2004.V Smith.Sid

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


Database

Script

Web Pages

Image Processing

Image Files

Text Processing

Image Server

Web Pages

Image Files


Database

Script

Web Pages

Image Processing

Image Files

Text Processing

Image Server

Database

Script

Web Pages


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


• Upload• Annotate• Label• Edit


Database

Script

Web Pages

Image Processing

Image Files

Text Processing


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 …




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 …




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


• On-line image labeling- Add labels to overlay image- 3 step process within web browser

Cool Features


• 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


• Taxonomy search via TNS

Image Discovery



• Extensive browse options- Taxon, keyword, type image, label

Image Discovery




• Two RSS feeds- Recent taxa/images

Image Discovery




• 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 …




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

2004.V Smith.Sid

Technology

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