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Connecting Specimens, Images and Vocabulary

Connecting Specimens, Images and Vocabulary. Specify, Morphbank, Morphster Beach, Noble, Spears – KU Mast, Riccardi – FSU Miranker, Tirmizi UT. Vision: a work process enhanced by online systems. Collect and digitize specimens Catalog metadata and images

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Connecting Specimens, Images and Vocabulary

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  1. Connecting Specimens, Images and Vocabulary Specify, Morphbank, Morphster Beach, Noble, Spears – KU Mast, Riccardi – FSU Miranker, Tirmizi UT

  2. 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

  3. Project: Repository and Tool Integration • 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

  4. Ontobrowser with Morphbank Keyword Search

  5. CTOL Images • Apparent workprocess • Collect • Image • Annotate

  6. CTOL in Morphbank

  7. 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 riccardi@ci.fsu.edu

  8. Our Cyber-Infrastructure Specify A TODO list of images and taxa Image deposit API Image retrieval Morphster Morphbank API API Retrieval of image annotations Ontology-based image search Ontobrowser API Publish images and annotations

  9. Retrieval of Annotations

  10. 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

  11. Morphster: Image Lookup

  12. Creating Characters and Character States

  13. Creating Characters and Character States

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