Knowledge Graphs in Ecology: Linking Data, Concepts, and Systems
Creators: name: Mietchen, Daniel
Publisher: name: Zenodo
Year: 2025

description: About: This repo contains part of the materials for a presentation given at the TU Munich on 8 May 2025 to students of ecology

 

Abstract: 

Ecology often deals with complex, interconnected systems and increasingly with large, diverse datasets. Knowledge graphs offer a practical approach to organizing and linking such information - connecting ecological principles with species, environments, interactions and processes in a way that supports integration and reasoning. In this lecture, we introduce the concept of knowledge graphs - without assuming a technical background - and explore their growing relevance in ecology, particularly in areas like invasion biology, biotic interactions and ecosystem modeling. We will then look at some examples of how knowledge graphs are being used to structure ecological data and make it more discoverable and interoperable. Alongside this, we will also sketch out how graph-based approaches relate to other elements of the broader AI landscape. Throughout the lecture, attendees are invited to share their own ideas on the matter or to pose questions.

 

 

The slide-based presentation was complemented by some practical examples from https://scholia.toolforge.org/ and https://globalbioticinteractions.org .

 

 



Some additional starting points for exploring the topic (with some formatting lost upon transfor from the source etherpad):





10-min no-slide talk in German https://youtu.be/l2cYtCxipK4 featuring Strelitzia reginae 







Poster: Biodiversity in NFDI Knowledge Graphs. https://doi.org/10.5281/zenodo.10997504







Slides: 12 years of Wikidata - zooming in on its scholarly content. Zenodo. https://doi.org/10.5281/zenodo.13997230







https://w.wiki/D$n5 - list of ecological concepts















https://w.wiki/E32X - a graph of their co-occurrence in the literature



















consider changing the LIMIT to 4000



















consider adding in images if available























https://w.wiki/E45C





















corresponding map



















list of co-occurring species



















formulas of co-occurring chemicals



















Phragmites australis















Invasion biology and the success of social collaboration networks, with application to Wikipedia https://scholia.toolforge.org/work/Q56524142













A conceptual classification scheme of invasion science https://scholia.toolforge.org/work/Q130735544













Knowledge graph examples

















studying pollination in a given geographic area with a known population of flowers and pollinators























start with one individual from one pollinator species





























let it visit one flower of one plant































then another flower of the same plant































then another plant































eventually, it may come back to a flower it had already visited































then it may go back to its nest



























bring in more individuals from this one pollinator species

























bring in more pollinator species

























consider microbes involved in pollination

























consider multiple pollination mechanisms

























consider using different methods (e.g. optical vs. acoustic vs. genetic vs. literature vs. mathematical modelling etc.)

























add disturbances like 





























predators































fires































floods































invasive species



































plant 









































herbivore







































pollinator









































predator



































deforestation































agricultural pesticides































climate change



























do it at another time (of the day/ week/ year) and/ or location (lat/ long/ alt/ proximity to key biogeographic features/ ecological gradients)

























start building a network of relevant ecological concepts

























combine this with ways to generate research questions and hypotheses and track progress on them