References

Detail for RxNorm

Class

Name or Properties

Definition

Occurrence Constraint (static: defined by OMV)

RxNorm

Comments

Ontology

URI

The URI of the ontology which is described by this metadata. It serves as a logical identifier and is not necessarily the physical location.

required

http://www.nlm.nih.gov/research/umls/rxnorm/

None

Ontology

name

The name by which an ontology is known

required

RxNorm

None

Ontology

acronym

A short name by which an ontology is formally known

optional

RxNorm

None

Ontology

description

Free text description of an ontology

required

RxNorm, a standardized nomenclature for clinical drugs and drug delivery devices, is produced by the National Library of Medicine (NLM). In this context, a clinical drug is a pharmaceutical product given to (or taken by) a patient with a therapeutic or diagnostic intent. A drug delivery device is a pack that contains multiple clinical drugs or clinical drugs designed to be administered in a specified sequence. In RxNorm, the name of a clinical drug combines its ingredients, strengths, and/or form.

While ingredient and strength have straightforward meanings, clarification of what is meant by form may be needed. In RxNorm, the form is the physical form in which the drug is administered or is specified to be administered in a prescription or order. The RxNorm clinical drug name does not refer to the size of the package, the form in which the product was manufactured, its form when it arrived at the dispensary or the intended route.

RxNorm's standard names for clinical drugs and drug delivery devices are connected to the varying names of drugs present in many different controlled vocabularies within the Unified Medical Language System (UMLS) Metathesaurus, including those in commercially available drug information sources. These connections are intended to facilitate interoperability among the computerized systems that record or process data dealing with clinical drugs.

None

Ontology

documentation

URL for further documentation

optional

http://www.nlm.nih.gov/research/umls/rxnorm/docs/index.html

None

Ontology

reference

List of bibliographic references describing the ontology and its applications

optional

http://www.nlm.nih.gov/research/umls/rxnorm/RxNorm.pdf

None

Ontology

notes

Additional information about the ontology that is not included somewhere else (e.g. information that you do not want to include in the documentation)

optional

---

This is where we may need to disambiguate true ontologies from non-ontologies. We also need guidelines on explicit definitions to guide classification (i.e. what is a non-ontology?)

Ontology

keywords

List of keywords related to the ontology

optional

Abstracting and Indexing as Topic, Algorithms, Ambulatory Care Facilities, Anesthesiology, Bibliometrics, Biomedical Research, Community Health Centers, Computer Communication Networks, Data Collection, Decision Support Systems: Clinical, Decision Support Techniques, Dictionaries: Pharmaceutic, Dietary Supplements, Drug Hypersensitivity, Drug Information Services, Drug Labeling, Drug Therapy, Drug Utilization Review, Electronic Prescribing, Epidemiologic Studies, Expert Testimony, Forms and Records Control, Government Regulation, Hospitals: Military, Humans, Information Management, Information Storage and Retrieval, Information Systems, International Classification of Diseases, International Cooperation, Internet, Knowledge Bases,Humans, Management Audit, Medical Audit, Medical Informatics, Medical Informatics Applications, Medical Order Entry Systems, Medical Order Entry Systems, Medical Record Linkage, Medical Records Systems: Computerized, Medically Uninsured, Medication Systems: Hospital, Natural Language Processing, Pharmaceutical Preparations, Pharmacy, Pharmacy Administration, Practice Guidelines as Topic, PubMed, Quality Assurance: Health Care, Safety Management, Semantics, Sensitivity and Specificity, Software, Software Design, Surgery Department: Hospital, Systems Integration, Tennessee, Terminology as Topic, Total Quality Management, Unified Medical Language System, United States, United States Department of Veterans Affairs, United States Food and Drug Administration, United States Government Agencies, User-Computer Interface, Virginia, Vocabulary: Controlled

We need to discuss a canonical taxonomy for keywords.
One suggestion is to use MeSH, similar to MeSH integration as topics such as HL7's InfoButtons (~ ST).

I derived these keywords by performing a literature search in PubMed, retrieving 18 articles, parsing out the keywords from the PubMed file, sorting and deduplicating using regular expressions (~ST).

An interesting exercise. Since the articles vary in their focus on RxNorm, many (most?) of these keywords are not relevant. To review further methods for keyword curation.

Ontology

Status

The tracking information for the contents of the ontology

---

---

None

Ontology

creationDate

Date when the ontology was initially created

required

2001 (see http://www.nlm.nih.gov/research/umls/rxnorm/history.html)

None

Ontology

modificationDate

Date of the last modification made to the ontology

optional

20100607

None

Ontology

naturalLanguage

The language of the content of the ontology (i.e. English, German, etc.)

---

English

None

Ontology

numberOfAxioms

---

---

n/a

None

Ontology

hasContributor

Contributors to the creation of the ontology

---

RxNorm has source vocabularies including:
SAB (Source Name), GS (Gold Standard Alchemy), MDDB (Medi-Span Master Drug Data Base), MMSL (Multum MediSource Lexicon), MMX (Micromedex DRUGDEX), MSH (Medical Subject Headings ;MeSH.), MTHFDA (FDA National Drug Code Directory), MTHSPL (FDA Structured Product Labels), NDDF (First DataBank NDDF Plus Source Vocabulary), NDFRT (Veterans Health Administration National Drug File - Reference Terminology), SNOMED CT (SNOMED Clinical Terms ;drug information.), VANDF (Veterans Health Administration National Drug File

None

Ontology

hasCreator

---

---

National Library of Medicine (NLM)

None

Ontology

usedOntologyEngineeringTool

Information about the tool used to create the ontology

optional

UMLS Metathesaurus (a source and a subset of the Metathesaurus)

None

Ontology

usedOntologyEngineeringMethodology

Information about the method model used to create the ontology

optional

The scope of RxNorm is determined by the combined scope of its source vocabularies. Many relationships (primarily synonymous), concept attributes, and some concept names are added by the NLM during the creation of RxNorm forms. The concepts themselves are derived from the names provided by the source vocabularies. RxNorm reflects and preserves the meanings, concept names, and relationships from its source vocabularies in the same way that the Metathesaurus preserves content and meaning.(reference to UMLS Reference Manual)

None

Ontology

conformsToKnowledgeRepresentationParadigm

Information about the paradigm model used to create the ontology

optional

Rich Release Format (RRF)

None

Ontology

endorsedBy

The parties (i.e. organizations, people) that have expressed support or approval of this ontology

optional

 

None

Ontology

hasDomain

The subject domain of the ontology

optional

Clinical drugs and drug delivery devices
Per NLM:
"Clinical Drug" is a "pharmaceutical product given to (or taken by) a patient with a therapeutic or diagnostic intent"

"Drug Delivery Device" is a "pack that contains multiple clinical drugs or clinical drugs designed to be administered in a specified sequence"

A quick perusal through MeSH yielded a very large subset of drug terms. Used the NLM overview page to classify the domain here (~ ST)

Ontology

isOfType

---

optional

terminology?

None

Ontology

designedForOntologyTask

The purpose for which the ontology was originally designed
Annotation Task : the ontology is used as a controlled vocabulary to annotate resources and data. This task includes the usage of a semantically rich ontology for representing arbitrarily complex annotation statements on these resources. The task can be performed manually or (semi-)automatically.

ConfigurationTask : the ontology is designed to provide a controlled and unambiguous means to represent valid configuration profiles in application systems. As the aim of the ontology is to support the operationalization of particular system-related pro- cesses; this task is performed automatically in that the ontology is processed in an automatic manner by means of reasoners or APIs.

FilteringTask : the task describes at a very general level how ontologies are applied to refine the solution space of a certain problem, such as information retrieval or personalization. The task is targeted at being performed semi-automatically or au- tomatically.

IndexingTask : in this scenario, the goal of the ontology is to provide a clearly defined classification and browsing structure for the information items in a repository. Again, the task can be performed manually by domain experts or as part of an application in an automatic or semi-automatic way.

Integration Task : the task characterizes how ontologies provide an integrating environ- ment, an inter-lingua, for information repositories or software tools. In this scenario the ontology is applied (semi-)automatically to merge between heterogeneous data pools in the same or in adjacent domains.

Matching Task : the goal of matching is to establish links between semantically similar data items in information repositories. In contrast to the previous task, matching does not include the production of a shared final schema/ontology as a result of aggregating the matched source elements to common elements. W.r.t. the automa- tization level the range varies from manual to fully-automatical execution.

Mediation Task : the ontology is built to reduce the ambiguities between communicating human or machine agents. It can act as a normative model which formally and clearly defines the meaning of the terms employed in agent interactions. In the context of programmed agents, the task is envisioned to be performed automatically.

Query FormulationTask : the ontology is used in information retrieval settings as a controlled vocabulary for representing user queries. Usually the task is performed au- tomatically in that the concepts of the ontology is are listed in a query formulation front-end in order to allow users to specifies their queries.

QueryRewritingTask : complementary to the query formulation dimension, this task applies ontologies to semantically optimize query expressions by means of the do- main knowledge (constraints, subsumption relations etc.) The task can be inter- preted as a particular art of filtering information. The task is performed automati- cally; however, it assumes the availability of patterns describing the transformations at query level.

PersonalizationTask : the ontology is used mainly for providing personalized access to information resources. Individual user preferences w.r.t. particular application set- tings are formally specified by means of an ontology, which, in conjunction with appropriate reasoning services, can be directly integrated to a personalization component for filtering purposes. The usage of
be carried out in various forms, from a direct involvement of the user who manually specifies ontological concepts which optimally describe his preferences, to the ontological modelling of user profiles.

SearchTask : the task characterizes how ontologies are used to refine common keyword- based search algorithms using domain knowledge in form of subsumption relations. Ontology-driven search is usually performed automatically by means of reasoning services handling particular aspects of an ontology representation language.

optional

Indexing, Integration, Matching, Query Formulation, Query Writing, Search

None

Ontology

hasFormalityLevel

Level of formality of the ontology
catalog, glossary, thesauri, taxonomy, frames and properties, value restrictions, disjointness, general logic constraints

optional

taxonomy

None

Ontology

knownUsage

The applications where the ontology is being used

optional

---

None

Ontology

hasOntologyLanguage

The ontology language

required

Rich Release Format

None

Ontology

hasOntologySyntax

The presentation syntax for the ontology language

---

---

None

Ontology

resourceLocator

The location where the ontology can be found. It should be accessible via a URL. It can be the same as the value for the URI property.

required

http://www.nlm.nih.gov/research/umls/rxnorm/

None

Ontology

version

The version information of the ontology

---

Versions are bound to UMLS Metathesaurus releases
http://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html
Current version is:
06/07/2010 | Version 2010-3

None

Ontology

hasLicense

Underlying license model

---

UMLS Metathesaurus License
http://wwwcf.nlm.nih.gov/umlslicense/snomed/license.cfm

This element does not parse out the license from a canonical source of the license description

Ontology

useImports

References another ontology containing definitions, whose meaning is considered to be part of he meaning of the ontology described by this ontology metadata instance.

---

RxNorm has source vocabularies including:
SAB (Source Name), GS (Gold Standard Alchemy), MDDB (Medi-Span Master Drug Data Base), MMSL (Multum MediSource Lexicon), MMX (Micromedex DRUGDEX), MSH (Medical Subject Headings ;MeSH.), MTHFDA (FDA National Drug Code Directory), MTHSPL (FDA Structured Product Labels), NDDF (First DataBank NDDF Plus Source Vocabulary), NDFRT (Veterans Health Administration National Drug File - Reference Terminology), SNOMED CT (SNOMED Clinical Terms ;drug information.), VANDF (Veterans Health Administration National Drug File

None

Ontology

hasPriorVersion

Contains a reference to another ontology metadata instance

---

http://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html

None

Ontology

isBackwardCompatibleWith

The ontology metadata instance which describes an ontology htat is a compatible prior version of the ontology described by this ontology metadata instance.

---

---

None

Ontology

IsCompatibleWith

The described ontology is a later version of the ontology described by the metadata specified, but is not backward compatible with it. It can be used to explicitly state that ontology cannot upgrade to use the new version without checking whether changes are required

optional

UMLS Metathesaurus

None

Ontology

numberOfClasses

Number of classes in the ontology

---

---

None

Ontology

numberOfProperties

Number of properties in the ontology

---

---

None

Ontology

numberOfIndividuals

Number of individuals in the ontology

---

---

None

OntologyType

 

This class categorizes ontologies by subsuming types of ontologies according to well-known classifications in the Ontology Engineering Literature (see Gomez-Perez, M. et al, in Ontological Engineering Springer, 2003)
Upper Level, Core, Domain, Task, Application

---

Domain?

None

OntologyType

name

The name by which an ontology type is formally known

---

Domain

None

OntologyType

acronym

A short name by which an ontology type is formally known

---

n/a

None

OntologyType

description

---

---

---

None

OntologyType

documentation

---

---

---

None

OntologyType

definedBy

---

---

---

None

License Model

---

A license model describing the usage conditions for an ontolog. NB: Identified licenses include Academic Free License (AFL), Common Public License (CPL), Lesser General Public License (LGPL), Open Software License (OSL), General Public License (GPL), Modified BSD License (mBSD), IBM Public License (IBM PL), Apple Public Source License (APSL), INTEL Open Source License (INTEL OSL), Mozilla Public License (MPL) Creative Commons Licenses (CCL) (Attribution (by) - Attribution-NoDerivs (by-nd) - Attribution-NonCommercial-NoDerivs (by-nc-nd) - Attribution-NonCommercial (by-nc) - Attribution-Noncommercial-Share Alike (by-nc-sa) - Attribution-ShareAlike (by-sa)), but can be extended to any.

---

RxNorm is based on the UMLS Metathesaurus License

http://wwwcf.nlm.nih.gov/umlslicense/snomed/license.cfm
Last updated: 5 February 2010
First published: 01 December 2004
Metadata| Permanence level: Permanence Not Guaranteed

None

License Mode

name

---

---

UMLS Metathesaurus License

None

License Mode

acronym

---

---

n/a

None

License Mode

description

---

---

---

Note: SNOMED license reference

License Mode

documentation

---

---

http://wwwcf.nlm.nih.gov/umlslicense/snomed/license.cfm

None

License Mode

specifiedBy

---

---

---

None

Ontology Engineering Methodology

 

---

---

---

None

Ontology Engineering Methodology

name

---

---

---

None

Ontology Engineering Methodology

acronym

---

---

---

None

Ontology Engineering Methodology

description

---

---

---

None

Ontology Engineering Methodology

documentation

---

---

---

None

Ontology Engineering Methodology

developedBy

---

---

---

None

Ontology Engineering Tool

---

A tool used to create the ontology

---

Would UMLS Metamorphosys apply here?

None

Ontology Engineering Tool

name

---

---

---

None

Ontology Engineering Tool

acronym

---

---

---

None

Ontology Engineering Tool

description

---

---

---

None

Ontology Engineering Tool

documentation

---

---

---

None

Ontology Engineering Tool

developedBy

---

---

---

None

Ontology Syntax

---

Individuals of the class OntologySyntax refers to well-known ontology syntax standards, such as: OWL-XML, or RDF/XML. The class can be extended to support additional classifications.

---

---

None

Ontology Syntax

name

---

---

---

None

Ontology Syntax

acronym

---

---

---

None

Ontology Syntax

description

---

---

---

None

Ontology Syntax

documentation

---

---

---

None

Ontology Syntax

developedBy

---

---

---

None

Ontology Language

---

Individuals of the class OntologyLanguage refer to well-known ontology language standards, such as:OWL, OWL-DL, OWL-Lite, OWL-Full, DAML-OIL, RDF(S). The class can be extended to support additional classifications.

---

---

None

Ontology Language

name

---

---

---

None

Ontology Language

acronym

---

---

---

None

Ontology Language

description

---

---

---

None

Ontology Language

documentation

---

---

---

None

Ontology Language

developedBy

---

---

---

None

Ontology Language

supportsRepresentationParadigm

The representation paradigm supported by the ontology language

---

---

None

Ontology Language

hasSyntax

The syntactical alternatives of the language

---

---

None

Knowledge Representation Paradigm

---

In this version we foresee two main classes of Knowledge Representation Paradigms: Description Logics, and Frames

--

---

None

Knowledge Representation Paradigm

name

---

---

---

None

Knowledge Representation Paradigm

acronym

---

---

---

None

Knowledge Representation Paradigm

description

---

---

---

None

Knowledge Representation Paradigm

documentation

---

---

---

None

Knowledge Representation Paradigm

specifiedBy

---

---

---

None

Formality Level

---

The pre-defined values for the formality level are based on the work presented in [8], which classifies ontologies in a spectrum of definitions according to the detail in their specification as: catalog, glossary, thesauri, taxonomy, frames and properties, value re- strictions, disjointness, general logic constraints. (See The Role of Frame Based Representation on the Semantic Web , PDF ~ ST)

---

---

None

Formality Level

name

---

---

---

None

Formality Level

description

---

---

---

None

Formality Level

---

---

---

---

None

Ontology Task

---

---

---

---

None

Ontology Task

taskName

---

---

---

None

Ontology Task

acronym

---

---

---

None

Ontology Task

description

---

---

---

None

Ontology Task

documentation

---

---

---

None

Ontology Domain

---

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. Only this way it can ensured that meaningful information about the relation of the domains of two separate ontologies can be deduced

---

---

None

Ontology Domain

URI

---

---

---

None

Ontology Domain

name

---

---

---

None

Ontology Domain

isSubDomainOf

---

---

---

None

Party

---

A party is a person or organization

---

---

None

Party

isLocatedAt

The geographical location of a party

---

---

None

Party

develops

An entity developed by a party

---

---

None

Party

specifies

Provenance information

---

---

None

Party

defines

---

---

---

None

Party

endorses

---

---

---

None

Party

hasAffiliatedParty

Another party that is affiliated with this party

---

---

None

Party

CreatesOntology

An ontology created by a party

---

---

None

Party

contributesToOntology

An ontology a party made contributions to

---

---

None

Person

 

Consider this in context of what is also represented in the FOAF Vocabulary Specification  ~ ST

---

There are multiple contacts:
Stuart Nelson
Simon Lieu
Wei Ma
Robin Moore
Vikraman Ganesan

There are multiple contacts. Need to describe this as a collection, cardinality and perhaps a subset of metadata to classify a role

Person

lastName

---

---

Nelson

None

Person

firstName

---

---

Stuart

None

Person

email

---

---

rxnorminfo@nlm.nih.gov

None

Person

phoneNumber

---

---

---

None

Person

faxNumber

---

---

---

None

Person

isContactPerson

Instance is contact person of an organization

---

True

Is this boolean?

Organization

---

---

---

---

None

Organization

name

---

---

National Library of Medicine

None

Organization

acronym

---

---

NLM

None

Organization

hasContactPerson

---

---

Stuart Nelson, MD, FACP

None

Location

---

The geographical location of a party. To keep things simple we use only DatatypeProperties instead of introducing classes for country, street, etc

---

---

None

Location

state

---

---

---

None

Location

country

---

---

---

None

Location

city

---

---

---

None

Location

street

---

---

---

None

NCBO Extensions

NB: This is a start of my attempt to populate BioPortal Metadata. Will need Natasha's help to complete (~ Stuart)

Class

Properties

Definition

Occurence/Constraint

LOINC, SNOMED-CT or NCI-T values

Comments

OntologyView (subclass of Ontology)

---

---

---

---

---

Party

Organization

---

---

---

---

Party

Person

---

---

---

---

OntologyGroup

urlHomepage

---

---

---

---

OntologyGroup

id

---

---

---

---

BioPortalUser

username

---

---

---

---

BioPortalUser

password

---

---

---

---

BioPortalUser

id

---

---

---

---

BioPortalUser

timestampCreation

---

---

---

---

BioPortalUserRole

id

---

---

---

---

EvaluationDimension

textualReview

---

---

---

---

EvaluationDimension

reviewOnDimension

---

---

---

---

EvaluationDimension

rating

---

---

---

---

ViewGenerationEngine

supportsViewDefinitionLanguage

---

---

---

---

ViewGenerationEngine

viewDefinitionLanguage

---

---

---

---

OntologyView

viewDefinition

---

---

---

---

Project

hasContactEmail

---

---

---

---

Project

hasContactName

---

---

---

---

VirtualOntology

virtualURI

---

---

---

---

VirtualOntology

id

---

---

---

---

VirtualOntology

isManual

---

---

---

---

VirtualOntology

oboFoundryId

---

---

---

---

VirtualOntology

hasVersions

---

---

---

---

VirtualOntology

currentVersion

---

---

---

---

VirtualView

---

---

---

---

---

relations

administers

---

---

---

---

relations

administeredBy

---

---

---

---

relations

supportedByViewGenerationEngine

---

---

---

---

relations

reviewOnDimension

---

---

---

---

relations

viewDefinitionLangauge

---

---

---

---

relations

belongsToGroup

---

---

---

---

Comments

Release Notes

For example, RxNorm updates releases, but uncertain about mechanism to identify most recent. A similar construct to NCBO's ontology version may be helpful for collections of artifacts that are updated, such as release notes, manuals/documentation, etc. Example:
Most recent: http://www.nlm.nih.gov/research/umls/rxnorm/docs/2010/rxnorm_releasenotes_full_06072010.html
General: http://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html

(ST 23 June 2010)

License

There is a single metadata element for license. Some licenses are certified and reused, but have versions and a canonical source (e.g. OSI approved open source licenses or Creative Commons licenses). Consider additional constructs for a canonical license URI, version, and any restrictions.

(ST 23 June 2010)

Ontology Domain

Found this challenging to populate. More than one domain applies here. Also, while there may be several, should this be constrained to the "best choice" or most appropriate representation?

(ST 23 June 2010)

Keywords

Consider supporting vocabularies to classify or annotate for keywords. In this case, I performed a literature search (PubMed) and pulled the keyword information from each article (18 total), sorted and removed duplicated to come up with a NLM-derived keyword list. Candidate vocabularies for classification including Medical Subject Headings (MeSH), similar to Infobuttons (HL7) use of MeSH for topics.

(ST 23 June 2010)

Ontology-Centric Metadata Often Poor Fit

Much of the metadata is targeted directly at true ontologies leading to a poor-fit for non-ontology knowledge representation artifacts (glossaries, taxonomies, etc.) and especially to more artifacts considerably more distant or dissimilar (e.g. specifications, "standards"), etc.

Disambiguation or Dublin-Core (and other) Metadata

I anticipate potential confusion by users of the subset of metadata used to classify those organizations and individuals that create and curate ontologies. Specifically these include "creator", "contributor", "author", "editor", etc. In Dublin Core parlance, the "creator" of this document is the "Vocabulary Representation WG" or "VCDE-WS" and a "Contributor" would be "Stuart Turner".

Domains

Should discuss creation of a set of values for "domain" that is sufficiently granular and expressive for use by the three organizations.

Task

OntologyTask, like domain, needs discussion of curation of a set of values that are sufficiently granular and expressive for use by all interested parties

Ontology Engineering Tool

Besides descriptive metadata, it would be beneficial to support community discourse around tooling, including issues, workarounds, features or other related information. Tooling (access, curation or editing, browsing, versioning, mapping, integration and other features) is especially important here. In light of this, is the tooling metadata sufficient for our use case(s)?