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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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Acknowledgements l.jpg

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

Ruth Dalton

SABO research project

European Commission funding of the ORIEL Project - IST-2001-32688

Outline of my presentation l.jpg
Outline of my presentation

  • Expert knowledge and tacit knowledge

  • The Semantic Web and ontologies

  • Ontologies in biology

  • The BioImage Database: its purpose, structure and ontology usage

  • Enabling ‘smart queries’ by importing external ontologies into BioImage

  • ImageBLAST: hypersearches across distributed biological databases

  • Concluding remarks and cautionary tales

Slide4 l.jpg

This is a fairly straightforward article, but nowhere in it are you told that:

  • Caenorhabditis elegans is a nematode worm, one of the handful of model organisms for which the complete genome has been sequenced

    or that

  • A transcription factor bind to nuclear DNA to control the readout of genetic information from a particular gene

  • These facts are so basic to the paper that they are assumed

Expert knowledge and tacit knowledge l.jpg
Expert knowledge and tacit knowledge are you told that:

  • Mutual understanding within any field of knowledge is based on a shared conceptualisationdeveloped by scholars over the years

  • This shared conceptualisation is often implicit through scholars’ choice of vocabulary and theories when speaking or writing

  • Furthermore, in order to communicate at the highest level (as in the Nature paper), scholars must assume that those listening to or reading their words are part of this community and share the conceptualization

  • Much of what is communicated in a paper or an academic lecture is first a reinforcement and then an extension of the shared tacit knowledge.

  • It is this assumed tacit knowledge, every bit as much as the technical jargon, that makes scientific literature so impenetrable to non-specialists

  • My next few slides are designed to make explicit some of the key points relating to ontologies, for the benefit of those for whom this may be new

Electronic communication of complex knowledge l.jpg
Electronic communication of complex knowledge are you told that:

  • In human society, much of our knowledge is implicit or tacit - we know more than we think we know!

  • However, today, as more and more knowledge is held on-line, more and more communication needs to be M2M, from one computer to another

  • To accomplish such communication successfully, and to permit semantic reasoning over distributed information resources

    • such tacit knowledge must be made explicit, and

    • the meaning of information must be specified unambiguously

  • This is difficult, and demands anal attention to detail

  • The next slide illustrates what I mean . . .

What is this l.jpg

This is are you told that:not a panda

This is not a photograph of a panda

What is this?

This is a caption for a projected digital image of a photograph of a panda

This is noteven a projected digital image of a photograph of a panda

In biology meanings may be complex l.jpg
In biology, meanings may be complex are you told that:

  • In normal conversation, “daughter” means a female human child conceived by sexual intecourse between mother and father, and then born after a gestation of nine months within the mother’s uterus

  • In non-mammalian animal species, development is usually from eggs

  • But sex is not always required: female aphids can give birth to daughters by parthenogenesis, without the need for fertilization of the eggs by male sperm

  • And in the field of cell biology, the word “daughter” has an entirely separate meaning: two genetically identical “daughter cells” are produced every time a single cell divides

  • Biological ontologies have thus to understand the context in which the word “daughter” is used, in order to apply the correct meaning

What is the semantic web and how can it help l.jpg
What is the Semantic Web, and how can it help? are you told that:

  • The concept of the Semantic Web was first clearly articulated in 2001 in an eponymous SciAm article by Tim Berners-Lee, Jim Hendler and Ora Lasilla

  • While the World Wide Web permits access to data in human-readable form, the Semantic Web provides access to information structured in a formal logical manner, such that computers can reason over it, extracting meaning

  • It involves three technologies, each resting hierarchically on the previous one:

    • The use of XML as a markup languagemore expressive than HTML

    • RDF triples that permits one to make simple logical statements (subject-verb-object) written in XML, in a form that a computer can understand

  • The use of ontologies – formal representations of a particular domain of knowledge (e.g. the GO ontology about genes and gene products) – written in a high level ontology language such as OWL (W3C’s Web Ontology Language), which is itself expressed as a set of RDF statements

Rdf triples l.jpg
RDF triples are you told that:

  • An RDF triple might state that amouseis_amammal, informing the computer that an entity ‘mouse’ is included in the more general category of ‘mammal’

  • This has the advantage that mouse inherits all class properties previously defined for mammal, such as the possession of four legs and fur

  • By using several RDF triples referring to the same subject, multiple attributes can be defined:

    Subject (Entity) = Mouse (class) This mouse (instance)

    Property (Attribute) = is_a / has_location / has_identifier

    Object (Value) = Mammal / Oxford / 667

  •  In RDF, the statement “This mouse is located in Oxford” is simply:


    <rdf:Description about=“Mouse”>




What type of animal is shown in this image l.jpg
What type of animal is shown in this image? are you told that:

Ailuropoda melanoleuca

German taxonomists claimed it was a bear

British taxonomists claimed it was a racoon

US taxonomists weren’t quite sure

Today the balance of opinion is bear l.jpg
Today, the balance of opinion is “bear” are you told that:

  • So what is an ontology? “An ontology is a formal explicit specification of a shared conceptualisation”

  • The role of an ontology is to facilitate the understanding, sharing, re-use and integration of knowledge through the construction of an explicit domain model

  • A panda is only a bear because we all now say it is!

We understand taxonomic hierarchies l.jpg
We understand taxonomic hierarchies are you told that:









  • Mouse

In an ontology, one can express more complex relationships about a mouse, other than just its taxonomy

A partial ontology of mouse l.jpg
A partial ontology of ‘mouse’ are you told that:

Group of

Mus musculusorganisms








(has_cardinality: 4)of_locomotion

(has_position: front / rear)

(has_handedness: left / right)

(has_length: number)



Fur hypothesised_

(default_colour: white)function

(has_length: number unit)

(has_density: number per unit area)


How do you build an ontology l.jpg
How do you build an ontology? are you told that:

  • You need to define all the terms within a domain of knowledge, and specify the relationships they have to one another

  • The structure of these relationships is a Directed Acyclic Graph, in which child terms can have more that one parent

  • The relationships of a child term to its two (or more) parent terms can be different, as shown in the previous example:

    • mouseis_a rodent – type relationship

    • mousemember_ofcolony – collective relationship

The thinking crow problem l.jpg
The thinking crow problem are you told that:

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!

Biological ontologies l.jpg
Biological ontologies are you told that:

  • There is good ontological coverage of the genes and gene products of model organisms in the form of the Gene Ontology (

  • But until very recently little work had been done at the other end of the biological spectrum, in the field of animal behaviour

  • However, my department is full of people undertaking whole animal biology

  • To be able to include their images and videos within the BioImage Database, we decided to develop a draft standard animal behaviour ontology, SABO

  • SABO is an upper level ontology designed to cover all of animal behaviour, build around Otto Tinbergen’s four questions: “How does it work? How did it develop? How is it used? and How did it evolve?”

  • Because interpretations of behavioural events can be very subjective, we have been careful to separate fact from hypothesis in the design of SABO, with emphasis on the authority for any claims

Fact and hypothesis in sabo l.jpg
Fact and hypothesis in SABO are you told that:

For example a courtship event l.jpg
For example, a courtship event are you told that:

Courtship behaviour in ducks l.jpg
Courtship behaviour in ducks are you told that:

  • Male mallard ducks attract their mates using a “grunt-whistle”, which Konrad Lorenz hypothesised in 1941 was derived from body shaking

  • Using the SABO ontology, this can be recorded in the following RDF triples:

  • Grunt-Whistle (a type of courtship behaviour)

    generates hypothesis

    Hypothesis About Evolutionary Origin (an ontology class)

  • Hypothesis About Evolutionary Origin

    hypothesised evolutionary origin

    Body Shaking (a type of behaviour)

  • Hypothesis About Evolutionary Origin

    has author

    “Lorenz, Konrad” (instance data)

  • Hypothesis About Evolutionary Origin

    has date

    “1941”(instance data)

The ethodata ontology l.jpg
The Ethodata Ontology are you told that:

  • SABO was used as one of the two starting points for a recent Animal Behaviour Metadata Workshop held at Cornell University, at which leading international ethologists worked together to create an Animal Behavior Metadata Standard

  • Our introduction of formal ontologies to this community was greatly helped by the fact that Chris Wilson, who had worked with us on SABO, recently started a Ph. D. at Cornell with Jack Bradbury, the workshop organiser

  • The Workshop output is a human-readable hierarchy of defined ethological terms, the draft Animal Behavior Metadata Standard (

  • The Workshop has commissioned us to develop this hierarchy into a fully-fledged computable ontology of animal behaviour, for the benefit of the whole ethological community

  • Based on the draft Animal Behavior Metadata Standard and on SABO, and written in OWL, this has the new agreed name of the Ethodata Ontology

  • We have already made a start on this work, and will use it to enter structured ethological image metadata into the BioImage Database

A view of the bioimage home page structure l.jpg
A view of the are you told that:BioImage home page structure

Note the hierarchical browse categories and the alternative Browse / Search arrangement

The bioimage database project l.jpg
The BioImage Database Project are you told that:

  • The value of digital image information depends upon how easily it can be located, searched for relevance, and retrieved

  • Detailed descriptive metadata about the images are essential, and without them, digital image repositories become little more than meaningless and costly data graveyards

  • The BioImage Database aims to provide a searchable database of high-quality multidimensional research images of biological specimens, both ‘raw’ and processes, with detailed supporting metadata concerning:

    • the biological specimen itself

    • the experimental procedure

    • details of image formation and subsequent digital processing

    • the people, institutions and funding agencies involved

    • the curation and provenance of the image and its metadata

  • to provide rich and accurate search results to queries over our data

  • and to integrate such multi-dimensional digital image data with other life science resources by providing links to literature and ‘factual’ databases

The organisation within bioimage l.jpg
The organisation within BioImage are you told that:

  • The basic unit of organisation within the BioImage Database is the BioImage Study, roughly equivalent to a scientific publication

  • A BioImage Study will contain one or more Image Sets, each corresponding to a particular scientific experiment or investigation

  • Each Image Set will contain one or more Imageson a common theme

  • Such an Image may be of any form or dimensionality

    • a 2D image, a 3D image, a video, or a 4D (x, y, z, time) image set

  • Users may browseor searchthe BioImage Database

    • by Study, by Image Set or by Image

  • For each representation, a thumbnail representative image and core metadata of the results (title, authors, description, LSID) are initially presented, and deeper metadata is available by clicking the title

  • Browses and searches may then be progressively refined

The basic bioimage metadata model l.jpg
The basic BioImage metadata model are you told that:

Cell or organism


Experimental study conditions or manipulations


Subject or specimen

Photographer or microscopist

Camera or microscope, illumination, focus, etc

Image capture

Image sets of multidimensional images, including videos

So people are related to objects and conditions / equipment through events

Things to note about the architecture external l.jpg
Things to note about the architecture: external are you told that:

  • User submission, searching and browsing activities are all mediated by the ImageStore Ontology

  • Submission forms are generated dynamically from the ontology, to suit the type of submission

  • Thus, for instance, people submitting light microscopy images are not asked for the accelerating voltage of their electron microscope

  • There is complete separation of content from presentation

  • Presentation to users is via HTML, while SOAP is used to communicate with Web Service clients

  • The Struts controller orchestrates data transfer between the system and the user

  • This permits simple customization of the appearance of the data

Multilingual capabilities enabled by struts l.jpg
Multilingual capabilities enabled by Struts are you told that:

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

Things to note about the architecture internal l.jpg
Things to note about the architecture: internal are you told that:

  • Data are exchanged within the system in XML format, using the BioImage schema

  • There is no hard-coded ‘business logic’ - structures and semantics are generated at run time

  • The ImageStore Ontology is the central data model

  • This single point of control greatly simplifies database maintenance, since changes are automatically and dynamically propagated throughout the system

  • The entire BioImage database structure can be automatically regenerated from the ImageStore Ontology whenever this is required (for example in a new form after updating the ImageStore Ontology), using metadata from a previous XML dump

  • This allows easy migration to a new DBMS, e.g. from PostgreSQL to Oracle

  • OWLBase is used to reference the ontology and to mediate data transfers

  • OWLBase thus provides an abstraction layer for submissions and queries

The imagestore ontology l.jpg
The ImageStore Ontology are you told that:

  • The ImageStore Ontology was constructed using the Jena toolkit ( and our own open source Ontology Organiser, an ontology constraint propagator and datatype manager

  • ImageStore:

    • uses a subset of the class model of the Advanced Authoring Format ( and to describe media objects

    • uses a subset of MPEG-7 to describe multimedia content, and

    • has its own data model to describe scientific experiments

  • It is currently written in DAML+OIL

  • We are in the process of upgrading BioImage to use Jena 2, which will permit us to convert the ImageStore Ontology into OWL

What is required of an image ontology l.jpg
What is required of an image ontology? are you told that:

  • Such a generic image ontology as the ImageStore Ontology must describe all aspects of the images themselves:

    • their acquisition (including details of who took the original micrograph, where, when, under what conditions, for what purpose, etc.)

    • the media object itself (source and derivation, image type, dynamic range, resolution, format, codec, etc.)

    • the denotation of the referent (a description of exactly what is recorded by the image, e.g. the nature, age and pre-treatment of the subject), and

    • the connotation of the referent (i.e. the interpretation, meaning, purpose or significance imparted to the image by a human, its relevance to its creator and others, and its semantic relationship to other images).

  • In addition to these ancillary metadata about the image, there is yet a further need to record semantic content metadata related directly to the information content of the images or videos themselves

  • These semantic content metadata carry very high information value, since they relate directly to spatial (or spatio-temporal) features that are of most immediate relevance to human understanding of media content, namely “Where, when and why is what happening to whom?”

Image description separating fact from hypothesis l.jpg
Image description – separating fact from hypothesis are you told that:

  • BioImage Study title: Xklp1:a Xenopus kinesin-like protein essential for spindle organisation and chromosome positioning

Denotation (raw fact):

Immunofluorescence localization of Xklp1 in XL177 cells

Connotation (interpretation):

Xklp1 is involved in chromosome localization during mitosis in embryonic Xenopus cells, since it is positioned at the metaphase plate

Vernos et al., 1995

Representing fact and hypothesis within imagestore l.jpg
Representing fact and hypothesis within ImageStore are you told that:

Narrative world

Media world

Real world

The bioimage advanced search interface l.jpg
The BioImage advanced search interface are you told that:

The Advanced Search Interface permits Boolean searches, search restrictions, and re-use of previous searches in combination with new terms

Automated sql query generation l.jpg
Automated SQL query generation are you told that:

In summary l.jpg
In summary: are you told that:

  • Queries are made by our ontology-driven database query engine, OWLBase

  • OWLBase passes a query via the ImageStore ontology to the underlying PostgreSQL metadata relational database

  • The database returns metadata of studies matching the search term:

    • authors

    • title

    • description

    • network locator (URI) for the representative thumbnail image

    • IDs of all the component datasets and images

  • These XML data are then used to populate the HTML Study Results Web page that is displayed to the user

  • Many of these items link to deeper metadata

  • If the user now clicks on one of the nodes linking to deeper metadata, a new OWLBase query is initiated that returns information about that component

Slide43 l.jpg

Search result, showing are you told that:Studies

What s so special l.jpg
What’s so special? are you told that:

  • For each query, OWLBase builds in memory an RDF ‘knowledge graph’ representing the structure of the components of each of the matching studies

  • As the user clicks on nodes linking to deeper metadata, each new OWLBase query return is used to extend the RDF graph of the resource

  • In this way, the in-memory representation of the relevant metadata is built up dynamically and incrementally, as required

  • At present, this would not seem to provide much additional functionality over and above a conventional relational database SQL query system

  • However, the fact that the searches use the ImageStore Ontology and build up an OWLBase RDF graph opens the possibility to three novel advances:

    • Use of external third-party ontologies

    • Smart querieswithin the BioImage Database


    • Hypersearchesacross distributed resources

People metadata within bioimage l.jpg
‘People’ metadata within BioImage are you told that:

  • People have attributes:

    • First and last names, dates of birth, addresses, phone numbers, etc

  • People have various affiliations:

    • Current membership of an institution, e.g a university

    • Former membership of another institution – e.g. undertook the research while a postdoc there

    • Simultaneous membership of a third organisation, e.g. an international research project partnership

  • People have grants:

    • “The work in this BioImage Study was funded by BBSRC”

  • People may have different roles within a BioImage Study:

    • This person planned the study – Principal investigator

    • That person prepared the specimen – Technician

    • A third person undertook the electron microscopy – Postdoc

    • Together they wrote the Nature paper – Authors

Use of external ontologies l.jpg
Use of external ontologies are you told that:

  • Because all BioImage queries are passed through the ImageStore ontology, and because ImageStore can be extended using external third-party ontologies, we have the possibility of using such external ontologies to enhance BioImage searches

  • In its simplest form, this can just be used to simplify metadata submission

  • For example, an organisation such as a pharmaceutical company might choose to use an instance of the BioImage Database System internally, behind its own firewall, for the organization of its own confidential research images

  • If that company already had an ontology-controlled database of all its employees’ details, there would be no need to re-enter those metadata for each image these people wished to record – all that would be required would be to link the BioImage Database System to the employee records ontology

  • But external ontologies can do much more for us . . .

Using external biological ontologies within bioimage l.jpg
Using external biological ontologies within BioImage are you told that:

  • Biological content can be described using external ontologies – currently

    • the GO ontology ( for genes and gene products, and

    • the NCBI taxonomy ( to identify species

    • and soon others will also be used, e.g. the Ethodata Ontology

  • We have already implemented the display of an interactive taxonomic hierarchy that permits the user to browse by narrowing or broadening the scope of the results displayed after a query, by clicking at different points in the taxonomy

    • Thus the images of specimens derived from all rodents can be refined to show only those from mice, or broadened to show all mammalian images

  • Similar modification of other parameters is also possible

    • For instance from confocal fluorescence images to real-time confocal images or to all fluorescence images (these relationships being structured within the ImageStore Ontology)

  • At present we can use third party ontologies only if we pre-import them

  • We wish now to extend this functionality by creating dynamic access to external ontologies that are published in XML on the Web, thus ensuring that we always access the most recent version

Smart queries within the bioimage database l.jpg
Smart queries within the BioImage Database are you told that:

  • We propose next to use external ontologies to provide the ability to undertake semantically rich searches of the BioImage Database that can handle

  • synonyms (‘mouse’ and ‘Mus musculus’)

  • hierarchies (‘rodent’ and ‘mammal’)

  • exclusions (not a computer mouse)

  • and related terms (‘laboratory animal’ and ‘model species’)

rather than being limited to conventional ‘Google-like’ searching by means of exact keyword matching, results of which are rather unpredictable!

  • We do not yet know how this Semantic Web approach to database querying will scale with increasing database size, and we will need to undertake comparative research after implementing it

Hypersearches of distributed information sources l.jpg
Hypersearches of distributed information sources are you told that:

  • At present, the BioImage Database gives users the straightforward capability of linking out from a BioImage study, dataset or image via standard Web hyperlinks to relevant material elsewhere on the Web

  • For example, the Advanced Search Interface enables users to enter BioImage queries of the type: “Retrieve all images of Drosophila testes showing expression of the gene always early (aly)”, and then enable users to link out from these BioImage studies both to the gene sequences and to literature publications of relevance

  • What we cannot do at present, however, is to send complex queries across a set of databases, of the type: “Retrieve images of whole Drosophila, Xenopus and mouse embryos showing the comparative neural expression of the most anterior of their Hox genes at different developmental stages, and show me these gene sequences aligned to maximise homology”

  • We wish to investigate how to undertake complex integrated ‘hypersearches’ simultaneously over the BioImage Database and relevant ontology-enabled and Web Services-enabled sequence, structural and literature databases

How to implement hypersearches l.jpg
How to implement hypersearches are you told that:

  • The conventional way to search across disparate databases would be to map their schemas onto some common system, and then use that to distribute a query across them in a manner that each database can understand.

  • Our approach is somewhat different, and relies on the fact that OWLBase dynamically builds up an RFD representation of the information space of interest, and that external ontologies can be integrated with ImageStore

  • Specifically, we plan to import relevant sub-graphsfrom published external ontologies (i.e. class data rather than instance data) dynamically into the RDF graph being built up within OWLBase during each query

  • We will then use this extended graph to structure the hypersearches, by providing ‘internal’ knowledge about the structure of external databases

  • OWLBase will thus act as more than just a query engine. It will build dynamic graphs of relationships between stuff within BioImage and stuff outside, and then run queries over that bigger graph

Imageblast l.jpg
ImageBLAST are you told that:

  • The ability to mount semantically rich queries over a variety of database resources opens the possibility of developing new bioinformatics search tools

  • Our first proposal for this, initially envisioned by our collaborator Michael Ashburner at the ORIEL Varenna conference last September, is ImageBLAST

  • By analogy with the BLAST tool for identifying homologous genes, Michael’s vision was for a tool in which a researcher could enter a nucleotide sequence and have returned images of the normal and mutant expression patterns of the protein encoded by that sequence, from all the model organism image databases, together with detailed metadata describing all that is known about that gene and its protein

  • Recently, my student Chris Holland and I have been designing some possible user interfaces for ImageBLAST

  • I will show them to you in fairly swift succession, to give you a glimpse of the vision we have in mind

The imageblast home page l.jpg
The ImageBLAST home page are you told that:

Gene name disambiguation l.jpg
Gene name disambiguation are you told that:

  • ‘SAP1’ is a synonym for three separate gene products:

    • beta 4 defensin (DEFB4, akaHBD-2)

    • EKT4 (aka ETS-domain protein), and

    • proposin (aka GLBA). Such homonyn / synonym ambiguities are common

  • We will use the system developed by our ORIEL partner Martijn Schuemie of the Erasmus University in Rotterdam for gene name disambiguation, in combination with the ‘conceptual fingerprinting’ software of our industrial partner Collexis BV of Rotterdam

  • Conceptual fingerprinting involves weighting terms in a piece of text on the basis of their frequency and proximity. Terms are defined using the MESH system and the UMLS biomedical thesaurus

  • Comparing numerical conceptual fingerprints permits rapid matching of related texts, and enables resolution of gene name ambiguity on the basis of the context of its usage

Summary results on adh in drosophila l.jpg
Summary results on ‘adh’ in are you told that:Drosophila

Dna results on adh in drosophila l.jpg
DNA results on ‘adh’ in are you told that:Drosophila

Product results on adh in drosophila l.jpg
Product results on ‘adh’ in are you told that:Drosophila

Structure of drosophila adh l.jpg
Structure of are you told that:Drosophila adh

Pathway results on adh in drosophila l.jpg
Pathway results on ‘adh’ in are you told that:Drosophila

Example of a specific pathway l.jpg
Example of a specific pathway are you told that:

Phenotype results on adh in drosophila l.jpg
Phenotype results on ‘adh’ in are you told that:Drosophila

One phenotype study on adh in drosophila l.jpg
One phenotype study on ‘adh’ in are you told that:Drosophila

Will imageblast work l.jpg
Will ImageBLAST work? are you told that:

  • To work, ImageBLAST will clearly requires intimate linkage between the ImageStore Ontology, the Gene Ontology, and the forthcoming Cell Ontology

  • It will also require integration with the Bio-MOBY Web Services for sequence bioinformatics ( developed by our Canadian colleague Mark Wilkinson

  • At present, our vision seems far from risk free

  • However, the pace of Semantic Web developments in which we have participated over the last two years has been truly astonishing

  • This gives reason to hope that, within a further two years, new developments in information space representation, and new methods for ontology integration and automated data extraction, will substantially aid us in attaining our goal

  • Such image bioinformatics tools, if indeed we succeed in developing them, will enormously facilitate knowledge mining within biological images, and will enable hitherto impossible types of on-line research to be undertaken

Populating the bioimage database l.jpg
Populating the BioImage Database are you told that:

  • But first the images must be made available in an ontology-driven database!

    The BioImage Database will receive regular images from three main sources:

  • Journals: Three major scientific publications have already agreed to provide the BioImage Database with biological images on a regular basis:

    • The EMBO Journal

    • EMBO Reports

    • The Journal of Microscopy

  • Research projects and specialist databases:

    • e.g. the Drosophila Testis Gene Expression Database

  • Laboratory image collections

    • The Open Microscopy Environment

  • If you have collections of high quality research images that you wish to publish, please let me know or contact us via

Final words of caution l.jpg
Final words of caution are you told that:

A cautionary tale l.jpg
A cautionary tale are you told that:

  • We recently wrote to a colleague requesting a copy of a beautiful confocal image that he had collected some years ago

  • His reply typifies the wasteful fate of an unfortunately large proportion of biological research images:

    ”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.“

  • It is perhaps the best possible argument

    • for the routine publication of images arising from publicly funded research in databases such as the BioImage Database, that can provide a safe repository for them and free access to them for the community

    • and for the funding of such databases from the public purse

Ontologies are supposed to fit together neatly like irregular four sided penrose tiles l.jpg
Ontologies are are you told that:supposed to fit together neatly - like irregular four-sided Penrose tiles

  • The blue shape

    represents our Ethodata Ontology

    – just one among many in the information landscape

Creating a harmonious whole l.jpg
. . . creating a harmonious whole are you told that:

“Penroses” by Ruth McDowell

But what if they don t l.jpg
. . . but what if they don’t? are you told that:

  • It is hoped that ontologies from different fields can be made ‘orthogonal’ to one another - non-overlapping and yet with no gaps between them

  • However, at present this is just an optimistic hope

  • As yet, there is insufficient ontological coverage of the universe of knowledge to know whether this particular vision of the Semantic Web can be realised

“Weeping woman” by Pablo Picasso

The data deluge and the paradigm trap l.jpg
The data deluge and the paradigm trap are you told that:

  • The volume of data generated in the Life Sciences is now estimated to be doubling every month

  • A single active cell biology lab may generate 10 to 100 Gbytes of multidimensional image data a month

  • Soon the only way to handle the data will be through the presuppositional ‘lens’ of an ontology – people will never have time to look at the raw data

  • Does that matter? After all, the ontology is a specification of the accepted paradigm established by the respected leading academics of the day

  • In other words, an ontology fossilized the prejudices of the old farts

  • Could this perhaps, maybe, just possibly, lead to a blinkered view of the world?

  • Might this hamper the process of discovery and inhibit the overthrow of incorrect hypotheses?

- what if Newton had written the ontology for physics? BEWARE!

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End are you told that:

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Additional slides of relevance are you told that:

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Entity-Attribute-Value storage are you told that:

  • Entity-Attribute-Value databases have recently found favour among healthcare professionals as a way of recording patient data

  • Like patient data, image descriptive data may be sparse – an image represents a small subset of the objects in the real world, just as a patient will have only a small subset of all possible diseases and treatments

  • Whereas in conventional relational database models, each description is stored in a specific column, the EAV approach uses row modelling - each description generates a row consisting of:

    • an entity(e.g. this_rose)

    • an attribute(a property of the entity, e.g. has_colour), and

    • a corresponding valueof the attribute (e.g. red)

  • These EAV triples are easily encoded in RDF

  • For the BioImage Database, we use conventional relational tables for those items upon which searches are frequently made – author, title, species, etc. - and have adopted the EAV approach for those metadata items that are not

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Patient records for blood parameters are you told that:

  • A conventional relational database table, with lots of blanks

  • Adding new columns to the table to accommodate new tests is not easy

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EAV tables to record patient details are you told that:

Units appropriate to each attribute are defined in the ontology, and so do not need to be specified in the table

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An example from everyday life . . . are you told that:


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.

  • “Is Emily Jane’s father a Yorkshire clergyman?”

  • Note that the only common element between the question and the press announcement is the child’s name

  • No conventional electronic query, formulated to interrogate a relational database containing the information within the press announcement, could possibly come up with the correct answer to this question

  • Why? People are able to employed deductive reasoning and extensive linguistic, cultural and geographical knowledge

  • Use of the correct ontology could help a computer to reach the same conclusion

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What would that ontology have to ‘know’? are you told that:

  • That a daughter is a female child, and that a male parent is a father

  • That “John” is a man’s name

  • That “Revd” is an abbreviation for “The Reverend”, the title given to an ordained minister of religion

  • That a typical employment for a minister of religion in the Anglican Church is to be a vicar, i.e. the minister of a parish church

  • That Anglican parish churches are named after Christian saints;

  • That a “vicarage” is a house provided for the accommodation of a vicar and his/her family

  • That since Revd Sanders lives in St Paul’s Vicarage, as well as being an ordained minister of religion, it is highly likely that he is indeed the Anglican vicar of St Paul’s church;

  • That a synonym for “vicar” is “clergyman”

  • That Leeds is an English city within the county of Yorkshire

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Do mountains exist? are you told that:

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Do mountains exist? are you told that:

Are we at the top of Everest?

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Do mountains exist? are you told that:

Are we on Mount Fuji at all?

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Ontologies are you told that:

  • Ontologies can describe many different kinds of relationships


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However, ontologies can have problems … are you told that:

  • We classify pandas as herbivores because 99% of their diet is bamboo

  • What about the other 1%?

    • Autopsy of one panda revealed bones of a bamboo rat in its stomach

    • In captivity, pandas will eat pork coated with honey

  • Does this make the panda an omnivore?

  • Humans make ‘reasonable judgements’ when classifying things

  • However, machines usually reason over facts that are either true or false, and cannot easily be programmed to make subtle distinctions

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Scientific imaging are you told that:

  • Images and videos form a vital part of the scientific record, for which words are no substitute

  • In the post-genomic world, attention is now focused on the functional analyses of gene expression, and on organization and integration within cells

  • In a month a single active cell biology lab may generate between 10 and 100 Gbytes of multidimensional image data

  • But at present little of this is published

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The problem of image publication are you told that:

  • Even when images are published, they are often only processed images, not the original image data

    • For example one might publish a single section or a projection from a complete 3D confocal image

    • or a couple of frames from a movie

  • It would be of great value if more original image data were published

    • This would both permit re-analysis and secondary meta-research

    • and would be useful for teaching and learning

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Ontology Organiser are you told that:A constraint propagator and datatype manager

  • Eliminates the cognitive overload of the user during ontology development while asserting relationships between resources

  • Ontology Organiser has capabilities not found in other editors like OilEd

  • First it can reduce the cognitive overload of the user during ontology development while asserting relationships between resources. It:

    • evaluate constraints placed on relationships

    • propagate any alterations necessary up through an ontology's hierarchy

    • thereby maintaining ‘semantic robustness'.

  • Second, it addresses the more technical problem regarding the lack of support for datatypes in existing ontology editing packages. Ontology Organiser goes some way to aid the user in defining, modifying and referencing custom datatypes in their ontologies

  • Ontology Organiser is available from SourceForge. Details can be found at