Transcript ppt - Morphbank ALA

Image management for effective
collaboration using presently existing Web
tools in Morphbank
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www.morphbank.net
SELTMANN2, Katja; PRIETO-MARQUEZ1,*, Albert; RONQUIST2, Fredrik; RICCARDI3, Gregory A.; DEANS5, Andy; JAMMIGUMPULA2, Neelima; MAST1, Austin; WINNER2, Steve; MANEVAJAKIMOSKA2, Karolina; PAUL2, Debbie; CPREK2, Christopher; 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. 4Department of Entomology,
North Carolina State University, Raleigh, NC 27607, USA.
Morphbank Team, Department of Computational Sciences, Florida State University
Morphbank Team
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Wilfredo Blanco, programmer/search and browse
Christopher Cprek, system administrator
Andrew Deans, biologist/Hymenoptera ontology project
Robert van Engelen, principal investigator /Department of Computer Science
Greg Erickson, principal investigator /paleontologist/paleohistological project
Cynthia Gaitros, technical writer
David Gaitros, programmer/annotations software/project coordinator
Neelima Jammigumpula, programmer/data base development/project coordinator
Peter Jörgensen, principal investigator /School of Computational Sciences
Corinne Jörgensen, principal investigator /School of Computational Sciences
Karolina Maneva-Jakimoska, programmer/Java development
Albert Prieto-Marquez, paleontologist/paleohistological project
Austin Mast, principal investigator /biologist/ herbarium curator/annotations software
Debbie Paul, curator/user manual and user trials
Fredrik Ronquist, principal investigator/biologist/project initiator
Greg Riccardi, principal investigator/ data base development /lead project coordinator
Katja Seltmann, curator/external links/annotation software
Steve Winner, programmer/Web development and GUI/collections software
What is Morphbank
 Morphbank is an open web repository of biological images serving the
research community. Any research biologist may use the morphbank tools
 First developed in 1998 by a Swedish-American-Spanish consortium as an
ftp site
 Now centered at the School of Computation Sciences (SCS), Florida State
University
 March 2005 - Morphbank team awarded 3-year NSF grant (BDI 0446224) to
develop the software
Morphbank 2.5.5
Morphbank 2.5.5
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Browse and search based on objects in Morphbank
Published vs. unpublished data
Group access/security
Reviewer Accounts
Access requires only a Web browser
Edit/upload from the Web & Excel upload
Darwin Core standard for data definitions
MorphbankID (mbID) but searchable by the origional file name for that image.
Online users manual and FAQ
Curators and a help desk and can arrange for a project workshop
User branding
Backup-second server + tape backup
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
View
Specimen
QuickTime™ and a
TIF F (LZ W) decompressor
are needed to see this picture.
Annotation
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
Image
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
Publication
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
Collection
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
Locality
External links
http://morphbank.net/Show/?id=80305
Morphbank 2.5.5
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Create Annotation (xml, determination, legacy and general) and Collections
Mirror images using ftp account
Maintain publication information
Web linking
– Use images in your own Web page using morphbank ID
– Link to any morphbank object (collection, annotation, image, specimen) using the morphbank ID.
Work with the Integrated Taxonomic Information System (ITIS). Use as the taxonomic name
service plus the ability to add names to Morphbank not presently in ITIS
– Annotate names already in ITIS
– collaboration with ITIS to submit names directly to their system from morphbank.
Collections: show, share, annotate, view and publish
Image hosting/linking
http://www.hymatol.org/Chalcidkey/
E. Grissell, M. E. Schauff & Mike Gates
Image hosting/linking
http://www.hymatol.org/Chalcidkey/
E. Grissell, M. E. Schauff & Mike Gates
Add links to publication records, search function for those publications
Mirrors/Image cache (2.5.5)
Future Directions
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Create tools to manage your objects
– These tools make it easier to limit records displayed
by user or group, and make changes to multiple records.
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Make upload and data management easier
Web services
Use ontologies and structured language
– Tagging, simple form of annotations
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Modification of the collection tool for creating Character/Character States
Build matrices for phylogenetics and key creation (see poster session)
Specific interface design for histological studies (see poster session)
Morphbank manager (beta)
Morphbank 2.7 - Character State Annotations
Import and export Nexus files
Morphbank 3.0 - ontologies
Morphbank 3.0 - Web services and Ontologies
http://www.specifysoftware.org/Specify
http://sourceforge.net/projects/mx-database
http://www.treebase.org/
http://www.gbif.org/
http://www.tolkin.org/
http://mesquiteproject.org
Acknowledgments
• National Science Foundation
- Biological Databases and Informatics (BDI) Program
(Grant DBI-0446224) for Morphbank
• 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