Tool Mapping
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SubtitleBioschemas specification for describing SoftwareApplication in the life-science.BioToolsBioJSBiocatalogueGalaxy tools shedGalaxyBridgeDBOntomatonZoomaRightFieldTavernaBioconductorUtrDBCLIMA 2MobiDBIFBRAINBioBioComputing UP
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Description[One paragraph description]
[References to supporting information like “use cases”, “bioschemas mapping” and “schema.org posted issues”]
<USE CASE URL>http://www.biojs.io/d/cttv.genomehttps://www.biocatalogue.org/https://toolshed.g2.bx.psu.edu/https://galaxyproject.org/http://www.bridgedb.org/https://github.com/ISA-tools/OntoMatonhttp://www.ebi.ac.uk/spot/zooma/about.htmlhttp://www.rightfield.org.uk/http://www.taverna.org.uk/https://www.bioconductor.org/packages/release/BiocViews.html#___Softwarehttp://www.bridgedb.org/http://bioinformatics.hsanmartino.it/clima2/http://mobidb.bio.unipd.it/https://www.france-bioinformatique.fr/en/services/toolshttp://rainbio.france-bioinformatique.fr/rainbio/http://protein.bio.unipd.it/services
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<CONTRIBUTOR1, CONTRIBUTOR2,..>RafaAleš & BraneRafaFedericoNormanAnnaFlavioPaoloIvanDomJonathan
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schema.orgbioschemas
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PropertyExpected TypeDescriptionBSC DescriptionMarginalityCardinalityControlled VocabularyName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCase
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Extends SoftwareApplication
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applicationCategoryText or
URL
Type of software application, e.g. 'Game, Multimedia'.labels/toolTypeMatchTypeRESTMatchTypeDatabaseMatchSubtitleDatabaseMatch
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applicationSubCategoryText or
URL
Subcategory of the application, e.g. 'Arcade Game'.
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applicationSuiteTextThe name of the application suite to which the application belongs (e.g. Excel belongs to Office).labels/collectionMatch
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availableOnDeviceTextDevice required to run the application. Used in cases where a specific make/model is required to run the application. Supersedes device.
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countriesNotSupportedTextCountries for which the application is not supported. You can also provide the two-letter ISO 3166-1 alpha-2 country code.
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countriesSupportedTextCountries for which the application is supported. You can also provide the two-letter ISO 3166-1 alpha-2 country code.
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downloadUrlURLIf the file can be downloaded, URL to download the binary.downloadNo Matchdownloads88613MatchDownloadDownload centerMatch
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featureListText or
URL
Features or modules provided by this application (and possibly required by other applications).MinimumMANYfunction/operationMatchCommandnpm install cytoscapeMatchfacilitates ontology search and tagging functionalities within Google SpreadsheetsPartial MatchFunctionCell line identification through STR profilePartial Match
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fileSizeTextSize of the application / package (e.g. 18MB). In the absence of a unit (MB, KB etc.), KB will be assumed.
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installUrlURLURL at which the app may be installed, if different from the URL of the item.summary/repositoryPartial MatchReleasehttps://github.com/ISA-tools/OntoMaton/releasesPartial MatchReleasehttps://github.com/myGrid/RightField/releasesPartial MatchUnique visitors304 last yearNo MatchURIPartial Match
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memoryRequirementsText or
URL
Minimum memory requirements.
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operatingSystemTextOperating systems supported (Windows 7, OSX 10.6, Android 1.6).labels/operatingSystemMatch
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permissionsTextPermission(s) required to run the app (for example, a mobile app may require full internet access or may run only on wifi).
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processorRequirementsTextProcessor architecture required to run the application (e.g. IA64).
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releaseNotesText or
URL
Description of what changed in this version.
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screenshotImageObject or
URL
A link to a screenshot image of the app.
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softwareAddOnSoftwareApplicationAdditional content for a software application.
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softwareHelpCreativeWorkSoftware application help.softwareHelp:url, softwareHelp:genre, softwareHelp:description/reviewMinimumMANYdocumentation, documentation/url, documentation/type, documentation/commentMatchDocumentation URLNoneMatchTraining materialIf you are new to ZOOMA, take a look at our getting started guide.Partial MatchHelpMatch
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softwareRequirementsText or
URL
Component dependency requirements for application. This includes runtime environments and shared libraries that are not included in the application distribution package, but required to run the application (Examples: DirectX, Java or .NET runtime). Supersedes requirements.contact/email, contact/url, contact/name, contact/tel, contact/typeMinimumMANYcontactMatchContact infoSantiago Schnel, E-mail: schnells@umich.eduMatchContactCNR ITB-Bari staffMatchFootnoteMobiDB created by BiocomputingUP Lab, University of Padua, Italy.MatchGautheret DanielMatchContactDepartment of Biomedical Sciences, University of PaduaMatch
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softwareVersionTextVersion of the software instance.summary/versionMatch
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storageRequirementsText or
URL
Storage requirements (free space required).
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supportingDataDataFeedSupporting data for a SoftwareApplication.MinimumONEsummary/descriptionMatchdescriptionLightweight genome browser for CTTV targets based on TnT GenomeMatchDescriptionDisorder Atlas is a web-based service that facilitates the interpretation of intrinsic disorder predictions using proteome-based descriptive statistics. This service is also equipped to facilitate large-scale systematic exploratory searches for proteins encompassing disorder features of interest, and further allows users to browse the prevalence of multiple disorder features at the proteome level. Disorder Atlas is freely available for non-commercial users at http://www.disorderatlas.org.MatchdescriptionMatchdescriptionGraph theory (a.k.a. network) library for analysis and visualisationMatchdescriptionBridgeDb is a framework for finding and mapping equivalent database identifiers. It has many facets: it is both a framework, live services, and are identifier mapping files for genes, proteins, and metabolites.MatchdescriptionZOOMA is an application for discovering optimal ontology mappings, developed by the Samples, Phenotypes and Ontologies Team at EBI. It can be used to automatically annotate "properties" (plain text, descriptive values about biological entities) with "semantic tags" (ontology classes).MatchdescriptionUTRdb is a curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs, derived from several sources of primary data. Experimentally validated functional motifs .....MatchAboutMobiDB was designed to offer a centralized resource for annotations of intrinsic protein disorder. The database features three levels of annotation: manually curated, indirect and predicted. As shown in the figure below, the different sources present a clear tradeoff between quality and coverage. By combining them all into a consensus annotation, MobiDB aims at giving the best possible picture of the "disorder landscape" of a given protein of interest.MatchDescriptionWeb service designed to display local syntenies in completely sequenced prokaryotic chromosomes.MatchDescription...Match
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aboutThingThe subject matter of the content.summary/homepagePartial MatchBase URLhttp://www.disorderatlas.orgMatchurlhttp://www.biojs.io/d/cytoscapeMatchRepo URLhttps://github.com/ISA-tools/OntoMatonPartial MatchRepo URLhttps://github.com/myGrid/RightFieldPartial Matchhomepagehttp://utrdb.ba.itb.cnr.it/MatchHomepagehttp://mobidb.bio.unipd.it/MatchHomepagehttp://protein.bio.unipd.it/servicesMatch
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accessModeTextThe human sensory perceptual system or cognitive faculty through which a person may process or perceive information. Expected values include: auditory, tactile, textual, visual, colorDependent, chartOnVisual, chemOnVisual, diagramOnVisual, mathOnVisual, musicOnVisual, textOnVisual.
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accessModeSufficientTextA list of single or combined accessModes that are sufficient to understand all the intellectual content of a resource. Expected values include: auditory, tactile, textual, visual.
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accessibilityAPITextIndicates that the resource is compatible with the referenced accessibility API (WebSchemas wiki lists possible values).
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accessibilityControlTextIdentifies input methods that are sufficient to fully control the described resource (WebSchemas wiki lists possible values).
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accessibilityFeatureTextContent features of the resource, such as accessible media, alternatives and supported enhancements for accessibility (WebSchemas wiki lists possible values).
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accessibilityHazardTextA characteristic of the described resource that is physiologically dangerous to some users. Related to WCAG 2.0 guideline 2.3 (WebSchemas wiki lists possible values).
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accessibilitySummaryTextA human-readable summary of specific accessibility features or deficiencies, consistent with the other accessibility metadata but expressing subtleties such as "short descriptions are present but long descriptions will be needed for non-visual users" or "short descriptions are present and no long descriptions are needed."
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accountablePersonPersonSpecifies the Person that is legally accountable for the CreativeWork.MinimumONEsummary/nameMatchnamecttv.genomeMatchNameDisorder AtlasMatchtool.nameConvert FASTQ to FASTAMatchnameBiojs-CytoscapeMatchnameBridgeDbMatchRepository nameOntoMatonPartial MatchtitleZOOMAMatchTitleRightFieldMatchNo MatchNo MatchNameUTRdb databaseMatchNameCell Line Integrated Molecular AuthenticationMatchNameMobiDBMatch?ABSYNTEMatchNameBWAMatchNameBioComputing UP servicesMatch
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aggregateRatingAggregateRatingThe overall rating, based on a collection of reviews or ratings, of the item.
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alternativeHeadlineTextA secondary title of the CreativeWork.
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associatedMediaMediaObjectA media object that encodes this CreativeWork. This property is a synonym for encoding.
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audienceAudienceAn intended audience, i.e. a group for whom something was created. Supersedes serviceAudience.
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audioAudioObjectAn embedded audio object.
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author
Organization or
Person
The author of this content or rating. Please note that author is special in that HTML 5 provides a special mechanism for indicating authorship via the rel tag. That is equivalent to this and may be used interchangeably.
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awardTextAn award won by or for this item. Supersedes awards.
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characterPersonFictional person connected with a creative work.
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citation
CreativeWork or
Text
A citation or reference to another creative work, such as another publication, web page, scholarly article, etc.MinimumMANYfunction/input/dataNo MatchsourceGoogle SpreadsheetsPartial MatchinputExcel spreadsheetMatchSTR profileMatchHelp (input)Search box, rest apiMatchDownloads820No Match
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commentCommentComments, typically from users.
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commentCountIntegerThe number of comments this CreativeWork (e.g. Article, Question or Answer) has received. This is most applicable to works published in Web sites with commenting system; additional comments may exist elsewhere.
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contentLocationPlaceThe location depicted or described in the content. For example, the location in a photograph or painting.
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contentRatingTextOfficial rating of a piece of content—for example,'MPAA PG-13'.
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contributor
Organization or
Person
A secondary contributor to the CreativeWork or Event.
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copyrightHolder
Organization or
Person
The party holding the legal copyright to the CreativeWork.
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copyrightYearNumberThe year during which the claimed copyright for the CreativeWork was first asserted.
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creator
Organization or
Person
The creator/author of this CreativeWork. This is the same as the Author property for CreativeWork.creditMatchProviderUniversity of Michigan Medical SchoolMatchRecommended citationWolstencroft K, Owen S, Horridge M, Krebs O, Mueller W, Snoep JL, du Preez F, Goble CA (2011), RightField: Embedding ontology annotation in spreadsheets, Bioinformatics (2011) 15;27(14):pp2021-2creditCNR-ITB, BariCiteCiting MobiDB
Emilio Potenza, Tomás Di Domenico, Ian Walsh, and Silvio C.E. Tosatto: MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins Nucl. Acids Res. (2014) doi:10.1093/nar/gku982
PlatformProvided by eBioCredit2016 © BioComputing UP. All Rights Reserved.
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dateCreatedDate or
DateTime
The date on which the CreativeWork was created or the item was added to a DataFeed.
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dateModifiedDate or
DateTime
The date on which the CreativeWork was most recently modified or when the item's entry was modified within a DataFeed.
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datePublishedDateDate of first broadcast/publication.
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discussionUrlURLA link to the page containing the comments of the CreativeWork.
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editorPersonSpecifies the Person who edited the CreativeWork.creditMatchProviderUniversity of Michigan Medical SchoolMatchRecommended citationWolstencroft K, Owen S, Horridge M, Krebs O, Mueller W, Snoep JL, du Preez F, Goble CA (2011), RightField: Embedding ontology annotation in spreadsheets, Bioinformatics (2011) 15;27(14):pp2021-2Partial MatchcreditCNR-ITB, BariMatchCiteCiting MobiDB
Emilio Potenza, Tomás Di Domenico, Ian Walsh, and Silvio C.E. Tosatto: MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins Nucl. Acids Res. (2014) doi:10.1093/nar/gku982
MatchPlatformProvided by eBioPartial MatchCredit2016 © BioComputing UP. All Rights Reserved.Match
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educationalAlignmentAlignmentObjectAn alignment to an established educational framework.
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educationalUseTextThe purpose of a work in the context of education; for example, 'assignment', 'group work'.
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encodingMediaObjectA media object that encodes this CreativeWork. This property is a synonym for associatedMedia. Supersedes encodings.
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exampleOfWorkCreativeWorkA creative work that this work is an example/instance/realization/derivation of.
Inverse property: workExample.
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fileFormatText or
URL
Media type, typically MIME format (see IANA site) of the content e.g. application/zip of a SoftwareApplication binary. In cases where a CreativeWork has several media type representations, 'encoding' can be used to indicate each MediaObject alongside particular fileFormat information. Unregistered or niche file formats can be indicated instead via the most appropriate URL, e.g. defining Web page or a Wikipedia entry.download/typeMatch
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funder
Organization or
Person
A person or organization that supports (sponsors) something through some kind of financial contribution.
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genreText or
URL
Genre of the creative work, broadcast channel or group.labels/toolTypePartial MatchTypeRESTMatchTypeDatabaseMatchSubtitleDatabaseMatch
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hasPartCreativeWorkIndicates a CreativeWork that is (in some sense) a part of this CreativeWork.
Inverse property: isPartOf.
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headlineTextHeadline of the article.
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inLanguageLanguage or
Text
The language of the content or performance or used in an action. Please use one of the language codes from the IETF BCP 47 standard. See also availableLanguage. Supersedes language.
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interactionStatisticInteractionCounterThe number of interactions for the CreativeWork using the WebSite or SoftwareApplication. The most specific child type of InteractionCounter should be used. Supersedes interactionCount.
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interactivityTypeTextThe predominant mode of learning supported by the learning resource. Acceptable values are 'active', 'expositive', or 'mixed'.
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isAccessibleForFreeBooleanA flag to signal that the publication is accessible for free. Supersedes free.
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isBasedOn
CreativeWork or
Product or
URL
A resource that was used in the creation of this resource. This term can be repeated for multiple sources. For example, http://example.com/great-multiplication-intro.html. Supersedes isBasedOnUrl.
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isFamilyFriendlyBooleanIndicates whether this content is family friendly.
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isPartOfCreativeWorkIndicates a CreativeWork that this CreativeWork is (in some sense) part of.
Inverse property: hasPart.
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keywordsTextKeywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.
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learningResourceTypeTextThe predominant type or kind characterizing the learning resource. For example, 'presentation', 'handout'.
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licenseCreativeWork or
URL
A license document that applies to this content, typically indicated by URL.labels/licenseMatchLicenceApache 2.0MatchLicense(s)No info yetMatchlicenseMITMatchLicenseCreative CommonsMatchLicense urlhttp://protein.bio.unipd.it/LICENSEPartial Match
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locationCreatedPlaceThe location where the CreativeWork was created, which may not be the same as the location depicted in the CreativeWork.
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mainEntityThingIndicates the primary entity described in some page or other CreativeWork.
Inverse property: mainEntityOfPage.
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material
Product or
Text or
URL
A material that something is made from, e.g. leather, wool, cotton, paper.
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mentionsThingIndicates that the CreativeWork contains a reference to, but is not necessarily about a concept.
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offersOfferAn offer to provide this item—for example, an offer to sell a product, rent the DVD of a movie, perform a service, or give away tickets to an event.
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positionInteger or
Text
The position of an item in a series or sequence of items.
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producer
Organization or
Person
The person or organization who produced the work (e.g. music album, movie, tv/radio series etc.).
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provider
Organization or
Person
The service provider, service operator, or service performer; the goods producer. Another party (a seller) may offer those services or goods on behalf of the provider. A provider may also serve as the seller. Supersedes carrier.
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publicationPublicationEventA publication event associated with the item.
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publisher
Organization or
Person
The publisher of the creative work.
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publishingPrinciplesURLLink to page describing the editorial principles of the organization primarily responsible for the creation of the CreativeWork.
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recordedAtEventThe Event where the CreativeWork was recorded. The CreativeWork may capture all or part of the event.
Inverse property: recordedIn.
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releasedEventPublicationEventThe place and time the release was issued, expressed as a PublicationEvent.
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reviewReviewA review of the item. Supersedes reviews.
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schemaVersionText or
URL
Indicates (by URL or string) a particular version of a schema used in some CreativeWork. For example, a document could declare a schemaVersion using an URL such as http://schema.org/version/2.0/ if precise indication of schema version was required by some application.
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sourceOrganizationOrganizationThe Organization on whose behalf the creator was working.
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spatialCoveragePlaceThe spatialCoverage of a CreativeWork indicates the place(s) which are the focus of the content. It is a subproperty of contentLocation intended primarily for more technical and detailed materials. For example with a Dataset, it indicates areas that the dataset describes: a dataset of New York weather would have spatialCoverage which was the place: the state of New York. Supersedes spatial.
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sponsor
Organization or
Person
A person or organization that supports a thing through a pledge, promise, or financial contribution. e.g. a sponsor of a Medical Study or a corporate sponsor of an event.
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temporalCoverage
DateTime or
Text or
URL
The temporalCoverage of a CreativeWork indicates the period that the content applies to, i.e. that it describes, either as a DateTime or as a textual string indicating a time period in ISO 8601 time interval format. In the case of a Dataset it will typically indicate the relevant time period in a precise notation (e.g. for a 2011 census dataset, the year 2011 would be written "2011/2012"). Other forms of content e.g. ScholarlyArticle, Book, TVSeries or TVEpisode may indicate their temporalCoverage in broader terms - textually or via well-known URL. Written works such as books may sometimes have precise temporal coverage too, e.g. a work set in 1939 - 1945 can be indicated in ISO 8601 interval format format via "1939/1945". Supersedes datasetTimeInterval, temporal.
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textTextThe textual content of this CreativeWork.
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thumbnailUrlURLA thumbnail image relevant to the Thing.
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timeRequiredDurationApproximate or typical time it takes to work with or through this learning resource for the typical intended target audience, e.g. 'P30M', 'P1H25M'.
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Schema.org mapping
Bioschemas fields
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