=string
An identifier of any form assigned by the source to identify the institution the record belongs to.
country=string
The 2-letter country code (as per ISO-3166-1) of the country in which the occurrence was recorded
continent=string
The continent in which the occurrence was recorded
Options: africa, antarctica, asia, europe, north_america, oceania, south_america

Table of contents

DESCRIPTION:

The module v.in.pygbif is a wrapper around the pygbif package.
Thus, pygbif is a dependency of v.in.pygbif. pygbif can be installed like this:

pip install pygbif

Through pygbif, the module allows to download data from the Global Biodiversity Information Facility (GBIF) using different search ⁄ filter criteria.

Since some of the Darwin Core attribute columns represent SQL key-words, the prefix "g_" was added to all attribute columns. The names of taxa provided at input to the search are written to the column "g_search".

The point data is downloaded and projected into the current location. By default import is limited to the current computational region in order to avoid possible projection errors, e.g. when projecting global data into UTM locations. However, in lat⁄lon location this limitation can be skiped using the -r flag.
Providing a mask automatically overrides the limitation of the search to the current computational region.

Terminology in v.in.pygbif is oriented on the Darwin Core standard: http://rs.tdwg.org/dwc/.

Please note that the GBIF Search API has a hard limit of 200,000 occurrences per request. If you want to fetch more records, either subivide your area of interest or split up your search by using different search criteria.
When a list of taxa is given as input, v.in.pygbif issues a search for each taxon individually. Thus, in order to split up a search it is recommended to either use different filters on time or space.

EXAMPLES:

# Check matching taxon names and alternatives in GBIF:
v.in.pygbif taxa="Poa,Plantago" rank=genus  -p

# Check matching taxon names and alternatives in GBIF and print output in table:
v.in.pygbif taxa="Poa pratensis,Plantago media,Acer negundo" rank=species -t

# Get number of occurrences for two geni:
v.in.pygbif taxa="Poa,Plantago" rank=genus  -o

# Get number of occurrences for two species:
v.in.pygbif taxa="Poa pratensis,Plantago media" rank=species  -o

# Fetch occurrences for two species into a map for each species:
v.in.pygbif taxa="Poa pratensis,Plantago media" rank=species output=gbif -i

SEE ALSO:

v.in.gbif

REFERENCES:

http://pygbif.readthedocs.io/en/latest/index.html
http://www.gbif.org
http://www.gbif.org/developer/summary

AUTHOR:

Stefan Blumentrath, Norwegian Institute for Nature Research, Oslo, Norway
Helmut Kudrnovsky

SOURCE CODE

Available at: v.in.pygbif source code (history)


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