Ontology Specifications for Self-Publishing of Experiment

Work in Progress
*** Seeking input from everyone ***

Status of this document:

8/6/06 Version 0.2, by AJ Chen
6/25/06 First draft (v0.1), by AJ Chen.

Authors:
AJ Chen

Contributors: (Add your name here after your contribution)
Thanks to everyone involved in the W3C Semantic Web Health Care and Life Sciences Interest Group (HCLSIG).

Purpose

To define an ontology for self-publishing of experiment as single unit and related information such as project, protocol, product, and researcher. The 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.

Development Process

(1) This specs is developed based on the requirements defined by the Scientific Publishing task force of HCLSIG.
(2) This specs should try to use as many terms as possible in other well-established ontologies including SKOS, DC, FOAF, FuGO, and Ebiquity ontologies.
(3) Everyone are welcome to contribute.

Overview of Classes and Properties

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

Class Relationship

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, see block diagram Fig. 1.

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.

.

Fig. 1 Class relationship of SPE ontology.

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

Relevant Ontologies and Vocabularies

RDF/XML
http://www.w3.org/TR/rdf-syntax-grammar/

RDFS
http://www.w3.org/TR/rdf-schema/

OWL
http://www.w3.org/TR/owl-ref/

XML
http://www.w3.org/TR/xmlschema-1/
http://www.w3.org/TR/2001/REC-xmlschema-2-20010502/

DC
http://dublincore.org/documents/dcmi-terms/
http://purl.org/dc/elements/1.1/
http://purl.org/dc/terms/

FOAF ontology:
http://xmlns.com/foaf/0.1/

vCard:
xmlns:vCard = "http://www.w3.org/2001/vcard-rdf/3.0#"
http://www.w3.org/TR/vcard-rdf

SUMO
http://ontology.teknowledge.com/

SKOS Core Vocabulary
http://www.w3.org/TR/swbp-skos-core-spec/

Ebiquity ontologies including project, publication, person, and contact
http://ebiquity.umbc.edu/ontology/

DOAP
http://usefulinc.com/doap

FuGO
http://fugo.sourceforge.net/ontologyInfo/ontology.php

BOSS
http://www.charlestoncore.org/ont/boss.html

EXPO
http://sourceforge.net/projects/expo