Acknowledgements. Chris Catton BioImage Development Manager: ImageStore Ontology and SABO developer. Simon Sparks BioImage Software Engineer: OWLBase query engine developer. John Pybus BioImage Systems Manager. Chris Wilson SABO research project. Chris Holland ImageBLAST research project.
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BioImage Development Manager: ImageStore Ontology and SABO developer
BioImage Software Engineer: OWLBase query engine developer
BioImage Systems Manager
SABO research project
ImageBLAST research project
SABO research project
European Commission funding of the ORIEL Project - IST-2001-32688
Subject (Entity) = Mouse (class) This mouse (instance)
Property (Attribute) = is_a / has_location / has_identifier
Object (Value) = Mammal / Oxford / 667
German taxonomists claimed it was a bear
British taxonomists claimed it was a racoon
US taxonomists weren’t quite sure
In an ontology, one can express more complex relationships about a mouse, other than just its taxonomy
(has_position: front / rear)
(has_handedness: left / right)
(has_length: number unit)
(has_density: number per unit area)
To properly annotate videos of Betty, we need to be able to structure not only people’s interpretations of the world, but also Betty’s view of what is going on!
Hypothesis About Evolutionary Origin (an ontology class)
hypothesised evolutionary origin
Body Shaking (a type of behaviour)
“Lorenz, Konrad” (instance data)
Note the hierarchical browse categories and the alternative Browse / Search arrangement
Cell or organism
Experimental study conditions or manipulations
Subject or specimen
Photographer or microscopist
Camera or microscope, illumination, focus, etc
Image sets of multidimensional images, including videos
So people are related to objects and conditions / equipment through events
achieved simply by re-setting the default language of the user’s browser
This shows the Access Control Interface
The same HTML page is being viewed in both cases, using alternate resource bundles
Denotation (raw fact):
Immunofluorescence localization of Xklp1 in XL177 cells
Xklp1 is involved in chromosome localization during mitosis in embryonic Xenopus cells, since it is positioned at the metaphase plate
Vernos et al., 1995
The Advanced Search Interface permits Boolean searches, search restrictions, and re-use of previous searches in combination with new terms
rather than being limited to conventional ‘Google-like’ searching by means of exact keyword matching, results of which are rather unpredictable!
The BioImage Database will receive regular images from three main sources:
”Concerning the image data you requested - this is a tough one. The image was recorded about ten years ago, and I never managed to write a paper about the work so it was never published. The original data (if they still exist) must be on some magneto-optical disk in one of many boxes in my flat - quite hopeless to find at short notice. All I can promise is that I’ll look into this once I am back from my travels – but that will take a few months. Whether anyone still has hardware capable of reading the disc is quite another matter! Sorry about this.“
represents our Ethodata Ontology
– just one among many in the information landscape
“Penroses” by Ruth McDowell
“Weeping woman” by Pablo Picasso
- what if Newton had written the ontology for physics? BEWARE!
Units appropriate to each attribute are defined in the ontology, and so do not need to be specified in the table
BIRTHS, MARRIAGES AND DEATHS
Born to Revd John and Mrs Marjorie Sanders of St Paul’s
Vicarage, Tadcaster Road, Leeds: a daughter Emily Jane,
at 11:25 a.m. on 25th December 2003, weight 3.6 Kg.
Are we at the top of Everest?
Are we on Mount Fuji at all?