2004.v smith.sid
DESCRIPTION
SID: Specimen Image DatabaseTRANSCRIPT
Specimen Image Database (SID)
Vince Smith*, Simon Rycroft & Rod Page
University of Glasgow, Glasgow, UK*Present Address: Illinois Natural History Survey, USA
http://sid.zoology.gla.ac.uk/
Design Requirements
• Distributed
• Cross Platform
• Generic (any taxa)
• Intuitive ?
• Free
• Web based
• Add user incentives?
Entity Relationships
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
Image Server
Entity Relationships
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
Image Server
Web Pages
Image Files
Entity Relationships
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
Image Server
Database
Script
Web Pages
Entity Relationships
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
Image Server
Image Processing
Text Processing
• Upload• Annotate• Label• Edit
• Browse• Search• RSS Feeds• Web Service
• Add/delete users• Set preferences
• Browse• Search• RSS Feeds• Web Service
• Upload• Annotate• Label• Edit
Entity Relationships
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
• Browse• Search• RSS Feeds• Web Service
Image Server
Registered Users AdministratorUnregistered Users
Taxonomy Name Server
http://darwin.zoology.gla.ac.uk/~rpage/MyToL/www/
Rod Page - Univ. of Glasgow
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
Image Server
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
Image Server
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
Image Server
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
Image Server
Centralized Taxonomy
Taxon X
Taxon Y
Taxon Z
Taxon …
Taxonomy Name Server
http://darwin.zoology.gla.ac.uk/~rpage/MyToL/www/
Rod Page - Univ. of Glasgow
Centralized TNS Advantages- Maintains data quality- Common vocab. for searches via TNS- Minimizes data redundancy- Centralized taxonomy updates
TNS Disadvantages- Taxonomy must be in TNS- User chooses ‘which’ taxonomy- TNS must be on-line
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
Image Server
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
Image Server
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
Image Server
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
Image Server
Taxon X
Taxon Y
Taxon Z
Taxon …
Taxonomy Name Server
http://darwin.zoology.gla.ac.uk/~rpage/MyToL/www/
Rod Page - Univ. of Glasgow
Taxonomic Ontology
Rapid Annotation
• Quick upload
• Group images
Rapid Annotation
• Quick upload
• Group images
• Bulk annotation
Rapid Annotation
• Quick upload
• Group images
• Bulk annotation
• Apply keywords
Rapid Annotation
• Quick upload
• Group images
• Bulk annotation
• Apply keywords
• Re-annotate later
Copyrights & wrongs
• Respect restrictions ofimage provider
• Prevent copying ofmain image
• Optionally preventaccess to original image
Copyrights & wrongs
• Respect restrictions ofimage provider
• Prevent copying ofmain image
• Optionally preventaccess to original image
• Dynamic generation ofcopyright holder on mainimage
Cool Features
• Exemplar images- Define taxon ‘type’ images- Useful for web-services
Cool Features
• Exemplar images- Define taxon ‘type’ images- Useful for web-services
• On-line image labeling- Add labels to overlay image- 3 step process within web browser
Cool Features
• Exemplar images- Define taxon ‘type’ images- Useful for web-services
• On-line image labeling- Add labels to overlay image- 3 step process within web browser
Cool Features
• Exemplar images- Define taxon ‘type’ images- Useful for web-services
• On-line image labeling- Add labels to overlay image- 3 step process within web browser
• Alias addressing- Rapidly cite/locate images- (not a proper GUID)
Cool Features
• Exemplar images- Define taxon ‘type’ images- Useful for web-services
• On-line image labeling- Add labels to overlay image- 3 step process within web browser
• Alias addressing- Rapidly cite/locate images- (not a proper GUID)
Image Discovery
• Standard search options
Image Discovery
• Standard search options
• Taxonomy search via TNS
Image Discovery
• Standard search options
• Taxonomy search via TNS
• Extensive browse options- Taxon, keyword, type image, label
Image Discovery
• Standard search options
• Taxonomy search via TNS
• Extensive browse options- Taxon, keyword, type image, label
• Two RSS feeds- Recent taxa/images
Image Discovery
• Standard search options
• Taxonomy search via TNS
• Extensive browse options- Taxon, keyword, type image, label
• Two RSS feeds- Recent taxa/images
- e.g., for taxon ‘type’ images• Web service access
Future Developments?
• Common image portal?
• Keyword ontologies- Generic anatomical vocabularies with ontologies
• Add proper image GUID’s- Unique identifiers for each image (LSID’s?)
e.g. urn:lsid:pdb.org:1AFT:1
• Improved integration with TNS- Access other TNS?
• Better web service support- Retrieve any image/information, WSDL files?
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
Image Server
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
Image Server
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
Image Server
Database
Script
Web Pages
Image Processing
Image Files
Text Processing
Image Server
Taxon X
Taxon Y
Taxon Z
Taxon …
Taxonomy Name Server
http://darwin.zoology.gla.ac.uk/~rpage/MyToL/www/
Rod Page - Univ. of Glasgow
Image Portal?
BioCorder?(B i o l o g i c a l R e c o r d e r)
• Web based• Distributed• Specimen DB
• Cross platform• Free
• Modular
David Reed et alSubmitted to NSF July, ‘04
Acknowledgements
• Wellcome Trust