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CIMI URI’s

CIMI URI’s. Digital Resources. Digital resources URI for the resource itself ( dURI ) Resolves to metadata about the resource Link to latest version Link to newer revisions URI for each version of the resource ( vdURI )

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CIMI URI’s

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  1. CIMI URI’s

  2. Digital Resources Digital resources • URI for the resource itself (dURI) • Resolves to metadata about the resource • Link to latest version • Link to newer revisions • URI for each version of the resource (vdURI) • Renderings and languages may be negotiated or variations on the resource itself.

  3. Digital Resource Metadata – Related Resource Resource Version URI Resource URI – does not change Resource Metadata Version Metadata

  4. Real World Resource Real World Resource • Individuals, kinds, categories, attributes (tropes), … • Have zero or more “signifiers” • Goal of this presentation is to argue that, in OMG context, at least one should be a URI. (eURI) • Described by digital resources, but description is NOT the resource • Description may undergo revisions, but the resource does not (!) • Need a catalog: f(eURI)  dURI*

  5. URI Needs The source of confusion is that, when it comes to URI’s, we have: • The URI of the resource “r” – the thing being described • The URI of a description of “r” according to version “v” of model/ontology/document/… “d” • The URI of version “v” • The URI of document “d” • Formats / translations / … of all of the above

  6. Identifier Questions Questions about any identifier can include: • What does identifier I reference? • Where can I go to find more information about the reference of I? • Is identifier I sanctioned/used by my community? • What is the identifier for X? • How do I get a identifier registered for X?

  7. Identifier Management System • What does identifier I reference? • f1(I,[language],[format/[schema]])  description(language, format/schema) • Where can I go to find more information about reference I? • f2(I,[language],[format/[schema]])  identifier_list(language, format/schema) • Is identifier I sanctioned by my community? • f3(I)  publisher_identifier … • What is the identifier for X? • f4(X, …)  Iopt

  8. URI Identifier Management System URI scheme, like many “universal” schemes includes a mechanism for absorbing other schemes…

  9. URI’s Internet URI Scheme consists of: urn:<scheme>:<identifier> • urn:oid:2.16.840.1.113883.6.1 • urn:lsid:example.com:paper:132187 • urn:guid:748C595C-A1D2-4323-B006-971B04981672 • …

  10. http: URI’s http://<host name>:port/<path>?<query>#<fragment> • Host name comes from existing domain name system: [subdomain.]*domain.domain • www.informatics.mayo.edu Domain – controlled by ICANN Subdomain – controlled by Mayo Foundation for Medical Education and Research Subdomain – controlled by Mayo Department of Biomedical Statistics and Informatics

  11. Identifier Management Systemusing HTTP • What does identifier I reference? • GET URI [Accept-language, Accept, ..] description(language, format/schema) • Where can I go to find more information about reference I? • GET URI [Accept-language, Accept, ..] hrefs embedded in description • Is identifier I sanctioned by my community? • http GET http://www.networksolutions.com/whois/index.jsp (or equiv)  owner of URI. Is this the primary publisher / owner of the target resource? • What is the identifier for X? • http GET http://www.google.com/search?q=appendicitis • For generic • http GET http://informatics.mayo.edu/cts2/rest/entities?matchvalue=appendicitis • For specialized • If I know ‘code’ for X, I can find (or figure out) what the identifier would be: • http://snomed.info/id/74400008 • http://id.who.int/icd/release/10/A00 • How do I get an identifier registered for X? • Identify the owner • Identifier (if published) will be using URI scheme as published by owner

  12. HTTP URI’s The combination of the HTTP protocol the DNS system and the internet infrastructure already solves many of the registry/repository/classification issues we face today… … as long as • We separate the URI thing being described from the URI of the description itself • Convince the creators to mint the URI’s (and keep them permanent!) • Settle on a community accepted standardized metadata scheme • Content – (structured) HTML / CTS2 / ADL1.5 / 11179 / … • Links – RDFA / hrefs and other links. Need to settle on tags (e.g. “a” in html…)

  13. HTTP Identifiers Mechanisms are well accepted for the namespace/name mix: http://snomed.info/id/74400008 • Header: sctid == http://snomed.info/id/ • <sctid:74400008> • <element a=“&sctid;74400008”>

  14. URI’s (http) are the basis of the Semantic Web

  15. Coded_Text“Data Type”

  16. Issues Data Type – “A data type is a type whose instances are identified only by their value.” <Meaningxsi:type = “CODED_TEXT” value = “Has indication” code = “230165009” terminology_id = “2.16.840.1.113883.6.96” terminology_version = “http://snomed.info/sct/version/20130131”/> is NOTthe same as <Meaningxsi:type = “CODED_TEXT” value = “Has indication” code = “230165009” terminology_id = “2.16.840.1.113883.6.96” terminology_version = “http://snomed.info/sct/version/20120731”/> or <Meaningxsi:type = “CODED_TEXT” code = “230165009” terminology_id = “2.16.840.1.113883.6.96”/>

  17. Issues <Meaningxsi:type = “CODED_TEXT” value = “Has indication” code = “578961551000160109” terminology_id = “2.16.840.1.113883.6.96” terminology_version = “http://snomed.info/sct/version/20130131”/> • Not always known • Should not matter • If it does, compute it from the context <Meaningxsi:type = “CODED_TEXT” value = “Has indication” code = “578961551000160109” terminology_id = “2.16.840.1.113883.6.96” terminology_version = “http://snomed.info/sct/version/20130131”/> Requires external machinery to look up (URI’s anyone)

  18. Issues <Meaningxsi:type = “CODED_TEXT” value = “Indication of” code = “230165009” terminology_id = “2.16.840.1.113883.6.96” terminology_version = “http://snomed.info/sct/version/20130131”/> • Values are language specific and mutable. They cannot be part of the identity <Languagexsi:type = “CODED_TEXT” value = “English” code = “900000000000507009” terminology_id = “2.16.840.1.113883.6.96” terminology_version = “http://snomed.info/sct/version/20130131”/> vs “text@en” • Something is wrong here (!).

  19. CODED_TEXT data typeCTS2 model Required – can be used to acquire all Of the other information. Identity of item Where to go to get more information Would not be stored. Data Type Human readable text Result of context-specific interpretation Of URI.

  20. List of value set members Could be <member uri=“&sctid:74400008”/>

  21. Completely filled out <core:namespace>sctfsn</core:namespace> <core:name>Appendicitis (Finding) </core:name>

  22. Equivalent <Entryxmlns:xsi=http://www.w3.org/2001/XMLSchema-instancexmlns=http://opencimi.org archetype_node_id = “at0000.1.1” name = “Blood_pressure_observation” uid = “123456”> <ArchetypeDetailsarchetype_id = “CIMI-ENTRY.blood pressure.v1” rm_version = “1.0.0-dstu.1” /> <Link> <Meaningxsi:type = “CODED_TEXT” uri= http://snomed.info/id/230165009> <namespace>sctid</namespace> <name>230165009</name> <designation>Indication of</designation> </Meaning> <Details> . . . </Details> <Target> 654321 </Target> </Link> <Participation> <Party> 456789 </Party> <Functionxsi:type = “CODED_TEXT” uri=http://snomed.info/id/116154003> <namespace>sctid</namespace> <name>116154003</name> <designation>patient</designation> </Function> <Details> ... </Details> </Participation> 230165009 <Data> <Item> . . . <Item> . . . </Item> </Item> </Data> </Entry>

  23. Units xmlns:sctid=“http://snomed.info/id/” xmlns:rm=“http://opencimi.org/rm/” <rm:result> <rm:value>17</rm:value> <rm:units about=“http://snomed.info/id/123456”>mAcre/deciMold</rm:units> (or) <rm:units about=“&sctid;12345>mAcre/deciMold</rm:units> </rm:result>

  24. Summary http URI’s: Already have validation / lookup / routing / metadata scheme Have ns:name shorthand Work with xml / rdf / owl and forseeable technologies

  25. Coded_Text The “data type” should be URI. No more, no less Namespace/code – optional, (e.g. sctid : 74400008) Text – optional (“Appendicitis”) Term-id, terminology-version and other stuff… Optional if needed or perhaps even a subclass

  26. Issues • Things minted in SNOMED namespace (or WHO namespace) need negotiation… • Transformation to and from HL7 needed • MIF to OWL has already addressed portions of this • http://hl7.org/ontology/vocab/uv/cs/ActClass#ACCM • (actually they have a “CURRENT” in there but…)

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