Package: pyobis
pyobisPython client for the `OBIS API(https://api.obis.org/).Source on GitHub at iobis/pyobisWhat is it?Pyobis is an interesting python package that helps users fetch data from OBIS API which
harvests occurrence records from thousands of datasets and makes them available as a
single integrated dataset.The Ocean Biodiversity Information System (OBIS)is a global open-access data and
information clearing-house on marine biodiversity for science, conservation, and sustainable
development, maintained by IOOS.Other OBIS clients:R:robis,iobis/robisMain FeaturesHere are just a few of things pyOBIS can do:Easy handling of OBIS data, easy fetching without handling the raw API response directly.Built-in functions foroccurrence,taxon,node,checklistanddatasetendpoints of OBIS API.Provides easy export of data toPandasDataFrame, and helps researchers focus more on analysis rather than data mining.For examples of how to use this repo, see the jupyter notebooks in the/notebooks/directory.
NOTE: GitHub's jupyter notebook display does not show interactive plots; open the notebooks in a jupyter hub (eg colab, binder, etc) for the full experience.InstallationInstall from PyPIpipinstallpyobisInstall from conda-forgeInstalling pyobis from the conda-forge channel can be achieved by adding conda-forge to your channels with:condainstallpyobis--channelconda-forgeMore information hereInstall latest development version from GitHubpipinstallgit+git://github.com/iobis/pyobis.git#egg=pyobisInstall editable dev version from github for local development. System prerequisites: python3, conda# fetch codegitclonegit@github.com:iobis/pyobis.gitcdpyobis# installpython-mpipinstall-rrequirements.txt
python-mpipinstall-rrequirements-dev.txt
python-mpipinstall-e.# test your installationpython-mpytest# test and generate a coverage reportpython-mpytest-rxs--cov=pyobistestsDocumentationThe official documentation is hosted on GitHub Pageshttps://iobis.github.io/pyobis.Library APIpyobisis 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 (includingdatasetid,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 ascientificname, extensions (e.g. DNADerivedData, MeasurementOrFacts, etc.)taxa- Taxonomic names. Get taxon records withtaxonidorscientificname, and scientific name annotations by the WoRMS team.You can import the entire library, or each module individually as needed.Usage GuideFor a detailed usage guide with information about inputs, output and module functions please read theUsage GuideSample analysisSome Jupyter Notebook based sample analysis and visualization of data grabbed throughpyobishave been made available through/notebooks/directory.
To get full experience of the interactive plots (eg. geoplots, etc) please open notebooks in a Jupyter Hub (eg. through Google Colab, Binder, local installation, etc.)MetaLicense: MIT, seeLICENSE fileHelp make this project even more useful! Please read theContributing Guide.Please note that this project is released with aContributor Code of Conduct. By participating in this project you agree to abide by its terms.Further ReadingIn case you face data quality issues, please look atOBIS QC repoFor issues with the package itself, feel free to open an issue here!