Presentation on theme: "Director, Image Bioinformatics Research Laboratory Oxford e-Science Centre Department of Zoology, University of Oxford Oxford OX1 3PS, UK e-mail: david.shotton."— Presentation transcript:
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 European Commission funding of the ORIEL Project - IST-2001-32688 Chris Wilson SABO research project Ruth Dalton SABO research project Chris Holland ImageBLAST research project
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
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 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
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...
What is this? This is not a pandaThis is not a photograph of a panda This 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
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 mothers 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? 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 (W3Cs Web Ontology Language), which is itself expressed as a set of RDF statements
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: Oxford
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 werent quite sure
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!
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
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 Locomotion proper_ is_a part_of Running Fur hypothesised_ (default_colour: white) function (has_length: number unit) (has_density: number per unit area) Escape A partial ontology of mouse
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
The thinking crow problem To properly annotate videos of Betty, we need to be able to structure not only peoples interpretations of the world, but also Bettys view of what is going on!
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 Tinbergens 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
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 Origin has author Lorenz, Konrad (instance data) Hypothesis About Evolutionary Origin has date 1941 (instance data)
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
A view of the BioImage home page structure www.bioimage.org Note the hierarchical browse categories and the alternative Browse / Search arrangement
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
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
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
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
Multilingual capabilities enabled by Struts This shows the Access Control Interface The same HTML page is being viewed in both cases, using alternate resource bundles achieved simply by re-setting the default language of the users browser
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
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
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, namelyWhere, when and why is what happening to whom?
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
Representing fact and hypothesis within ImageStore Real world Media world Narrative world
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
Stage one: user inputs a query Find images of bears
Stage two: the ontology reasons over the request
Stage three: OWLBase convert the request to SQL
Stage four: metadata is retrieved from the database
Stage five: metadata is returned to OWLBase as XML
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
Whats 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
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
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...
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
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
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
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
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, Michaels 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
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
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
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
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 Ill 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 The blue shape represents our Ethodata Ontology – just one among many in the information landscape
... creating a harmonious whole Penroses by Ruth McDowell
... but what if they dont? 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
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!
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
Patient records for blood parameters Patient Values First name Last name DiseaseWhite cell count CholesterolEthyl alcohol Prostate -specific antigen Lots more columns... MarySmithAlcoholism0.3 mg/dlLots of blank values... JohnSmithCancer40 ng/ml KenJonesHeart disease 340 mg/dl BarryBrownAIDS630 cells/µl A conventional relational database table, with lots of blanks Adding new columns to the table to accommodate new tests is not easy
Person table FirstLastID MarySmith125 JohnSmith126 KenJones127 BarryBrown128 Auxiliary table Resource Name Resource ID Property ID Person1251 Person1262 Person1273 Person1284 Attribute - Value table IDAttributeValue 1Ethyl alcohol0.3 2Prostate specific antigen40 3Cholesterol340 4White cell count630 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
Is Emily Janes father a Yorkshire clergyman? BIRTHS, MARRIAGES AND DEATHS Born to Revd John and Mrs Marjorie Sanders of St Pauls Vicarage, 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 childs 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...
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 mans 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 Pauls Vicarage, as well as being an ordained minister of religion, it is highly likely that he is indeed the Anglican vicar of St Pauls church; That a synonym for vicar is clergyman That Leeds is an English city within the county of Yorkshire
Do mountains exist? Are we on Mount Fuji at all?
Ontologies Ontologies can describe many different kinds of relationships is_a
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
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
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
Using Protégé to define a class in the ontology
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