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Moving to Fully Distributed, Interoperable Repositories for Biodiversity Images and Information

SELTMANN2, Katja; PRIETO-MARQUEZ1,*, Albert; RONQUIST2, Fredrik; RICCARDI3, Gregory A.; DEANS2, Andy; JAMMIGUMPULA2, Neelima; MAST1, Austin; WINNER2, Steve; MANEVA-JAKIMOSKA2, Karolina; PAUL2, Debbie; BLANCO2, Wilfredo; GAITROS4, David; ERICKSON1, Gregory M.; and GAITROS2, Cynthia

1Department of Biological Science, Florida State University, Tallahassee, FL 32306-1100, USA. 2School of Computational Science, Florida State University, Tallahassee, FL 32306-4120, USA. 3College of Information, Florida State University, Tallahassee, FL 32306-4530, USA. 4Department of Computer Science, Florida State University, Tallahassee, FL 32306-4530, USA

Morphbank Team, School of Computational Sciences, Florida State University


Overview Biodiversity Images and Information

  • Long term goals

  • Update on Morphbank information interchange

  • Morphbank as an image repository, what’s the future?

  • Moving to a fully distributed image repository for Morphbank

    • Creating a highly reliable Internet repository

    • Caching images for dynamic image management

    • Distributing the Morphbank metadata

  • Moving to fully interoperable image repositories

    • Sharing images between repositories

    • Sharing metadata between repositories

    • Searching across repositories

  • What can we do to make this move?


Long-Term Goals Biodiversity Images and Information

  • Fully distributed image repository

    • The network is the repository: nobody/everybody owns the repository

    • Cheap: commodity systems for storage

    • Scalability: more users - more storage space

    • Long-term archiving, minimum downtime, fast access: guaranteed by redundancy

  • Coordinated international open source development of collaboratory software

    • Free for all - best way to help developing countries

    • Resources exist but how coordinate and fund distributed open source development of sophisticated software?

    • Should TDWG get involved? Separate non-profit organization?


Interaction through Web Services Biodiversity Images and Information


Web Services XML and RDF Biodiversity Images and Information


OCR to Facilitate Specimen Metadata Entry Biodiversity Images and Information


Reliable Data Repository Biodiversity Images and Information

  • People ask, “How much do you charge and how long will you keep my images?

    • Last year, Riccardi said, “Forever, or until June 30, 2008, whichever comes first.”

  • Server system at Morphbank to support claim

    • UPS, 24 hour on-call system administrators, high-bandwidth network

  • New strategy is evolving to give more satisfying answer

    • “As long as people find it useful.”

  • We need low cost, reliable, shared management

    • Off-the-shelf hardware

    • Open source software

    • Resources provided by contributors at low cost


Morphbank Server Biodiversity Images and Information

Browser

request

doc

Database

Web Server

img

Image File Store


Morphbank Mirror Server Biodiversity Images and Information

Browser

Morphbank

request

doc

Database

Web Server

img

Image File Store

Mirror management

Mirror

Web Server

Image File Store


Morphbank Reliability Biodiversity Images and Information

Browser

Morphbank

request

doc

Database

Web Server

img

Image File Store

Mirror

Web Server

Web Server

Web Server

Web Server

Web Server

Image File Store

Image File Store

Image File Store

Image File Store

Image File Store


Morphbank Caching Server Biodiversity Images and Information

Browser

Morphbank

request

doc

Database

Web Server

img

Image File Store

img

Mirror management

Mirror

Web Server

Image File Store


Morphbank Distribution Biodiversity Images and Information

Browser

Morphbank

request

doc

Database

Database

Web Server

Web Server

request

Active searching

Shared metadata

Image File Store

Image File Store

doc

Morphbank


Interoperability with Caching Biodiversity Images and Information

Browser

Morphbank

request

doc

Database

Database

Web Server

Web Server

request

doc

Image File Store

Image File Store

Shared Metadata

NBII


Full Interoperability Biodiversity Images and Information

Browser

Morphbank

request

doc

Database

Database

Web Server

Web Server

request

doc

Image File Store

Image File Store

Active searching

NBII


Summary
Summary Biodiversity Images and Information

  • Morphbank mirror

    • You can participate

    • Computer with disk, network, Apache, ftp

  • Need some technical improvements

    • Will occur outside the biodiversity informatics community

  • Need people to agree to share

    • Provide resources

    • Make improvements to information process

  • Workshops at FSU

    • Interoperability for images and metadata – Fall 07

    • Developer interaction – Spring 08

      • Integrate clients and services on top of the morphbank data model


Acknowledgments Biodiversity Images and Information

• National Science Foundation

- Biological Databases and Informatics (BDI) Program

(Grant DBI-0446224) for Morphbank

- PEET and DDIG Programs (DEB-041544081 and DEB-0328922) for mx

• Florida State University:

- School of Computational Science

- College of Information

- Department of Computer Science

- Department of Biological Science

- Department of Mathematics

• National Evolutionary Synthesis Center (NESCent)

• Swedish Research Council

• Uppsala University, Sweden

• Morphbank biologists and collaborators: AToL, PEET, PBI, MX, HERBIS, CBG,…

• TDWG supporters


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