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Medical and metrological vocabulary - Dynamic NPU Manual

Medical and metrological vocabulary

by Mikkel | Feb 6, 2020 | NPU Concept model, General rules and principles

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))	https://pubchem.ncbi.nlm.nih.gov/search/#collection=compounds https://www.ebi.ac.uk/chebi/ 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.