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![Page 1: Director, Image Bioinformatics Research Laboratory Oxford e-Science Centre Department of Zoology, University of Oxford Oxford OX1 3PS, UK e-mail: david.shotton.](https://reader036.fdocuments.in/reader036/viewer/2022070306/5516034155034694308b4cdd/html5/thumbnails/1.jpg)
Director, Image Bioinformatics Research LaboratoryOxford e-Science Centre
Department of Zoology, University of OxfordOxford OX1 3PS, UK
e-mail: david.shotton @zoo.ox.ac.uk
David Shotton
Bio-Ontologies Meeting
Glasgow
30/07/04
© David Shotton 2004
Using ontologies to provide semantic richness in biological image databases
(Sub-title: In Praise of Good Colleagues)
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Acknowledgements
Chris CattonBioImage Development Manager: ImageStore Ontology and SABO developer
Simon SparksBioImage Software Engineer: OWLBase query engine developer
John PybusBioImage Systems Manager
European Commission funding of the ORIEL Project - IST-2001-32688
Chris WilsonSABO research project
Ruth DaltonSABO research project
Chris HollandImageBLAST research project
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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
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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
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Expert knowledge and tacit knowledge
Mutual understanding within any field of knowledge is based on a shared conceptualisation developed 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
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Electronic communication of complex knowledge
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 . . .
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What is this?This is not a pandaThis is not a photograph of a pandaThis is not even a projected digital image of a photograph of a panda
This is a caption for a projected digital image of a photograph of a panda
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In biology, meanings may be complex
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
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What is the Semantic Web, and how can it help?
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 language more 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
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RDF triples
An RDF triple might state that a mouse is_a mammal, 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:RDF><rdf:Description about=“Mouse”>
<Location>Oxford</Location></rdf:Description>
</rdf:RDF>
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What type of animal is shown in this image?
German taxonomists
claimed it was a bear
British taxonomists
claimed it was a racoon
Ailuropoda melanoleuca
US taxonomists weren’t quite sure
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Today, the balance of opinion is “bear”
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!
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Animal
is_a
Vertebrate
is_a
Mammal
is_a
Rodent
is_a
Mouse
We understand taxonomic hierarchies
In an ontology, one can express more complex relationships about a mouse, other than just its taxonomy
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Group of Mus musculus organisms
is_a Colony
has_species_name member_of Mouse
proper_part_of has_ID
Leg has_mode_ 667(has_cardinality: 4) of_locomotion
(has_position: front / rear) (has_handedness: left / right)
(has_length: number)
used_for Locomotionproper_ is_apart_of Running
Fur hypothesised_(default_colour: white) function
(has_length: number unit) (has_density: number per unit area)
Escape
A partial ontology of ‘mouse’
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How do you build an ontology?
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:
mouse is_a rodent – type relationship
mouse member_of colony – collective relationship
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The thinking crow problem
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!
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Biological ontologies
There is good ontological coverage of the genes and gene products of model organisms in the form of the Gene Ontology (http://www.geneontology.org)
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
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Fact and hypothesis in SABO
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For example, a courtship event
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Courtship behaviour in ducks
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 Originhas author
“Lorenz, Konrad” (instance data)
Hypothesis About Evolutionary Origin has date
“1941” (instance data)
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The Ethodata Ontology
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 (ethodata.comm.nsdl.org)
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
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A view of the
BioImage home page structure
www.bioimage.org
Note the hierarchical
browse categories and the alternative Browse / Search
arrangement
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The BioImage Database Project
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
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The organisation within BioImage
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 Images on 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 browse or search the 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
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The basic BioImage metadata model
Cell or organism
Preparation
Image capture
Image sets of multidimensional images, including videos
Subject or specimen
Researcher
Photographer or microscopist Camera or
microscope, illumination,
focus, etc
Experimental study conditions or manipulations
So people are related to objects and conditions / equipment through events
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The structure of the BioImage Database
BioIm age S erver
V ideoW ork s W eb se rv e r
Browser interfaces
Jav a app le ts
A pac he W eb se rve r
Tax onom ies
Ontologies
O B O se rv e r
N C B I se rve r
K ey In te rna l p roc esses H T TP S O A P p ro toco ls
Tomcat
V iew X S L , JS P and S iteM esh
B io Im agem e tada ta - P ostg reS Q L
Loca lim age
file s to re
Log ic laye r (se rv le ts )
S O A Pin te r-faces
A dm in is tra tion se rv le t
Q ue ry s e rv le t
S O A P c lien ts
C o n tro l le r Stru ts
M ode l
(Javabeans)
O W LB ase que ry eng ine
S ubm iss ion se rv le t
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Things to note about the architecture: external
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
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Multilingual capabilities enabled by Struts
This shows
the Access Control Interfac
e
The same HTML
page is being
viewed in both cases, using
alternate
resource
bundles
achieved simply by re-setting the default language of the user’s browser
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Things to note about the architecture: internal
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
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The ImageStore Ontology
The ImageStore Ontology was constructed using the Jena toolkit (www.hpl.hp.com/semweb) 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 (sourceforge.net/projects/aaf and www.aafassociation.org) 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
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What is required of an image ontology?
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?”
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Image description – separating fact from hypothesis
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
Vernos et al., 1995
Connotation (interpretation):
Xklp1 is involved in chromosome localization during mitosis in embryonic Xenopus cells, since it is positioned at the metaphase plate
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Representing fact and hypothesis within ImageStore
ClassSegment
range
RestrictionsubClassOf
onProperty
ObjectProperty
has
ClassConnotation
ClassDenotation
subClassOf
subClassOf
ClassEvent
Restriction
subClassOf
ObjectProperty
states
ObjectProperty
tool
ObjectProperty
participant
ClassFormOfExpression
Restriction
subClassOf
DataTypePropery
CameraMotionType
Restriction
subClassOf
onProperty
xsd:Mpeg7:cameraMotionType
range
ObjectProperty
location
subPropertyOf
subPropertyOf
subPropertyOf
DataTypePropery
weather
onProperty
DataTypePropery
habitat
onProperty
DataTypePropery
RegionOf Interest
onProperty
subClassOf
ClassNarrativeContentDescription
xsd:Mpeg7:SpatialMask D
range
Narrative WorldReal World
subClassOf
Media
RestrictionObjectProperty
hassubClassOf onProperty range
ClassEventContentDescription
subClassOf
Restriction
onProperty
ObjectProperty
has
rangerange
range
subPropertyOf
Collection
Rdf:Statement Rdf:Statement
intersectionOf
intersectionOf
Restriction
ObjectProperty
states
ObjectProperty
tool
ObjectProperty
participant
ObjectProperty
location
subPropertyOf
subPropertyOf
subPropertyOf
DataTypePropery
weather
onProperty
DataTypePropery
habitat
onProperty
range
subPropertyOf
Collection
Rdf:Statement Rdf:Statement
intersectionOf
intersectionOf
Real world Media world Narrative world
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The BioImage advanced search interface
The Advanced Search Interface permits Boolean searches, search restrictions, and re-use of previous searches in combination with new terms
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Automated SQL query generation
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Stage one: user inputs a query “Find images of bears”
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Stage two: the ontology reasons over the request
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Stage three: OWLBase convert the request to SQL
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Stage four: metadata is retrieved from the database
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Stage five: metadata is returned to OWLBase as XML
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In summary:
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
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Search result,
showing Studies
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What’s so special?
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 queries within the BioImage Database
and Hypersearches across distributed resources
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‘People’ metadata within BioImage
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
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Use of external ontologies
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 . . .
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Using external biological ontologies within BioImage
Biological content can be described using external ontologies – currently the GO ontology (www.geneontology.org) for genes and gene products, and the NCBI taxonomy (www.ncbi.nlm.nih.gov/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
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Smart queries within the BioImage Database
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
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Hypersearches of distributed information sources
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
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How to implement hypersearches
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-graphs from 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
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ImageBLAST
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
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The ImageBLAST home page
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The ImageBLAST hypersearch interface
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Gene name disambiguation
‘SAP1’ is a synonym for three separate gene products: beta 4 defensin (DEFB4, aka HBD-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
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Summary results on ‘adh’ in Drosophila
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DNA results on ‘adh’ in Drosophila
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Product results on ‘adh’ in Drosophila
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Structure of Drosophila adh
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Pathway results on ‘adh’ in Drosophila
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Example of a specific pathway
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Phenotype results on ‘adh’ in Drosophila
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One phenotype study on ‘adh’ in Drosophila
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Will ImageBLAST work?
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 (biomoby.org) 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
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Populating the BioImage Database
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 www.bioimage.org
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Final words of caution
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A cautionary tale
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
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Ontologies are 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
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. . . creating a harmonious whole
“Penroses” by Ruth McDowell
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. . . but what if they don’t?
“Weeping woman” by Pablo Picasso
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
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The data deluge and the paradigm trap
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
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Additional slides of relevance
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Entity-Attribute-Value storage
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 value of 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
Patient Values
First name
Last name
Disease White cell count
Cholesterol Ethyl alcohol
Prostate-specific antigen
Lots more columns . . .
Mary Smith Alcoholism 0.3 mg/dl Lots of blank values . . .John Smith Cancer 40 ng/ml
Ken Jones Heart disease
340 mg/dl
Barry Brown AIDS 630 cells/µl
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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Person table
First Last ID
Mary Smith 125
John Smith 126
Ken Jones 127
Barry Brown 128
Auxiliary table
Resource Name
Resource ID
Property ID
Person 125 1
Person 126 2
Person 127 3
Person 128 4
Attribute - Value table
ID Attribute Value
1 Ethyl alcohol 0.3
2 Prostate specific antigen 40
3 Cholesterol 340
4 White cell count 630
Units appropriate to each attribute are defined in the
ontology, and so do not need to be specified in the table
EAV tables to record patient details
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“Is Emily Jane’s father a Yorkshire clergyman?”
BIRTHS, MARRIAGES AND DEATHSBorn to Revd John and Mrs Marjorie Sanders of St Paul’sVicarage, Tadcaster Road, Leeds: a daughter Emily Jane,at 11:25 a.m. on 25th December 2003, weight 3.6 Kg.
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
An example from everyday life . . .
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What would that ontology have to ‘know’?
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?
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Do mountains exist?
Are we at the top of Everest?
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Do mountains exist?
Are we on Mount Fuji at all?
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Ontologies
Ontologies can describe many different kinds of relationships
Bears
OmnivoreHerbivore
Diet
is_a
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However, ontologies can have problems …
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
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
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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Using Protégé to define a class in the ontology
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Ontology Organiser 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 www.bioimage.org/publications.do