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SERONTO: Framework for Biodiversity Data Management

ALTER-Net is a European network addressing major biodiversity issues. SERONTO is their framework to manage and make biodiversity data available to scientists, policy makers, and the public.

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SERONTO: Framework for Biodiversity Data Management

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  1. SERONTO Bert van der Werf Mihai Adamescu Minu Ayromlou Nicolas Bertrand Jakub Borovec Hugues Boussard Constatin Cazacu Toon van Daele Sabina Datcu Mark Frenzel Volker Hammen Helena Karasti Miklos Kertesz Pirjo Kuitunen Mandy Lane Juraj Lieskovsky Barbara Magagna Johannes Peterseil Sue Rennie Herbert Schentz Katharina Schleidt Liisa Tuominen A Socio-Ecological Research and Observation Ontology

  2. ALong Term Biodiversity, Ecosystem, and Awareness Research Network funded by the European Union. ALTER-Net addresses major biodiversity issues at a European scale. The network is a partnership of 24 organizations from 17 European countries ALTER-Net

  3. A framework for effective information and knowledge management Objective: To construct a framework within which can be built a system to manage biodiversity data, information and knowledge from the Network of Excellence, and to make them available to scientists, policy makers and the public. Work Package I6

  4. Different domains ecological, meteorological, chemical, geographical, sociological, economic, etc. Different languages real language differences; scientific language differences Different scaling Global, regional, site; surveys, ... Different purpose monitoring versus experiments; exploration versus parameter fitting Different storage methods spreadsheets, databases; local or distributed Biodiversity data

  5. data conservation data sharing data quality provenance (ISO ...) scientific data integration data mining analysis and meta analysis graphically advanced techniques workflows Purpose of framework

  6. Dependent variables measurements/observations Independent variables treatments classifications in stratified sampling measurements often time Sources of variation sampling structure observer method design (blockings) etc. Measurement scale distributional assumptions preferred analysis Assumptions Components for analysis

  7. methods used relationship between methods units and dimensions conversion between units the entity of observation/treatment how to group them how are they selected Aspects important for combining data from different sources

  8. Distributed databases Ontologies semantics for concepts hierarchical structure of concepts relationships/properties reasoning and restriction logic mappings and derivation Approach for Framework

  9. SERONTO • Core ontology • observation ontology • units and dimensions ontology • Domain ontologies • taxonomy • ecology • chemistry • sociology • etc.

  10. Repeatability: The ontology should be capable of holding enough meta-data that another person can repeat the experiment or observation at another place and time. Transparency: It must be possible to record and retrieve meta-data describing what actually happened. Designing the core

  11. Structures for domain knowledge Base classes for derivation Hierarchical reference lists Data and meta data for observations What, When, Where, Who, How? What went wrong? Meta data for administration Project information Units and dimensions Versioning methods Core contains:

  12. Core classes:

  13. SERONTO: basic classes

  14. basics: example

  15. Method Derived classes: • Measurement method • Treatment method • Classification method

  16. Method: simple example

  17. selection_description

  18. Example

  19. grouping_description: design (treatment, measurement, layout in field, block’s, etc.) membership “group by” functions (mean, variance, ...) reference lists species other nominal value lists actors: persons, institutions project etc. Other classes:

  20. Proof of concept F-Logic / OntoStudio F-Logic / OntoStudio JOKL cultural landscapes ECN Summary Database Proof of Concept JOKL cultural landscapes ECN Summary Database Proof of Concept JOKL cultural landscapes ECN Summary Database Proof of Concept 2835 foodplain Pythia vegetation JODI vegetation 2835 foodplain Pythia vegetation JODI vegetation 2835 foodplain Pythia vegetation JODI vegetation Connect Databases Connect Databases Connect Databases Import OWL Ontology Import OWL Ontology Import OWL Ontology SERONTO SERONTO Results SERONTO Results Results Query Query

  21. http://www5.umweltbundesamt.at/ALTERNet/index.php?title=Main_Pagehttp://www5.umweltbundesamt.at/ALTERNet/index.php?title=Main_Page

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