Medical and metrological vocabulary

Scope

Description of why and how concepts are traceable and defined by international vocabulary

Principle

All concepts must be defined by international nomenclature, ontology or terminology (Principles of NPU terminology)

Description

Sources to bodies of terms used with a particular technical application in medical, clinical laboratory and metrological fields (see Table of terminology references)

Example

A NPU definition can be defragmented into individual concepts

Reference

 

Concept field

Terminology

Identifiers

Homepages

Allergenes

Clinical and Laboratory Standards Institute – Approved Guideline I/LA20-A2 Clinical and Laboratory Standards Institute – Approved Guideline I/LA20-A2  (previously NCCLS) CLSI identifiers http://clsi.org/

Blood types

International Society of Blood Transfusion (ISBT 128) None http://www.isbtweb.org/

Certified Reference Material (CRM, preparations)

World Health Organization, International Biological Reference Preparations WHO Reference Preparation http://www.who.int/biologicals/reference_preparations/en/

Chemical substances (substances with low molecular weight)

Chemical Abstract Services (CAS)

Inchi system (IUPAC)

CAS registry (Inchi key (IUPAC))
  1. https://chem.nlm.nih.gov/chemidplus/
  2. https://www.ebi.ac.uk/chebi/
  3. https://pubchem.ncbi.nlm.nih.gov/search/#collection=compounds
  4. http://www.hmdb.ca/

Note: The chemical substances are termed according to the above homepages in that order. In practice, if the first homepage can’t identify or define the chemical substance, the chemical substance termed according to the next (if found).

Enzymes

International Union of Biochemistry and Molecular Biology Enzyme Committee

Note: Focus on protein function

Enzyme Commission (EC) www.expasy.org

Gene phenotypes

Mendelian Inheritance in Man OMIM database www.omim.org

General medical concepts, and substances without chemical definitions

Medical Subject Headings (MeSH)

NCI Thesaurus

MeSH Unique ID

NCI Thesaurus ID

https://meshb.nlm.nih.gov/#/fieldSearch

https://ncit.nci.nih.gov/ncitbrowser/

Note: Both references above can be used but the definitions should be scrutinized in both references. Selective choices (cherry picking) can appear.

Genomic DNA sequences

Locus Reference Genomic LRG http://www.lrg-sequence.org/

Human genes

HUGO Gene Nomenclature Committee HGNC gendatabase www.genenames.org

Internal definitions

Established terms that do not exist in any international terminology references QU ID

http://www.labterm.dk/Enterprise%20Portal/NPU_download.aspx

(Download the CSV-file termed: ‘English version: All concept elements in use this date’)

International Nonproprietary Name (INN)

International Nonproprietary Nameof medicines None https://www.who.int/medicines/services/inn/en/

Living organisms

Taxonomy for organisms NCBI ID www.ncbi.nlm.nih.gov/taxonomy

kind-of-property

IFCC-IUPAC

None

”Silver book” [2]

DynamicNPUmanual

Metrological terms

International vocabulary of metrology None https://www.bipm.org/en/publications/guides/vim.html

Measurement units

Bureau International des Poids et Mesures None www.bipm.org

Prokaryotic organisms

List of prokaryotic names with standing nomenclature (LPSN) NCBI ID

http://www.bacterio.net/index.html

Note: For administration purposes, the NCBI taxonomy ID is chosen.

Proteins

Universal Protein Resource (UniProt)

Note: Focus on protein structure

UP ID

https://www.uniprot.org/

Note: Name of protein with a catalytic property use above enzyme nomenclature

Virus

International Commitee on Taxonomy of Viruses (ICTV) NCBI ID

https://talk.ictvonline.org/

Note: For administration purposes, the NCBI taxonomy ID is chosen.

Scope

 

Principle

 

Description

The terms and their corresponding identifiers can be downloaded: http://www.labterm.dk/Enterprise%20Portal/NPU_download.aspx

(Download the CSV-file termed: ‘English version: All concept elements in use this date’). Each term has a unique NPU term identifier, e.g. arbitrary concentration has QU50081 as identifier.

Example

 

 

Reference

 

Date

Subjects

Notes

Examples

  Glycoproteins and glycolipids At this point, there are no stable and international terminology references for these two subjects  
  Avoiding duplicate terms (two or more terms that have same definitions) The threshold between similar terminology references can be discrete for a given term. Establishing a term in the NPU terminology must be used with caution to avoid duplicate terms.

Aspartate transaminase (Identifier E.C. 2.6.1.1) is termed in Expasy and Aspartate transaminase, cytoplasmatic in UNIPROT (P17174).

Note: In this case, the first term was chosen.

  Criteria to the terminology reference

Terminology references are chose by the following criteria:

  • Stable organisation behind the terminology
  • Online available
  • Internationally approved
  • Well defined content

Note: C-NPU approves or disapproves a potential terminology reference in interest.

 
  Terms with internal definitions To establish a term that is not identified in any terminology references, terms with internal definitions may be neccessary to establish, using the vocabulary of the NPU terminology. This should be the last resort. ‘Zolpidem/Creatininium’ is defined as: “the  coefficient of the quantity of Zolpidem (CAS82626-48-0) relative to the quantity of Creatininium (CAS60-27-5)”
  Inchi system IUPAC’s Inchi system is  under trial.