Working with Data Sources

Overview

Teaching: 10 min
Exercises: 10 min

Questions

• How does GloBI discover interaction data?

• How does GloBI integrate interaction data?

• Is GloBI a data repository or a search index?

Objectives

• Understand where to find GloBI data sources

• Understand where to find GloBI data reviews

Data Sources: GloBI’s Building Blocks

Global Biotic Interactions (https://globalbioticinteractions.org, GloBI) relies on existing species interaction datasets, or data sources. These data sources are regularly re-indexed by GloBI to include recent updates. So, rather than a data management system or repository, GloBI is more like a search engine that helps find biotic interaction data in openly available datasets.

The kinds of data sources indexed by GloBI are pretty diverse: some datasets come from professionally managed natural history collections or specialized data portals, whereas others are manually transcribe interaction records from literature, or observation records provided by citizen scientists.

A list of GloBI data sources can be found at https://globalbioticinteractions.org/sources.

Exercise 1: Find Data Sources

Visit https://globalbioticinteractions.org/sources and locate:

• the USNM Ixodes Collection,

• Seltmann’s Tick Interaction Database, and

• iNaturalist observation records.

For each data source, click on the badge to explore some of their indexed interactions.

Describe one interaction for each data source in the collaborative notes.

GloBI builds the search index in the following steps:

1. Find registered interaction data in Github and Zenodo.
2. Access/download and version digital dataset
3. Integrate interaction records using translation tables into a knowledge graph
4. allow for Reuse by publishing integrated data products and services

These steps are repeated regularly, often many times a week, to include new additions or other updates.

Want to Learn More about Data Indexing Steps?

Visit https://globalbioticinteractions.org/process and learn more about the GloBI indexing process and the tools.

Data Source Reviews

To help better understand how GloBI interprets data sources, automated data reviews are made available for each data source, or dataset.

These dataset specific reviews include:

• lists of review notes and summaries (e.g., review.tsv files),
• checklists of taxonomic names (e.g., indexed-names.tsv), and
• indexed interaction data records (e.g., indexed-interactions.tsv).

Exercise 2: Parasite Tracker Data Source: CAS

Visit the GloBI’s Parasite Tracker project page at https://globalbioticinteractions.org/parasitetracker and locate the California Academy of Sciences / Entomology Collection.

Click on each of the buttons and describe the function of the “review”, “GloBI”, “config”, “issues” and “names” badges.

Also, in the review log, note how many interactions GloBI found in the California Academy of Sciences Entomology collection.

In this lesson episode, you’ve learned that GloBI is a search index that helps to explore interaction data in existing data sources.

Also, you found the list of GloBI data sources and discovered the search-by-datasource, review and configuration links.

Next Up: Reviewing the Reviews

If you’d like to learn more about what a data review is, please jump to Reviewing Interaction Records.

If you are specifically interested in how GloBI links to taxonomic names, please visit lesson episode Reviewing Taxonomic Names.

Key Points

• GloBI is built using existing data sources

• Data sources are continously and automatically indexed by GloBI

• GloBI provides automated reviews of data sources