Specimen Image Database (SID) Vince Smith, Simon Rycroft & Rod Page University of Glasgow, Glasgow, UK Present Address: Illinois Natural History Survey,

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 ?

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.





• Free

• Web based

• Add user incentives?

• 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 FilesQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.

Text Processing

• Browse

• Search

• RSS Feeds

• Web Service

Image Server

Registered Users AdministratorUnregistered Users



Web Pages

Image Files





Database

Script

Web Pages

Image Processing

Text Processing

Taxonomy Name Server

QuickTime™ and aTIFF (LZW) decompressorare needed to see this picture.

http://darwin.zoology.gla.ac.uk/

~rpage/MyToL/www/

Rod Page - Univ. of Glasgow



Database

Script

Web Pages

Image Processing


Text Processing

Image Server



Database

Script

Web Pages

Image Processing


Text Processing

Image Server



Database

Script

Web Pages

Image Processing


Text Processing

Image Server



Database

Script

Web Pages

Image Processing


Text Processing

Image Server

Centralized Taxonomy

Taxon X

Taxon Y

Taxon Z

Taxon …



http://darwin.zoology.gla.ac.uk/

~rpage/MyToL/www/


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


Text Processing

Image Server



Database

Script

Web Pages

Image Processing


Text Processing

Image Server



Database

Script

Web Pages

Image Processing


Text Processing

Image Server



Database

Script

Web Pages

Image Processing


Text Processing

Image Server

Taxon X

Taxon Y

Taxon Z

Taxon …



http://darwin.zoology.gla.ac.uk/~rpage/MyToL/www/


Taxonomic Ontology

Rapid Annotation

• Quick uploadQuickTime™ and a

TIFF (Uncompressed) decompressorare needed to see this picture.

• Group images



• Bulk annotationQuickTime™ and a


• Apply keywords



• Re-annotate later



Copyrights & wrongs

• Respect restrictions of image provider

• Prevent copying of main imageQuickTime™ and a


• Optionally prevent access to original image

• Dynamic generation of copyright holder on main image

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

• Taxonomy search via TNSQuickTime™ and a


QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.• 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?

QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.



Database

Script

Web Pages

Image Processing


Text Processing

Image Server



Database

Script

Web Pages

Image Processing


Text Processing

Image Server



Database

Script

Web Pages

Image Processing


Text Processing

Image Server



Database

Script

Web Pages

Image Processing


Text Processing

Image Server

Taxon X

Taxon Y

Taxon Z

Taxon …



http://darwin.zoology.gla.ac.uk/~rpage/MyToL/www/


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 TrustQuickTime™ and aTIFF (LZW) decompressorare needed to see this picture.

Specimen Image Database (SID) Vince Smith, Simon Rycroft & Rod Page University of Glasgow, Glasgow, UK Present Address: Illinois Natural History Survey,

Documents

image lsids

main image slide

glasgow image portal

webservices online image

common image portal

copying of main image

free web

server http

Specimen Image Database (SID) Vince Smith*, Simon Rycroft & Rod Page University of Glasgow, Glasgow, UK *Present Address: Illinois Natural History Survey,

Specimen Image Database (SID) Vince Smith, Simon Rycroft & Rod Page University of Glasgow, Glasgow, UK Present Address: Illinois Natural History Survey,