|
spe:Experiment dc:title dc:type dc:subject spe:associatedProject spe:hypothesis spe:introduction spe:procedure spe:protocolUsed spe:productUsed spe:data spe:dataLink spe:result spe:conclusion spe:discussion spe:mainConcept spe:conductedBy spe:PI boon:startTime boon:endTime boon:status dc:references spe:publishedIn dc:isReferencedBy boon:fundingSource dc:description dc:publisher dc:license dc:rights boon:altwebpage boon:createdBy boon:createTime boon:updatedBy boon:updateTime boon:webpage |
spe:Project dc:title dc:type dc:subject spe:objectives spe:design spe:resources boon:startTime boon:endTime boon:status boon:owner spe:projectLead boon:currentMember boon:pastMember spe:hasPublication dc:references dc:isReferencedBy boon:fundingSource dc:license dc:rights boon:altwebpage boon:createdBy boon:createTime boon:updatedBy boon:updateTime boon:webpage |
spe:Protocol
dc:titledc:type dc:subject dc:description spe:procedure spe:productUsed boon:author dc:references dc:isReferencedBy dc:publisher dc:rights dc:license boon:altwebpage boon:createdBy boon:createTime boon:updatedBy boon:updateTime boon:webpage |
spe:Publication dc:title dc:type dc:subject dc:abstract spe:content dc:source boon:author spe:firstAuthor spe:correspondingAuthor spe:citationSource dc:references dc:isReferencedBy dc:issued dc:publisher dc:description dc:license dc:rights boon:altwebpage boon:createdBy boon:createTime boon:updatedBy boon:updateTime boon:webpage |
| 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 to 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 (type of experiment) dc:subject (related disciplines like biology, medicine, chemistry, computer, software, etc. using keywords or key phrases, may be chosen from controlled vocabularies) spe:associatedProject (project composed of the experiment) spe:introduction spe:hypothesis (hypothesis for the experiment if any) 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:dataLink (URI to additional data source that can't be represented here) spe:result (result of the experiment) spe:conclusion (articulate if the hypothesis is supported or rejected) spe:discussion spe:mainConcept (URI to some main concepts, uniquely identified by URI ) spe:conductedBy (who conducts the experiment, by URI) spe:PI (principle investigator for the experiment, by URI) boon:startTime (experiment start time ) boon:endTime (experiment end time) boon:status (an experiment may be published while it's still in progress) 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) boon:fundingSource dc:description dc:publisher dc:license dc:rights boon:createdBy (someone who publishes the experiment, not necessarily the experimenter) boon:createTime boon:updatedBy boon :updateTime boon:altwebpage (related or alternative web page, URL) boon:webpage (a web presentation of the same data, URL) |
| Superclass |
| 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) dc:description spe:procedure (detailed steps of the procedure) spe:productUsed (URI to tools used) boon:author dc:references dc:isReferencedBy dc:publisher dc:rights dc:license boon:createdBy boon:createTime boon:updatedBy boon:updateTime boon:altwebpage (related or alternative web page, URL) boon:webpage (a web presentation of the same data, URL) |
| Superclass |
| 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 dc:subject (related disciplines like biology, medicine, chemistry, computer, software, etc.) spe:objectives (project objectives, goals) spe:design spe:resources (related and useful resources) boon:startTime boon:endTime boon:status (past, current, active, inactive, in progress, etc.) boon:owner (owner of the project, may be a PI, a group, or an organization) spe:projectLead (project lead, manager, etc.) boon:currentMember boon:pastMember spe:hasPublication dc:references dc:isReferencedBy boon:fundingSource (funding sources, by URI) dc:license dc:rights boon:createdBy boon:createTime boon:updatedBy boon:updateTime boon:altwebpage (related or alternative web page, URL) boon:webpage (a web presentation of the same data, URL) |
| Superclass |
| 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, Project. 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)) dc:source (URL to full text content source if available) boon: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:license dc:rights boon:createdBy boon:createTime boon:updatedBy boon:updateTime boon:altwebpage (related or alternative web page, URL) boon:webpage (a web presentation of the same data, URL) |
| Superclass |
| 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 | boon:Person |
| ObjectProperty | spe:correspondingAuthor |
| Description | Publication's corresponding
author |
| Domain | spe:Publication |
| Range | boon:Person |
| ObjectProperty | spe:firstAuthor |
| Description | Publication's first author |
| Domain | spe:Publication |
| Range | boon:Person |
| ObjectProperty | spe:hasPublication |
| Description | A publication own by a resource |
| Domain | spe:Project |
| Range | spe:Publication |
| ObjectProperty | spe:PI |
| Description | Principle investigator
responsible for an experiment, a project or a group. |
| Domain | spe:Project |
| Range | boon: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 | boon:Product |
| ObjectProperty | spe:projectLead |
| Description | A person who leads the project |
| Domain | spe:Project |
| Range | boon: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 |
| 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: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 | content of a publication |
| Domain | spe:Publication |
| Range | xsd:string |
| 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:dataLink |
| 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:design |
| Description | Project design |
| Domain | spe:Project |
| Range | xsd:string |
| DatatypeProperty | spe:discussion |
| Description | Further discussions about an
experiment, its data and results. |
| Domain | spe:Experiment |
| 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:introduction |
| Description | Experiment introduction |
| Domain | spe:Experiment |
| 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:objectives |
| Description | Objectives of a project |
| Domain | spe:Project |
| Range | xsd:string |
| 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: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 |