Getting Interaction Data

Overview

Teaching: 5 min
Exercises: 5 min

Questions

• 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?

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