connecting specimens, images and vocabulary specify, morphbank, morphster beach, noble, spears –...
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Connecting Specimens, Images and VocabularySpecify, Morphbank, MorphsterBeach, Noble, Spears – KU Mast, Riccardi – FSUMiranker, Tirmizi UT
Vision: a work process enhanced by online systems Collect and digitize specimens Catalog metadata and images
Add to online digital repositories ASAP Protect digital information from outsiders
Create phenome descriptions Extend ontology Annotate images and anatomy
Share online among collaborators
Specify specimen management Desktop tool for specimen metadata management
Morphbank Image Repository Web presence for collaboration and publication
Morphster and Ontobrowser Ontology Management for Phylogenetics Extension of ontology to incorporate phenotypes and
annotations Integration of Specify, Morphster and Morphbank
Searching for images using ontology terms Linking images and other digital objects to ontology
terms Access to information from any user interface
Illustrate a key for legumes of the southeast
Project: Repository and Tool Integration
Ontobrowser with Morphbank Keyword Search
CTOL Images
Apparent workprocess Collect Image Annotate
CTOL in Morphbank
Illustration of Ontology
• Associate feature that can be seen in an image with ontology terms that describe the image– Area of interest in the image– Terms that describe anatomy, shape, etc.
• Replace– The (un) controlled vocabulary of Morphbank – With the controlled vocabulary of Morphster
• Resulting system is– Better for users because it is illustrated– Better for harvesters because it is precise
Ontobrowser
API
API
API
API
Specify
Morphbank Morphster
Publish images and annotations
A TODO list ofimages and taxa
Image retrieval
Image deposit
Ontology-based image
search
Retrieval of image annotations
Our Cyber-Infrastructure
Retrieval of Annotations
Morphster Image lookup from Morphbank
Currently: keyword based Later: ontology-based, taxon, specimen,
character … Ontology-based creation of character
statements Currently: EQ (EAV) model Later: Tirmizi’s taxonomy of character types
Image annotation: anatomical entities and phenotypes Export to Ontobrowser
Image search strategies Expanding scope
Ask for ‘wrist’, if no match, ask for ‘forearm’, ‘hand’, etc.
Harvest and
Morphster: Image Lookup
Creating Characters and Character States
Creating Characters and Character States