About SID

SID was conceived by Simon Rycroft and Vince Smith as a general-purpose web repository of high-quality digital images for phylogenetic and biodiversity research. Key features of SID include:

• Web upload/download of images
  (supports multiple image formats)
• Bulk and single image annotation via web forms
  (permits quick, simple, and detailed annotation of images)
• Extensive browse and search options
  (includes advanced taxonomic search options)
• Web service facility
  (allows external websites to display images and annotations stored by SID)
• Web utility to label specific image features
  (displays optional labels overlaying an image, useful for highlighting key features)
• Taxonomy served and validated independently by the Glasgow Taxonomy Name Server
  (maintains integrity of the data and helps "future-proof" the taxonomy)
• Alias addresses for images by accession number
  (permits rapid citation of images in publications e.g. http://darwin.zoology.gla.ac.uk/~sid/id/15
• Freeware - available for download from the "Host SID" link
  (allows anyone to set up the database and serve their own images)

Screen shots

• Multiple image upload* [1]
• Group images for bulk annotation* [1]
• Bulk or individual image annotation* [1,2,3]
• Label image features as a layer over the image* [1,2,3]
• Administrator page* [1]
• Advanced search [1]

* Requires registration to access this feature within the database.

History and Credits

Database and website design and implementation was completed by Simon Rycroft. This was initially performed as part of his dissertation requirement for an MSc in Information Technology at the University of Glasgow. Testing, support and ideas for development were provided by Vince Smith and Rod Page.

Software

The site uses an Apache web server, running PHP with a MySQL database. Image conversion is done using the command line interface to imagemagick. The multiple file upload applet was written by Simon Rycroft using Java.

The site has been tested using the latest versions of Mozilla Firebird, Mozilla, Opera, Safari and Internet Explorer on Mac, Windows and Linux platforms (current as of Winter, 2004) . Extensive use of Mozilla Firebird was made during development.

Similar Sites

Morphbank
A fantastic site with similar goals to SID. Morphbank is a centralized image repository, cf SID which is designed to be distributed. It currently lacks web service support, taxonomy validation and several other utilities that have been incorporated into SID.

Future Developments

• Implement a controlled vocabulary and ontology for keywords with definitions.
  This would facilitate better keyword searching and maintain data quality by enforcing consistency of nomenclature. The list would include synonyms. An excellent example of a controlled vocabulary for Drosophila is available from FlyBase.
• Greater web service support.
  Support for DiGIR queries (Distributed Generic Information Retrieval), development of a WSDL file, and better integration with the Glasgow Taxonomy Name Server for taxonomy name validation.
• Taxonomic name validation for associate taxa.
  e.g. hosts of parasites Taxonomic names are presently only validated for the taxon displayed in the image and not for associated taxa such as the hosts of parasites.
• Taxon type images for different image formats.
  Presently only one type image is designated for each taxon. Support for taxon type images unique to different image formats (e.g. SEM and light microscope images) would be desirable.
• Help boxes
  The image submission and user interface is designed to be intuitive. Further support could be provided with the addition of help boxes.
• Additional browse and search features.
  Searching by associate taxa (e.g. the host name of a parasite) or browsing by taxonomic hierarchy served by the Glasgow Taxonomy Name Server.

Funding

SID received no direct funding but has been indirectly supported with funds from a Wellcome Trust Biodiversity Fellowship to Vince Smith.