CTS2

Status ReportPresentation to Ontology PSIG

Dec 9, 2010

Outline

• Background and Approach• Specification outline via. Compliance points• Status

Background and Approach

CTS2

BackgroundCommon Terminology Services Edition 2Derived from:• OMG LQS Specification (1999)– OO Model, read only, but laid most of the

groundwork• HL7 CTS Specification (2004)– ANSI and ISO Standard– SOA Model, read only, reduced scope from LQS

CTS2

Brief HistoryWorking through the HSSP Process• Issued by HL7 as a SFM Fall 2009• RFP issued by OMG 2010• Preliminary submissions June 2010– Mayo– II4SM

• Final submissions due Feb 21, 2011– For March OMG meeting

CTS2

General Requirements• CTS Functionality (but not signatures)• Ontology versioning and incremental update• “Authoring”• Data binding model (value sets / ISO 11179)• Reasoning and inference

CTS2

Additional Drivers and Requirements• NCI/Mayo LexEVS compatibility• Semantic Web / Ontology community buy-in• BioPortal compatibility– RESTful compatible architecture

• Alignment w/ II4SM model– Reasoning– Z representation

• OMV alignment• API4KB Alignment• Addl: Phin VADS, HL7 MIF, IHE Implementations and

Profiles (SVS)

Approach

PIM – “Platform Independent Model”, mapped to multiple Platform Specific Models (PSMS):

• REST • SOA(p)• iRDF

Specification – combination of UML, text and Z

Challenges

What, exactly is a PIM?How do we create one model that aligns with

REST (our primary target), SOA(p), RDF minimalists and POJO?

No easy answers, but Z specification seems to help considerably

Other Challenges

LexEVS – built, runs and already incorporates a significant portion of what is in the requirements

• LexEVS (XML / POJO) to PIM is a non-trivial transformation

• Reproducible behavior is a non-trivial processDecision was made to build CTS2

implementation on top of LexEVS vs changing core API

RDF implementation pending in 2011 for NCBO

Before we get started

Specification approachUML / text / Z• (At the moment, Z is most current)• Text and UML follow (or not) at varying rates

Do I need to know Z to read it?– At the moment, it would help a lot but…– … the intent is that the text faithfully, clearly and

accurately reflects what is said in the Z

Other details

Z means LaTeX (more or less) • Your faithful narrator is not a LaTeX expert,

meaning that it tends to be odd, clumsy, etc.• … any assistance would be greatly appreciatedBrowsing and authoring access is available

online (!)

Compliance

Compliance

Resource orientation provides fine-grained implementation / compliance points

• Resource Axis – Which resources are represented by the service

• Functional Axis - What functionality the service provides

• Representational Axis – How the resources are represented

• Structural Detail – Structured [+ “semi”-structured + [RDF]]

ComplianceResource Axis

ComplianceResource Axis

Service provider can implement any combination of:

Code System – metadata about code system (ontology) purpose, provider, release cycle, etc.

(rdf:type skos:ConceptSystem or Owl:Ontology)Code System Version – metadata about a

collection of statements (ontology) . (rdf:type skos:ConceptSystem or Owl:Ontology)

ComplianceResource Axis (cont)

Entity – structured assertions about classes / individuals and/or predicates

. (rdf:type skos:Concept, owl:Class, owl:Individual, rdf:Predicate)

Association – metadata about a collection of statements about Entities

(rdf:type rdf:Statement where rdf:subject type Entity)

ComplianceResource Axis (cont)

Value Set – metadata about set of entity references

. (rdf:type iso11179:EnumeratedConceptDomain)

Value Set Definition – rules for constructing a value set

. (rdf:type ???)

Value Set Resolution Rule - rules for applying a value set definition in a particular context

. (rdf:type ???)

ComplianceResource Axis (cont)

Concept Domain – metadata about the scope, purpose, etc. of a data element concept

(rdf:type iso11179:DataElementConcept)

Concept Domain Binding – contextual association between a concept domain and a value set.

(rdf:type iso11179:DataElement)

ComplianceResource Axis (cont)

Mapping – metadata about a set of relationships between classes, roles and/or individuals in two or more ontologies

Mapping Version – collection of relationships for a mapping at a given point in time

(a) Need examples(b)Need mapping and mapping version for

public health reporting (CDC notifiable conditions) – Anthrax Lab tests (LOINC) and SCT Microorganism codes

ComplianceFunctional Axis

ComplianceFunctional Axis

For a given resource:• Get - return resource by identifier• Search / Filter – directories w/ constraints• Load / Export - from external sources and formats• Incremental Update – change sets• Authoring – construct change sets• History – change history of a resource• Service State – state of service at point in time• Resource Specific

ComplianceFunctional Axis (cont)

Resource Specific:• Code System Version– Latest / tagged version for code system– Lookup by entity

• Association– Reasoning Service– Graph retrieval and navigation

ComplianceFunctional Axis (cont)

Resource Specific:• Value Set Definition– Latest / tagged definition for given value set– Resolve Value Set– Membership Inquiry

ComplianceFunctional Axis (cont)

Resource Specific:• Mapping Version– What is mapped / not mapped– (Beginning of) rule based mapping

ComplianceRepresentation Axis

ComplianceRepresentation Axis

Resource Representation:• XML• JSON• RDF• (i)RDFFunctional Representation:• REST• SOAP• POJO

ComplianceRepresentation Axis

Still an outstanding issue on granularity• PIM is (more or less) agnostic when it comes

to granularity…• … invariants / preconditions / postconditions

are the same whether you lump or split the operations

• SOA / REST granularity can be choreographed• … so how far do we need to go?

ComplianceStructural Detail

Structural Detail

1) Traditional UML / XML Structure2) Collection of Structured Statements

- provenance, history, statement origin

3) (i)RDF- “cannonical” RDF rendering of statements w/o provenance, history

Status

Current Status

Specification is still undergoing significant change• Remaining faithful in spirit to the June submission• Beginning to incorporate II4SM functionality (but not

yet complete)Feb 21 deadline is still doable but very tight

Status

• Fundamental Model and Functionality remains consistent with first submission(s)

• Work continues on:– Refactoring and refinement: each community has

its own needs and “non-negotiables”– Naming: each community has its own names– Formal semantics: a precise specification is a lot of

work• For next 2-3 weeks, online resource will be a

“sausage factory”… then settling.

Notes

• Meaningful Use Vocabulary Task Force• USHIK – contact (who?)• DOA (Department of Agriculture)• UMLS services – check w/ Jim Case• VA • DoD• http://informatics.mayo.edu/cts2