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The Dendro research data management platform: Applying ontologies to long-term preservation in a collaborative environment
The document discusses the Dendro research data management platform, emphasizing the importance of early engagement with researchers for effective metadata production and data preservation. It highlights the use of linked open data for interoperability and collaboration, as well as the platform's ability to integrate with existing repository systems. The conclusion stresses the need for a collaborative approach in research data management, utilizing ontologies to enhance the metadata framework.
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The Dendro research data management platform: Applying ontologies to long-term preservation in a collaborative environment
- 1. The Dendro researchdata management platform ! Applying ontologies to long-term preservation in a collaborative environment João Rocha da Silva joaorosilva@gmail.com Faculdade de Engenharia da Universidade do João Aguiar Castro Porto / INESC TEC joaoaguiarcastro@gmail.com Cristina Ribeiro mcr@fe.up.pt DEI—Faculdade de Engenharia da Universidade do Porto / INESC TEC João Correia Lopes jlopes@fe.up.pt iPRES 2014, October 06 - 10 2014, Melbourne, Australia
- 2. Contents • Researchdata management in the long tail • Linked Open Data: why do we need it? • Collaboration for easier metadata production • The Dendro platform • Conclusions 2
- 3. Research Data Management in the long tail of research Why we need to start early 3
- 4. The long tailof research 2011: Science magazine reviewers are asked about their data requirements ~1700 replied 4
- 5. Source Dealing withdata. Challenges and opportunities. Introduction. (2011). Science (New York, N.Y.), 331(6018), 692–3. doi:10.1126/science.331.6018.692 5
- 6. Source Dealing withdata. Challenges and opportunities. Introduction. (2011). Science (New York, N.Y.), 331(6018), 692–3. doi:10.1126/science.331.6018.692 6
- 7. Gathering Processing Paperwriting Preservation, Sharing 7
- 8. Gathering Processing Paperwriting Researcher leaves Metadata 8
- 9. Gathering Processing Paperwriting Project ends 9
- 10. Gathering Processing Paperwriting “Where is the data?” “How / when / by whom was the data produced?” 10
- 11. Curators cannot copewith a posteriori description Researchers must participate in RDM from the start They are the domain experts 11
- 12. Linked Open Data What is it? Why do we need it? 12
- 13. Linked Open Data • Simplicity! - LOD is a very simple model for representing knowledge • Meaning! - Resources are interlinked by properties with established meaning • Interoperability! - Standard methods for querying data - SPARQL - Representations use standard formats - RDF, OWL 13
- 14. nie:isLogicalPartOf !!!! http://dendro.fe.up.pt/ project/datanotes/data “Base data of the DCB experiments” dc:title nie:title base data.xls rdf:type nie:File dcb:initialCrackLength 180mm ! ! !!! ! http://dendro.fe.up.pt/project/ datanotes/data/base %20data.xls 14
- 15. Analytical Chemistry Dataset Fracture Mechanics Dataset … Generic Author Description Creation date … Author Description Creation date … … Domain Specific Sample Count Analysed Substance … Initial Crack Length Specimen Type … 15
- 16. Collaboration For metadatauseful now and in the future 16
- 17. Gathering Processing Paperwriting Preservation, Sharing 17
- 18. Gathering Deposit CollaborationDescription “Freeze” in repository Sharing 18
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- 21. The Dendro platform An open-source platform for Linked Open Data in research environments 21
- 22. Metadata Ontologies Description • Data store fully built on Linked Data • No relational database to preserve • Model can grow by loading more ontologies • External systems can retrieve resources via SPARQL 22
- 23. Metadata Ontologies File Storage ! ! Deposit • GridFS cluster for large or numerous files • Can work in the cloud if needed 23
- 24. Metadata Ontologies Business Logic File Storage ! ! Collaboration • Flexible access control system • Backup / Restore • Versions history • File type previews • Integration • DSpace (SWORD) • ePrints (SWORD) • CKAN • Figshare • …….. 24
- 25. Metadata Ontologies API Business Logic File Storage ! ! Sharing • All operations available via RESTful API using JSON • All resources are de-referenceable (HTTP content negotiation) • Plugin architecture allows integration with external systems Web UI 25
- 26. For curators •Curators can work with researchers to build more ontologies using existing tools (e.g. Protégé) • Established ontologies can be loaded (DC, FOAF…) • Ontologies mature (reuse across Dendro instances) • Data, metadata and its meaning go together Beyond ! INSPIRE: An ontology for biodiversity metadata records Creating lightweight ontologies for dataset description: Practical applications in a cross-domain research data management workflow Rocha da Silva, J., Castro, J., Ribeiro, C., Honrado, J., Lomba, A., Gonçalves, J. Castro, J., Rocha da Silva, J., Ribeiro, C. 10th International Workshop on Ontology Content (OntoContent 2014) Digital Libraries 2014 (DL2014) (pre-print available at http://dendro.fe.up.pt/) (pre-print available at http://dendro.fe.up.pt/) 26
- 27. For programmers •100% Open-source software • Rich API allows Dendro to be connected to almost any system (e.g. mobile apps) Ontology-based multi-domain metadata for research data management using triple stores LabTablet: semantic metadata collection on a multi-domain laboratory notebook Rocha da Silva, J., Ribeiro, C., Correia Lopes, J. Amorim,R., Castro, J., Rocha da Silva, J., Ribeiro, C. 18th International Database Engineering & Applications Symposium (IDEAS 2014) 8th Metadata and Semantics Research Conference (MTSR 2014) (pre-print available at http://dendro.fe.up.pt/) (pre-print available at http://dendro.fe.up.pt/) 27
- 28. Dendro dies, datalives on Triple Store Ontologies “Database” “Documentation” 28
- 29. Conclusions • Researchdata management should start early • Linked Open Data: simple, interoperable, flexible • Collaboration support helps researchers while gathering metadata for later deposit • Dendro: a fully open-source platform for RDM, built on Linked Open Data • Dendro integrates with major repository platforms 29
- 30. Conclusions (cont’d) •Ontologies: source of metadata descriptors • Data model grows as more ontologies are loaded • Curators can model and share the ontologies • Domain ontologies evolve with reuse 30
- 31. Visit us at http://dendro.fe.up.pt
- 32. João Rocha daSilva! PhD Student, Senior Web Developer, Semantic Web at INESC TEC João Rocha da Silva is an Informatics Engineering PhD student at the Faculty of Engineering of the University of Porto. He specializes on research data management, applying the latest Semantic Web Technologies to the adequate preservation and discovery of research data assets.! ! He is also an experienced freelancer iOS Developer with several Apps published on the App Store, and a self-taught DIY mechanic with a special interest in classic cars, particularly his 1987 Toyota Corolla GT Twin Cam, also known as Hachi- Roku or AE86.! João Aguiar Castro! PhD Student, Research Data Management researcher at INESC TEC João Aguiar Castro holds a Masters degree in Information Science, and is currently a Digital Platforms PhD student at the Faculty of Engineering of the University of Porto. He is a research data management researcher, particularly in the definition of application profiles that meet the metadata needs of different research domains Cristina Ribeiro! João Correia Lopes! João Correia Lopes is an Assistant Professor in Informatics Engineering at Universidade do Porto and a researcher at INESC TEC. He has graduated in Electrical Engineering in the University of Porto in 1984 and holds a PhD in Computing Science by Glasgow University in1997. His teaching includes undergraduate and graduate courses in databases and web applications, software engineering and object-oriented programming, markup languages and semantic web. He has been involved in research projects in the area of long-term preservation, service-oriented architectures and e- Science. Currently his main research interests are e- Science and the management of research data. Assistant Professor in Informatics Engineering at Universidade do Porto, Researcher at INESC TEC Cristina Ribeiro is an Assistant Professor in Informatics Engineering at Universidade do Porto and a researcher at INESC TEC. She has graduated in Electrical Engineering, holds a Master in Electrical and Computer Engineering and a Ph.D. in Informatics. Her teaching includes undergraduate and graduate courses in information retrieval, digital libraries, knowledge representation and markup languages. She has been involved in research projects in the areas of cultural heritage, multimedia databases and information retrieval. Currently her main research interests are information retrieval, digital preservation and the management of research data. Assistant Professor in Informatics Engineering at Universidade do Porto, Researcher at INESC TEC
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- 34. RDF/XML, SPARQL Endpoint HTML JSON API DB Adapter ES Endpoint GridFS Client Presentation Graph Database (LOD) Web Interface Distributed document index AngularJS (JavaScript) NodeJS (JavaScript) File Storage Cluster Business Logic Logic Openlink Virtuoso 7 ElasticSearch MongoDB (GridFS) Web Human Users JSON JSON JSON Data
- 35. Curated Dataset Working Files Deposit Curator Dendro FOAF DC dc:title nie:isPartOf dcb:specimenLength Ontology concept reuse Web Portal SPARQL Endpoint Sharing & evolution “Mature” ontologies on the web Metadata validation Data producers Free-Text Search API CKAN Dryad Domain-Specific Lightweight Ontologies dcb dcb Data reuser dcb Specification of new metadata ontologies 1 2 3 4