Sadie Mills - Mapping Marine Diversity: using QGIS to visualise and extract biodiversity data

Summary

In this presentation, Sadie Mills from NIWA discusses the management of New Zealand’s marine and freshwater invertebrate collections, focusing on the use of the Specify database software. She outlines the challenges of data management and how integration with QGIS allows for real-time updates, spatial analysis, and the creation of high-quality maps. The solution facilitates the visualization and validation of large biological datasets, providing researchers with the tools to analyze species distribution and environmental factors. This powerful system enables better data access and improved mapping for biodiversity and fisheries research.

Takeaways

• 😀 The National Institute for Water and Atmospheric Research (NIWA) focuses on the stewardship of New Zealand's marine and freshwater biodiversity.
• 😀 The NIWA invertebrate collection contains approximately 300,000 preserved marine and terrestrial specimens, covering 8,500 species across 21 phyla.
• 😀 NIWA manages significant biological resources, including invasive species data, marine and freshwater ecosystems, and samples from Antarctic waters and the Southwest Pacific.
• 😀 The tool Specify, an open-source software developed by the University of Kansas, is used to manage NIWA's extensive natural history collection.
• 😀 Specify helps store data in an underlying MySQL database, including spatial data such as latitude and longitude coordinates for specimen collection locations.
• 😀 The software includes a Google Earth plugin for visualizing data points but has limitations, such as only supporting single data queries and restricting export to 20,000 records.
• 😀 To address limitations, NIWA integrated QGIS, a powerful mapping tool, to access and visualize data from the live database in real time.
• 😀 QGIS allows NIWA to overlay multiple map layers, such as benthic protected areas and vent activity polygons, to analyze data distribution effectively.
• 😀 QGIS also supports spatial data analysis, including intersection tools that allow researchers to extract points within defined polygons for deeper analysis.
• 😀 NIWA now produces high-quality, publication-ready maps using QGIS, with the ability to visualize data across various projections and layers using free and open-source tools.
• 😀 Specify's customizable fields, including taxonomic and geographic trees, make it adaptable for managing natural history collections and other types of data.

Q & A

What is the role of the National Institute for Water and Atmospheric Research (NIWA)?

NIWA is a crown research institute in New Zealand that focuses on water and atmospheric research, maintaining important databases, and providing knowledge related to biodiversity, particularly in freshwater and marine ecosystems.

What is the primary focus of Sadie Mills' work at NIWA?

Sadie Mills works as the collection manager of the NIWA invertebrate collection, focusing on enhancing the stewardship of New Zealand's marine biodiversity through the collection and management of marine invertebrate specimens.

How large is the NIWA invertebrate collection, and where do the specimens come from?

The NIWA invertebrate collection houses about 300,000 jars of preserved marine invertebrates, covering species from New Zealand, the Ross Sea, and the wider Southwest Pacific.

What software does Sadie Mills' team use to manage their collection data?

Sadie Mills' team uses Specify, an open-source software developed by the University of Kansas, to manage natural history collection data. It is especially designed for biological and taxonomic records.

What challenges does the Specify software face when handling spatial data?

Specify has limitations when managing large datasets or when querying multiple polygons. It only supports basic spatial functionality, such as exporting data into Excel, but struggles with real-time data validation, complex queries, and displaying large amounts of data at once.

What solution did Sadie Mills' team find for the limitations of Specify in managing spatial data?

The team used QGIS, a powerful geographic information system, in combination with Specify to directly access their live database, enabling real-time validation, spatial analysis, and the creation of publication-quality maps.

How does QGIS help in visualizing and analyzing the data?

QGIS allows the team to plot data points from the Specify database directly onto a map, visualize the distribution of species, perform spatial analysis (e.g., extracting points within certain polygons), and generate customizable maps with multiple layers for further analysis.

What are the key benefits of using QGIS for this type of data management?

The main benefits of using QGIS include live access to data, real-time data validation, the ability to perform spatial analysis, and the production of high-quality maps. It also allows the integration of other spatial data layers to enrich the analysis.

How does QGIS help in ensuring the accuracy of the data?

QGIS helps ensure accuracy by allowing the team to check if data points are plotted correctly on the map, preventing errors like points being placed on land, and providing tools to correct and validate the data in real time.

What kind of data can be integrated into QGIS for spatial analysis?

QGIS can integrate a wide range of data types, including spatial data such as points, lines, and polygons, as well as external layers such as benthic protected areas, vent polygons, and other geospatial datasets, enabling comprehensive analysis of biodiversity distribution.