Refactoring HUBzero for Linked Data


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This the presentation file from the JCDL'12 which talks about HUBzero and linked data. We refactored HUBzero and exposed the metadata information in a linked data style. One salient contribution of our work is that we implemented OAI-ORE in HUBzero and exposed the aggregation relationships in linked data. To show how user agents and human users can benefit from our work, we design and implement 3 tools, OAI-PMH data provider, RDF crawler and graph browser. The first two tools show how user agents can leverage our refactoring process to make use of the metadata and the last tool can serve as a debugging tool for human users.

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  • How can we model the data in HUBzero with the help of linked data? Leverage the linked data for hub resource to enhance HubzeroHow can users and user agents benefit from this refactoring procedure?3 tools here: oai-pmh, hub crawler, graphical browser
  • LAMP is a solution stack of free, open source software, referring to Linux, Apache HTTP server, MySQL database and PHPJoomla is a free and open source content management framework, written in PHPOne salient advantage of Joomla is that developers can implement independent component and plugins to serve specific purposes
  • A resource for the entire nanotechnology discovery and learning community
  • Use URIs (uniform resource identifier) to identify thingsUse HTTP URIs such that these things can be referred to and dereferenced by people and “user agents”Provide useful information about the thing when its URI is dereferenced, using standard formats such as RDF/XMLInclude links to other, related URIs in the exposed data to improve discovery of other related information on the Web
  • Use Dublin Core as a convenient and generic vocabulary for mapping metadata of the hub resource to RDF predicates.
  • OAI-ORE: defines standards for the description and exchange aggregation of Web resources. OAI-ORE specification implements the ORE model which introduces the RM that makes it possible to associate an identity with aggregations of resources and make assertions about their structures and semantics.the aggregations may combine distributed resources together, and with multiple media types, including text, images, data and videos.Aggregation itself identified by its URI is a conceptual resource. Since it is uniquely identified by its URI, this makes aggregations of aggregations possible.aggregated resource : any resource that is part of another aggregationRM; a resource describing an aggregation based on a set of assertions. RM must contain the information that which aggregation it is describing. Other assertions indicated the aggregated resources.Mentions: proxy aggregation
  • OAI-PMH(protocol for metadata harvesting) : a protocol developed by open archives initiative. It can be used to harvest or collect the metadata descriptions of the records in an archive. Usually, an implementation of OAI-PMH must support representing metadata in Dublin Core. For our implementation, it also supports OAI-ORE metadata.
  • Refactoring HUBzero for Linked Data

    1. 1. RefactoringHUBzero forLinked Data Michael Witt Yongyang Yu Purdue University JCDL’12, Washington DC
    2. 2. OutlineHUBzeroLinked DataData ModelingSoftware &ToolsConclusion
    3. 3. What is HUBzero?• Web-based virtual research environment• Publish and reuse resources (software, videos, datasets, etc.)• LAMP stack (Linux, Apache, MySQL, PHP)• Joomla! framework
    4. 4. HUBzero• Platform for scientific collaboration• Create and upload resources by types• Courses, seminars, tools, downloads, series, workshops, publications, and teaching materials• Tag, rank, discuss, etc.
    5. 5. HUBzero Features• Interactive simulation tools – zoom in on a graph, rotate a molecule, etc.• Online presentations – deliver online presentation in flash format• Tool development areas – source code management and version control
    6. 6. HUBzero Reference•• M.McLennan and R. Kennell, HUBzero: a platform for dissemination and collaboration in computational science and engineering
    7. 7. What is Linked Data?
    8. 8. Linked Data• URIs (names for various things)• HTTP URIs• Publish linked data in RDF format on the Web• Links to other URIs
    9. 9. Data Modeling Linked Data OAI-ORE Dublin Core Creative Commons
    10. 10. Object Reuse and Exchange (OAI-ORE)• Aggregation• Aggregated Resources (Nested Aggregations)• Resource Maps
    11. 11. Dublin Core Mapping to HUBzero Dublin Core HUBzero table dc:title jos_resources.title dc:creator jos_resources.created_by dc:subject jos_tags.raw_tag dc:date jos_resources.created dc:identifier dc:description jos_resources.introtext dc:type jos_resources.type dc:publisher (statically assigned) dc:rights jos_resources.params
    12. 12. Example: Modeling HUBzero with OAI-ORE RM <http://hub#agg> <ore:aggregates> <http://hub/downloads#agg> Hub downloads RM Slimy salamander Slimy.m4v RM …
    13. 13. Implementation• Resource component• Exposing metadata from MySQL RDB• Serialized in RDFa+XHTML
    14. 14. AggregationResource Mapore:aggregates
    15. 15. Software & Tools We Have Developed• Implementation of OAI-ORE for HUBzero• OAI-PMH Data Provider• RDF Crawler• Graph Browser
    16. 16. OAI-PMH Data Provider• Implemented as a stand-alone component in Joomla• Serialized as RDF/XML• Each resource type  OAI-PMH set• OAI-ORE Resource Maps  ListMetadataFormats• ore:aggregates  ListRecords
    17. 17. RDF Crawler• A demonstration of utilizing linked data from the Web• Starting from the top level of the hub• Parsing XHTML and dereferencing URIs• RDF triples to N-Triple file• N-Triple to Jena TDB triple store• Basis of the graph browser
    18. 18. Graph Browser
    19. 19. Graph Browser string literalsshared boundaryof a larger graph HTTP URIs
    20. 20. Graph Browser
    21. 21. Graph Browser
    22. 22. Summary• Successfully extended and refactored HUBzero for Linked Data• Exposed Hub resources with OAI-ORE, Dublin Core, Creative Commons, etc.• Built software and tools to implement and utilize Linked Data from HUBzero
    23. 23. Future work• Incorporate richer and more specific vocabularies e.g. Library of Congress Subject Headings (LCSH)• Enable users to create and publish their own collections (Aggregations)• Enable semantic search
    24. 24. Acknowledgements• National Leadership Grant(LG-05-10-0117-10) from Institute of Museum and Libraries Services