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It has been shown that data management should start as early as possible in the research workflow to minimize the risks of data loss. Given the large numbers of datasets produced every day, curators may be unable to describe them all, so researchers should take an active part in the process. However, since they are not data management experts, they must be provided with user-friendly but powerful tools to capture the context information necessary for others to interpret and reuse their datasets. In this paper, we present Dendro, a fully ontology-based collaborative platform for research data management. Its graph data model innovates in the sense that it allows domain-specific lightweight ontologies to be used in resource description, acting as a staging area for later deposit in long-term preservation solutions.
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The Dendro research data management platform
!Applying ontologies to long-term preservation in a collaborative
environment
João Rocha da Silva [email protected]
Faculdade de Engenharia da
Universidade do Porto / INESC TECJoão Aguiar Castro
Cristina Ribeiro [email protected] DEI—Faculdade de
Engenharia da Universidade do
Porto / INESC TECJoão Correia Lopes [email protected]
iPRES 2014, October 06 - 10 2014, Melbourne, Australia
Contents• Research data management in the long tail
• Linked Open Data: why do we need it?
• Collaboration for easier metadata production
• The Dendro platform
• Conclusions
2
Research Data Management in the long tail of research
Why we need to start early
3
2011: Science magazine reviewers are asked about their data requirements
~1700 replied
The long tail of research
4
Dealing with data. Challenges and opportunities. Introduction. (2011). Science (New York, N.Y.), 331(6018), 692–3. doi:10.1126/science.331.6018.692
Source
5
Dealing with data. Challenges and opportunities. Introduction. (2011). Science (New York, N.Y.), 331(6018), 692–3. doi:10.1126/science.331.6018.692
Source
6
Gathering
Processing
Paper writing
Preservation, Sharing
7
Gathering
Processing
Paper writing
Researcher leaves
Metadata
8
Gathering
Processing
Paper writing
Project ends9
“Where is the data?”“How / when / by whom was the data
produced?”
Gathering
Processing
Paper writing
10
Researchers must participate in RDM from the start
They are the domain experts
Curators cannot cope with a posteriori description
11
Linked Open DataWhat is it? Why do we need it?
12
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
!!!!
http://dendro.fe.up.pt/project/datanotes/data
nie:isLogicalPartOf
“Base data of the DCB experiments”
dc:title
base data.xls
nie:title
rdf:type
nie:File
180mm
dcb:initialCrackLength
!!!!!!
http://dendro.fe.up.pt/project/datanotes/data/base
%20data.xls
14
Analytical Chemistry Dataset
Fracture Mechanics Dataset …
GenericAuthor
Description Creation date
…
Author Description
Creation date …
…
Domain Specific
Sample Count Analysed Substance
…
Initial Crack Length Specimen Type
…
15
CollaborationFor metadata useful now and in the future
16
Gathering
Processing
Paper writing
Preservation, Sharing
17
Gathering
Deposit
“Freeze” in repository
Collaboration Description
Sharing
18
Gathering
…19
Demo
Dendroβ
20
The Dendro platformAn open-source platform for Linked Open Data in
research environments
21
Metadata
Ontologies
• 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
Description
22
Metadata
Ontologies
File Storage !
!
• GridFS cluster for large or numerous files
• Can work in the cloud if needed
Deposit
23
Metadata
Ontologies
File Storage !
!
Business Logic
• Flexible access control system
• Backup / Restore
• Versions history
• File type previews
• Integration • DSpace (SWORD)
• ePrints (SWORD)
• CKAN
• Figshare
• ……..
Collaboration
24
Metadata
Ontologies
File Storage !
!
Business Logic
API
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
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
Creating lightweight ontologies for dataset description: Practical applications in a cross-domain research data management workflow Castro, J., Rocha da Silva, J., Ribeiro, C. Digital Libraries 2014 (DL2014) (pre-print available at http://dendro.fe.up.pt/)
Beyond INSPIRE: An ontology for biodiversity metadata records !Rocha da Silva, J., Castro, J., Ribeiro, C., Honrado, J., Lomba, A., Gonçalves, J. 10th International Workshop on Ontology Content (OntoContent 2014) (pre-print available at http://dendro.fe.up.pt/) 26
For programmers
• 100% Open-source software
• Rich API allows Dendro to be connected to almost any system (e.g. mobile apps)
LabTablet: semantic metadata collection on a multi-domain laboratory notebook Amorim,R., Castro, J., Rocha da Silva, J., Ribeiro, C. 8th Metadata and Semantics Research Conference (MTSR 2014) (pre-print available at http://dendro.fe.up.pt/)
Ontology-based multi-domain metadata for research data management using triple stores Rocha da Silva, J., Ribeiro, C., Correia Lopes, J. 18th International Database Engineering & Applications Symposium (IDEAS 2014) (pre-print available at http://dendro.fe.up.pt/) 27
Triple Store Ontologies
Dendro dies, data lives on
“Database” “Documentation”28
Conclusions• Research data 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
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
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.!
PhD Student, Senior Web Developer, Semantic Web at INESC TEC
João Rocha da Silva!
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.
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
Cristina Ribeiro! João Correia Lopes!Assistant Professor in Informatics Engineering at Universidade do Porto, 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
PhD Student, Research Data Management researcher at INESC TEC
João Aguiar Castro!
Extras
Graph Database(LOD)
Distributed document index
File Storage Cluster
Business Logic
Web Interface
Openlink Virtuoso 7 ElasticSearch MongoDB
(GridFS)
NodeJS (JavaScript)
AngularJS (JavaScript)
DB Adapter ES Endpoint GridFS Client
Human UsersWeb
JSON JSON JSON
RDF/XML, SPARQL Endpoint
JSON API
HTML
Data
Logic
Presentation
CuratedDataset
Curator
WorkingFiles
Dendro
FOAF
DC
dc:titlenie:isPartOfdcb:specimenLength
Ontology concept reuse
SPARQLEndpoint
Sharing & evolution
“Mature”ontologies on the web
Metadatavalidation
Deposit
Data producers
Free-TextSearch
API
CKANDryad
Web Portal
Domain-Specific Lightweight Ontologies
dcbdcb
Data reuser
dcb
Specification of new metadata ontologies
1
2
3
4
