Define specs for SPE ontology self-publishing experiment, web publishing, semantic web, ontology, open data]]> Ontology]]> To define an ontology for self-publishing of experiment as single unit and related information such as project, protocol, product, and researcher. The SPE ontology is designed for self-publishing of experiments in RDF/XML. There are three specific goals: (1) The terms are intended to be used by applications that should appeal to users across all scientific disciplines. This means a shallow ontology is more appropriate. Fine-grained terms can be added in future versions. (2) Although it may be used for any number of applications, its primary focus at current stage is to enable more precise search of related information at single experiment level across the web. This is in contrast to searching a journal article, which is usually synthesized from many experiments. (3) It should enable application developers to develop easy-to-use publishing tools for end users (researchers). User-friendly self-publishing tools are critical for adoption of the new publishing option. Users should be able to easily publish their experiment information without any knowledge of semantic web technology or ontology. ]]>
  • This specs is developed based on the requirements defined by the Scientific Publishing task force of W3C HCLSIG.
  • Review all relevant ontologies available. This specs should try to use as many terms as possible in other well-established ontologies including SKOS, DC, FOAF, FuGO, and Ebiquity ontologies.
  • I will create the first draft and then put it up on the wiki for the group to review and comment. Everyone are welcome to contribute.
  • Integrate comments and feedback from the group into the specs and create a newer version for further review by the group.
  • Repeat the review and revision cycles until a stable version is reached.
    • During the review process, the intermediate version will be also used in implementation of the self-publishing tool, which will provide more feedback to ontology development. ]]>     Overview of Classes and Properties This version of SPE ontology is a shallow one with only a few classes representing the top level objects involved in conducting experiment and publishing experiment information.The central class is Experiment, representing the information about a single experiment. The content of an experiment is organized as hypothesis, procedure, data, result and conclusion, which are data properties of Experiment class and are not shown in the diagram. The same experiment also uses protocols (class Protocol) and additional tools (class Product). It can be part of a publication (class Publication) and associated with a project (class Project). A project consists of a collection of experiments. There are researchers (class Person) who conduct the experiment. A researcher may belong to a group (class Group), which is part of an organization (class Organization). Researcher and groups can have projects and publications. Research tools are used by the procedures of experiments and protocols. Information on research tool are published by their manufacturers. An established experiment procedure is usually written as a protocol for sharing. A research publication traditionally is a composite of many experiments. But, a broader view taken by this specs considers any information published on the web as a form of publication, including experiment, protocol and product information self-published by researchers and tool providers as semantic data. This type of semantic publication has one clear difference from the traditional publication, that is, it uses one semantic object to represent not only the contents but also the so-called metadata. Because the relationships between the objects used in self-publishing are semantically represented, it will power the discovery of related information and potential data sharing.
    spe:Experiment dc:title dc:type dc:subject spe:associatedProject dc:description spe:hypothesis spe:procedure spe:protocolUsed spe:productUsed spe:data spe:supplementalData spe:result spe:conclusion spe:discussion spe:mainConcept spe:publishedIn dc:references dc:isReferencedBy spe:conductedBy spe:PI spe:startTime spe:endTime spe:status dc:license dc:rights spe:createdBy spe:createTime spe:updatedBy spe:updateTime foaf:homepage spe:webpage spe:Project dc:title dc:type dc:subject spe:objectives dc:description spe:startTime spe:endTime spe:status spe:ownBy spe:projectLead spe:currentMember spe:pastMember spe:hasPublication dc:references dc:isReferencedBy spe:resources foaf:fundedBy spe:createTime spe:updateTime foaf:homepage spe:webpage

    spe:Protocol

    dc:title dc:subject dc:type spe:procedure spe:productUsed dc:references dc:isReferencedBy spe:ownBy dc:rights dc:license spe:createdBy spe:createTime spe:updatedBy spe:updateTime foaf:homepage spe:webpage    		 spe:Publication dc:title dc:type dc:subject dc:abstract spe:content spe:contentURL spe:author spe:firstAuthor spe:correspondingAuthor spe:citationSource dc:issued dc:publisher dc:references dc:isReferencedBy dc:description dc:isVersionOf dc:license dc:rights spe:createdBy spe:createTime spe:updatedBy spe:updateTime foaf:homepage spe:webpage
    spe:Product dc:title dc:type dc:subject spe:model spe:specs spe:userManual dc:references dc:isReferencedBy spe:manufacturedBy spe:distributedBy spe:price spe:promotion spe:createTime spe:updateTime foaf:homepage spe:webpage spe:Person foaf:name foaf:title dc:type dc:subject spe:role spe:expertise spe:interest spe:hasPublication spe:currentProject spe:pastProject spe:inGroup spe:address spe:phone spe:cellphone spe:fax spe:email spe:updateTime foaf:homepage spe:webpage spe:Group foaf:name dc:type dc:subject spe:interest spe:currentMember spe:pastMember spe:currentProject spe:pastProject spe:hasPublication spe:inOrganization spe:responsiblePerson foaf:fundedBy spe:address spe:phone spe:cellphone spe:fax spe:email spe:updateTime foaf:homepage spe:webpage spe:Organization foaf:name dc:type dc:subject spe:address spe:phone spe:cellphone spe:fax spe:email spe:updateTime foaf:homepage spe:webpage

    Classes

    Class spe:Experiment
    Description A single experiment, usually done by a defined procedure, including but not limited to scientific experiments. A specific type of self-publication. An experiment may start from a hypothesis and if so, the conclusion should articulate results in relation to the hypothesis, e.g. rejection, supported, etc. This allows a search engine to discover what has happened to what hypothesis. Some main concepts like proteins or genes can be identified by URI in a list so that one can unambiguously search all the works that have been done related any specific concept. It should uniquely identify the protocols, additional tools, and references, which serve as important links for effective discovery of related information. In current version, the experiment contents are divided into several smaller parts, which are represented by string or literal. It enables field-based text search and provide specific search contexts for search engine. In future version, the contents may be represented by object properties if it facilitates data sharing.
    Properties (and quick comments) dc:title (experiment name) dc:type (i.e. category, can be chosen from controlled vocabularies) dc:subject (related disciplines like biology, medicine, chemistry, computer, software, etc. using keywords or key phrases, may be chosen from controlled vocabularies) spe:associatedProject dc:description spe:hypothesis spe:procedure (specific to this experiment, may use protocols for some of the steps) spe:protocolUsed (protocols used in the procedure, by URIs) spe:productUsed (list critical tools that are used in the procedure but not covered in any protocol used, by URI) spe:data spe:supplementalData (URI to additional data source that can’t be represented here) spe:result spe:conclusion (articulate if the hypothesis is supported or rejected) spe:discussion spe:mainConcept (URI to some main concepts, uniquely identified by URI ) spe:publishedIn (publications using the experiment’s data and results, by URI) dc:references (URIs to publications this experiment refers to, by URI) dc:isReferencedBy (may list the publications that make reference to this experiment, by URI) spe:conductedBy (who conducts the experiment, by URI) spe:PI (principle investigator for the experiment, by URI) spe:startTime spe:endTime spe:status (an experiment may be published while it’s still in progress) dc:license dc:rights spe:createdBy (someone who publishes the experiment, not necessarily the experimenter) spe:createTime spe:updatedBy spe:updateTime foaf:homepage (related or alternative web page, URL) spe:webpage (a web presentation of the experiment, URL)
    Superclass spe:Publication
    Class spe:Protocol
    Description An established procedure for doing an experiment or part of an experiment. A specific type of self-publication.
    Properties (and quick comments) dc:title (protocol title) dc:type dc:subject (research areas where the protocol can be used for) spe:procedure (detailed steps of the procedure) spe:productUsed (URI to tools used) dc:references dc:isReferencedBy spe:author dc:rights dc:license spe:createdBy spe:createTime spe:updatedBy spe:updateTime foaf:homepage spe:webpage
    Superclass spe:Publication
    Class spe:Product
    Description Materials, reagents, instrument, and software used by the experiment procedure or protocol. A specific type of self-publication. Product providers can publish their research tools in semantic format and make it available to researchers. This allows unique identification of each tool used in research. A search engine will help researchers to evaluate tools by uniquely identifying what experiments have used the tools before.
    Properties (and quick comments) dc:title (product name) dc:type (product type, such as chemical, assay kit, instrument, software, etc) dc:subject (research areas where the product can be used for) spe:model (product model) spe:specs (product specifications) spe:userManual (URL to user manual or instructions) dc:references dc:isReferencedBy spe:manufacturedBy spe:distributedBy spe:price spe:promotion spe:createTime spe:updateTime foaf:homepage spe:webpage
    Superclass spe:Publication
    Class spe:Project
    Description Usually a large undertaking that requires a series of experiments. Can be used to organize experiments. A specific type of self-publication.
    Properties (and quick comments) dc:title (project name) dc:type (functional category, such as research, development, production, etc.) dc:subject (related disciplines like biology, medicine, chemistry, computer, software, etc.) spe:objectives (project objectives, goals) dc:description spe:startTime spe:endTime spe:status (past, current, active, inactive, in progress, etc) spe:ownBy (owner of the project, may be a PI, a group, or an organization) spe:projectLead (project lead, manager, etc) spe:currentMember spe:pastMember spe:hasPublication dc:references dc:isReferencedBy spe:resources (related and useful resources) foaf:fundedBy (funding sources, by URI) spe:createdBy spe:createTime spe:updatedBy spe:updateTime foaf:homepage spe:webpage
    Superclass spe:Publication
    Class spe:Publication
    Description Any publication including research paper, industry article, report, etc. A semantic publication represents both contents and metadata in one place. This data object can be used to self-publish any information online. Three specific types of self-publications are defined in this ontology, i.e. Experiment, Protocol, Product. Publication object also can be used to wrap a traditional publication (e.g. journal article) and provide an URI for it.
    Properties (and quick comments) dc:title dc:type (publication type like self-published, peer-reviewed, open-standard, etc.) dc:subject (related disciplines, keywords) dc:abstract spe:content (full text content if available, enabling full-text search by search engine)) spe:contentURL (URL to full text content source if available) spe:author spe:firstAuthor spe:correspondingAuthor spe:citationSource (the source part of citation, i.e. journal/volume/number/pages) dc:issued (publishing date) dc:publisher dc:references dc:isReferencedBy dc:description dc:isVersionOf (version) dc:license dc:rights spe:createdBy spe:createTime spe:updatedBy spe:updateTime foaf:homepage spe:webpage
    Class spe:Person
    Description Any person including researcher. A researcher may belong to a group and multiple projects, and have a list of publications and specific interest and expertise. These relationships allows any researcher to accurately find out what other researchers are doing what.
    Properties (and quick comments) foaf:name foaf:title (Dr., Mr., Ms., etc.) spe:role (job tittle, job function, etc) dc:type (functional category, such as research, development, production, etc.) dc:subject (related disciplines like biology, medicine, chemistry, computer, software, etc.) spe:expertise (skill set, experience, etc) spe:interest (professional interest areas) spe:hasPublication (URI to publication) spe:currentProject (URI to current project) spe:pastProject (URI to past project) spe:inGroup (URI to the group the person belongs to) spe:address spe:phone spe:cellphone spe:fax spe:email spe:updateTime foaf:homepage spe:webpage
    Superclass foaf:Person
    Class spe:Group
    Description Any group including research group.
    Properties (and quick comments) foaf:name dc:type (functional category, such as research, development, production, etc.) dc:subject (related disciplines like biology, medicine, chemistry, computer, software, etc.) spe:interest (interest areas) spe:currentMember (URI to current group members) spe:pastMember (URI to past members) spe:currentProject (URI to current projects) spe:pastProject (URI to past projects) spe:hasPublication (URI to the group’s publications) spe:inOrganization (URI to the organization that the group is in) foaf:fundedBy (funding sources, by URI) spe:responsiblePerson (PI, manager, director, etc) spe:address spe:phone spe:cellphone spe:fax spe:email spe:updateTime foaf:homepage spe:webpage
    Superclass foaf:Group
    Class spe:Organization
    Description Any organization such as university, institute, or company. Categorizing organization in terms of type and subject provides the right contexts for search engine
    Properties (and quick comments) foaf:name dc:type (academic, commercial, government, other) dc:subject (related disciplines like life science, health care, chemistry, IT, computer, software, publishing, etc.) spe:address spe:phone spe:cellphone spe:fax spe:email spe:updateTime foaf:homepage spe:webpage
    Superclass foaf:Organization
    Class spe:PostalAddress
    Description Postal address.
    Properties spe:pobox spe:street spe:city spe:state spe:postalcode spe:country
    Superclass  

    Object Properties

    ObjectProperty spe:author
    Description Publication’s author
    Domain spe:Publication, spe:Protocol
    Range spe:Person
    ObjectProperty spe:address
    Description Postal address
    Domain spe:Person, spe:Group, spe:Organization
    Range spe:PostalAddress
    ObjectProperty spe:associatedProject
    Description A Project that an experiment is associated with.
    Domain spe:Experiment
    Range spe:Project
    ObjectProperty spe:conductedBy
    Description A person who conducted the experiment.
    Domain spe:Experiment
    Range spe:Person
    ObjectProperty spe:correspondingAuthor
    Description Publication’s corresponding author
    Domain spe:Publication
    Range spe:Person
    ObjectProperty spe:createdBy
    Description A person who created the semantic resource.
    Domain spe:Experiment, spe:Project, spe:Protocol, spe:Product, spe:Publication
    Range spe:Person
    ObjectProperty spe:currentMember
    Description A current member of a project or group
    Domain spe:Project, spe:Group
    Range spe:Person
    ObjectProperty spe:currentProject
    Description Current project.
    Domain spe:Person, spe:Group
    Range spe:Project
    ObjectProperty spe:distributedBy
    Description A distributor that distributes the product.
    Domain spe:Product
    Range spe:Organization
    ObjectProperty spe:firstAuthor
    Description Publication’s first author
    Domain spe:Publication
    Range spe:Person
    ObjectProperty spe:hasPublication
    Description A publication own by a resource
    Domain spe:Project, spe:Person, spe:Group
    Range spe:Publication
    ObjectProperty spe:inGroup
    Description A group that a person belongs to or is associated with.
    Domain spe:Person
    Range spe:Group
    ObjectProperty spe:inOrganization
    Description An organization that a group or person belongs to or is associated with.
    Domain spe:Group, spe:Person
    Range spe:Organization
    ObjectProperty spe:manufacturedBy
    Description A manufacturer that makes the product.
    Domain spe:Product
    Range spe:Organization
    ObjectProperty spe:ownBy
    Description A person (PI or manager), group or organization who owns or is responsible for the project
    Domain spe:Project
    Range foaf:Agent
    ObjectProperty spe:pastMember
    Description A past member of a project or group
    Domain spe:Project, spe:Group
    Range spe:Person
    ObjectProperty spe:pastProject
    Description Past project.
    Domain spe:Person, spe:Group
    Range spe:Project
    ObjectProperty spe:PI
    Description Principle investigator responsible for an experiment, a project or a group.
    Domain spe:Experiment, spe:Project, spe:Group
    Range spe:Person
    ObjectProperty spe:productUsed
    Description Materials or tools used by an experiment procedure or protocol, including reagents, instruments, software. Product providers can define their product as semantic resources, which are available for researcher to use in semantic publishing.
    Domain spe:Protocol, spe:Experiment
    Range spe:Product
    ObjectProperty spe:projectLead
    Description A person who leads the project
    Domain spe:Project
    Range spe:Person
    ObjectProperty spe:protocolUsed
    Description A protocol used by an experiment.
    Domain spe:Experiment
    Range spe:Protocol
    ObjectProperty spe:publishedIn
    Description A publication using the experiment data and result
    Domain spe:Experiment
    Range spe:Publication
    ObjectProperty spe:responsiblePerson
    Description A person who is responsible for the group, such as PI, manager, director, etc.
    Domain spe:Group
    Range spe:Person
    ObjectProperty spe:updatedBy
    Description A person who updated the resource.
    Domain spe:Experiment, spe:Project, spe:Protocol, spe:Product, spe:Publication
    Range spe:Person

    Datatype Properties

    DatatypeProperty spe:cellphone
    Description Cell phone number
    Domain spe:Person, spe:Group, spe:Organization
    Range xsd:string
    DatatypeProperty spe:citationSource
    Description The source part of a citation, including journal, volume, number and pages for an article, or book title and chapter for book chapter, etc.
    Domain spe:Publication
    Range xsd:string
    DatatypeProperty spe:city
    Description City name
    Domain spe:PostalAddress
    Range xsd:string
    DatatypeProperty spe:conclusion
    Description Conclusion drawn from an experiment. If a hypothesis is proposed, conclusion should be made in relation to the hypothesis, such as rejection, supporting, verification, proven, etc.
    Domain spe:Experiment
    Range xsd:string
    DatatypeProperty spe:content
    Description Full text content of a publication.
    Domain spe:Publication
    Range xsd:string
    DatatypeProperty spe:contentURL
    Description URL of the content source.
    Domain spe:Publication
    Range xsd:anyURI
    DatatypeProperty spe:country
    Description Country name
    Domain spe:PostalAddress
    Range xsd:string
    DatatypeProperty spe:createTime
    Description Date and time when a resource is created
    Domain spe:Experiment, all classes
    Range xsd:dateTime
    DatatypeProperty spe:data
    Description Data generated from an experiment. In current version, data are expressed as strings or literal. Future version will figure out how to represent more complex data types like graph, image and table.
    Domain spe:Experiment
    Range xsd:string
    DatatypeProperty spe:discussion
    Description Further discussions about an experiment, its data and results.
    Domain spe:Experiment
    Range xsd:string
    DatatypeProperty spe:email
    Description Email address
    Domain spe:Person, spe:Group, spe:Organization
    Range xsd:string
    DatatypeProperty spe:endTime
    Description Date and time when an experiment or a project ends
    Domain spe:Experiment, spe:Project
    Range xsd:dateTime
    DatatypeProperty spe:expertise
    Description Expertise that a person has.
    Domain spe:Person
    Range xsd:string
    DatatypeProperty spe:fax
    Description Fax number
    Domain spe:Person, spe:Group, spe:Organization
    Range xsd:string
    DatatypeProperty spe:hypothesis
    Description Experiment hypothesis if any. Fine-grained properties of hypothesis will be defined in future version.
    Domain spe:Experiment
    Range xsd:string
    DatatypeProperty spe:interest
    Description Interest areas that a person or group has.
    Domain spe:Person, spe:Group
    Range xsd:string
    DatatypeProperty spe:mainConcept
    Description A main concept associated with an experiment, such as a protein or gene being studied.
    Domain spe:Experiment
    Range xsd:anyURI
    DatatypeProperty spe:model
    Description Model of a product
    Domain spe:Product
    Range xsd:string
    DatatypeProperty spe:objectives
    Description Objectives of a project
    Domain spe:Project
    Range xsd:string
    DatatypeProperty spe:phone
    Description Phone number
    Domain spe:Person, spe:Group, spe:Organization
    Range xsd:string
    DatatypeProperty spe:pobox
    Description PO box number
    Domain spe:PostalAddress
    Range xsd:string
    DatatypeProperty spe:postalcode
    Description Zip code
    Domain spe:PostalAddress
    Range xsd:string
    DatatypeProperty spe:price
    Description Current price for a product
    Domain spe:Product
    Range xsd:float
    DatatypeProperty spe:procedure
    Description A procedure for doing an experiment, usually having multiple steps. May use protocols for some of the steps.
    Domain spe:Experiment, spe:Protocol
    Range xsd:string
    DatatypeProperty spe:promotion
    Description Promotion for a product
    Domain spe:Product
    Range xsd:string
    DatatypeProperty spe:resources
    Description Related and useful resources
    Domain spe:Project
    Range xsd:string
    DatatypeProperty spe:result
    Description Results and conclusions drawn from an experiment
    Domain spe:Experiment
    Range xsd:string
    DatatypeProperty spe:role
    Description A role that a person plays, such as PI, student, postdoc, scientist, researcher, manager, etc.
    Domain spe:Person
    Range xsd:string
    DatatypeProperty spe:specs
    Description Product specifications.
    Domain spe:Product
    Range xsd:string
    DatatypeProperty spe:startTime
    Description Date and time when an experiment or a project starts
    Domain spe:Experiment, spe:Project
    Range xsd:dateTime
    DatatypeProperty spe:state
    Description State name
    Domain spe:PostalAddress
    Range xsd:string
    DatatypeProperty spe:status
    Description Status of an experiment or a project: in progress, active, inactive, past, or current, etc.
    Domain spe:Experiment, spe:Project
    Range xsd:string
    DatatypeProperty spe:street
    Description Street address
    Domain spe:PostalAddress
    Range xsd:string
    DatatypeProperty spe:supplementalData
    Description A pointer to additional data that are generated from an experiment but can’t be expressed in the experiment’s semantic resource.
    Domain spe:Experiment
    Range xsd:anyURI
    DatatypeProperty spe:updateTime
    Description Date and time when a resource is updated.
    Domain spe:Experiment, all classes
    Range xsd:dateTime
    DatatypeProperty spe:userManual
    Description A pointer to the user manual or instructions for a product.
    Domain spe:Product
    Range xsd:anyURI
    DatatypeProperty spe:webpage
    Description A webpage presenting a resource for human consumption, usually a URL to HTML page. It’s the equivalent web document of a semantic data resource.
    Domain all classes
    Range xsd:anyURI
    ]]>     AJ Chen 6/18/2006]]> in progress 2006-08-24 21:08:41 2006-12-05 00:01:39     0.3