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Microbiology Editorial Guidelines 

The current page will no longer provide the SNOMED CT Content Development Canadian Editorial Guidelines for Microbiology.

All implementers are requested to align to

the current SNOMED CT Editorial Guide

and follow the guidelines listed in the Observable Entity and Microbiology Test Results

English Generic Editorial Guidelines

Canada Health Infoway (Infoway) publishes English Generic Editorial Guidelines. These guidelines should be consulted, along with the SNOMED International Guidelines prior to creating and submitting any new content for submission to Infoway.

. These pages describe the National Standards Release Centre (NSRC) approach to applying the Editorial Guidelines from SNOMED International to create SNOMED CT concepts for Microbiology. This includes:

• H antigen
• Organism Naming conventions
• Serotypes

Microbiology References

Authoritative references recognized by SNOMED International

References are required when submitting requests for new concepts .

Here is the list of a few resources that SNOMED International considers when reviewing the changes applicable to the Organism hierarchy:

Bacteria:

• LPSN (http://www.bacterio.net/) --Site is in alignment and follows the ‘International Committee on Systematics of Prokaryotes’ (ICSP) (http://www.the-icsp.org/) recommendation as published by the International Journal of Systematic and Evolutionary Microbiology (https://www.microbiologyresearch.org/)
• DSMZ-Prokaryotic Nomenclature Up-to-date (https://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date.html)

Fungus:

• http://www.mycobank.org/
• http://www.indexfungorum.org/names/names.asp

Viruses:

• https://talk.ictvonline.org/taxonomy/ --requires review of additional scientific papers for concepts that are more specific than species

Parasites:

so that these concepts can be promoted internationally.

See section 8. References for a non-exhaustive list of references suggested by SNOMED International.

SNOMED Canadian Edition

If you cannot provide any reference from these recognized and authoritative sources, here is a list of some resources that may be considered when submitting requests for new concepts or for modifications applicable to the Organism hierarchy for publication only in the Canadian Edition of SNOMED CT. 

General: 

• https://www.uniprot.org/taxonomy/ 
• httpshttp://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/-- Although not an authoritative source, it will provide useful links to other sources. It is also used in UMLS as a QA source

General

• Integrated Taxonomic Information System (ITIS) -- ITIS is limited in coverage, but it is validated for those organisms it contains.

Organism Naming Conventions

• The SNOMED Editorial Guide includes naming conventions that apply to all SNOMED CT concepts. However, additional principles apply to the naming of concepts in the Organism hierarchy, and these differ from the general naming conventions, so it’s important to familiarize themselves with the detailed rules found in the Organism Naming Conventions in section of the Editorial Guide. (https://confluence.ihtsdotools.org/display/DOCEG/Organism+Naming+Conventions)
• When considering a name, the first task is to consider if the  whether the concept represents an organism or taxonomic group of organisms that has a scientific name in the Linnaean taxonomy e.g. Escherichia coli (organism) or Genus Escherichia coli (organism) or Family Enterbacteriaceae (organism) . 

• The non-Linnaean categories of organisms are reflected in SNOMED CT concepts which identifies a staining property, a physiological characteristic (that the organism requires oxygen) and a description of the organism’s morphology (that it is rod-shaped). These are among the properties used in a laboratory to determine the identity of a bacterial organism in a specimen, culture, or isolate. e.g Gram-negative aerobic rod (organism) or Deoxyribonucleic acid virus (organism) 

• The Editorial guide specifies the source listed above to be considered when determining an organisms current name.

Serotypes and Serogroup in Microbiology

A serotype or serovar is a distinct variation within a species of bacteria or virus or among the immune cells of different individuals. Microorganisms, viruses, or cells are classified together based on their cell surface antigens, allowing the epidemiologic classification of organisms to the subspecies level. Microorganisms of a given serotype are classified together based on "cell surface" antigens, allowing the epidemiological classification of organisms that is more specific than the species level. Antigens are surface proteins that based on its location on the organism are classified as types O, H and K. Serotype biology does vary with the organism category and includes the location of the antigens on the bacteria as well as the complexity and number of serotypes.

A group of serotypes with common antigens is called a serogroup or sometimes serocomplex. An example of this is the Salmonella enterica subsp. arizonae (organism) (ConceptID 397502001) which infects the human gut and is responsible for various diarrheal infections across the globe

• Browser/wwwtax.cgi
• Public Health Agency of Canada reported diseases published in "The Canada Communicable Disease Report"
• Organisms reported by provincial public health authorities
• National Microbiology Laboratory (NML Winnipeg) "National Microbiology Laboratory publications"