Ontologies & Ontology tools for the
CCLRC Neutron & Muon Facility
Louisa Casely-Hayford
e-Science
ISIS a CCLRC Neutron & Muon Facility
• ISIS is the worlds leading pulsed Neutron & Muon source situated at
the CCLRC Rutherford Appleton Laboratory. ISIS supports an
international community of around 1600 scientists in a range of
scientific disciplines.
• Currently ISIS produces about 700GB of combined Neutron & Muon
data each year and this figure is set to rise with the addition of a new
target station.
• The ISIS Metadata Catalogue (ICAT) is a twenty year back
catalogue of experiments conducted at ISIS it contains
approximately 3GB of metadata which references 3TB of data.
• In order to maximise the value of data produced from the facility, it
must be fully searchable.
• To address this problem, e-Science is developing numerous
software solutions and ontologies are seen one of these useful
approaches.
Presenter Name
Louisa Casely-Hayford
Facility
Name
e-Science
Why Ontologies are a useful solution?
• Ontologies offer a powerful means to formally express the nature of
a domain.
• To share common understanding of the structure of information
among people
• To enable reuse of domain knowledge
• To make domain assumptions explicit
• They provide central controlled vocabularies that can be integrated
into catalogues, databases, web publications and knowledge
management applications
• Ontologies will facilitate searching of data by category and grouping
of data into keywords across studies
Presenter
Name
Louisa Casely-Hayford
Facility
Name
e-Science
Building an Ontology
• Defining terms in a domain and relations between them.
– Defining concepts in the domain (classes)
– Arranging the concepts in a hierarchy (subclass-superclass
hierarchy)
– Defining which attributes and properties (slots) classes can have and
constraints on their values
– Defining individuals and filling in slot values
• Involves collaboration between domain experts and ontology builders.
• Ontologies are expressed in a formal language and developed within an
editing environment.
Presenter
Name
Louisa Casely-Hayford
Facility
Name
e-Science
A Protégé-OWL Ontology
• Classes
• Individuals
• Properties
Italy
livesIn
America
Gemma
England
hasSibling
A class is a concept in the domain
- a class of People
- a class of Pets
- a class of Countries
A class is a collection of elements with
similar properties.
Instances of classes
- America can be an instance of the
class Country.
Class Country
Mathew
hasPet
Class Person
Fluffy
Fido
Class Pet
Presenter
Name
Louisa Casely-Hayford
Facility
Name
e-Science
Building of the ISIS Facilities Ontology
of keywords
in these five
categories
are:
•Examples
The ISIS
facilities ontology
is based
on keywords
in the ISIS
Metadata catalogue (ICAT).
• HRP00145.RAW - a datafile name.
•
Over 10,000 keywords housed in ICAT and many are synonyms.
- a High
Resolution
Powder into
Diffractometer
one of the many
•• HRPD
Keywords
in ICAT
were grouped
5 main categories:
instruments used in experiments at the ISIS facility.
1. Datafile name
2. Instrument
• Hydrazinium
- an investigation title, chemical names and
3. Investigation
compounds
were used astitle
investigation titles of experiments in
ICAT. 4. Investigator
5. Year
• 1986 - the year in which a particular experiment was conducted
• JINR (Joint Institute for Nuclear Research) - the name of an
investigator.
Presenter
Name
Louisa Casely-Hayford
Facility
Name
e-Science
ISIS Facilities Ontology Hierarchy
Presenter
Name
Louisa Casely-Hayford
Facility
Name
e-Science
ISIS Facilities Ontology
Class ISISExperiment
hasTitle
Hydrazinium
Protein Crystallography
GroupExperiment
Class InvestigationTitle
wasConductedIn
Class CrystallographyGroupExperiment
1986
hasInvestigator
hasDataFileName
Class Year
hasUsedInstrument
Pete Jones
HRPD
HRP00145.RAW
Class Investigator
Class Instrument
Class DataFile
Presenter
Name
Louisa Casely-Hayford
Facility
Name
e-Science
Presenter
Name
Louisa Casely-Hayford
Facility
Name
e-Science
ISIS Online Proposal System
• Scientists can submit applications for beamtime at ISIS through an
online application form which is known as the ISIS Online Proposal
System
• The ICAT(Metadata catalog) not only holds the 20 year back catalog
of data, but will also hold data from approved proposals and data
generated from experiments conducted at ISIS
• Three separate modular ontologies for Sample, Investigator and
Experiment are being developed to mark up the Proposal system
• These ontologies are partly based on the proposal system database
schema
Presenter
Name
Louisa Casely-Hayford
Facility
Name
e-Science
Sample, Investigator and Experiment Ontologies
Sample
Investigator
Experiment
Presenter
Name
Louisa Casely-Hayford
Facility
Name
e-Science
OntoMaintainer
• Consensus on Concepts modelled in the ISIS Facilities ontology,
was achieved through a series of interviews with domain experts.
• During the design and creation process, there was a difficulty in
sharing current versions of the ontology with our collaborators at
ISIS.
• This is because to view the hierarchical structure of the ontology,
scientists would have to download and install Protégé locally.
• The Ontology Maintainer was developed to facilitate the community
in remotely viewing current versions of the ontology.
Presenter
Name
Louisa Casely-Hayford
Facility
Name
e-Science
Screen Shot of OntoMaintainer
Presenter
Name
Louisa Casely-Hayford
Facility
Name
e-Science
Benefits of OntoMaintainer
• It is easily accessible because it is available over the web
• Allows domain experts to contribute towards the maintenance of the
ontologies
• Encourages collaboration between domain experts (scientists) and
ontology builders by allowing members of the community to be involved
in the development and maintenance of ontologies
• Makes collaboration between domain experts and ontology builders more
efficient
Presenter
Name
Louisa Casely-Hayford
Facility
Name
e-Science
Future Work
• Completion of Sample, Investigator, Experiment and ISIS Facilities
Ontologies
• Ontology Maintainer will be improved through the addition of properties
to enable relationships between individuals in classes to be shown.
• Graphical view of hierarchies of the ontology will be added to the user
interface of the Ontology Maintainer.
• Tree hierarchy will be made more dynamic through automatic updating of
classes.
Presenter
Name
Louisa Casely-Hayford
Facility
Name
e-Science
Conclusion
• Ontologies to mark up the ICAT back catalogue and new approved
studies submitted through Online Proposal System to improve the search
and navigation of data and search of concepts across scientific
disciplines.
• Ontology Maintainer will facilitate the process of creating and maintaining
ontologies by providing a means of getting feedback directly from domain
experts.
• Major challenge scope, modularity and integration of ontologies.
Presenter
Name
Louisa Casely-Hayford
Facility
Name
e-Science
Question Time
Presenter
Name
Louisa Casely-Hayford
Facility
Name
e-Science