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.
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 (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.
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.
Authoring E Coli Serogroup for H
Conventional Escherichia coli (E. coli) O:H serotyping by agglutination of somatic and flagellar antigens with the use of anti - E. Coli polyclonal antiserum is time-consuming, expensive, and available only in a small number of reference laboratories. When reporting the H antigen, it should be remembered that the O antigen is always present. In Canada, it is only a few that have reported it over the years untyped or untypable O antigens. For all organisms, the flagellar has to have the somatic.
For the Ecoli with H typed we have examples like Escherichia coli serotype O7: H18, where the parent is
458090002 |Escherichia coli serogroup O7 (organism)| Parent
458099001 |Escherichia coli serotype O7: H18 (organism)| Child
For E Coli where the O antigen is not typed or was unable to be typed, the guidance is to use E coli serogroup O undetermined: H
Escherichia coli serogroup O undetermined: H (organism), indicate that the O is textual as undetermined as it is not known
Escherichia coli serogroup O (organism)| Parent
• E coli serogroup O undetermined: H (Child)
o Escherichia coli serogroup O undetermined:H19 (organism) Child