Skip to end of metadata
Go to start of metadata

7.12.1 FSN 

    • The fully specified name of organism concept classes that are officially recognized Linnaean taxonomic classes, (other than species), will include a designation of rank. Specifically, those Linnaean classes involved include but may not be limited to Phylum, Order, Suborder, Class, Family, Genus, and subspecies. 
    • Properly constructed FSN terms are composed of the single word term indicating the taxonomic rank + the recognized name of that rank + hierarchy designator e.g., 106544002 | Family Enterobacteriaceae (organism).

The convention is not applied to a concept that merely refers to a rank: e.g., 113727004 | Vancomycin resistant Enterococcus (organism) is correct because it refers to a subclass of the genus (e.g., Enterococcus species that are resistant).   "Vancomycin resistant Genus Enterococcus" would not be correct.

7.12.2 Organism subspecies descriptions

Fully specified names of organism subspecies descriptions should use the word "subspecies" and not an abbreviation of same, e.g. Pelecanus occidentalis subspecies californicus

7.12.2.1 Superkingdom bacteria

Official names of subspecies in the Superkingdom bacteria include the abbreviation subsp. The list of synonyms for subspecies should include one description that is the official name of the class, e.g. Aeromonas salmonicida subsp. pectinolytica.

7.12.3 Organism class variants

Fully specified names of organism classes that are variants (of their superclass) may include the terms “variant,”  “biovar”, “serovar”, and “pathovar.” An example is Brucella suis biovar 4 (organism). Other abbreviations “var,” “var.”, “sv”, “sv.”, “bv”, “bv.”, “pv”, “pv.”  should not be used in the FSN.

7.12.3.1 Allowable abbreviations

Where the abbreviation is part of the official name, the list of synonyms should include one description that is the official name with the appropriate abbreviation.

7.12.3.2 Salmonella serotype nomenclature

The binomial format for representing an organism species includes capitalizing the genus name and beginning the species name with a lower case letter, e.g. Brucella abortus. Salmonella serotypes have a quadrinomial format of "Genus species subspecies Serotype" where the serotype name is capitalized, e.g. Samonella enterica subsp. enterica ser. Doer. Additional terms omitting the species and subspecies name for brevity, e.g., Salmonella Doer, are in common usage for Salmonella serotypes.  In SNOMED CT these Salmonella serotype descriptions should be capitalized and not confused with traditional binomial species representation. 

7.12.4 US/GB spelling variants for taxonomic concepts 

Taxonomic resources e.g.Integrated Taxonomic Information System (ITIS); List of Prokaryotic names with Standing in Nomenclature (LPSN) use the scientific name for organisms. Similarly in SNOMED CT the scientific name should be used in FSN and PT. If the preferred spelling in a jurisdiction is not the official scientific name, the preferred name should be added in the language RefSet extension.

7.12.5 Use of "X species"

The use of terms of the form "X species", such as "Salmonella species", is routine in laboratory reporting, but in the context of the Linnaean organism hierarchy there is no difference between "Salmonella species" and simply "Salmonella" the genus. In the context of a laboratory report, the term "Salmonella species" sometimes is intended to convey additional information beyond the place of the identified organism in the Linnaean hierarchy, but the intended connotation may vary from lab to lab and from organism to organism. Since the organism code represents a class of organisms, it cannot also represent what was or was not done, or what will be done, to identify the organism. It also cannot properly represent other information about the result. If there is additional information that needs to be communicated, it should be in a separate statement or comment (e.g. "further species identification pending" or "sent to reference laboratory for further identification", or "further identification to be done if clinically indicated"
  • When there is a request for "X species", it will be reviewed for consideration as a synonym to "X genus".
  • All of the existing content of X species that occurred as a sibling or a child of the Genus-level organism have been deprecated from SNOMED CT core as of January 2015 release.

7.12.6 Microorganism name changes:

Microorganism taxonomic names may change from time to time. One of the primary reasons for these changes is advances in science e.g. application of molecular techniques to compare the nucleic acid similarities among organisms, which may result in:

  • An organism previously assigned to a particular taxon (e.g. Genus) is found to be significantly unrelated to other members of the taxon on a molecular basis
  • Reassessing the taxonomic groupings originally established based on phenotypic characteristics
  • Proposal to reassign the organism to a different taxon--either a new taxon or an existing one

As a taxonomic name changes for an organism, our goal is to display the organism with the most current name while preserving the old names. Our approach currently is ad-hoc: if we get a request for changing the name, we recommend the changes based on the following use cases:

    • When the name of one organism changes to another name, the recommendation is to change the FSN for affected concepts without changing the concept ID, while the old name is retained as a synonym:
      • The original FSN term and its description ID will be made inactive (OLD description FSN)
      • A new FSN and description ID will be created and made Active (New description FSN)
      • A a new Synonym and description ID will be created and made Active (Old description) 
    • When a single species is later classified into multiple species, the recommendation is to retire original concept as ambiguous, create new required concepts, and set a "MAY BE" relationship between the old concept and the new ones.
    • When 2 (or more) organisms are later classified as one: create a new concept and retire the existing ones with a "replaced by" relationship to the new one.

7.12.7 Resources for Organism Naming

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

For details on the Organism hierarchy, see 6.8.6 Organism.
For details on how Organisms are used in microbiology reporting, see 6.3.5 Observables and results for microbiology tests.

Feedback