MOBIKO

Mountain Biodiversity Knowledge Graph

Started
April 15, 2025
Status
In Progress
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Abstract

Much knowledge about mountain biodiversity is “trapped” inside scientific publications as unstructured text that is not machine-understandable and difficult to link and summarise. With advances in natural language processing, large language models, and computational power, unstructured text can increasingly be mined and relations between concepts explored and stored in a structured way as linked open data. Here we propose to develop the Mountain Biodiversity Knowledge Graph ‘MoBiKo’, by extracting knowledge about mountain biodiversity status and trends from literature and store it in a graph database for analysis in the context of a first ever global mountain biodiversity assessment.

The project builds on existing biodiversity knowledge infrastructures and databases, rule-based approaches, and on artificial intelligence, machine learning, and natural language processing tools. It delivers a state-of-the-art machine-based approach to knowledge and relation extraction applicable beyond the mountain context. MoBiKo will allow users to query, analyse, and visualise mountain biodiversity status and trends information in space and time and to access and manipulate linked data in support of open and collaborative science and policy. As a collaborative project with existing open research data initiatives and by adopting FAIR principles, this project contributes to, and benefit from open science in Switzerland and beyond.

People

Collaborators

SDSC Team:
Yousra El-Bachir
Carl Remlinger
Anisia Katinskaia
Luis Salamanca

PI | Partners:

Global Mountain Biodiversity Assessment (GMBA), PLAZI, Swiss Institute of Bioinformatics

Global Mountain Biodiversity Assessment (GMBA)

  • Prof. Markus Fischer
  • Prof. Antoine Guisan
  • Dr. Donat Agosti
  • Prof. Patrick Ruch

description

Motivation

‍The corpus of scientific literature is growing exponentially, approaching 500 million pages for biodiversity. Accordingly, reviewing or synthesizing it is close to impossible without technological support. Yet, because most literature consists of non-machine-readable unstructured text, the knowledge it contains is ‘trapped’ and its analysis limited. Advances in artificial intelligence (AI) and NLP represent a game changer towards ‘liberating’ these data. Despite these developments, no solution exists yet for the machine-based processing of extensive biodiversity literature and for supporting large-scale assessments with readily available knowledge repositories. Our project is an attempt to address this situation by applying and further evolving AI approaches for meaning and relationship extraction.

Proposed Approach / Solution

‍The Swiss Data Science Center (SDSC) contributes to the MoBiKo project by designing and implementing a robust, scalable pipeline that transforms unstructured biodiversity literature into structured, machine-interpretable knowledge. Our mission in this project is to bridge advances in natural language processing, knowledge representation, and graph technologies with the concrete needs of large-scale biodiversity assessment. SDSC leads the development and evaluation of state-of-the-art named entity recognition and relationship extraction methods, combining transformer-based models, large language models, and ontology-driven normalization to extract biodiversity states, trends, and drivers from scientific texts. These extracted statements are formalized as traceable RDF entities and relations and integrated into an interoperable knowledge graph aligned with FAIR principles. Throughout the project, SDSC works closely with domain experts and existing biodiversity infrastructures to ensure methodological rigor, transparency, and reusability, while delivering a generalizable approach applicable beyond the mountain biodiversity domain.

Impact

‍The project delivers a step change in how biodiversity knowledge can be accessed, assessed, and reused by converting thousands of publications into a structured, transparent, and queryable knowledge graph. Scientifically, this reduces the reliance on purely manual literature synthesis and enables reproducible, large-scale assessments of biodiversity trends and drivers. Societally, the resulting infrastructure supports evidence-based environmental policy and leaves a durable open resource for researchers, practitioners, and decision-makers.

‍

Figure 1. Overview of the research plan and WPs. Italics: processes, boxes: inputs / outputs.

Gallery

Annexe

Additional resources

Bibliography

  1. Wilkinson, M. D. et al. The FAIR Guiding Principles for scientific data management and
    stewardship. Sci Data 3, 160018 (2016).
  2. Page, R. D. M. Ozymandias: a biodiversity knowledge graph. PeerJ 7, e6739 (2019).
  3. Thessen, A. E., Cui, H. & Mozzherin, D. Applications of Natural Language Processing in
    biodiversity science. Advances in Bioinformatics 2012, 1–17 (2012).
  4. Dagdelen, J. et al. Structured information extraction from scientific text with large language
    models. Nat Commun 15, 1418 (2024).
  5. Penev, L. et al. OpenBiodiv: a knowledge graph for literature-extracted Linked Open Data in
    biodiversity science. Publications 7, 38 (2019).

Publications

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