In the SemanticWeb, URIs are used to support a marketplace of terms.
In DTS (#268), all namespaces are either by subscription or local. There is no concept of a marketplace, of terminologies, from afternoon-hack to small workgroup product to multi-site collaboration to commercial product or open standard. To be fair, that is what it says on the tin:
Apelon DTS integrates standard vocabulary, including local enhancements, into an enterprise healthcare-computing environment. -- DTS Server Guide
And like i2b2, there are no URIs for concepts/terms, unfortunately. I think I explained why that's important in my 2009 project report; if not, I should find a good written argument. If nothing else, it's a backbone concept in OWL, a W3C standard with a lot of application in biomedical informatics:
Key bio-medical ontologies, such as SNOMED-CT and the NCI thesaurus migrated to OWL and to an OWL based toolchain, allowing them to move from proprietory[sic] languages and their vender[sic] locked in toolchains.
-- OWL 2: A Medical Informatics Perspective, Bijan Parsia October 4, 2009
FishingVisit discussion
Major Vocabularies
Jim Campbell (Nebraska) said NCVHS is an important set of guidelines.
some of this is from memory; verification/citation in progress
see also HERON#TerminologyMapping
| Domain | Vocabulary | Usage/Structure | Governance | License |
| Problems/Diagnoses | ||||
| SNOMED-CT | clinical terminology... | CAP (was NIH?) | free for research | |
| ICD-9 | diagnoses for billing | published by the World Health Organization (WHO) | Non-commercial research license | |
| Procedures | ||||
| CPT | "medical nomenclature used to report medical procedures and services under public and private health insurance programs" | maintained by the American Medical Association | "The AMA is committed to making CPT widely available at low cost." | |
| Labs | ||||
| LOINC | "laboratory and other clinical observations" | "Regenstrief Institute maintains the LOINC database" | royalty free re-distrubtion; limitations on derivative works | |
| Medications | ||||
| RxNorm | "clinical drugs and drug delivery devices" | part of UMLS | ||
| NDFRT | "NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model." | "The National Drug File - Reference Terminology (NDF-RT) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF-RT is updated monthly. " | Part of UMLS | |
| NCI Thesaurus | "clinical care, translational and basic research, and public information and administrative activities" | "A Service of the National Cancer Institute" | ||
| FDB | First Databank (Hearst) | proprietary | ||
| literature indexing | ||||
| MeSH | pubmed | |||
| Terminology Alignment | ||||
| UMLS | many controlled vocabularies in the biomedical sciences | maintained by the US National Library of Medicine | free for research |
hope to clean this up a bit... caregraf has nice browsers... http://schemes.caregraf.info/loinc#!14747-0 this one is cool too... http://terminologie.nictiz.nl/snomed
RRF UMLS Data Format
Metathesaurus - Rich Release Format (RRF)
ICD-11 in OWL
- Using Semantic Web in ICD-11: Three Years Down the Road
Tania Tudorache, Csongor I. Nyulas, Natalya F. Noy, Mark A. Musen
Stanford Center for Biomedical Informatics Research, Stanford University, USA
ISWC 2013
NCI Thesaurus in OWL
A caBIG page on the NCI Thesaurus says "The NCI Thesaurus is authored using the open-source Protege editor. On a monthly basis the Thesaurus is exported as an OWL file for publication." ooh! EVS Downloads says "EVS encourages you to begin using NCI Thesaurus in the Web Ontology Language (OWL). " And lo: Thesaurus.owl
SNOMED-CT in OWL
Where are the SNOMED-in-OWL bits? Not clear that they're published, but see:
Unlocking SNOMED-CT for the uninitiated
SNOMED CT, even when presented in the more user-friendly Manchester OWL syntax, can be impenetrable to the uninitiated. To address this problem, we have developed a system (named OntoVerbal?) that automatically translates SNOMED CT concepts/classes into natural language text. We invite you to help us test the system by participating in a short (20 min) experiment that involves reading 10 such texts and translating them back into the corresponding OWL.
Ontology/Concept Mapping
Possible tool:
The CTSA Health Ontology Mapper (HOM) is an open source general purpose instance mapper running as an i2b2 cell designed for academic research and hospital environments. It can convert locally obtained data (which may not be encoded using any nationally recognized standard format) into standard ontologies as defined by the IEC111-79 data model format
