OBIS created some packages and pipelines to help users work with OBIS data within a programming environment. Our main packages were developed for the R language.
Chose your programming language:
R
robis
robis, our flagship R package, is a client for the OBIS API. It includes functions for data access, as well as a few helper functions for visualizing occurrence data and extracting nested MeasurementOrFact or DNADerivedData records.
Available through CRAN (use install.packages("robis"))
GitHub: https://github.com/iobis/robis
obistools
obistools is an R package designed with tools for data enhancement and ensuring data quality. It includes a range of functions to support comprehensive quality control checks, such as: taxon matching, verifying required OBIS fields, verifying identifiers, and detecting issues with geographic coordinates such as depth inconsistencies or points located on land.
This package requires devtools to be installed:
install.packages("devtools")
devtools::install_github("iobis/obistools")
See the GitHub for more documentation: https://github.com/iobis/obistools
obisdi
Python
pyobis
pyobis is a python package to help users fetch data from the OBIS API. It has similar functions as robis for obtaining data, including occurrence, taxon, node, checklist and dataset. For more information see: https://github.com/iobis/pyobis