BioMe - The butterfly monitoring Germany usecase
Creators: name: Harpke, Alexander
name: Brünecke, Jörg
name: Bohring, Hannes
name: Grescho, Volker
name: Haase, Kristina
name: Kühn, Elisabeth
name: Kuhnert, Tobias
name: Musche, Martin
name: Petruschke, Sven
name: Schnicke, Thomas
name: Sielaff, Daniel
name: Strätling, Jeremy
name: Bumberger, Jan
Publisher: name: Zenodo
Year: 2024
Subjects: biodiversity
biodiversity monitoring
datahub
UFZ
pollinators
butterflies
indicator
nfdi4biodiversity

description: Butterfly Monitoring Germany - Based on the modular BioMe - infrastructure for biodiversity monitoring projects

Butterfly Monitoring Germany (Tagfalter-Monitoring Deutschland / TMD) is a citizen science project to assess the status and trends of butterfly populations in Germany. The data collected is used to analyse the impacts of environmental change such as habitat loss and climate change, to support evidence-based conservation, and to inform decision makers and the general public about the state of biodiversity. Citizen science programs like TMD are also used in other fields, e.g. the monitoring of other insect groups, small watercourses and streams, or certain vertebrate species. 

The TMD apps and BioMe 

Programmes for biodiversity monitoring require complex infrastructures to collect, manage and prepare the data for various purposes. The TMD project is the first use case using the BioMe framework. The project aimes to provide a framework and infrastructure to implement applications for data collection and data curation in the context of biodiversity monitoring initiatives. This primarily addresses species or environmental status monitoring, but also data management, in particular the data quality workflow and data visualisation. For this purpose, BioMe supports data integration and synthesis for cross-thematic/interdisciplinary networking as a prerequisite for data products and further analyses. The role/rights-based data access and options for aggregated data preparation and its visualisation in diagrams or maps contribute to knowledge transfer and facilitate the involvement of strategic stakeholders. 

Requirements for the technical platform 



Focused on science - modular approach with reusable components for content-driven requirements of scientific communities within the scope of monitoring projects and field trails/data collection projects 

Open and FAIR by design providing data and metadata based on community proven standards using open interfaces

Flexible and location independent through support of mobile apps

Support for data collection through the use of AI


Technical Features 



Future proof modular technical stack built on open source products

Integrated into a portable container microservice architecture 

Identity and access management supporting Helmholtz AAI  

Customized, encapsulated web application based on project specific adaptable packages 

Project specific database 

Additional project independent databases  



trait/taxonomic database (project taxonomic concept) 

geo/spatial database 



Role-based communication between databases front and backend based on respective APIs (data views can be managed based on roles)

Cloud based asset management and object storage based on S3 technology 




Modular construction toolbox for content related components 
BioMe pursues the most generic, modular approach possible in order to fulfil a wide range of requirements in various projects. This should enable simple deployment for other projects and enable  integration into the local it infrastructure.





 Table 1: components of BioMe and their features 







Module



Features







user management 








Implements



basic roles and permissions 

show and edit user data 

show user lists 










base layout








Enables customization through 



project title 

colour scheme

logo & favicon  

navigation menu 

footer with links 










landing page 








 


Provides slots for



presentation of project-specific content

user-specific news feeds

individual messages e.g. through the integrated quality assurance-system 









tables 








Generates and manages



tables with specific configuration and settings  

user-specific visibility of columns 






filters






Handles  



definition and management of individual queries

services to load list of filters 

possibility to save and remove specific filterconfigurations 






 publications
 The editorial module allows to





manage categories 




create and edit e.g.



news 

legal documents 

tutorials 






 



observations and quality assurance 








Provide the possibility to



define qa-status 

propose qa-status 

set qa-status 






 



transects 


 Allows to manage





a transect establishing workflow

transect proposals

release of transect proposals

transect specific habitat characteristics





 



species catalogue 




 Allows to visualize and manage



taxonomic trees

characteristics for taxonomic items like species or genus

a search function within the taxonomic tree and catalogue




 



species identification guide




 Provides



dichotomous determination key for several species groups

supports correct identification of species







 







Additional project specific features for TMD 




Extended customization of the landing page based on widget system 



Most recent observations or images 

Several basic project statistics 

Most active users 

Individual diagram views 



Basic Webgis functionalities, e.g. geographical location of transects and species observation 

Diagram-based visualisation of the data 

Mobile app for TMD that uses the same backend. The mobile app has an offline mode that enables the data to be entered even without an internet connection. The app is available in the respective store for iOS free of charge 



https://apps.apple.com/de/app/tagfaltermonitoringdeutschland/ 









The mobile App can be reused when using the same methodological approach as for butterfly monitoring but then has to be treated as a separate app that needs to be customised and further developed independently.

Contact Information





In case of any question please contact: biome@ufz.de. 

 



Techstack, dependencies and third party open source products 



Vue / Vuetify Vue.js - The Progressive JavaScript Framework | Vue.js (vuejs.org) 

Capacitor Capacitor by Ionic - Cross-platform apps with web technology (capacitorjs.com) 

Leaflet Leaflet - a JavaScript library for interactive maps (leafletjs.com) 

NodeJS  

PHP / Symfony Symfony, High Performance PHP Framework for Web Development 

PostgreSQL / PostGIS PostgreSQL: The world's most advanced open source database 

Keycloak with integrated Helmholtz ID Keycloak 

MinIO MinIO | S3 & Kubernetes Native Object Storage for AI 

Docker CE / Docker Compose Docker: Accelerated Container Application Development 





 



Internal Interfaces: 




ApiPlatform API Platform (api-platform.com) 



GraphQL GraphQL | A query language for your API 

REST 








Available basic data:  






The plattform contains an extandable taxonomy backbone for the used target species groups




This includes the taxonomy tree of the species with scientific names and the trivial synonyms




Short descriptions of the species characteristics 



BioMe architecture

The architecture of a BioMe usecase includes the frontend components, consisting of a web application and a mobile app. The backend structure consists of a project-specific API and database, as well as trait/taxonomy and geo API and databases shared across all BioMe projects.

Acknowledgements

 RDM

This project was made possible by the Research Data Management Team (RDM) at the Helmholtz Center for Environmental Research - UFZ. RDM at the UFZ is part of of the Helmholtz Earth and Environment DataHub initiative.

DataHub

We thank the Helmholtz Association and the Federal Ministry of Education and Research (BMBF) for supporting the DataHub Initiative of the Research Field Earth and Environment.

The DataHub enables an overarching and comprehensive research data management, following FAIR principles, for all Topics in the Program Changing Earth – Sustaining our Future.

NFDI4Biodiversity

The realisation of the project was made possible by NFDI4Biodiversity flexfund resources and personnel support.

Natura Incognita

The AI-supported identification of butterflies was realised as part of the AI lighthouse project ‘Natura Incognita’ funded by the Federal Ministry for the Environment, Nature Conservation, Nuclear Safety and Consumer Protection (BMUV) in close cooperation with the Ilmenau University of Technology and the Max Planck Institute for Biogeochemistry.