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Sharing Data-Rich Research
Through Repository Layering
Stephen Abrams
California Digital Library
Angela Rizk-Jackson
Julia...
Why is data curation important?
 Accelerating scientific progress
 Enabling appropriate scrutiny and verification of res...
The library’s role
 A continuation of its long-standing mission and practice to
connect patrons with content of interest ...
Merritt
 Curation repository available to the UC community and
external partners
 Preservation and access
 Content agno...
Merritt
Storage node
Storage
broker
Inventory
ONEShare UNM
storage node
Storage node
UI/API
UI/API
UI/API
LDAP
LDAP
LDAP
R...
(Some) issues to address
 Scale
 Individual objects ranging from 0 to 47,000 files
 Individual files ranging from 0 to ...
(Some) issues to address
 Scale
 Individual objects ranging from 0 to 47,000 files
 Individual files ranging from 0 to ...
Scale
 Avoiding client timeout
 ≤ 2 GB: File-based  stream-based AIP-to-DIP processing
 > 2 GB: Asynchronous delivery
...
Control
 Data use agreements (DUAs)
 Explicit assertion of license requirements and terms of use
 Curatorial and consum...
User experience
 Due to its open eligibility policy, Merritt will always provide a
more generic UX than special-purpose o...
User experience
 Due to its open eligibility policy, Merritt will always provide a
more generic UX than special-purpose o...
DataShare
 “The goal of the DataShare project is to catalyze widespread
sharing of scientific research data”
datashare.uc...
DataShare
 Prepare
 Describe
 Upload
 Curate
 Discover
 Share
DataShare
 Prepare
 Best practice advice
 Describe
 Upload
 Curate
 Discover
 Share
DataShare
 Prepare
 Describe
 Schema-directed
metadata editor
 DataCite schema
schema.datacite.org
 Upload
 Curate
...
DataShare
 Prepare
 Describe
 Upload
 File browse or
drag-n-drop
 Curate
 Discover
 Share
DataShare
 Prepare
 Describe
 Upload
 File browse or
drag-n-drop
 Curate
 Discover
 Share
DataShare
 Prepare
 Describe
 Upload
 Curate
 Manage datasets
 Discover
 Share
DataShare
 Prepare
 Describe
 Upload
 Curate
 Discover
 Faceted search and
browse
 Share
DataShare
 Prepare
 Describe
 Upload
 Curate
 Discover
 Share
 DataONE
 DataCite
 (soon) Primo
Web of Knowledge
...
Merritt + DataShare
Storage node
Storage
broker
Inventory
ONEShare UNM
storage node
Storage node
UI/API
UI/API
UI/API
LDAP...
Research Hub
 “Research Hub provides powerful tools for content
management and collaboration”
hub.berkeley.edu
 Alfresco...
Research Hub
 Prepare
 Acquire and
arrange
 Describe
 Upload
 Curate
 Discover
 Share
Research Hub
 Prepare
 Describe
 Schema-directed
metadata editors
 Upload
 Curate
 Discover
 Share
Research Hub
 Prepare
 Describe
 Upload
 Direct action
 Curate
 Discover
 Share
 Prepare
 Describe
 Upload
 Direct action
 Curate
 Discover
 Share
Research Hub
Research Hub
 Prepare
 Describe
 Upload
 Policy-based
workflow rules
 Curate
 Discover
 Share
Research Hub
 Prepare
 Describe
 Upload
 Drag-and-drop
 Curate
 Discover
 Share
Research Hub
 Prepare
 Describe
 Upload
 Confirmation
 Curate
 Discover
 Share
Research Hub
 Prepare
 Describe
 Upload
 Curate
 Manage datasets
 Discover
 Share
Research Hub
 Prepare
 Describe
 Upload
 Curate
 Discover
 Share
Research Hub
 Prepare
 Describe
 Upload
 Curate
 Discover
 Share
Merritt + DataShare + Research Hub
Storage node
Storage
broker
Inventory
ONEShare UNM
storage node
Storage node
UI/API
UI/...
Next steps
 Self-service account
registration
 UCTrust and InCommon
Shibboleth federations
 Additional cloud-based
repl...
Sharing research through repositories
 Conform to institutional policy, publication requirements, and
funder mandates
 P...
Sharing research through repositories
 Conform to institutional policy, publication requirements, and
funder mandates
 P...
For more information
 Merritt
www.cdlib.org/uc3/merritt
uc3@ucop.edu
Stephen Abrams David Loy
Patricia Cruse Mark Reyes
S...
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Or 2013-abrams-sharing-data-rich-research

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Merritt’s micro-services-based architecture provides a number of options for easy integration with diverse external discovery services with specific disciplinary focus on scientific data sharing. By removing many of the barriers faced by researchers interested in data publication, the integrations of Merritt with DataShare and Research Hub exemplify a new service model for cooperative and distributed data sharing. The widespread adoption of such sharing is critical to open scientific inquiry and advancement.

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  • Copyright © 2013 by The Regents of the University of CaliforniaThis work is made available under the terms of the Creative Commons Attribution-ShareAlike 3.0 license
  • MatijaGrguric, Scale up! – Curved elements!, http://www.flickr.com/photos/32195273@N05/5107685264Tom Rafferty, Remote control!, http://www.flickr.com/photos/67945918@N00/4319529821Barry Egan, File rio 2006, http://www.flickr.com/photos/vixon/116447718
  • Kevin Smith, Converting 8.24 bit samples in CoreAudio on iOS, http://www.kevatron.co.uk/converting-8-24-bit-samples-in-coreaudio-on-ios/Paul B. Hartzog, Server room, http://www.flickr.com/photos/paulbhartzog/680749585
  • Transcript of "Or 2013-abrams-sharing-data-rich-research"

    1. 1. Sharing Data-Rich Research Through Repository Layering Stephen Abrams California Digital Library Angela Rizk-Jackson Julia Kochi University of California, San Francisco Noah Wittman University of California, Berkeley
    2. 2. Why is data curation important?  Accelerating scientific progress  Enabling appropriate scrutiny and verification of results  Promoting integrity and debate  Facilitating new collaborations  Avoiding needless duplication of effort  Increasingly, complying with institutional policies, publication requirements, and funder mandates Cf. White and Teds (2011), “Making the case for research data management” DCC briefing paper, www.dcc.ac.uk/resources/briefing-papers/making-case-rdm
    3. 3. The library’s role  A continuation of its long-standing mission and practice to connect patrons with content of interest in meaningful ways across barriers of space and time Cf. Tenopir et al. (2012), “Academic librarians and research data services: Preparation and attitudes,” 78th IFLA General Conference and Assembly, Helsinki, conference.ifla.org/past/ifla78/116-tenopir-en.pdf  Offering solutions that enhance the natural points of alignment between the scholarly research and information lifecycles Publish Reuse ShareCreate Discover Collect PreserveAccessResearchResearch CurationCuration Scholarly lifecycle Information lifecycle
    4. 4. Merritt  Curation repository available to the UC community and external partners  Preservation and access  Content agnostic, model free  Highly decentralized micro-services architecture Cf. Abrams, Cruse, Kunze, and Minor (2011), “Curation micro-services: A pipeline metaphor for repositories,” Journal of Digital Information 12(2), journals.tdl.org/jodi/article/view/1605  26 curatorial units  271 collections  325,000 objects  450,000 versions  4,500,000 files  13 TB www.cdlib.org/uc3/merritt merritt.cdlib.org
    5. 5. Merritt Storage node Storage broker Inventory ONEShare UNM storage node Storage node UI/API UI/API UI/API LDAP LDAP LDAP RDBMS Fixity User agent Message queue RDBMS Load balancer Ingest Load balancer Ingest Ingest EZID No-SQL DataCite … DataONE member node RDBMS RDBMS DataONE coord’ing node … IDF Load balancer Web of Knowledge Primo SAN SDSC cloud
    6. 6. (Some) issues to address  Scale  Individual objects ranging from 0 to 47,000 files  Individual files ranging from 0 to 14 GB  Maintaining control  Concern over potential loss of control over dissemination and use of data  User experience  Switch from organizational to individual interaction www.flickr.com/photos/vixon/116447718www.flickr.com/photos/traftery/4319529821www.flickr.com/photos/32195273@N05/51076852642
    7. 7. (Some) issues to address  Scale  Individual objects ranging from 0 to 47,000 files  Individual files ranging from 0 to 14 GB  Maintaining control  Concern over potential loss of control over dissemination and use of data  User experience  Switch from organizational to individual interaction Augment repository function by composition (when possible) and addition (when necessary)  Loosely-coupled integration with external community supported systems and services
    8. 8. Scale  Avoiding client timeout  ≤ 2 GB: File-based  stream-based AIP-to-DIP processing  > 2 GB: Asynchronous delivery  Email notification with personalized, time-limited URL  Streamlined storage provisioning  SDSC cloud cloud.sdsc.edu www.kevatron.co.uk/converting-8-24-bit-samples-in-coreaudio-on-ios www.flickr.com/photos/paulbhartzog/680749585
    9. 9. Control  Data use agreements (DUAs)  Explicit assertion of license requirements and terms of use  Curatorial and consumer notification of acceptance Cf. Brazhnik and Jones (2007), “Anatomy of data integration,” Journal of Biomedical Informatics 40(3): 252- 69, doi:10.1016/j.jbi.2006.09.001 From: no-reply-merritt@ucop.edu Subject:Merritt DUA acceptance Name: Stephen Abrams Affiliation: California Digital Library Collection: UCSF DataShare Object: Frontotemporal Lobar Degeneration (FTLD) Date: 2013-05-3109:50:34PDT Terms of use: As part of this agreement, Consumer submits to the following statements: (1) I will receive access to de-identified data and will not attempt to establish the identity of any of the study subjects. (2) I will share these data only with my immediate co-workers, and I will not transfer these data to other research groups. I understand that these data are available to other research groups through the process by which I obtain them. (3) I will require anyone in my group who utilizes these data, or anyone with whom I share these data to comply with this data use agreement ...
    10. 10. User experience  Due to its open eligibility policy, Merritt will always provide a more generic UX than special-purpose or disciplinary systems  Shifting user roles, shifting expectations  Institutional  individual researcher  Behavioral expectations set by the commercial/mobile web
    11. 11. User experience  Due to its open eligibility policy, Merritt will always provide a more generic UX than special-purpose or disciplinary systems  Shifting user roles, shifting expectations  Institutional  individual researcher  Behavioral expectations set by the commercial web  Integration with extant services that better provide the desired UX  DataShare  Research Hub
    12. 12. DataShare  “The goal of the DataShare project is to catalyze widespread sharing of scientific research data” datashare.ucsf.edu  UCSF Clinical and Translational Science Institute ctsi.ucsf.edu  UCSF Library www.library.ucsf.edu  UCSF Center for Imaging of Neurodegenerative Disease www.radiology.ucsf.edu/cind  Architecture  DataShare submission client (Ruby/Rails)  Merritt curation repository  DataShare discovery portal (XTF/Java)
    13. 13. DataShare  Prepare  Describe  Upload  Curate  Discover  Share
    14. 14. DataShare  Prepare  Best practice advice  Describe  Upload  Curate  Discover  Share
    15. 15. DataShare  Prepare  Describe  Schema-directed metadata editor  DataCite schema schema.datacite.org  Upload  Curate  Discover  Share
    16. 16. DataShare  Prepare  Describe  Upload  File browse or drag-n-drop  Curate  Discover  Share
    17. 17. DataShare  Prepare  Describe  Upload  File browse or drag-n-drop  Curate  Discover  Share
    18. 18. DataShare  Prepare  Describe  Upload  Curate  Manage datasets  Discover  Share
    19. 19. DataShare  Prepare  Describe  Upload  Curate  Discover  Faceted search and browse  Share
    20. 20. DataShare  Prepare  Describe  Upload  Curate  Discover  Share  DataONE  DataCite  (soon) Primo Web of Knowledge  SEO
    21. 21. Merritt + DataShare Storage node Storage broker Inventory ONEShare UNM storage node Storage node UI/API UI/API UI/API LDAP LDAP LDAP RDBMS Fixity User agent Message queue RDBMS Load balancer Ingest Load balancer Ingest Ingest EZID No-SQL DataCite … DataONE member node RDBMS RDBMS DataONE coord’ing node … IDF Load balancer Web of Knowledge Primo SAN SDSC cloud DataShare upload Collection Atom feed XTF xtf.cdlib.org DataShare portal Lucene
    22. 22. Research Hub  “Research Hub provides powerful tools for content management and collaboration” hub.berkeley.edu  Alfresco CMS www.alfresco.com  770 projects, 3,900 users  Personal file management  Project collaboration  Departmental resource pooling  Research data management  Desktop sync, mobile app, Adobe Creative Suite  UC Berkeley Information Services and Technology ist.berkeley.edu
    23. 23. Research Hub  Prepare  Acquire and arrange  Describe  Upload  Curate  Discover  Share
    24. 24. Research Hub  Prepare  Describe  Schema-directed metadata editors  Upload  Curate  Discover  Share
    25. 25. Research Hub  Prepare  Describe  Upload  Direct action  Curate  Discover  Share
    26. 26.  Prepare  Describe  Upload  Direct action  Curate  Discover  Share Research Hub
    27. 27. Research Hub  Prepare  Describe  Upload  Policy-based workflow rules  Curate  Discover  Share
    28. 28. Research Hub  Prepare  Describe  Upload  Drag-and-drop  Curate  Discover  Share
    29. 29. Research Hub  Prepare  Describe  Upload  Confirmation  Curate  Discover  Share
    30. 30. Research Hub  Prepare  Describe  Upload  Curate  Manage datasets  Discover  Share
    31. 31. Research Hub  Prepare  Describe  Upload  Curate  Discover  Share
    32. 32. Research Hub  Prepare  Describe  Upload  Curate  Discover  Share
    33. 33. Merritt + DataShare + Research Hub Storage node Storage broker Inventory ONEShare UNM storage node Storage node UI/API UI/API UI/API LDAP LDAP LDAP RDBMS Fixity User agent Message queue RDBMS Load balancer Ingest Load balancer Ingest Ingest EZID No-SQL DataCite … DataONE member node RDBMS RDBMS DataONE coord’ing node … IDF Load balancer Web of Knowledge Primo SAN SDSC cloud DataShare upload Collection Atom feed XTF xtf.cdlib.org DataShare portal Lucene Research Hub
    34. 34. Next steps  Self-service account registration  UCTrust and InCommon Shibboleth federations  Additional cloud-based replication  Outreach  Integration with Open Context archaeological portal opencontext.org  Atom-based submission  Integration with Nuxeo www.nuxeo.com  UC system-wide DAMS solution  Integration with Islandora islandora.ca  Collaboration with UCLA Library  Tuque API  Integration with DPN www.dpn.org
    35. 35. Sharing research through repositories  Conform to institutional policy, publication requirements, and funder mandates  Pro-active curation of valuable research outputs  Stable citation and access  High visibility publication and discovery  Use metrics
    36. 36. Sharing research through repositories  Conform to institutional policy, publication requirements, and funder mandates  Pro-active curation of valuable research outputs  Stable citation and access  High visibility publication and discovery  Use metrics  Repository layering as an appropriate division of labor  Exploiting existing capabilities already in local use
    37. 37. For more information  Merritt www.cdlib.org/uc3/merritt uc3@ucop.edu Stephen Abrams David Loy Patricia Cruse Mark Reyes Shirin Faenza Joan Starr Scott Fisher Carly Strasser Erik Hetzner Marisa Strong Joshua Hubbard Bhavitavya Vedula Greg Janée Kenneth Weiss John Kunze Perry Willet Rosalie Lack  DataShare datashare.ucsf.edu Geoffrey Boushey Julia Kochi Anirvan Chatterjee Angela Rizk-Jackson Maninder Kahlon Michael Weiner  Research Hub hub.berkeley.edu Ian Crew Michael McCarthy (Tribloom) Noah Wittman Patrick McGrath www.slideshare.net/UC3/or-2013abramssharingdatarichresearch
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