SRRO 2023-12-15 A minimal ontology that identifies RDF graphs loaded in the SPARQL service, and identifies various commonly used properties in these resources to facilitate common SPARQL queries. Service RDF Resource Ontology Developed by Anthony Huffman of the He Lab (U.Michigan) and the Semantic Infrastructure group of the NCI. The core SRRO reuses or derives elements from other RDF schemas or vocabularies: VANN: A vocabulary for annotating vocabulary descriptions http://purl.org/vocab/vann/ https://github.com/iand/vocabdotorg/tree/main/www/src/vann license: http://creativecommons.org/licenses/by/1.0/ dcat: Data Catalog Vocabulary https://www.w3.org/TR/vocab-dcat-3/ https://github.com/w3c/dxwg/tree/gh-pages/dcat/rdf license: https://creativecommons.org/licenses/by/4.0/ OMV - Ontology Metadata Vocabulary https://sourceforge.net/projects/omv2/ license: unknown sd: Service Description Vocabulary https://www.w3.org/TR/sparql11-service-description/#vocab https://www.w3.org/ns/sparql-service-description.rdf terms of use: https://www.w3.org/copyright/software-license-2023/ prov: PROV Ontology https://www.w3.org/TR/2013/NOTE-prov-overview-20130430/ http://www.w3.org/ns/prov.ttl terms of use: https://www.w3.org/copyright/software-license-2023/ The git tag of the release version 1.0 of srro.owl is 1.4.0. 1.0 Declared as owl:ObjectProperty in the prov ontology. Used here as an owl:AnnotationProperty to refer to external objects without having to import them or pun when the object of the triple is a property. A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity. Declared as ObjectProperty in the prov ontology. Used here as an owl:AnnotationProperty to refer to external objects and remain in OWL without punning. download from A property that links a Service RDF Resource to a download location where the resource can be downloaded from. has conversion authority A property that relates a Service RDF Resource to the Organization that processes the original resource to a form that is then used in the current SPARQL service. has date A property that relates a Service RDF Resource to the property that the resource uses to refer to its version release date. has definition A property that relates a Service RDF Resource to the property that the resource uses for an entity's textual definition. has identifier A property that relates a Service RDF Resource to the property that the resource uses for an entity's identifier. has intent A property that relates a Service RDF Resource to the general intent or purpose of the resource. has namespace A property that relates a Service RDF Resource to the namespace of the resource, or the namespace of a resource referenced by a Service RDF Resource. has preferred term A property that relates a Service RDF Resource to the property that the resource uses for its entity's preferred term. has source authority A property that relates a Service RDF Resource to the authoritative Organization that develops, maintains, and publishes the resource. has term A property that relates a Service RDF Resource to the property that the resource uses for an entity's non-preferred terms, e.g. synonyms. has version A property that relates a Service RDF Resource to the property that the resource uses to refer to its release version. in named graph A property that relates a Service RDF Resource to the Named Graph that identifies it in the SPARQL service. has domain A property that relates the Service RDF Resource to the Ontology Domain that it covers. has license A property that is used to relate an RDF resource to a license such that the license governs the terms of use permitted for that resource. An RDF resource might reuse entities from multiple resources with their own namespaces. has namespace IRI A namespace IRI used in a resource. Modified to refer to IRIs rather than URIs. has ontology IRI The IRI that an ontology may declare to identify itself. omv:acronym A data property that links an organization to an acronym. omv:description omv:email omv:name dcat:accessURL is an RDF property also typed as owl:ObjectProperty. It is used here as a datatype property. has access URL dcat:accessURL A URL of a resource that gives access to a distribution of the dataset. E.g. landing page, feed, SPARQL endpoint. Use for all cases except a simple download link, in which case downloadURL is preferred. dcat:downloadURL is an RDF property also typed as owl:ObjectProperty. It is used here as a datatype property. has download URL dcat:downloadURL The URL of the downloadable file in a given format. E.g. CSV file or RDF file. The format is indicated by the distribution's dct:format and/or dcat:mediaType. sd:name is rdf:type rdf:Property. Here it is used as an owl:DatatypeProperty sd:name Relates a named graph to the name by which it may be referenced in a FROM/FROM NAMED clause. The object of the sd:name property is an IRI. has namespace prefix vann:preferredNamespacePrefix A commonly-used prefix for a namespace used by a resource. 1 It is used here for a landing page, or FTP directory, that needs to be navigated to obtain the (mutable) link to the downloadable distribution file. Access Site Definition The class of properties that relate a resource's entities to their textual definition. The specific property used by a resource for this purpose is an instance of this class. 1 It is used here to obtain the URL that links directly to the downloadable distribution file. The scheme of the URL can be http, ftp, or any other scheme supporting downloads. Download Link An FTP site's directory listing served by an http web server is considered a landing page. Download Location The class of web and internet locations from which a resource can be downloaded from. This includes anonymous FTP sites, and http web sites, either via direct links or landing pages. Identifier The class of properties that relate a resource's entities to their identifiers. The specific property used by a resource for this purpose is an instance of this class. 1 1 Each namespace is an instance of this class. Namespace The class of namespaces used by the resources in this service, each of which is the common substring beginning each IRI in the RDF or OWL resource. Preferred Term The class of properties that relate a resource's entities to the preferred term used by its user community to denote that entity. The specific property used by a resource for this purpose is an instance of this class. Resource Description The class of entities that relate an RDF resource to information about the resource as a whole, such as version and release date information, namespaces. Resource Entity Description The class of properties used by RDF resources to describe the entitities of the resource, such as textual definitions and terms, among others. Resource Intent Resource Intent Type The main purpose of the RDF Graph resource. For example, to document the terminology of some domain. Individuals of this class are types of intent. 1 1 1 1 1 1 Each individual RDF resource is an instance of this class. Each individual IRI is in the present namespace, with a recognizable name of the resource used for the short name of the IRI. The resource's Ontology IRI is obtained from the 'has Ontology IRI' property. Service RDF Resource The class of RDF Graph resources accessible in the SPARQL service. Term The class of properties that relate a resource's entities to the various terms used by its user community to denote that entity, such as synonyms, abbreviations, acronyms, among other term types. The specific property used by a resource for this purpose is an instance of this class. If an RDF resource is versioned by its date, the version date property is likely non-existent. Version The class of properties that relate a resource to its release or modification version. The specific property used by a resource to indicate its version is an instance of this class. Version Date The class of properties that relate a resource to its release or modification date. The specific property used by a resource for this purpose is an instance of this class. A Service RDF Resource loaded into production; note this should be kept up-to-date by populating further instances of ontology. Supporting Service RDF Resource Supporting Service RDF Resource LicenseModel A license model describing the usage conditions for an ontology While the domain can refer to any topic ontology it is advised to use one of the established general purpose topic hierarchy like DMOZ or domain specific topic hierarchy like ACM for the computer science domain. Ontology Domain The subject of knowledge that is covered by a service resource. While the domain can refer to any topic ontology it is advised to use one of the established general purpose topic hierarchy like DMOZ or domain specific topic hierarchy like ACM for the computer science domain. 1 Organisation Organization An organisation of some kind. Represents social institutions such as universities, companies, societies etc. Location A location can be an identifiable geographic place (ISO 19112), but it can also be a non-geographic place such as a directory, row, or column. As such, there are numerous ways in which location can be expressed, such as by a coordinate, address, landmark, and so forth. 1 The graph name of a resource gets set by an administrator or developer on data load to an RDF quadstore database, it is not specified by the RDF resource. Named Graph An instance of sd:NamedGraph represents a named graph having a name (via sd:name) and an optional graph description (via sd:graph). Anthony Huffman ORCID: 0000-0002-5735-7540 change to IAO_0000708 https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International license CCBY 4.0 CCBY 4.0 http://purl.obolibrary.org/obo/go.owl The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms. GO Gene Ontology NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. NCIm NCIm Label NCIm Atom NCIm graph http://ncim.nci.nih.gov/NCIMetathesaurus# mts NCIm Namespace NCIm Description http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl NCI Thesaurus, a controlled vocabulary in support of NCI administrative and scientific activities. Produced by the Enterprise Vocabulary System (EVS), a project by the NCI Center for Biomedical Informatics and Information Technology. National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U.S.A. NCIt NCI Thesaurus http://ncicb.nci.nih.gov/xml/owl/EVS/ThesaurusInferred.owl NCI Thesaurus inferred version, a controlled vocabulary in support of NCI administrative and scientific activities. Produced by the Enterprise Vocabulary System (EVS), a project by the NCI Center for Biomedical Informatics and Information Technology. National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U.S.A. NCIt inferred NCI Thesaurus inferred version http://cbiit.nci.nih.gov/srro A minimal ontology that identifies RDF graphs loaded in the SPARQL service, and identifies various commonly used properties in these resources to facilitate common SPARQL queries. SRRO Service RDF Resource Ontology biological domain biomedical domain http://cbiit.nci.nih.gov/caDSR The Cancer Data Standards Registry and Repository (caDSR) is a metadata repository based on the ISO/IEC 11179 Metadata Registry standard. Freely available, released without a license. caDSR Cancer Data Standards Registry and Repository https://cadsr.nci.nih.gov/ftp/caDSR_Downloads/CDE/XML/ Download location of the caDSR is an FTP site fronted by a web server. The user needs to read or parse the directory to select the correct file. cadsr download location http://cbiit.nci.nih.gov/caDSR cadsr graph http://cbiit.nci.nih.gov/caDSR# cmdr cadsr namespace clinical domain The mission of the GO Consortium is to develop a comprehensive, computational model of biological systems, ranging from the molecular to the organism level, across the multiplicity of species in the tree of life. help@geneontology.org GO Consortium GO Consortium https://purl.obolibrary.org/obo/go.owl Download location of GO is a URL, can be downloaded with a direct link to the file. go download location http://www.geneontology.org/GO go graph http://purl.obolibrary.org/obo/ obo1 go namespace information technology domain license none license unknown metadata A resource type whose primary purpose is to describe in a standard format, for instance ISO 11179, the information that describes an entity or other resources. caDSR The project in the National Cancer Institute's Center for Biomedical Informatics and Information Technology (CBIIT) responsible for developing standard data elements and case report forms, among other metadata, in support of the NCI mission. It's main product is also named the Cancer Data Standards Repository, based on the ISO/IEC 11179 metadata registry standard. The project is run by the Semantic Infrastructure (SI) group of CBIIT. caDSR.RA@mail.nih.gov NCI Cancer Data Standards Registry and Repository NCI Cancer Data Standards Registry and Repository caDSR EVS The project in the National Cancer Institute's Center for Biomedical Informatics and Information Technology (CBIIT) responsible for developing vocabulary products and services in support of the NCI mission. It's main products are the NCI Thesaurus and the NCI Metathesaurus, a cancer-centric UMLS derivative. The project is run by the Semantic Infrastructure (SI) group of CBIIT. NCIThesaurus@nih.gov NCI Enterprise Vocabulary Service EVS creates, compiles, and cross-maps biomedical terminology needed by NCI and its community. EVS publishes NCI Thesaurus (NCIt) as its core reference terminology and biomedical ontology. EVS also makes available standalone versions of other terminologies and ontologies of special interest, and provides access with extensive cross-mappings to more than 75 terminologies in the NCI Metathesaurus. NCI Enterprise Vocabulary Service SI A program within the Clinical & Translational Research Informatics Branch in the Informatics and Data Science Program of the Center for Biomedical Informatics & Information Technology (CBIIT) of the NCI. It runs the EVS and caDSR projects. NCI Semantic Infrastructure A program within the Clinical & Translational Research Informatics Branch in the Informatics and Data Science Program of the Center for Biomedical Informatics & Information Technology (CBIIT) of the National Cancer Institute. It runs the EVS and caDSR projects. NCI Semantic Infrastructure NCI SI ftp://ftp1.nci.nih.gov/pub/cacore/EVS/NCI_Thesaurus/Thesaurus.OWL.zip Download location of NCIt is a URL, can be downloaded with a direct link to the file. ncit download location http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl ncit graph http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# ncit ncit namespace http://ncicb.nci.nih.gov/xml/owl/EVS/ThesaurusInferred.owl ncit inferred graph A resource type whose primary purpose is to provide a detailed specification or representation of a resource. Although an ontology with intent terminology could be considered a schema of a domain, it's primary purpose is to specify the terminology of the domain. schema https://raw.githubusercontent.com/NCI-Semantic-Infrastructure/si-schemas/main/metadata-SI/production/srro-production.owl Download location of SRRO is a URL, can be downloaded with a direct link to the file. srro download location http://cbiit.nci.nih.gov/srro srro graph http://cbiit.nci.nih.gov/srro# srro srro namespace A resource type that contains a set of terms and definitions, among other attributes, for the elements of a domain of knowledge, e.g. clinical care, biological molecules. Terms from this type of resource can be used to annotate other artifacts, i.e. serve as metadata. The distinction with the metadata type in the present resource is that a terminology doesn't include all the necessary information required by e.g. a standard data element in one defined data structure. terminology A property used as an identifier in the caDSR for data elements. cmdr:publicId A property used as an identifier in the NCIt. ncit:NHC0 code A property used for preferred terms in the NCI Thesaurus. ncit:P108 Preferred Name A property used to denote the various terms associated with a concept, synonyms, abbreviations, acronyms, among others, in the NCIt. ncit:P90 FULL_SYN The property used for definitions in the NCIt. ncit:P97 DEFINITION A property used for definitions in GO and other OBO vocabularies. iao:definition definition A property used to denote release dates in the caDSR, NCIt, and other RDF resources. dc:date Date A property used to denote release dates in the SSRO and other RDF resources. dcterms:date A property used for synonyms in GO and other OBO vocabularies. oboInOwl:hasExactSynonym has exact synonym A property used for identifiers in GO and other OBO vocabularies. oboInOwl:id The rdfs:label is used for preferred terms in caDSR, GO and other vocabularies. rdfs:label An annotation property that provides version information for an ontology or another OWL construct. Used by the NCIt and GO among other RDF resources. owl:versionInfo A property used to denote various terms associated with a data element in the caDSR. skos:altLabel A property used for definitions of data element in the caDSR. skos:definition