myExperiment describes itself as a "Social Virtual Research Environment" that provides the ability to share Research Objects (ROs) over a social infrastructure to facilitate actioning of research. The myExperiment Ontology is a logical representation of the data model used by this environment, allowing its data to be published in a standard RDF format, whilst providing a generic extensible framework that can be reused by similar projects. ROs are data structures designed to semantically enhance research publications by capturing and preserving the research method so that it can be reproduced in the future. This paper provides some motivation for an RO specification and briefly considers how existing domain-specifific ontologies might be integrated. It concludes by discussing the future direction of the myExperiment Ontology and how it will best support these ROs

Bechhofer, Sean

De Roure, David

Newman, David

English

Southampton (e-Prints Soton)

myExperiment: An ontology for e-ResearchDavid R Newman1, Sean Bechhofer2, David De Roure11 School of Electronics and Computer Science, University of Southampton,Southampton, UKdrn05r@ecs.soton.ac.uk2 School of Computer Science, The University of Manchester, Manchester, UKAbstract. myExperiment describes itself as a \Social Virtual ResearchEnvironment" that provides the ability to share Research Objects (ROs)over a social infrastructure to facilitate actioning of research. The my-Experiment Ontology is a logical representation of the data model usedby this environment, allowing its data to to be published in a standardRDF format, whilst providing a generic extensible framework that can bereused by similar projects. ROs are data structures designed to seman-tically enhance research publications by capturing and preserving theresearch method so that it can be reproduced in the future. This paperprovides some motivation for an RO specication and briey considershow existing domain-specic ontologies might be integrated. It concludesby discussing the future direction of the myExperiment Ontology andhow it will best support these ROs.1 IntroductionThis paper describes the design of an OWL DL [1] ontology for myExperiment,within the context of e-Research. [2] states that myExperiment is a \Social Vir-tual Research Environment" (Social VRE) and as such denes the four requisitecapabilities for such a system:1. Facilitate management and sharing of Research Objects (ROs)2. Support a social model3. Provide an open extensible environment4. Provide a platform to action researchSection 2 describes the myExperiment model and presents an insight to someof the motivation and design decisions taken in its construction, in particularhow it has been inuenced by these four capabilities. It demonstrates how thisinsight informed the design decisions for the ontology itself. It also explains thetechniques used to try to promote reuse of the ontology in other VRE and socialnetworking projects.Section 3 describes the purpose of ROs in semantically enhancing researchpublications. It briey considers the requirements of an RO to ensure a scientistcan reproduce the research it encompasses and how its design should facilitatethis. In particular how the design will provide support for integration of domain-specic ontologies / vocabularies.2myExperiment currently only supports a few basic types of RO. This papertherefore concludes by considering how the myExperiment Ontology needs toevolve to provide greater support for all ROs.2 Building the myExperiment Ontology2.1 The myExperiment ModelThe myExperiment model has three main features that are motivated by thefour capabilities of a Social VRE:1. Content Management2. Social Networking3. Object AnnotationmyExperiment's initial user group was bioinformaticians that wanted to be ableto manage and share workows [3]. However, it quickly became apparent that tofull its capabilities, a model that allows scientists from wide ranging elds toshare many dierent types of research was needed. myExperiment allows usersto manage dierent types of les as well as more abstract concepts and denesthese items as Contributions.When a user joins myExperiment, they can make friends and join Groups,(represented by Friendship and Membership records), to build their social net-work. Beyond this myExperiment allows users to send each other Messages andmake Announcements to their groups. With this social network it makes it pos-sible for Contributions to be shared in a highly customizable way through theuse of additive Policies.Object Annotation allows users to annotate Contributions with Annotations,such as Tags, Ratings Reviews and Comments to enhance search and to supportcuration.2.2 DesignThe purpose for building an ontology was so to produce a consistent specicationfor publishing myExperiment's data as RDF and contributing to the web of data.All of myExperiment's public data can be accessed via the web3 and queriedusing myExperiment's SPARQL endpoint4.The myExperiment website has been built using the Ruby-on-Rails5 frame-work. Ruby-on-Rails was chosen because it provides a Model-View-Controller(MVC) architecture for agile development of web projects allowing rapid innova-tion [4]. The model component of the architecture is designed to be a thin veneerover a database engine giving the developer freedom to choose the database thatsuits them, in the case of myExperiment MySQL was chosen.3 http://rdf.myexperiment.org/4 http://rdf.myexperiment.org/sparql5 http://rubyonrails.org/3Having the myExperiment model already represented in the structured formof a MySQL database provided both benets and disadvantages when design-ing the myExperiment Ontology. The initial construction of the ontology wasstraightforward, as much of the database schema could be transcribed directlyinto OWL DL. A number of tools exist that can automate this process [5], (e.g.RDBtoOnto [6], DB2OWL [7], etc.). However, several factors made using sucha tool unsuitable for building the myExperiment Ontology as a whole.Ruby-on-Rails uses the database to store information to manage the webinterface. In some cases this data would be inappropriate to represent, such asusers' encrypted passwords and salts. In other cases this data is irrelevant suchas HTTP session data.Ruby-on-Rails supports polymorphism. This allows a Contributions table tostore generic information about items users want to share and then referencetables such as Workows and Files that store information specic to that typeof Contribution. However, this means that it is impossible to determine fromthe database schema the dierent types of Contribution so that they can berepresented as subclasses of Contributions within the ontology.Capturing myExperiment's customizable sharing model was a key aspect tobuilding the myExperiment Ontology. This is because it is one of the featuresthat makes myExperiment unique in the VRE community. Further to this, theway that Contributions are shared greatly eects the data generated withinmyExperiment, such as who has tagged a Workow or how many times a File hasbeen downloaded. Therefore it is important that there is a way of capturing thisinformation concisely. However, this task was complicated by having subjectivegroups such as friends that vary depending on the user as well as over time.The Simple Network Access Rights Management (SNARM) Ontology6 allowsadditive policies to be dened by assigning dierent types of permissions to users,groups and abstract groups such as friends or all the groups a user belongs to. Itis extensible to allow the denition of new types of permission and new abstractgroups.myExperiment subscribes to the Web 2.0 model of being a \perpetual beta".This means that it evolves over time as users request new features. This in-evitably means the database model is not perfect. In the process of manuallybuilding the ontology it became clear where abstractions could be made and thishas fed back into the design of the database model to make it simpler and moreextensible.2.3 Promoting ReuseOne of myExperiment's goals is to encourage reuse of Workows and other Con-tributions. For the design of the ontology this ethos was adopted so that it bothreuses existing specications and makes itself as reusable as possible throughcareful consideration of design decisions.6 http://rdf.myexperiment.org/ontologies/snarm/4A number of core ontologies / schemata already exist for representing proper-ties and classes that exist within myExperiment. The reuse of these gives myEx-periment's RDF data a graceful degradation of understanding. I.e. if a machineis presented with some myExperiment RDF, it does not have to be aware of themyExperiment Ontology to have some understanding of the type of object it isdealing with. A major tasks in the Semantic Web world is co-reference resolution[8]. One technique for performing this task is comparing properties, this is morelikely to be successful if an object uses recognized properties from core ontologies/ schemata.The myExperiment Ontology reuses both properties and classes from DublinCore7, Friend of a Friend (FOAF)8, Semantically Inter-linked Online Commu-nities (SIOC)9 and the Open Archives Initiative's Object Reuse and Exchange(OAI-ORE)10 ontologies / schemata.Reusing elements from core ontologies / schemata helps to promote reuse ofthe ontology, as it makes it easier to understand the purpose of the ontologyand it gives condence that consideration has been given to the classes andproperties dened within. However, this in itself is not enough. The ontologyneeds to be suciently generic so that potential users do not disregard it forbeing too specic or bloated. At the same time it needs to be expressive enoughto represent the whole myExperiment model. To achieve this the myExperimentOntology was constructed as a set of modules allowing anyone who reuses themto pick and choose the modules they need. Figure 1 diagrams how the modulesbolt together to build the complete myExperiment Ontology. Each module sitsatop the modules it requires to dene any subclass or sub-property relationships.Fig.1. myExperiment Ontology Modules ArchitectureThe Base module with the assistance of the SNARM ontology provides thebulk of the features described in section 2.1, the remaining modules supportthe capability to provide an extensible environment with denitions for specic7 http://dublincore.org/8 http://www.foaf-project.org/9 http://sioc-project.org/10 http://www.openarchives.org/ore/5Contributions, Annotations, usage statistics, etc. In particular the Experimentmodule is designed to represent the process of actioning research. The Specicmodule sits over the top and amalgamates all these modules using OWL's importproperty to generate an ontology for the whole myExperiment model. It alsoprovides classes and objects that are highly specic to myExperiment instanceat http://www.myexperiment.org/.A more detailed document describing the ontology specication can be foundat http://rdf.myexperiment.org/ontologies/.3 Research Objects3.1 MotivationAt present the accepted way of publishing research is to have a paper acceptedby a conference or journal. These papers are just text documents. They may ref-erence tools and data sources that were used and result sets that were produced.However, there is no certainty that these references will be sucient to repro-duce the research the paper describes. Even if they are, there is no guaranteethat these references will still resolve to the item the paper described.Even if it is possible to repeat the research of the paper, this has overlookedthe problem of actually nding this relevant paper in the rst place. [9] describeshow in the eld of bioinformatics there are already so many papers that it isquite dicult to nd the one that discusses a particular gene in a specic context.Text-mining tools can help with this task but this begs to question why was itburied in the rst place.A Semantic Web approach can assist in such a task, by associating inter-operable metadata with these papers. Much of this process can quite easily beautomated but when it comes to dening the interrelationships of resources (e.g.data sources, tools and result sets), this requires both an extensible specicationand a sea-change in attitudes to what constitutes a research publication.3.2 ROs in myExperimentBuilding the myExperiment Ontology has helped to clarify the concept of ROsand how myExperiment \facilitates [the] management and sharing" of them.myExperiment currently has three entities that could be considered ROs: Work-ows, Packs and Experiments.When a Workow is uploaded various supporting les can also be uploaded orautomatically generated, such as SVG and PNG visualizations of the Workow,all these resources are grouped together. New WorkowVersions can also beuploaded and are then associated with the original Workow.Packs are designed to allow users to collaboratively aggregate resources to-gether by hand. They very closely resemble OAI-ORE Aggregations (see section3.3). A Pack contains items that are either myExperiment Contributions or ex-ternal resources. Packs allow metadata to be recorded about these items that isonly relevant within the context of that Pack.6Fig.2. The Anatomy of a Pack (credit to Jiten Bhagat)Experiments are aggregations of Jobs which in themselves are aggregationsof an enacted Workow with its inputs, outputs and the Runner used to enactit.These three entities currently require an explicit denition in the databasestructure / ontology. Supporting all conceivable ROs in this way is impractical.Rather ROs should describe their own structure so that this does not need tobe dened in any system that stores them.3.3 Anatomy of a Research ObjectResearch Objects (ROs) are designed to aggregate together resources, (e.g. data-sets, workows, etc.), to represent an investigation, experiment or question [10].They need to be machine-processable so that they can be automated and demon-strate the research they encompass.OAI-ORE is a specication dening how resources can be aggregated [11]. Itwas designed for the Open Repositories community to allow them to exchangeobjects between repositories in a standard format. OAI-ORE's rst class objectis an Aggregation that can then have one or more items associated with it asAggregated Resources. Aggregations can be serialized into concrete syntax, suchas RDF, Atom Feeds or RDFa, as Resource Maps. The specication allows formetadata to be assigned to all these objects. Metadata pertinent to AggregatedResources only in the context of the Aggregation can also be assigned usingProxies.OAI-ORE provides a suitable mechanism for making ROs machine-readable,to make them machine-processable a further specication is needed to help denethe interrelationships between resources and the provenance, lifecycle, sharing,curation and usage proles. The e-Laboratory Technical Architecture Group11are currently working on dening such a specication.11 A collaboration between VRE and related projects at the University of Manchesterand University of Southampton.7Domain-specic ontologies already exist for representing entities compara-ble to ROs, such as the MGED Ontology12 and the SWAN Ontology13. TheSWAN Ontology id designed to represent scientic discourse, it has extensionsfor supporting domain-specic concepts such as Life Science Entities and theGene Ontology [12]. Scientic discourse is an important component in deningreproducible research within an RO.In many cases it should be possible to use these domain-specic ontologies ormodules thereof to describe the resources and interrelationships of the RO withminimal integration required. Otherwise a simple specication of these domain-specic classes and properties could be dened to accomplish this task and in-tegrate with the RO specication ontology.4 ConclusionmyExperiment stores a large amount of structured data and required a way ofproviding this data in a standard, consistent and atomic way to make integrationwith similar systems easier. Building the myExperiment Ontology has facilitateddelivering this data as RDF and allowing it to be queried using SPARQL. Havingan ontology provides a machine-readable specication that mechanisms such asRepresentational State Transfer (REST) APIs do not have.The design of the myExperiment Ontology is a continual process but throughcareful analysis of the underlying data model it has been designed in an genericway to ensure that future modications should be additions or minor alterationsrather than signicant structural changes.Through the reuse of existing classes and properties from core ontologies /schemata and the modularization of the ontology, a concerted eort has beenmade to promote reuse of the ontology in similar projects. Modularization shouldalso allow any signicant modications to the myExperiment model to be iso-lated in new modules rather than requiring changes to existing ones.In particular, as the concept of ROs becomes more evolved a new modulecan be constructed to support them. This module will need to integrate with theRO specication ontology to provide an interface with the provenance, lifecycle,sharing, curation and usage proles stored within an RO, allowing the user tomanage these within myExperiment.If ROs are to be successful and provide a mechanism for publishing repro-ducible research there needs to be a system to allow their management and shar-ing prior to as well as post publication. This system should also facilitate thecollaborative building of ROs, where multiple researchers, potentially situatedin dierent locations, are involved in the same experiment or investigation. Inte-grating the myExperiment Ontology with the RO specication ontology shouldmake myExperiment well placed to achieve this.12 http://mged.sourceforge.net/ontologies/MGEDOntology.owl13 http://swan.mindinformatics.org/ontology.html8References1. 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myExperiment: An ontology for e-Research

myExperiment: An ontology for e-Research

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