seltmann 2, katja; prieto-marquez 1,*, albert; ronquist 2, fredrik; riccardi 3, gregory a.; deans 5,...

SELTMANN2, Katja; PRIETO-MARQUEZ1,*, Albert; RONQUIST2, Fredrik; RICCARDI3, Gregory A.; DEANS5, Andy; JAMMIGUMPULA2, Neelima; MAST1, Austin; WINNER2, Steve; MANEVA-JAKIMOSKA2, 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

Image management for effective collaboration using presently existing Web

tools in Morphbank------------------------------

www.morphbank.net

• 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

Morphbank Team

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

What is Morphbank

Morphbank 2.5.5

• 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

Morphbank 2.5.5

QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.QuickTime™ and a

TIFF (LZW) decompressorare needed to see this picture.

QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.QuickTime™ and a

TIFF (LZW) decompressorare needed to see this picture.

QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.QuickTime™ and a

TIFF (LZW) decompressorare needed to see this picture.View Specimen Annotation Image Collection Locality

QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.Publication

http://morphbank.net/Show/?id=80305

External links

• 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.

Morphbank 2.5.5

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)

• 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.

• Make upload and data management easier• Web services• Use ontologies and structured language

– Tagging, simple form of annotations

• 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)

Future Directions

Morphbank manager (beta)

Morphbank 2.7 - Character State Annotations

Import and export Nexus files

Morphbank 3.0 - ontologies

http://www.specifysoftware.org/Specify

http://mesquiteproject.orghttp://www.tolkin.org/

Morphbank 3.0 - Web services and Ontologies

http://sourceforge.net/projects/mx-database

http://www.treebase.org/

http://www.gbif.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