Getting Interaction Data
Overview
Teaching: 5 min
Exercises: 5 minQuestions
Where can I download interaction data?
What formats are the data available?
Objectives
Understand the available ways to get interaction data
Understand the columns of the downloaded data
Getting oriented with GloBI interaction data
Let’s get oriented with the interaction data found on GloBI. GloBI data products are interpreted in order to bring together disparate data sources (literature, observations, collections, etc.). This means that GloBI data products are opinionated and may be incomplete compared to the original data sources. Original data can be found from the citations and these should still be considered the detailed building blocks for the entire interaction dataset.
Some of the different sources of data include natural history collection records, observations extracted from the literature, interaction and network datasets, observations from community science programs and other, larger aggregated datasets.
Where to find data
Navigate to the GloBI Data Products page and explore the Original Data Sources.
What is what?
stable versions of the data are versioned in the doi:10.5281/zenodo.3950589 GloBI data publication. A new version is done about every six months.
snapshot are the most recent, live data. Thus, this could change daily! Great for exploration and preliminary analysis.
How many records are in the GloBI dataset. It is a lot!
wc -l interactions.csv
Data publication
For research or other data intensive project, it is suggested to use GloBI’s stable versioned integrated data published via doi:10.5281/zenodo.3950589 or create a new data publication that contains the data you are using.
Other ways of accessing GloBI data
Exploratory, interactive queries can be executed through SPARQL and Cypher endpoints, GloBI Search/Browse pages, or by using the REST-y GloBI Web API. For those that use R, rglobi is available to explore interaction data. rglobi can also be used to execute Cypher queries. However, it is best to consider these as methods for exploring data rather than data access points. If you are doing research, download the full dataset and create a version of it.
Discussion: Why is it important to version the GloBI data in research?Take a moment to discuss as a group why it is important to version, publish, or archive a copy of the GloBI dataset you use for research. What are some ways to archive datasets?
Next Up: Reviewing the Reviews
If you’d like to follow along while working with the entire dataset, please jump to Working with the Whole Dataset.
If you would like to explore GloBI data through the GloBI webpage, please visit lesson episode Point and Click.
Key Points
GloBI has interaction data that can be accessed as a full dataset
Better to use the full or whole dataset than the APIs