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. These pages describe Infoway’s approach to applying the Editorial Guidelines from SNOMED International to create SNOMED CT concepts for Microbiology. This includes:
Microbiology References
Authoritative references recognized by SNOMED International are required when submitting requests for new concepts
SNOMED International
For content that meet the International inclusion criteria, 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:
Viruses:
- https://talk.ictvonline.org/taxonomy/ --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.
- Catalogue of Life is the result of cooperation between ITIS (https://www.itis.gov) and Species 2000 (https://www.sp2000.org/). Please note, Catalogue of Life may not be up to date for all areas. For bacteria, fungus, and virus, consult resources noted above as primary references.
- International Code of Zoological Nomenclature (ICZN)
- International Code of Nomenclature for algae, fungi, and plants (IAPT) https://www.iapt-taxon.org/nomen/main.php
- World Checklist of Selected Plant Families
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
SNOMED Canadian Edition
For content that meet the only National inclusion criteria, here is the list of a few resources that is suitable for SNOMED Canadian Edition considers when reviewing the changes applicable to the Organism hierarchy. These references are suitable when a request does not meet the inclusion criteria for submission for SNOMED International.
General:
- https://www.uniprot.org/taxonomy/
- https://www.ncbi.nlm.nih.gov/Taxonomy/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"