1 / 22

What is Morphbank

Building Relationships between Images and other Biological Objects using the Morphbank Repository ( www.morphbank.net ) and Morphbank Collaboratory Tools.

ramirezr
Download Presentation

What is Morphbank

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Building Relationships between Images and other Biological Objects using the Morphbank Repository (www.morphbank.net) and Morphbank Collaboratory Tools 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, Department of Computational Sciences, Florida State University

  2. What is Morphbank • Morphbank is an open web repository and collaboratory for biological images primarily serving the specimen-based research community • Started in 1998 by a Swedish-American-Spanish consortium as an open ftp image archive • Centered at the School of Computational Science (SCS), Florida State University, since 2004 • 2005 - 2008 NSF grant (DBI 0446224) to develop the system, in particular for three use cases: • Remote annotation of natural history specimens • Morphological phylogenetics • Paleohistology

  3. Long-Term Goals • 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?

  4. Morphbank 2.5.5

  5. Browse and search images based on metadata Alphabetic index of taxon names Taxon hierarchy Single Google-like search box Field-specific search and filtering Security model Private vs. public data (‘unpublished’ and ‘published’) Group access, different roles within the group, user-managed Each user has a ‘privilege taxon’ Reviewer accounts Edit and upload From Web form or batch upload through Excel workbook From new Specify client plug-in User support Curators and help desk Online users manual and FAQ Workshops for users and programmers Morphbank 2.5.5

  6. Morphological Ontology Taxa View Specimen Annotation Publication Collection Locality Morphbank 2.5.5 Morphbank objects External objects Morphbank image

  7. External links http://morphbank.net/Show/?id=80305

  8. http://morphbank.net/Show/?id=142605 Collections: show, share, annotate, view and publish

  9. Linking Online Papers to Collections

  10. Image hosting/linking http://morphbank.net/Show/?id=111266 http://www.morphbank.net/?id=111266&imgType=jpeg http://www.hymatol.org/Chalcidkey/ E. Grissell, M. E. Schauff & Mike Gates

  11. Image hosting/linking http://www.hymatol.org/Chalcidkey/ E. Grissell, M. E. Schauff & Mike Gates

  12. Morphbank users addition, correction peer review, validation community consensus Taxon Name Management (2.5.5) Morphbank ITIS cache ITIS+

  13. Taxon Name Annotations (2.5.5)

  14. Morphbank 2.7 - Character State Annotations Import and export Nexus files

  15. Using Ontologies

  16. Mx - ontology/controlled vocabulary builder

  17. Illustrating the Ontology

  18. Using Ontologies in Morphbank

  19. Acknowledgments • 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

More Related