index.rst

pyobis

Python client for the OBIS API.

Source on GitHub at iobis/pyobis

Other OBIS clients:

• R: robis, iobis/robis

Installation

from pypi

pip install pyobis

dev version

pip install git+git://github.com/iobis/pyobis.git#egg=pyobis

Library API

pyobis is split up into modules for each of the groups of API methods.

• checklist - Checklist. Generate a checklist of species under a taxa, IUCN Red List, or most recently added species.
• dataset - Dataset. Get metadata of datasets (including datasetid, owner, institution, number of records, etc) for a queried spatiotemporal region or taxa.
• nodes - Nodes. Get records or activities for an OBIS node.
• occurrences - Occurrence. Fetch occurrence records, geopoints, lookup for a scientificname, extensions (e.g. DNADerivedData, MeasurementOrFacts, etc.)
• taxa - Taxonomic names. Get taxon records with taxonid or scientificname, and scientific name annotations by the WoRMS team.

You can import the entire library, or each module individually as needed.

Taxa module

from pyobis import taxa

query = taxa.search(scientificname="Mola mola")
query.execute()
query.data  # Returns the data
query.api_url  # Returns the API URL

data = taxa.search(scientificname="Mola mola").execute()
taxa.search(geometry="POLYGON((30.1 10.1, 10 20, 20 40, 40 40, 30.1 10.1))")
taxa.taxon(10332)
taxa.taxon(127405)

Occurrence module

from pyobis import occurrences

query = occurrences.search(scientificname="Mola mola")
query.execute()
query.data  # Returns the data
query.api_url  # Returns the OBIS API URL
query.mapper_url  # Returns the OBIS Mapper URL

data = occurrences.search(scientificname="Mola mola", size=10).execute()
occurrences.search(
    geometry="POLYGON((30.1 10.1, 10 20, 20 40, 40 40, 30.1 10.1))", size=20
)

Dataset module

from pyobis import dataset

query = dataset.search(scientificname=["Mola", "Abra", "Lanice", "Pectinaria"])
query.execute()
query.data  # Returns the data
query.api_url  # Returns the API URL

data = dataset.get(id="ec9df3b9-3b2b-4d83-881b-27bcbcd57b95").execute()

Nodes module

from pyobis import nodes

query = nodes.search(scientificname=["Mola", "Abra"])
query.execute()
query.data  # Returns the data
query.api_url  # Returns the API URL

Checklist module

from pyobis import checklist

query = checklist.list(scientificname="Cetacea")
query.execute()
query.data  # Returns the data
query.api_url  # Returns the OBIS API URL

Meta

• License: MIT, see LICENSE file
• Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Contents

.. toctree::
   :maxdepth: 2

   occurrences
   taxa
   dataset
   nodes
   checklist
   changelog_link

License

MIT

Indices and tables

• :ref:`genindex`
• :ref:`modindex`
• :ref:`search`