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BIOFIN-EU: Training "FAIR Data Principles and Metadata: or Why Build Ontologies"
This tutorial introduces the FAIR Data Principles—Findable, Accessible, Interoperable, and Reusable—and their application to Nature-based Solutions (NbS) and scientific data management. It walks you through key concepts like metadata and ontologies, explaining why they matter and how to use them to make data machine-readable and shareable. Through real-world examples and semantic web technologies (e.g., RDF, OWL, SPARQL), it demonstrates how to structure and label data effectively to support collaboration, transparency, and reuse across platforms and institutions.
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BIOFIN-EU: Training "FAIR Data Principles and Metadata: or Why Build Ontologies"
- 1. biofin-project.eu 1 FAIR dataprinciples and Metadata: or why build ontologies Christopher Brewster (University of Maastricht): Christopher.Brewster@maastrichtuniversity.nl
- 2. biofin-project.eu 2 Of metadata,of ontologies, and of FAIR data Principles ∙ Strange terms, strange concepts for most people ∙ Why are we interested in this in the BioFIN project? ∙ What is this? ∙ How do we do it? ∙ Why do we do this? ∙ ... but first a little story ... almost a history lesson The time has come,' the Walrus said, To talk of many things: Of shoes — and ships — and sealing-wax — Of cabbages — and kings — And why the sea is boiling hot — And whether pigs have wings.' The time has come,' the Walrus said, To talk of many things: Of shoes — and ships — and sealing-wax — Of cabbages — and kings — And why the sea is boiling hot — And whether pigs have wings.’ -- Lewis Caroll
- 3. biofin-project.eu 3 Story 1– The Web of Data ∙ 1992 Tim Berners-Lee invents the World-Wide-Web. This was designed as a web of documents. ∙ TBL realises that a web of documents was insufficient and what was needed was a “web of data”. ∙ From this realization arose a series of technologies we generally call "semantic web" - to gradually turn a web of documents into a web of data ∙ Includes standards such RDF, RDFS, OWL, SPARQL, .... and lots more under the aegis of W3C ∙ In 00s, TBL proposed the idea of "Linked Data“: ∙ One for online in any format – “open data” ∙ Two for online in machine readable format e.g Excel ∙ Three for online, in non-proprietary format e.g. csv ∙ Four for online, non-proprietary format, use open standards to identify stuff (i.e. use URIs, RDF etc.) ∙ Five for online, non-proprietary format, use open standards, link to other data sets
- 4. biofin-project.eu 4 Story 2Linked Open Data Cloud
- 5. biofin-project.eu 5 Story 3Open Science ∙ Two contrary movements ∙ Panic about "open data", problem especially in health but general move towards respecting privacy, ownership etc. ∙ Frustration with research being paid for but not open, accessible, frustration both from scientists and funding agencies, some parts of general public/politicians ∙ Frustration also research gets lost, inaccessible, loss of context etc. ∙ Result (cutting a long story short) ∙ European Open Science Cloud - from the EC ∙ FAIR Data Principles - from the Life Science community https://unsplash.com/photos/PdDBTrk GYLo
- 6. biofin-project.eu 6 The FAIRData Principles ∙ Important paper laid the foundations: Wilkinson, M. D., et al. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3, 160018. https://doi.org/10.1038/sdata.2016.18 ∙ Has had a huge impact … generally adopted by the EC and many other funding agencies ∙ What does it mean?
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- 8. biofin-project.eu 8 FAIR Consequences– semantic technologies ∙ Metadata for a NbS to be findable ∙ Need to use an ontology/taxonomy/vocabulary that is widely used to label the NBS/data with appropriate keywords/concepts ∙ Need have unique identifiers ∙ Metadata for NBS to be accessible ∙ Need to use a commonly used protocol to access the NbS/data ∙ Need to have access controls – who is allowed to have access to that data? ∙ Metadata for aNbS to be interoperable ∙ Need to agreed ontology to describe the NbS/data, even more important if data is to be machine readable ∙ Ontology must be following FAIR principles as well ∙ Metadata for a NbS to be reusable ∙ Need for provenance data – where did this NbS come? Who made it? ∙ Need for suitable machine readable licences
- 9. biofin-project.eu 9 Example Metadata Zenodo– some article - DC format Wikidata – Maastricht – in RDF <rdf:RDF> <rdf:Description rdf:about="https://www.wikidata.org/wiki/Special:EntityData/Q1309"> <rdf:type rdf:resource="http://schema.org/Dataset"/> <schema:about rdf:resource="http://www.wikidata.org/entity/Q1309"/> <cc:license rdf:resource="http://creativecommons.org/publicdomain/zero/1.0/"/> <schema:softwareVersion>1.0.0</schema:softwareVersion> <schema:version rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1831142180</schema:version> <schema:dateModified rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2023-02-10T18:20:04Z</schema:date Modified> <wikibase:statements rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">178</wikibase:statements> <wikibase:sitelinks rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">121</wikibase:sitelinks> <wikibase:identifiers rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">51</wikibase:identifiers> </rdf:Description> <rdf:Description rdf:about="http://www.wikidata.org/entity/Q1309"> <rdf:type rdf:resource="http://wikiba.se/ontology#Item"/> </rdf:Description> <rdf:Description rdf:about="https://af.wikipedia.org/wiki/Maastricht"> <rdf:type rdf:resource="http://schema.org/Article"/> <schema:about rdf:resource="http://www.wikidata.org/entity/Q1309"/>
- 10. biofin-project.eu 10 Ontologies ∙ Whatis an ontology? Just a machine readable, formal way of describing a part of the world. ∙ There are lost of ontologies …. Central to Linked Data, central to any form of “knowledge representation” ∙ Typically use RDF/RDFS/OWL formalisms to be machine readable ∙ Lots and lots of agriculture, forestry and environment ontologies e.g. AGROVOC, FOODON, AGRO, ENVO ∙ Too many, often lack of agreement means every organisation goes and creates another one … ∙ However, necessary to achieve interoperability http://finto.fi/yso/en/page/p5454 Agrovoc ENVO
- 11. biofin-project.eu 11 Why dowe do this? • An NbS is for the platform a bundle of data. • We need to be able to clearly specify what data is necessary and what is optional. • We need to be able to share this data e.g. with financial institution is a machine-readable format. • We need to get other actors to provide data is a standardized a manner as possible. • Creating a standard enables other people to provide services that interact with the platform.