Microbiology Editorial Guidelines
The current pages form the SNOMED page will no longer provide the SNOMED CT Content Development Canadian Editorial Guidelines for Microbiology. They have been reviewed against the latest version of the SNOMED International Editorial Guidelines to ensure alignment between the guidelines. These pages describe Infoway’s 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 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
- SerotypesGuidelines currently being followed:
- Guidelines that have been resolved and approved by SNOMED International Guidelines that are still under discussion at SNOMED International
Microbiology References
for submissionsEnglish Generic Editorial Guidelines
Canada Health Infoway (Infoway) publishes English Generic Editorial Guidelines. These guidelines should be consulted, along with the guidelines in the following pages prior to creating any new content for submission to Infoway.
Implementers should be familiar with the SNOMED International Guidelines prior to creating submissions for new content.
Authoritative references recognized by SNOMED International
Microbiology References
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:
Viruses:
- http://www.ictvonline.org/virusTaxonomy.asp--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/
- https: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.
Impacting Editorial Guidelines
In order to provide input to SNOMED International regarding the development of Microbiology Editorial Guidelines, submitters must first register with SNOMED International Confluence. (https://confluence.ihtsdotools.org/display/ILS/Confluence+User+Accounts)
Once the Confluence account has been created, submitters must then request to join a specific project they want to follow or provide input to. The Micro Editorial Guidelines project ended on Dec 15, 2014.
- Find the project you are looking for under the ‘All Projects’ tab
- Click on the project to open it up
- On the left side will be a ‘Join this project’ button, click it
- Once the request is approved, submitters will have access to the files and be notified of any news or meetings
- 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"