[::Associated Project::]
Ontology
[::Subject::]
self-publishing experiment, web publishing, semantic web, ontology, open data
[::Introduction::]
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.
[::Hypothesis::]
[::Procedure::]
- 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.
[::Protocols Used::]
[::Tools Used::]
[::Data::]
[::Data Links::]
[::Result::]
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 |
[::Conclusion::]
[::Discussion::]
[::Main Concepts::]
[::Published In::]
[::References::]
[::Researcher::]
AJ Chen
[::PI::]
[::Start Time::]
6/18/2006
[::End Time::]
[::Status::]
in progress
[::Alternative Web Page::]
http://esw.w3.org/topic/HCLS/ScientificPublishingTaskForce?action=AttachFile&do=get&target=SPE_specs_v0_2.html
[::Rights::]