Microbiology

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.

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 (http://ijs.sgmjournals.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:

• http://www.ictvonline.org/virusTaxonomy.asp--requires review of additional scientific papers for concepts that are more specific than species

Parasites:

• http://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.