Ontology Specifications for Self-Publishing Experiment

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


Status of this document:
    6/25 First draft, by AJ Chen.
 
Contributors: (add your name here after you contribute to this document!)
    AJ Chen

Purpose

To define vocabularies to be used in self-publishing of experiments in RDF/XML. There are three specific goals for this set of vocabularies:
(1) The terms are intended to be used by applications that appeal to users across all scientific disciplines. 
(2) Although it may be used for any number of applications, its primarily focus at current stage will be enabling more efficient search of information at single experiment level on the web. This is in contrast to searching a paper, which is usually synthesized from many experiments.
(3) It should be easy to use by end users as well as easy to implement by application developers.

Development Process

(1) This specs is developed based on the requirements defined by this group.
(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.

Classes

Class
spe:Experiment
Description
A single experiment, part of a project. Any type of experiment that is usually done by a defined procedure and generates some sort of data and results. Including but limited to scientific experiments.
Properties
spe:associatedProject
dc:subject
dc:description
spe:hypothesis
spe:procedure
spe:protocolUsed
spe:data  (dc:dataset?)
spe:result
spe:discussion
spe:publication
dc:isReferencedBy
spe:conductedBy
spe:startTime
spe:endTime
spe:updateTime
foaf:homepage

Class
spe:Project
Description
Usually a large undertaking that requires a series of experiments. A collection of experiments.
Properties
dc:title
dc:subject
dc:description
spe:startTime
spe:endTime
spe:ownBy
foaf:fundedBy
foaf:member  (a list of foaf:Person)
dc:isReferencedBy
dc:references
spe:publication
foaf:homepage

Class
spe:Protocol
Description
An established procedure for doing experiments or studies.
Properties
dc:title
dc:subject
spe:procedure
spe:productUsed
dc:references
dc:isReferencedBy
spe:ownBy
spe:updatedBy
spe:updateTime
foaf:homepage

Class
spe:Product
Description
For materials, reagents, instrument, and software that are used by the experiment procedure or protocol.
Properties
dc:title
spe:model
dc:type
spe:specs
spe:manufacturedBy
spe:distributedBy
foaf:homepage

Class
spe:Researcher
Description
A person who performed the experiment.
Properties
foaf:name
foaf:title
spe:role
spe:expertise
foaf:interest
foaf:publications
foaf:weblog
spe:inGroup
spe:contactInfo
foaf:homepage
Superclass
foaf:Person

Class
spe:Group
Description
A research group.
Properties
foaf:name
dc:type
foaf:member
spe:inOrganization
foaf:fundedBy
spe:contactInfo
foaf:homepage
Superclass
foaf:Group

Class
spe:Organization
Description
An organization such as university, institute, company.
Properties
foaf:name
dc:type
spe:contactInfo
foaf:homepage
Superclass
foaf:Organization


ObjectProperties

ObjectProperty spe:associatedProject
Description A Project that the experiment is associated with.
Domain spe:Experiment
Range spe:Project

ObjectProperty spe:protocolUsed
Description A protocol used by the experiment.
Domain spe:Experiment
Range spe:Protocol

ObjectProperty spe:conductedBy
Description A experimenter who conducted the experiment.
Domain spe:Experiment
Range spe:Researcher

ObjectProperty spe:ownBy
Description A person or group who owns or is responsible for the project
Domain spe:Project
Range foaf:Agent

ObjectProperty spe:updatedBy
Description A person or group who updated the resource.
Domain spe:Protocol
Range foaf:Person

ObjectProperty spe:productUsed
Description Materials or tools used by the experiment procedure or protocol, including reagents, instruments, software.
Domain spe:Protocol
Range spe:Product

ObjectProperty spe:manufacturedBy
Description A manufacturer that makes the product.
Domain spe:Product
Range spe:Organization

ObjectProperty spe:distributedBy
Description A distributor that distributes the product.
Domain spe:Product
Range spe:Organization

ObjectProperty spe:inGroup
Description A group that a person belongs to or is associated with.
Domain spe:Researcher
Range spe:Group

ObjectProperty spe:inOrganization
Description An organization that a group belongs to or is associated with.
Domain spe:Group
Range spe:Organization

ObjectProperty spe:contactInfo
Description Contact information for a person. group, or organization.
Domain spe:Researcher, spe:Group, spe:Organization
Range contact:ContactInformation


DatatypeProperties

DatatypeProperty spe:hypothesis
Description Experiment hypothesis if any
Domain spe:Experiment
Range xsd:string

DatatypeProperty spe:procedure
Description A procedure that is used to carry out the experiment, usually having multiple steps.
Domain spe:Experiment
Range xsd:string

DatatypeProperty spe:data
Description data generated from the experiment.
Domain spe:Experiment
Range xsd:string  (how to represent image and table data type?)

DatatypeProperty spe:result
Description results and conclusions drawn from from the experiment data.
Domain spe:Experiment
Range xsd:string

DatatypeProperty spe:discussion
Description further discussions about the experiment, its data, results and conclusions.
Domain spe:Experiment
Range xsd:string

DatatypeProperty spe:startTime
Description data and time when an experiment started
Domain spe:Experiment
Range xsd:dateTime

DatatypeProperty spe:endTime
Description date and time when an experiment ended
Domain spe:Experiment
Range xsd:dateTime

DatatypeProperty spe:updateTime
Description date and time when this resource for the experiment is updated; the first update time being the creation time.
Domain spe:Experiment
Range xsd:dateTime

DatatypeProperty spe:publication
Description A publication using the data and results from the experiment.
Domain spe:Experiment
Range xsd:anyURI

DatatypeProperty spe:webpage
Description A webpage displaying the information about the experiment, usually represented by a URL.
Domain spe:Experiment
Range xsd:anyURI

DatatypeProperty spe:model
Description Model of a product
Domain spe:Product
Range xsd:string

DatatypeProperty spe:specs
Description Product specifications.
Domain spe:Product
Range xsd:string

DatatypeProperty spe:role
Description A role a person plays, such as PI, student, postdoc, scientist, researcher, etc.
Domain spe:Researcher
Range xsd:string

DatatypeProperty spe:expertise
Description Expertise that a person or experimenter has.
Domain spe:Researcher
Range xsd:string


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/

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